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Xylem

Xylem is the major water-conducting tissue in vascular plants, responsible for transporting water and dissolved nutrients from the roots to the leaves and other parts of the plant.
It is composed of various cell types, including tracheary elements (such as vessels and tracheids), parenchyma cells, and fibers.
Xylem plays a crucial role in plant growth, development, and adaptation to environmental stresses.
Its structure and function have been extensively studied to understand plant physiology and improve agricultural practices.
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Most cited protocols related to «Xylem»

1
Annotated Whitefly EPG Data Analysis
Cited 45 times
Raw EPG data recorded by EPG Systems Stylet+d was manually annotated using EPG Systems Stylet+a software v01.30 (13-04-2016)/B27. Annotated waveforms were non-probing (np), pathway (C), phloem salivation (E1), phloem ingestion (E2), derailed stylet mechanics (F), xylem feeding (G) and intracellular puncture—potential drop (pd). Waveforms were identified based on the waveform pattern, amplitude, relative voltage level, R/emf origin, frequency, and the context of the waveform as described in the previous EPG studies of B. tabaci (Jiang et al., 1999 (link); Johnson and Walker, 1999 (link); Liu et al., 2012 (link); Civolani et al., 2014 (link); Zhou, 2014 ; Prado Maluta et al., 2017 (link)).
Annotation files were then directly passed to a modified version of the Ebert 3.0 program in SAS Enterprise Guide 7.1, SAS 9.4 statistical software (SAS Institute, Cary, NC, USA) for further analysis which produces the same parameters as the popular Sarria excel workbook (Sarria et al., 2009 (link); Ebert et al., 2015 (link)). The modified version is provided in the Supplementary Material. The modified version utilizes the series of BoxCox power transformation to determine the best possible transformation, as implemented in the PROC TRANSREG statement (Osborne, 2010 ). The results of this power transformation were inspected visually using histogram and Q-Q plots. For certain parameters, power transformations are unsuitable as they cannot approximate the necessary S-curve. Therefore, the Arcsine transformation was applied before the BoxCox transformation if this was necessary. The modification of the original Ebert 3.0 program also utilizes a macro script developed by Piepho (2012 ) that mitigates the case when varying standard error of a difference causes the traditional algorithm to fail to represent all significant differences of the means using the letter grouping. The Piepho algorithm solves the problem as it is able to generate a discontinous line display (Piepho, 2012 ). As a consequence, seeing discontinous assigned letters such as “ac” or “acd” is not uncommon (Piepho, 2014 (link); Poosapati et al., 2014 (link); Santos et al., 2015 (link); McCaghey et al., 2017 (link)).
Milenovic M., Wosula E.N., Rapisarda C, & Legg J.P. (2019). Impact of Host Plant Species and Whitefly Species on Feeding Behavior of Bemisia tabaci. Frontiers in Plant Science, 10, 1.
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Publication 2019
Genes, vpr Mechanics Phloem Protoplasm Punctures Sialorrhea Walkers Xylem
2
Phloem and Xylem Sap Collection from Wheat Seedlings
Cited 31 times
The collection of phloem and xylem saps from wheat seedlings was performed according to the method of Hazama et al. (2015) (link). Treated and untreated seedlings of 27 days cut on surfaces of the stems near the petioles of mature leaves with a razor blade and exuded drops (excluding the first drop) collected as phloem sap using micropipettes. Samples of phloem sap were stored in eppendorf previously washed with 0.1 M HNO3 for 2 days and then with double distilled water three times to eliminate metals. The samples were stored at -20°C until analysis.
After the collection of phloem sap, stems were cut at 2 cm above the interface of the shoot and root, and xylem sap exudates were collected for 30 min using micropipettes. The measured pH of the xylem sap was 6.0–6.4. Samples of xylem sap were also stored at -20°C until analysis.
For the estimation of Zn in phloem and xylem saps above, the described procedure (for Zn) was followed.
Tripathi D.K., Mishra R.K., Singh S., Singh S., Vishwakarma K., Sharma S., Singh V.P., Singh P.K., Prasad S.M., Dubey N.K., Pandey A.C., Sahi S, & Chauhan D.K. (2017). Nitric Oxide Ameliorates Zinc Oxide Nanoparticles Phytotoxicity in Wheat Seedlings: Implication of the Ascorbate–Glutathione Cycle. Frontiers in Plant Science, 8, 1.
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Publication 2017
Exudate Metals Phloem Plant Roots Seedlings SKAP2 protein, human Stem, Plant Triticum aestivum Xylem
3
Phytohormone Analysis by HPLC-MS
Cited 28 times
Cytokinins (zeatin, Z, and zeatin riboside, ZR), indole-3-acetic acid (IAA), and abscisic acid (ABA) were extracted and purified according to the method of Dobrev and Kaminek (2002) (link). One gram of fresh plant material (leaf or root) was homogenized in liquid nitrogen and placed in 5 ml of cold (–20 °C) extraction mixture of methanol/water/formic acid (15/4/1 by vol., pH 2.5). After overnight extraction at –20 °C solids were separated by centrifugation (20 000 g, 15 min) and re-extracted for 30 min in an additional 5 ml of the same extraction solution. Pooled supernatants were passed through a Sep-Pak Plus †C18 cartridge (SepPak Plus, Waters, USA) to remove interfering lipids and plant pigments and evaporated to dryness. The residue was dissolved in 5 ml of 1 M formic acid and loaded on an Oasis MCX mixed mode (cation-exchange and reverse phase) column (150 mg, Waters, USA) preconditioned with 5 ml of methanol followed by 5 ml of 1 M formic acid. To separate different CK forms (nucleotides, bases, ribosides, and glucosides) from IAA and ABA, the column was washed and eluted stepwise with different appropriate solutions indicated in Dobrev and Kaminek (2002) (link). ABA and IAA were analysed in the same fraction. After each solvent was passed through the columns, they were purged briefly with air. Solvents were evaporated at 40 °C under vacuum. Samples then dissolved in a water/acetonitrile/formic acid (94.9:5:0.1 by vol.) mixture for HPLC/MS analysis. Analyses were carried out on a HPLC/MS system consisting of an Agilent 1100 Series HPLC (Agilent Technologies, Santa Clara, CA, USA) equipped with a μ-well plate autosampler and a capillary pump, and connected to an Agilent Ion Trap XCT Plus mass spectrometer (Agilent Technologies, Santa Clara, CA, USA) using an electrospray (ESI) interface. Prior to injection, 100 μl of each fraction extracted from tissues or a similar volume of xylem sap were filtered through 13 mm diameter Millex filters with 0.22 μm pore size nylon membrane (Millipore, Bedford, MA, USA). 8 μl of each sample, dissolved in mobile phase A, was injected onto a Zorbax SB-C18 HPLC column (5 μm, 150×0.5 mm, Agilent Technologies, Santa Clara, CA, USA), maintained at 40 °C, and eluted at a flow rate of 10 μl min−1. Mobile phase A, consisting of water/acetonitrile/formic acid (94.9:5:0.1 by vol.), and mobile phase B, consisting of water/acetonitrile/formic acid (10:89.9:0.1 by vol.), were used for the chromatographic separation. The elution programme maintained 100% A for 5 min, then a linear gradient from 0% to 6% B in 10 min, followed by another linear gradient from 6% to 100% B in 5 min, and finally 100% B maintained for another 5 min. The column was equilibrated with the starting composition of the mobile phase for 30 min before each analytical run. The UV chromatogram was recorded at 280 nm with a DAD module (Agilent Technologies, Santa Clara, CA, USA). The mass spectrometer was operated in the positive mode with a capillary spray voltage of 3500 V, and a scan speed of 22 000 m/z s−1 from 50–500 m/z. The nebulizer gas (He) pressure was set to 30 psi, whereas the drying gas was set to a flow of 6.0 l min−1 at a temperature of 350 °C. Mass spectra were obtained using the DataAnalysis program for LC/MSD Trap Version 3.2 (Bruker Daltonik GmbH, Germany). For quantification of Z, ZR, ABA, and IAA, calibration curves were constructed for each component analysed (0.05, 0.075, 0.1, 0.2, and 0.5 mg l−1) and corrected for 0.1 mg l−1 internal standards: [2H5]trans-zeatin, [2H5]trans-zeatin riboside, [2H6]cis,trans-abscisic acid (Olchemin Ltd, Olomouc, Czech Republic), and [13C6]indole-3-acetic acid (Cambridge Isotope Laboratories Inc., Andover, MA, USA). Recovery percentages ranged between 92% and 95%.
ACC (1-aminocyclopropane-1-carboxylic acid) was determined after conversion into ethylene by gas chromatography using an activated alumina column and a FID detector (Konik, Barcelona, Spain). ACC was extracted with 80% (v/v) ethanol and assayed by degradation with alkaline hypochlorite in the presence of 5 mM HgCl2 (Casas et al., 1989 ). A preliminary purification step was performed by passing the extract through a Dowex 50W-X8, 50–100 mesh, H+-form resin and later recovered with 0.1 N NH4OH. The conversion efficiency of ACC into ethylene was calculated separately by using a replicate sample containing 2.5 nmol of ACC as an internal standard and used for the correction of data.
Albacete A., Ghanem M.E., Martínez-Andújar C., Acosta M., Sánchez-Bravo J., Martínez V., Lutts S., Dodd I.C, & Pérez-Alfocea F. (2008). Hormonal changes in relation to biomass partitioning and shoot growth impairment in salinized tomato (Solanum lycopersicum L.) plants. Journal of Experimental Botany, 59(15), 4119-4131.
Publication 2008
1-aminocyclopropane-1-carboxylic acid Abscisic Acid acetonitrile Capillaries Centrifugation Chaperone-Mediated Autophagy Chromatography cis-acid Cold Temperature CREB3L1 protein, human Cytokinins DNA Replication Dowex Ethanol Ethylenes formic acid Gas Chromatography Glucosides High-Performance Liquid Chromatographies Hypochlorite indoleacetic acid Isotopes Lipids Mass Spectrometry Mercuric Chloride Methanol Nebulizers Nitrogen Nucleotides Nylons Oxide, Aluminum Pigmentation Plant Leaves Plant Roots Plants Pressure Radionuclide Imaging Resins, Plant Sep-Pak C18 Solvents Strains Tissue, Membrane Tissues Vacuum Xylem Zeatin zeatin riboside
4
Phytohormone Extraction and Quantification
Cited 17 times
The fourth main-stem leaf from the apex and the whole roots were harvested before and
after xylem sap collection to determine CKs and ABA. About 0.5g of fresh samples was
extracted and homogenized in 2ml of 80% methanol (containing 40mg l–lbutylated hydroxytoluene as an antioxidant). The extract was incubated at 4 °C for
48h, and then centrifuged at 4000rpm for 15min at 4 °C. The supernatant was passed
through C18 Sep-Pak cartridges (Waters Corp., Millford, MA, USA), and the phytohormone
fraction was eluted with 10ml of 100% (v/v) methanol and then 10ml of ether. The eluate
was dried down by pure N2 at 20 °C, and then stored at –40
°C.
Wang Y., Li B., Du M., Eneji A.E., Wang B., Duan L., Li Z, & Tian X. (2012). Mechanism of phytohormone involvement in feedback regulation of cotton leaf senescence induced by potassium deficiency. Journal of Experimental Botany, 63(16), 5887-5901.
Publication 2012
Antioxidants Ethyl Ether Methanol Plant Leaves Plant Roots Xylem
5
Transcript Profiling of Plant Tissues
Cited 10 times
All of the libraries were comprised of a single organ or tissue, and the majority of libraries were developed by pooling samples collected at different points along a time course, along the diurnal cycle, at several stages of differentiation or from different treatments (Supplemental data 2 and [58 ]). Treatments known to affect plant physiology were applied to saplings (young trees) aiming to stimulate different transcript profiles. These treatments included N and P fertilization as well as stem girdling. Three libraries were made from whole root systems of very young spruce seedlings, produced through tissue culture, grown in sterile growth media. Most of the libraries were derived from one genotype (pg-653), however four libraries were comprised of two or more genotypes. The secondary xylem collected from saplings (library GQ007) was comprised of the entire sampling of woody tissues collected from seedlings; however, only the differentiating partly-lignified secondary xylem was collected from mature trees as previously described [16 (link)]. The secondary xylem tissues were collected by first gently separating the bark from the underlying wood and scraping the soft tissues inward of the cambial area. The secondary phloem of mature trees was collected by gently scrapping the inner surface of the bark with a scalpel blade. All tissue samples were frozen in liquid nitrogen and then stored at -80°C until RNA extraction immediately upon removal from the tree, seedling or tissue culture vessel.
Pavy N., Paule C., Parsons L., Crow J.A., Morency M.J., Cooke J., Johnson J.E., Noumen E., Guillet-Claude C., Butterfield Y., Barber S., Yang G., Liu J., Stott J., Kirkpatrick R., Siddiqui A., Holt R., Marra M., Seguin A., Retzel E., Bousquet J, & MacKay J. (2005). Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters. BMC Genomics, 6, 144.
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Publication 2005
Adrenal Cortex Blood Vessel Cambium cDNA Library Culture Media Fertilization Freezing Genotype Nitrogen Phloem Picea Plant Physiological Phenomena Plant Roots Stem, Plant Sterility, Reproductive Tissues Trees Xylem

Most recents protocols related to «Xylem»

1
Scanning Electron Microscopy of Xylem in Cut Stems
The xylem at the base of cut stems was examined using scanning electron microscopy (TESLA BS- 300). Stem samples were collected on day 9. Cross-sectional segments of the stem bases were obtained using razor blades. Segments were fixed in FAA solution (90 mL: 5 mL: 5 mL of formalin (37–40%), alcohol (70%), and acetic acid) according to the protocol reported by Li et al. [45 ] after which they were dried at the critical point of CO2 (Balzers CPD-020) and coated with gold (30 nm) in a sputter coater (Balzers SCD-040). The segments were then examined and photographed.
Gururani M.A., Atteya A.K., Elhakem A., El-Sheshtawy A.N, & El-Serafy R.S. (2023). Essential oils prolonged the cut carnation longevity by limiting the xylem blockage and enhancing the physiological and biochemical levels. PLOS ONE, 18(3), e0281717.
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Publication 2023
Acetic Acid Ethanol Formalin Gold Scanning Electron Microscopy Stem, Plant Xylem
2
Clonal rRBD Protein Production Process
Clonal rRBD producing cell lines were seeded at 0.3 × 106 cells/mL in 125 mL shake flasks at a 30 mL working volume and cultured at 37 °C. Samples were taken daily to measure VCD and cell viability with a Vi-Cell XR, and glucose and lactate levels with a YSI 2950 biochemistry analyzer (Xylem). Starting on day 3, cells were fed 3.3% v/v BalanCD HEK293 feed (Irvine Scientific) supplemented with 4 mM GlutaMAX and bolus additions of 45% glucose solution (Sigma-Aldrich) to reach 7 g/L of glucose. Batches were terminated once cell viability was < 80%. Supernatants were harvested for titer analysis using the same protocol as for transient batch harvest.
Green E.A., Hamaker N.K, & Lee K.H. (2023). Comparison of vector elements and process conditions in transient and stable suspension HEK293 platforms using SARS-CoV-2 receptor binding domain as a model protein. BMC Biotechnology, 23, 7.
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Publication 2023
Cell Lines Cells Cell Survival Clone Cells Glucose Lactate Transients Tremor Xylem
3
Structural and Flow Characteristics of Panax notoginseng Xylem
The detailed structural parameters of the Panax notoginseng xylem were shown in the scanning electron microscopy images. The flow resistance characteristics of the vessel were analyzed by the computational fluid dynamics method [11 (link), 18 (link)]. Based on the microscopic images of the cross-section and axial-section, the structural parameters of the annular thickening and pitted thickening vessel were measured. The measurements were taken for each character listed in Table 1.
The types of vessel cross-sections were shown in Fig 2. The terms of the annular thickening and pitted thickening vessel were shown in Fig 3, which R was inscribed circle diameter, W was width, S was spacing, H was height, L was length.
The actual structural parameters of the xylem were obtained from the Panax notoginseng samples (Table 1), and the computational domain model of the annular thickening and pitted thickening vessel was established based in SolidWorks. The hexagon vessels of Panax notoginseng were shown in Fig 4.
The computational domain models contained a flow area with a secondary wall thickening pattern of 250 μm in length. To avoid effects at the entrance and exit, an extended smooth segment with length 25 μm was added at both ends of the vessel (Fig 5).
The boundary conditions were that the pressure was zero at the model outlet, and the flow velocity was 0.3 mm/s at the model inlet. The irregularity of the vessel structure was generated by tetrahedral and hexahedral unstructured meshes. The maximum and minimum of the unit size were 4.4×10-6m and 4.4×10-8m, respectively. In this part, the scale of the mesh was based on the prediction accuracy of the inlet/outlet pressure drop, and the mesh size independence test was performed (Table 2). The pressure drop difference between the standard mesh and the fine mesh was 0.22%. The mesh number has no effect on the calculation results, so the standard mesh number was used to analyze flow resistance characteristics, and the total number of meshes in the model was approximately 728680 (Fig 6). The PowerCube-S01 with a high-performance computing system was used for the simulation.
Xu T., Li Z., Bao S., Su Y., Su Z., Zhi S, & Zheng E. (2023). Xylem vessel type and structure influence the water transport characteristics of Panax notoginseng. PLOS ONE, 18(3), e0281080.
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Publication 2023
Blood Vessel Character Hydrodynamics Microscopy Panax notoginseng Pressure Scanning Electron Microscopy Vascular Resistance Xylem
4
Modeling Fluid Dynamics in Xylem Vessels
The hexagonal xylem vessel model (Fig 7) can analyze the flow characteristics by the energy conservation law (Bernoulli equation). The flow between arbitrary sections satisfies the Bernoulli equation, which was written in sections from the inlet to the exit sections Z1, Z2, ···, Zn as:
P1ρg+V122g+z1=P2ρg+V222g+z2+ξ1V222g+λl1V228DgP2ρg+V222g+z1=P3ρg+V322g+z3+ξ2v322g+λl2V328Dg⋅⋅⋅⋅⋅⋅⋅⋅⋅⋅⋅⋅Pn−1ρg+Vn−122g+zn−1=Pnρg+Vn22g+zn+ξn−1Vn22g+λln−1Vn28Dg
Where Pn and Vn were the average pressure and flow velocity at section n, ρ was fluid density, g was the acceleration of gravity, Zn was the position head of water at the section, ξn−1 was the local loss coefficient of section n-1 to section n, λ was friction factor of head loss, ln−1 was the length between two adjacent sections. D was the hydraulic radius of the xylem vessel, the expression of D was:
D=Aχ
Add the two sides of the equations of Eq (1) in order:
P1−Pnρg=zn−z1+ξ1V222g+ξ2V322g+⋯+ξn−1Vn22g+λLVn28Dg
Where l1+l2+l3+···+ln-1= L, L was the total length of the xylem vessel.
Known by the continuity equation:
V1A1=V2A2=V3A3=⋯=VnAn
In Eq (4), Ai(i = 1,2…,n) was the flow area at the corresponding section, Substituting Eq (4) into Eq (3) give:
ΔPρg=L+[λ(A1An)2L4D+∑i=1n−1ξi(A1Ai+1)2]V122g
Where
ξ=[λ(A1An)2L4D+∑i=1n−1(A1Ai+1)2ξi]
Eq (6) was simplified to:
ΔPρg=L+ξV122g
Expressed as:
ξ=2V12(ΔPρ‐Lg)
Expressed by flow rate:
ξ=24R4q2(ΔPρ−Lg)
In Eqs (8A, 8B), was the flow resistance coefficient of hexagonal xylem vessel, q was the average flow rate.
For pentagon, quadrilateral and circular xylem vessel model, the expressions were:
ξ=50R4(tan36∘)2q2(ΔPρ−Lg)
ξ=32R4q2(ΔPρ−Lg)
ξ=2π2R4q2(ΔPρ−Lg)
Xu T., Li Z., Bao S., Su Y., Su Z., Zhi S, & Zheng E. (2023). Xylem vessel type and structure influence the water transport characteristics of Panax notoginseng. PLOS ONE, 18(3), e0281080.
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Publication 2023
Acceleration Blood Vessel Friction Gravity Head Pressure Radius Vascular Resistance Xylem
5
Transcriptome Analysis of Plant Tissues
Phloem and xylem tissue were homogenised in liquid nitrogen with mortar and pestle and then stored at at -80 °C for further RNA or protein extraction. 100 mg of the homogenized tissue was placed in a frozen 2 mL tube containing a ceramic bead and ground for 60 s at a frequency of 26 1/S with a TissueLyser II (Qiagen, Cat. 85,300). Total RNA was isolated using RNeasy Plant Mini kit (Qiagen, Cat. 74,903) with DNase treatments (RNase-Free DNase Set cat. No. 79254) according manufacturer’s instructions. The RNA was quantified using the Qubit 4 fluorometer (ThermoFisher) with the Qubit RNA BR Assay Kit (ThermoFisher, Cat. Q10211). RNA integrity (RIN) was tested with the Agilent RNA 6000 Nano Kit (Agilent, Cat. 5067–1511) on a 2100 Bioanalyzer instrument (Agilent, Cat. G2939BA) and all samples used for RNA-Seq had a RIN greater than 7.
The Illumina NeoPrep Library Prep System was used to prepare samples from 50 ng of total RNA extraction (Illumina, Documents: 15049720v01, 15049725v03, 15059581v02). TruSeq Standard mRNA Library Prep (Illumina, NP-202–1001) was used with the default indexes adapters A to P. At the last step, each processed sample collected from the library card was analysed for library quality check using a DNA 1000 chip on the 2100 Bioanalyzer (Agilent, Cat. 5067–1504). Finally, each sample was normalized manually at 10 nM and then pooled (5 μL × 16 samples) in one library for the Illumina sequencing platform.
The libraries composed of the 16 samples were sequenced into two lines in Rapid-Run Mode (16 samples/line) in a single flow cell for paired-end 100 bp with an Illumina HiSeq 2500 sequencing system. The samples were sequenced at the Centre Hospitalier de l'Université Laval sequencing platform (Quebec City, Canada).
Chiu C.C., Pelletier G., Stival Sena J., Roux-Dalvai F., Prunier J., Droit A, & Séguin A. (2023). Integrative analysis of green ash phloem transcripts and proteins during an emerald ash borer infestation. BMC Plant Biology, 23, 123.
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Publication 2023
Biological Assay BP 100 Cells Deoxyribonucleases DNA Chips DNA Library Endoribonucleases Freezing Nitrogen Phloem Plants Proteins RNA, Messenger RNA-Seq Tissues Xylem

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Rneasy plant mini kit by Qiagen
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More about "Xylem"

Xylem is the crucial water-conducting tissue found in vascular plants, responsible for transporting water and essential nutrients from the roots to the leaves and other parts of the plant.
This complex tissue is composed of various cell types, including tracheary elements (such as vessels and tracheids), parenchyma cells, and fibers.
Xylem plays a pivotal role in plant growth, development, and adaptation to environmental stresses.
Understanding the structure and function of xylem has been a key focus of plant physiology research, with techniques like HiSeq 2000 and HiSeq 2500 sequencing platforms, RNeasy Plant Mini Kit and RNeasy Plant Kit for RNA extraction, RNase-Free DNase Set for DNA removal, and Agilent 2100 Bioanalyzer for quality assessment being commonly used.
Researchers can leverage innovative AI-powered platforms like PubCompare.ai to locate relevant protocols from literature, preprints, and patents, and use AI-driven comparisons to identify the best methods for their xylem-related studies, enhancing reproducibility and research accuracy.
By optimizing xylem-related protocols and leveraging cutting-edge tools, researchers can gain deeper insights into plant physiology and improve agricultural practices.
For example, the ClonExpress II One Step Cloning Kit and Xcalibur software version 2.2 can be used to streamline molecular biology workflows and data analysis, respectively, in xylem-focused studies.