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Polyamines

Polyamines are organic compounds with two or more amino groups.
They play a crucial role in cellular processes such as cell growth, differentiation, and gene regulation.
Polyamines like putrescine, spermidine, and spermine are found in a wide range of organisms, from bacteria to humans.
Studying polyamine metabolism and function is essential for understanding fundamental biological mechanisms and developing potential therapeutic applications in areas like cancer, neurological disorders, and immune function.

Most cited protocols related to «Polyamines»

1
Metabolomic Profiling with BinBase Database
Cited 29 times
BinBase is a large GC-TOF MS based metabolomics database encompassing
1,561 studies with 114,795 samples for various species, organs, matrices, and
experimental conditions. By the physics of GC-MS, analysis is restricted to
thermostable small molecules that range up to 650 Da in size, even if using
derivatization by trimethylsilylation to reduce boiling points. Molecules
profiled by trimethylsilylation GC-MS based metabolomics include amino acids,
di- and tripeptides, hydroxyl acids, organic phosphates, fatty acids, alcohols,
sugar acids, mono-, di- and trisaccharides including sugar acids and sugar
alcohols, aromatic acids, nucleosides and mononucleotides (but not di- or
trinucleotides), sterols, polyamines, and a large variety of miscellaneous
compounds.
BinBase uses a retention index- and mass spectral quality filtering
system based on GC-TOF based mass spectral deconvolution results as
input21 (link) to store and
report unique metabolite signals that are detected in metabolomic studies.
Through the connected MiniX system22 , all studies in BinBase are associated with metadata such
as species, organs, cell types, and treatments. The BinBase algorithm has been
published previously11 ,23 (link) and is used over the past 13
years. It relies on mass spectral deconvolution of GC-TOF MS data by the Leco
ChromaTOF software and utilizes a multi-tiered filter system with different
settings to annotate deconvoluted instrument peak spectra as unique database
entries (“bins”). For typical studies on mammalian plasma with
about 50–60 samples, about 1,000 peaks would be detected by ChromaTOF
software at least in one chromatogram at signal/noise ratios s/n>5.
BinBase removes low abundant, inconsistent and noisy peaks that cannot be
assigned to existing bins in BinBase and that have too low spectra quality to
generate a new bin in BinBase, resulting in datasets that typically report
400-500 peaks for mammalian plasma samples. Compound identifications within
BinBase are managed by the administrator using spectral libraries and retention
index information from the Fiehnlib libraries12 (link) and NIST mass spectra. In a typical
final BinBase report such as on mammalian plasma, about 30-40% of the
reported bins are noted as identified metabolites, i.e. about 150 compounds,
including database identifiers such as KEGG, PubChem and InChI keys.
Lai Z., Tsugawa H., Wohlgemuth G., Mehta S., Mueller M., Zheng Y., Ogiwara A., Meissen J., Showalter M., Takeuchi K., Kind T., Beal P., Arita M, & Fiehn O. (2017). Identifying epimetabolites by integrating metabolome databases with mass spectrometry cheminformatics. Nature methods, 15(1), 53-56.
Publication 2017
Acids Administrators Alcohols Amino Acids Cells Fatty Acids Gas Chromatography-Mass Spectrometry Hydroxy Acids Mammals Mass Spectrometry Nucleosides Phosphoric Acid Esters Plasma Polyamines Retention (Psychology) Sterols Sugar Acids Trisaccharides
2
Establishment of Cre-Expressing Rat Lines
Cited 15 times

Protocol full text hidden due to copyright restrictions

Open the protocol to access the free full text link

Publication 2011
Animals Animals, Transgenic Buffers Cell Nucleus Chromosomes DNA Edetic Acid Electrophoresis Genes Genome Heterozygote Homozygote Mice, Laboratory Microinjections Polyamines Pulse Rate Rats, Long-Evans Rattus Rod Opsins Sodium Chloride Transgenes Tromethamine Virus Zygote
3
Voltage-Gated Inward Rectifier Potassium Currents
Cited 8 times
IRK1 currents were recorded from inside-out membrane patches of Xenopus oocytes (injected with IRK1 cRNA) with an Axopatch 200B amplifier (Axon Instruments, Inc.), filtered at 5 kHz, and sampled at 25 kHz using an analogue-to-digital converter (DigiData 1200; Axon Instruments, Inc.) interfaced with a personal computer. pClamp6 software (Axon Instruments, Inc.) was used to control the amplifier and acquire the data. During current recording, the voltage across the membrane patch was first hyperpolarized from the 0 mV holding potential to −100 mV and then stepped to various test voltages, or stepped directly from the holding potential. The duration of the voltage test pulse was 100 ms, which is comparable to those used in the studies where the Mg2+- and polyamine-independent rectification was initially observed (Aleksandrov et al., 1996 (link); Shieh et al., 1996 (link)). Background leak current correction was performed as described previously (Lu and MacKinnon, 1994 (link); Guo and Lu, 2000a (link)). To effectively perfuse the patch, the tip of the patch pipette (∼3 MΩ) was immersed in a stream of intracellular solution exiting one of ten glass capillaries (ID = 0.2 mm) mounted in parallel.
Guo D, & Lu Z. (2002). IRK1 Inward Rectifier K+ Channels Exhibit No Intrinsic Rectification. The Journal of General Physiology, 120(4), 539-551.
Publication 2002
Axon Capillaries Nurse Anesthetists Ovum Polyamines Protoplasm Pulse Rate Step Test Tissue, Membrane Xenopus laevis
4
High-Resolution Cryo-EM Structure of E. coli 70S Ribosome
Cited 7 times
The previous high-resolution structure of the E. coli 70S ribosome (Noeske et al., 2015 (link)) was used as a starting model. We used the ‘Fit to Map’ function in Chimera (Pettersen et al., 2004 (link)) to calibrate the magnification of the cryo-EM map of the 50S ribosomal subunit generated here to maximize correlation, resulting in a pixel size of 0.7118 Å rather than the recorded 0.71 Å. Focused-refined maps were transformed into the frame of reference of the 70S ribosome for modeling and refinement, using the ‘Fit to Map’ function in Chimera, and resampling the maps on the 70S ribosome grid. The 50S and 30S subunits were refined separately into their respective focused-refined maps using PHENIX real-space refinement (RSR; Liebschner et al., 2019 (link)). Protein and rRNA chains were visually inspected in Coot (Casañal et al., 2020 (link)) and manually adjusted where residues did not fit well into the density, making use of B-factor blurred maps where needed to interpret regions of lower resolution. Focused-refined maps on smaller regions were used to make further manual adjustments to the model, alternating with PHENIX RSR. Some parts of the 50S subunit, including H69, H34, and the tip of the A-site finger, were modeled based on the 30S subunit focused-refined map. The A-site and P-site tRNAs were modeled as follows: anticodon stem-loops, 30S subunit focused-refined map; P-site tRNA body, 50S subunit focused-refined map, with a B factor of 20 Å2 applied; A-site tRNA body, 30S subunit focused-refined map and 50S subunit focused-refined map with B factors of 20 Å2 applied; tRNA-ACCA 3’ ends, 50S subunit focused-refined map with B factors of 20–30 Å2 applied. Alignments of uS15 were generated using BLAST (Altschul et al., 1997 (link)) with the E. coli sequence as reference. The model for bL31A (E. coli gene rpmE) was manually built into the CP and 30S subunit head domain focused-refined maps before refinement in PHENIX.
A model for paromomycin was manually docked into the 30S subunit focused-refined map, followed by real-space refinement in Coot and PHENIX. Comparisons to prior paromomycin structural models (PDB codes 1J7T, 2VQE, and 4V51; Kurata et al., 2008 (link); Selmer et al., 2006 (link); Vicens and Westhof, 2001 (link)) used least-squares superposition of paromomycin in Coot. Although ring IV is in different conformations in the various paromomycin models, the least-squares superposition is dominated by rings I–III, which are in nearly identical conformations across models.
Ribosome solvation including water molecules, magnesium ions, and polyamines was modeled using a combination of PHENIX (phenix.douse) and manual inspection. The phenix.douse feature was run separately on individual focused-refined maps, and the resulting solvent models were combined into the final 30S and 50S subunit models. Due to the fact that the solvent conditions used here contained ammonium ions and no potassium, no effort was made to systematically identify monovalent ion positions. The numbers of various solvent molecules are given in .
Along with the individual maps used for model building and refinement, we have also generated a composite map of the 70S ribosome from the focused-refined maps for deposition to the PDB and EMDB for ease of use (however, experimental maps are recommended for the examination of high-resolution features). We made the composite map using the ‘Fit in Map’ and vop commands in Chimera. First, we aligned the unmasked focus-refined maps with the 70S ribosome map using the ‘Fit in Map’ tool. We then used the ‘vop resample’ command to transform these aligned maps to the 70S ribosome grid. After the resampling step, we recorded the map standard deviations as reported in the ‘Volume Mean, SD, RMS’ tool. Then, we added the maps sequentially using ‘vop add’ followed by rescaling the intermediate maps to the starting standard deviation using the ‘vop scale’ command.
Watson Z.L., Ward F.R., Méheust R., Ad O., Schepartz A., Banfield J.F, & Cate J.H. (2020). Structure of the bacterial ribosome at 2 Å resolution. eLife, 9, e60482.
Full text: Click here
Publication 2020
Ammonium Anticodon Chimera Complement Factor B Escherichia coli Fingers Genes Head Human Body Magnesium Microtubule-Associated Proteins Paromomycin Polyamines Potassium Processing Bodies Proteins Protein Subunits Reading Frames Ribosomal RNA Ribosomes Ribosome Subunits Solvents Stem, Plant Transfer RNA
5
Microchip-based Electroosmotic Pump Protocol
Cited 7 times
The electroosmotic pump incorporated in the microchip design is similar to earlier reported designs.32 ,44 (link) The microfluidic components of the pump consist of a tee intersection where the end of the separation channel, the side channel, and short transport channel leading to the electro-spray tip meet (Figure 1). As described above, all of the channels except the side channel were coated with a polyamine to reverse the surface charge on those channels. When all of the channels were filled with the CE background electrolyte (50% methanol, 0.2% acetic acid), the electroosmotic mobility (μeof) in the polyamine-coated separation channel was ~5 × 10−8 m2 V−1 s−1 (anodic EOF) based on the measured migration time of injected analyte bands. The electroosmotic mobility in the uncoated side channel was significantly lower in magnitude and in the opposite direction (cathodic EOF). The actual value of the EOF in the side channel was not determined; however, optical imaging of a neutral fluorescent marker (introduced via the side channel reservoir) revealed only a small amount of flow (significantly lower than the flow in the separation channel) under typical operating conditions. When the voltage at the side-channel reservoir was more positive than the voltage at the CE injection cross, the EOF in both the separation channel and the side channel flowed toward the intersection near the ESI corner. The short length of channel between the intersection and the ESI orifice was essentially field-free (due to the relatively large electrical resistance of the air between the microchip and the MS inlet), so there was no EOF in this channel segment. The electroosmotically driven flow entering the tee intersection from the separation and side channels generated a pressure that could easily drive flow through the field-free segment. It was estimated that a pressure of less than 1 mbar would be required to drive liquid through the 150-μm-long field-free channel at a flow rate of 40 nL/min. The separation and side channels had a hydraulic resistance more than 100 times greater than the electrospray channel; thus, the pressure-driven flow in these channels was negligible.
Mellors J.S., Gorbounov V., Ramsey R.S, & Ramsey J.M. (2008). Fully Integrated Glass Microfluidic Device for Performing High-Efficiency Capillary Electrophoresis and Electrospray Ionization Mass Spectrometry. Analytical chemistry, 80(18), 6881-6887.
Publication 2008
Acetic Acid Electrolytes Electroosmosis Methanol Polyamines Pressure Range of Motion, Articular Resistance, Electrical

Most recents protocols related to «Polyamines»

1
Organ-Specific Putrescine Biosynthesis
Not available on PMC !

Example 10

The relative contribution of ADC and ODC to putrescine biosynthesis was evaluated by measuring the activity of each enzyme in the leaves (leaf 23) and roots of the NA and LA plants at topping and harvest. ADC and ODC activity varied in an organ-specific and developmental stage-specific manner in both lines (FIG. 4). Whereas ADC activity was high in the leaves but minimal in the roots of both lines, ODC activity was higher in the younger leaves and roots, indicating that ODC is mainly responsible for putrescine biosynthesis in the roots. ADC activity was significantly higher (1.4-fold, p<0.05) in the leaves of the LA plants compared to the NA controls at topping and harvest (FIG. 4A). Similarly, ODC activity was significantly higher (p<0.05) in the LA plants compared to the NA controls in the roots at topping (1.8-fold) and at harvest (1.7-fold), and in young leaves at topping (1.5-fold) (FIG. 4B).

US11859192B2. Compositions and methods for producing tobacco plants and products having altered alkaloid levels with desirable leaf quality (2024-01-02). Altria Client Services LLC [US]. Inventors: Marcos Fernando de Godoy Lusso [US], James A. Strickland [US], Jesse Frederick [US], Dongmei Xu [US], Chengalrayan Kudithipudi [US].
Full text: Click here
Patent 2024
Anabolism Biosynthetic Pathways enzyme activity Plant Roots Plants Polyamines Putrescine
2
Lignosulfonate-Polyamine Composite Synthesis
Not available on PMC !

Example 1

Calcium lignosulfonate (Borrement CA 2120) was provided by Borregaard LignoTech. Sodium lignosulfonate was purchased from Aldrich, and ammonium lignosulfonate was obtained from TemBac.

Sodium carboxymethylcellulose (NaCMC), hydroxypropylcellulose (HPC) and hydroxyethylcellulose (HEC) were obtained from Aldrich and showed a Mw of approx. 250 kDa, 100 kDa and 100 kDa, respectively.

The amine functional material such as hexamethylene diamine (HMDA) and diethylenetriamine (DETA) were obtained from Aldrich. Different types of polyethylenimines (Lupasol® EO, Lupasol® PS, Lupasol® P and Lupasol® G100), polyvinyl amines (Luredur® VM, Luredur® VH and Luredur® VI), were obtained from BASF Chemical Company, and polyetheramines (JeffamineED600, JeffamineEDR148, JeffamineT403) from Huntsman Holland BV.

The required amounts of polymer and lignosulfonate (LS) were dissolved in water individually. The required amount of polyamine functional compound was added to the LS solution followed by homogenization. The polymer solution and LS-amine solution were then combined at ambient temperature and stirred at 500 rpm for 30 minutes.

US11879063B2. Binder compositions and uses thereof (2024-01-23). KNAUF INSULATION SPRL [BE], KNAUF INSULATION, INC. [US]. Inventors: Carl Hampson [GB], Ferdous Khan [GB].
Full text: Click here
Patent 2024
Amines Ammonium calcium lignosulfonate Cyclohexane Diamines diethylenetriamine hydroxyethylcellulose hydroxypropylcellulose lignosulfonates Polyamines Polyethyleneimine Polymers Polyvinyls Sodium Sodium Carboxymethylcellulose TLR4 agonist G100
3
Synthesis of Polyam-N-Cu2+ Resin
A commercially available weak base anion exchanger (Purolite weak base anion, details in table S4) with primary amine functional groups was used as the parent polymer for preparing Polyam-N-Cu2+. The parent polyamine resin has an average particle size of 500 ± 50 μm and was conditioned by rinsing with distilled water (DI) for 1 hour before use. Similar products are likely to be available from other manufacturers; no endorsement is implied. To convert the parent polyamine resin into Polyam-N-Cu2+, a CuCl2 solution (1000 mg/liter) at pH ≈ 4.0 was passed through the parent resin in a fixed-bed column. After loading the Cu, the resin beads were rinsed with DI to remove the residual chemicals, and the as-prepared Polyam-N-Cu2+ resin beads were used in this study after air drying. A chelating polymeric resin with iminodiacetate functionality (Amberlite IRC718; details in table S2) was treated through the same Cu(II)-loading protocol to prepare polyiminodiacetate-Cu and compare with Polyam-N-Cu2+.
Chen H., Dong H., Shi Z, & SenGupta A.K. (2023). Direct air capture (DAC) and sequestration of CO2: Dramatic effect of coordinated Cu(II) onto a chelating weak base ion exchanger. Science Advances, 9(10), eadg1956.
Publication 2023
amberlite Amines Anions AS resin cupric chloride Debility Parent Polyamines Polymers Resins, Plant
4
Constructing and Characterizing pI-SceI and pCut Plasmids
pI-SceI was constructed by cloning the I-sceI nuclease from pSLTS [a gift from Shelley Copley, Addgene plasmid #59386, (61 (link))] cloned into the expression vector pHERD30T between the EcoRI and XbaI sites using primers I-SceI F and I-SceI R (Table 2). Restriction cloning sites in primer sequences are indicated by capital letters. pCut was constructed by cloning the I-SceI recognition sequence (TAGGGATAACAGGGTAAT) into pUCP18 between the HindIII and EcoRI sites. pEmpty is simply the empty pUCP18 vector. Primers used to screen for the presence/absence of circular and linear plasmid DNA are as follows: pCutF and M13R produce a 1-kb product indicating the presence of circular pCut (these primers will not amplify linearized pCut DNA). pCutF and pCutR produce a 0.5-kb product indicating the presence of both linear and circular forms of pCut. Clones carrying pI-SceI and confirmed linearized pCut plasmid DNA or those carrying pEmpty were grown with or without 50 mM putrescine in LB broth for the indicated times. Intracellular polyamines were measured as described above.
de Mattos C.D., Faith D.R., Nemudryi A.A., Schmidt A.K., Bublitz D.C., Hammond L., Kinnersley M.A., Schwartzkopf  C.M., Robinson A.J., Joyce A., Michaels L.A., Brzozowski R.S., Coluccio A., Xing D.D., Uchiyama J., Jennings L.K., Eswara P., Wiedenheft B, & Secor P.R. (2023). Polyamines and linear DNA mediate bacterial threat assessment of bacteriophage infection. Proceedings of the National Academy of Sciences of the United States of America, 120(9), e2216430120.
Publication 2023
Clone Cells Cloning Vectors Deoxyribonuclease EcoRI Oligonucleotide Primers Plasmids Polyamines Protoplasm Putrescine
5
Quantifying Bacterial Polyamine Levels
Polyamines were measured using the Total Polyamine Assay Kit (MAK349, Sigma). A 100 µL aliquot of the indicated bacterial cultures was collected, centrifuged, washed with 1× PBS, and resuspended in PBS. Bacteria were lysed with 1:10 vol/vol chloroform, vortexed, and incubated at room temperature for 2 h. The solution was centrifuged, and the top aqueous layer was collected. Following the manufacturer’s instructions, 1.0 µL of the collected sample was mixed with the Total Polyamine Assay Kit reagents, incubated at 37 °C for 30 min, and read using a CLARIOStar plate reader using end point fluorescence (λex = 535 nm/λem = 587 nm). Polyamine concentrations were determined by comparing values to a standard curve constructed from known concentrations of putrescine. Values were then normalized to OD600 measurements taken from the original bacterial cultures.
de Mattos C.D., Faith D.R., Nemudryi A.A., Schmidt A.K., Bublitz D.C., Hammond L., Kinnersley M.A., Schwartzkopf  C.M., Robinson A.J., Joyce A., Michaels L.A., Brzozowski R.S., Coluccio A., Xing D.D., Uchiyama J., Jennings L.K., Eswara P., Wiedenheft B, & Secor P.R. (2023). Polyamines and linear DNA mediate bacterial threat assessment of bacteriophage infection. Proceedings of the National Academy of Sciences of the United States of America, 120(9), e2216430120.
Publication 2023
Bacteria Biological Assay Chloroform Fluorescence Polyamines Putrescine Specimen Collection

Top products related to «Polyamines»

1
Spermidine by Merck Group
Sourced in United States, Germany, China, United Kingdom, Sao Tome and Principe, Italy
Spermidine is a laboratory product offered by Merck Group. It is a naturally occurring polyamine compound found in various living organisms. Spermidine plays a role in cellular processes, but a detailed description of its core function is not available without potential for bias or extrapolation.
2
Dansyl chloride by Merck Group
Sourced in United States, Germany, Italy, China, United Kingdom, Canada
Dansyl chloride is a fluorescent labeling reagent commonly used in analytical chemistry. It is a small molecule that reacts with primary amines, resulting in the formation of a fluorescent dansyl derivative. Dansyl chloride is employed in various analytical techniques, such as high-performance liquid chromatography (HPLC) and fluorescence spectroscopy, to facilitate the detection and quantification of labeled compounds.
3
Spermine by Merck Group
Sourced in United States, Germany, United Kingdom, Portugal
Spermine is a laboratory reagent used in various scientific applications. It is a naturally occurring polyamine that plays a role in cellular processes. As a laboratory product, Spermine's core function is to serve as a chemical compound for research and analysis purposes. No further interpretation or extrapolation on its intended use is provided.
4
Putrescine by Merck Group
Sourced in United States, Germany, France, United Kingdom, Spain, Canada, Japan
Putrescine is a chemical compound that is used as a building block in various laboratory experiments and applications. It has a core function as a reagent or intermediate in scientific research and analysis.
5
Polyamine by Merck Group
Sourced in United States, Japan
Polyamines are a class of organic compounds that contain multiple amino groups. They are commonly used in various laboratory applications, including biochemistry, cell biology, and molecular biology. Polyamines play a crucial role in cellular processes such as nucleic acid synthesis, cell growth, and gene expression.
6
Fetal bovine serum (fbs) by Thermo Fisher Scientific
Sourced in United States, China, United Kingdom, Germany, Australia, Japan, Canada, Italy, France, Switzerland, New Zealand, Brazil, Belgium, India, Spain, Israel, Austria, Poland, Ireland, Sweden, Macao, Netherlands, Denmark, Cameroon, Singapore, Portugal, Argentina, Holy See (Vatican City State), Morocco, Uruguay, Mexico, Thailand, Sao Tome and Principe, Hungary, Panama, Hong Kong, Norway, United Arab Emirates, Czechia, Russian Federation, Chile, Moldova, Republic of, Gabon, Palestine, State of, Saudi Arabia, Senegal
Fetal Bovine Serum (FBS) is a cell culture supplement derived from the blood of bovine fetuses. FBS provides a source of proteins, growth factors, and other components that support the growth and maintenance of various cell types in in vitro cell culture applications.
7
Proline by Merck Group
Sourced in United States, Germany, United Kingdom, Japan, China, Belgium, Switzerland, Spain, Australia, Italy
Proline is a lab equipment product manufactured by Merck Group. It is a versatile instrument designed for performing various laboratory tasks. The core function of Proline is to provide accurate and reliable measurements and analysis in a wide range of scientific applications.
8
Synergy 2 multi function microplate reader by Agilent Technologies
Sourced in United States
The Synergy 2 Multi-Function Microplate Reader is a versatile laboratory instrument designed to perform various detection methods for microplate-based assays. It can measure absorbance, fluorescence, luminescence, and time-resolved fluorescence within microplates.
9
Toluene by Merck Group
Sourced in United States, Germany, Italy, United Kingdom, India, Spain, Japan, Poland, France, Switzerland, Belgium, Canada, Portugal, China, Sweden, Singapore, Indonesia, Australia, Mexico, Brazil, Czechia
Toluene is a colorless, flammable liquid with a distinctive aromatic odor. It is a common organic solvent used in various industrial and laboratory applications. Toluene has a chemical formula of C6H5CH3 and is derived from the distillation of petroleum.
10
Total polyamine assay kit by Abcam
Sourced in United States, Canada
The Total Polyamine Assay Kit is a quantitative colorimetric assay that measures the total polyamine content in biological samples. The kit provides a simple and reliable method to determine the overall polyamine levels.

More about "Polyamines"

Polyamines are a class of organic compounds featuring two or more amino groups.
These versatile biomolecules play a pivotal role in various cellular processes, including cell growth, differentiation, and gene regulation.
Key polyamines include putrescine, spermidine, and spermine, which are found across a wide range of organisms, from bacteria to humans.
Studying polyamine metabolism and function is crucial for understanding fundamental biological mechanisms and developing potential therapeutic applications in areas such as cancer, neurological disorders, and immune function.
Researchers can leverage advanced tools like PubCompare.ai to optimize their polyamine research.
This AI-driven platform helps scientists easily locate reliable protocols from literature, preprints, and patents, using sophisticated search and comparison features.
By enhancing reproducibility and accuracy through AI-driven analysis, scientists can identify the most effective and reliable approaches, driving breakthroughs in this dynamic field of study.
Polyamine research often involves techniques such as dansyl chloride derivatization and total polyamine assays using platforms like the Synergy 2 Multi-Function Microplate Reader.
Additionally, factors like fetal bovine serum (FBS) and amino acids like proline can influence polyamine metabolism and cellular processes.
By incorporating these related terms and concepts, researchers can gain a comprehensive understanding of the polyamine landscape and unlock new insights.