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Lingzhi

Lingzhi, also known as Ganoderma lucidum, is a popular medicinal mushroom prized for its potential health benefits.
This fungus has been used in traditional Chinese medicine for centuries and is the subject of ongoing scientific research.
The PubCompare.ai platform leverages AI-driven analysis to help researchers optimize their Lingzhi studies by identifying the most accurate and reproducible protocols from academic literature, preprints, and patents.
This intelligent comparison feature ensures users can find the best Lingzhi products and procedures to enhance their research outcomes and experince seamless, data-driven Lingzhi research.

Most cited protocols related to «Lingzhi»

1
Phylogenomic Analysis of Fungal Diversity
Together with V. volvacea, 14 fungal species assigned mainly to the Basidiomycota (phyla are not italicized) and Ascomycota were used in the phylogenomic analysis. Genomic data for eight species (Agaricus bisporus, Aspergillus niger, Ganoderma lucidum, Phanerochaete chrysosporium, Puccinia graminis, Saccharomyces cerevisiae, Schizophyllum commune and Trichoderma reesei) were obtained from the Joint Genome Institute (JGI), and for five species (Coprinopsis cinerea, Cryptococcus neoformans, Neurospora crassa, Rhizopus oryzae, Ustilago maydis) from the Broad Institute. Single-copy orthologous protein sequences from the genomes of 14 species were obtained using our custom perl program. The tandem concatenated sequences consisting of 178 single-copy orthologous sequences from the 14 species were then used to construct a phylogenomic tree using the neighbor-joining method [85] (link) (bootstrap  = 1000, JTT matrix). Timescale estimation of phylogenomic analysis with calibration was implemented in the codeml program [86] (link) of the PAML package (version 4) [70] (link). The divergence time between species was estimated using PAML [87] (link) by calibrating against the reassessed origin of U. maydis at 550 million years ago [88] (link). We used both global and local clock methods [89] (link) to estimate the timescale of species divergence, and linear regression was applied to test the congruence between the global and local clocks.
Bao D., Gong M., Zheng H., Chen M., Zhang L., Wang H., Jiang J., Wu L., Zhu Y., Zhu G., Zhou Y., Li C., Wang S., Zhao Y., Zhao G, & Tan Q. (2013). Sequencing and Comparative Analysis of the Straw Mushroom (Volvariella volvacea) Genome. PLoS ONE, 8(3), e58294.
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Publication 2013
Agaricus bisporus var. albidus Amino Acid Sequence Ascomycetes Aspergillus niger Basidiomycota CLOCK protein, human Coprinus cinereus Cryptococcus neoformans Genome Joints Lingzhi Neurospora crassa Phanerochaete chrysosporium Puccinia graminis Rhizopus oryzae Saccharomyces cerevisiae Schizophyllum commune Trees Trichoderma reesei Ustilago maydis
2
Comprehensive Basidiomycete P450 Monooxygenase Survey
P450 monooxygenases of selected basidiomycete species were obtained from the published data and publicly available data bases. The literature that was consulted on the respective species included the following publications: Phanerochaete chrysosporium: Syed and Yadav [19] (link) and Hirosue et al., [41] (link); Phanerochaete carnosa: Sukuzi et al., [10] (link); Postia placenta: Ide et al., [20] (link) and Ganoderma sp.: Syed et al., [12] (link). Annotated P450s for Agaricus bisporus, Serpula lacrymans and Tremella mesenterica were downloaded from the Fungal Cytochrome P450 Database (FCPD) (http://p450.riceblast.snu.ac.kr/index.php?a=view) [44] (link). The revised FCPD represents fungal P450 nomenclature equivalent to the standard P450 nomenclature [45] (link). P450s for the medicinal mushroom Ganoderma lucidum strain 260125-1 [9] (link) were kindly provided by Dr David Nelson, University of Tennessee, USA. The cytochrome P450 webpage (http://drnelson.uthsc.edu/P450seqs.dbs.html) [46] (link) was also visited for analysis of P450 signature domains and confirmation of pseudo P450s. Furthermore, the annotated P450s of animal pathogen/parasite Cryptococcus neoformans were downloaded from the cytochrome P450 webpage [46] (link).
Among the P450 sequences resourced, as mentioned above, only the authentic P450s, i.e. those P450s containing both P450 signature motifs (heme-binding sequence motif FXXGXXXCXG and the EXXR motif in the K-helix), were selected for analysis. Hence, the P450 count reported in this study for the P450 family is slightly different from the P450 count presented in published literature and public data bases (Table S1). Pseudo P450s and alleles (for Postia placenta) are not included in this study.
Syed K., Shale K., Pagadala N.S, & Tuszynski J. (2014). Systematic Identification and Evolutionary Analysis of Catalytically Versatile Cytochrome P450 Monooxygenase Families Enriched in Model Basidiomycete Fungi. PLoS ONE, 9(1), e86683.
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Publication 2014
Agaricales Agaricus bisporus var. albidus Alleles Animals Basidiomycota Cryptococcus neoformans Cytochrome P450 Ganoderma Helix (Snails) Heme Lingzhi Mixed Function Oxygenases Parasites Pathogenicity Phanerochaete carnosa Phanerochaete chrysosporium Postia placenta Serpula lacrymans Strains Tremella mesenterica
3
Reishi Inhibits Breast Cancer Growth in SCID Mice
Female severe combined immunodeficient (SCID) mice (21 d of age) were purchased from Charles River Laboratories International Inc. (Wilmington, MA) and housed under specific pathogen-free conditions. The mice received autoclaved AIN 76-A phytoestrogen-free diet (Tek Global, Harlan Teklad, Madison, WI) and water ad libitum. Cell inoculations were performed as previously described by us [20] (link). SUM-149 cells (∼1×106) in Matrigel (BD Biosciences, San Jose, CA) were injected into the mammary fat pad under isofluorane inhalation as described in [20] (link), [21] (link). After tumor establishment (1 week post-inoculation), the animals were randomly divided into control (n = 11) and experimental (n = 11) groups. Mice were gavaged every day with vehicle or 28 mg/kg BW of Reishi for a period of 13 week. Mice were weighed weekly and tumor volume was measured once a week along two major axes using calipers measurements. Tumor volume (mm3) was calculated as follows: π/6 (L)(W)(H). The relative tumor volumes were calculated as the ratio of the average tumor volume on week n divided by the average tumor volume on week one. Tumor weights were obtained at the end of the study.
Suarez-Arroyo I.J., Rosario-Acevedo R., Aguilar-Perez A., Clemente P.L., Cubano L.A., Serrano J., Schneider R.J, & Martínez-Montemayor M.M. (2013). Anti-Tumor Effects of Ganoderma lucidum (Reishi) in Inflammatory Breast Cancer in In Vivo and In Vitro Models. PLoS ONE, 8(2), e57431.
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Publication 2013
Animals Breast Cells Epistropheus Inhalation Lingzhi matrigel Mus Neoplasms Pad, Fat Phytoestrogens Rivers SCID Mice Specific Pathogen Free Therapy, Diet Vaccination Woman
4
Genome assembly and annotation of Ganoderma lingzhi
A DNA library with 350-bp inserts was constructed and sequenced under an Illumina HiSeqX-Ten. For the PacBio RSII platform, a 20-kb library was generated and sequenced. The genome size of G. lingzhi was estimated by the k-mer method using sequencing data from the Illumina DNA library. Quality-filtered reads were subjected to 17-mer frequency distribution analysis using Jellyfish v2.2.1058 (link). Then, the genome size, heterozygosity and repeat content were estimated by Genome-Scope web tools59 (link). The de novo assembly of contigs was performed with FALCON (version 0.7.0). Pilon (v 1.23) was utilized to further correct the PacBio-corrected contigs with accurate Illumina short reads and to generate the genome assembly of G. lingzhi. The genome assembly was evaluated using BUSCO 3.1.0 (Benchmarking Universal Single-Copy Orthologues) with comparison to the lineage dataset fungi_odb9 (Creation date: 2016-10-21, number of species: 85, number of BUSCOs: 290).
For genome annotation, both homologous comparison and de novo prediction were used to annotate the repeated sequences within the G. lingzhi genome. A more detailed description can be found in previous reports60 (link). The assembly reported in this paper is associated with NCBI BioProject: PRJNA738334 and BioSample: SAMN19718602. The data have been deposited in NCBI’s Sequence Read Archive under accession numbers SRR14933280 and SRR14933281.
Liu Y.N., Wu F.Y., Tian R.Y., Shi Y.X., Xu Z.Q., Liu J.Y., Huang J., Xue F.F., Liu B.Y, & Liu G.Q. (2023). The bHLH-zip transcription factor SREBP regulates triterpenoid and lipid metabolisms in the medicinal fungus Ganoderma lingzhi. Communications Biology, 6, 1.
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Publication 2023
DNA Library Fungi Genome Heterozygote Lingzhi Repetitive Region
5
Genome-wide SREBP bHLH Binding Profiling
DAP-seq genomic DNA library preparation: Fresh G. lingzhi mycelia were ground to fine powder using liquid nitrogen. DNA was extracted by CTAB and dissolved in Tris-EDTA buffer. DNA libraries were constructed by fragmenting genomic DNA to an average of 200 bp using a Covaris M220 (Woburn, MA, USA) according to the manufacturer’s recommended setting. DAP-seq protein expression: The coding sequence of the SREBP bHLH domain was cloned into a pFN19K HaloTag T7 SP6 Flexi expression vector61 (link). The halo–SREBP bHLH fusion protein was expressed using the TNT SP6 Coupled Wheat Germ Extract System (Promega) following the manufacturer’s specifications and was directly captured using Magne Halo Tag Beads (Promega). DAP-seq binding assay and sequencing: The protein-bound beads were incubated with gDNA fragments, and the bound DNA fragments were released by heating to 98 °C. The bound DNA fragments were amplified by employing the KAPA HiFi HotStart ReadyMixPCR Kit (Roche, Basel, Switzerland). The PCR product was purified using AMPure XP beads (Beckman) and sequenced on an Illumina NavoSeq. DAP-seq data processing: Reads were mapped to the G. lingzhi genome sequence (this study) using BOWTIE262 (link). The reads are enriched at a certain location, which is called the peak. Peak calling was conducted using Macs263 (link). Associations of DAP-seq peaks located upstream or downstream of the transcription start site within 3.5 kb were analysed using Homer64 (link), based on the general feature format (gff) files. Gene function annotation was blasted against the NR, NT, SwissProt, and Pfam databases. FASTA sequences were obtained using BEDTools for motif analysis65 (link). Motif discovery was performed using MEME-Chip suite 5.0.534 (link).
Liu Y.N., Wu F.Y., Tian R.Y., Shi Y.X., Xu Z.Q., Liu J.Y., Huang J., Xue F.F., Liu B.Y, & Liu G.Q. (2023). The bHLH-zip transcription factor SREBP regulates triterpenoid and lipid metabolisms in the medicinal fungus Ganoderma lingzhi. Communications Biology, 6, 1.
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Publication 2023
Biological Assay Cetrimonium Bromide DNA Chips DNA Library Edetic Acid Gene Annotation Genome Genomic Library HaloTag Lingzhi Mycelium Nitrogen Open Reading Frames Powder Promega Proteins Sterol Regulatory Element Binding Proteins Transcription Initiation Site Triticum aestivum Tromethamine

Most recents protocols related to «Lingzhi»

1
Trichoderma-Ganoderma Interaction Transcriptome
Trichoderma hengshanicum “1009” and G. lingzhi “11GL-16” were used in all experiments and preserved in the Development and Utilization Laboratory of Fungi Resource of Jilin Agricultural Science and Technology College. G. lingzhi was grown in an edible fungus base. For G. lingzhi-back inoculation, the fruiting bodies of some growth vigor were strictly selected. T. hengshanicum isolated on potato dextrose agar (PDA) was propagated in a constant temperature incubator at 25°C for 4 days. The G. lingzhi fruiting bodies were inoculated with 5-mm-diameter mycelial blocks (from PDA culture plates). The control group inoculated PDA agar blocks without mycelium. At 0, 2, 12, and 24 h after inoculation, the G. lingzhi fruiting bodies were cut off with a sterile scalpel at a distance of 5 mm from the lesions and stored at −80°C after quick freezing with liquid nitrogen. At 0, 2, 12, and 24 h after inoculation, three fruiting bodies were taken from each replicate of each treatment group. The frozen samples were used for RNA sequencing.
Wang T., Li X., Zhang C, & Xu J. (2023). Transcriptome analysis of Ganoderma lingzhi (Agaricomycetes) response to Trichoderma hengshanicum infection. Frontiers in Microbiology, 14, 1131599.
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Publication 2023
Agar Cardiac Arrest DNA Replication Freezing Fungi Glucose Human Body Lingzhi Nitrogen Solanum tuberosum Sterility, Reproductive Trichoderma hengshanicum Vaccination
2
Validation of RNA-seq Results in Ganoderma lingzhi
RNA-seq results were validated by selecting six DEGs to examine the consistency of their expression profiles. Total RNAs were extracted from collected G. lingzhi materials using the Trizol (Invitrogen, USA) kit according to the manufacturer’s instructions. First-strand cDNAs were synthesized by the PrimeScript™ 1st stand cDNA Synthesis Kit. The internal transcribed spacer (ITS) gene was used as an internal control. Volume for all the reactions was 20 μL; 1 μL cDNA, 10 μL 2 × SYBR real-time PCR (Applied Biosystem, Carlsbad, CA, USA), and 0.4 μL of each primer. The PCR procedure was 5 min at 95°C, followed by 40 cycles of 15 s at 95°C and 30 s at 60°C. Three biological replicates were performed per sample. The formula of 2–ΔΔCT was used to calculate gene relative expression levels.
Wang T., Li X., Zhang C, & Xu J. (2023). Transcriptome analysis of Ganoderma lingzhi (Agaricomycetes) response to Trichoderma hengshanicum infection. Frontiers in Microbiology, 14, 1131599.
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Publication 2023
Anabolism Biopharmaceuticals DNA, Complementary Gene Expression Genes Lingzhi Oligonucleotide Primers Real-Time Polymerase Chain Reaction RNA RNA-Seq trizol
3
Extraction and Characterization of EBF-2 Herbal Formula
EBF-2 was generated by purification of FAHF-2 with a safe solvents consisting of butanol and ethyl acetate (52 (link)). 8 herb constituents (Prunus mume, Zanthoxylum schinifolium, Angelica sinensis, Zingiber officinalis, Cinnamomum cassia, Phellodendron chinense, Coptis chinensis, and Panax ginseng) were extracted using butanol, while the Ganoderma lucidum was extracted using ethyl acetate and the dried extracts were combined to generate the EBF-2 powder substance. Three batches of FAHF-2 and EBF-2 were tested in this study-manufacturing date and shelf life are listed in Supplemental Table 1. Botanical information for individual herbs, including geographical location, harvest season, pre-processing, heavy metal and pesticide residues, and quality control methods, have been published previously (54 (link)).
Yang N., Maskey A.R., Srivastava K., Kim M., Wang Z., Musa I., Shi Y., Gong Y., Fidan O., Wang J., Dunkin D., Chung D., Zhan J., Miao M., Sampson H.A, & Li X.M. (2023). Inhibition of pathologic immunoglobulin E in food allergy by EBF-2 and active compound berberine associated with immunometabolism regulation. Frontiers in Immunology, 14, 1081121.
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Publication 2023
Angelica sinensis Butyl Alcohol Cinnamomum cassia Coptis chinensis ethyl acetate Lingzhi Metals, Heavy Panax ginseng Pesticide Residues Phellodendron Powder Prunus Solvents Zanthoxylum
4
Ganoderma lucidum Mouse Study Protocol

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Publication 2023
Animal Ethics Committees Buffers Distillation Edetic Acid Lingzhi Mice, Inbred C57BL Oligonucleotide Primers paraform Sodium Chloride
5
Extraction of Ganoderma lucidum Polysaccharides

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Publication 2023
Bath Centrifugation Ethanol Lingzhi Polysaccharides Sterility, Reproductive

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More about "Lingzhi"

Lingzhi, also known as Ganoderma lucidum, is a renowned medicinal mushroom revered in traditional Chinese medicine for its potential health benefits.
This fungus, scientifically classified as Ganoderma, has been utilized for centuries and continues to be the subject of extensive research.
The PubCompare.ai platform leverages advanced AI-driven analysis to help researchers optimize their Lingzhi studies.
By identifying the most accurate and reproducible protocols from academic literature, preprints, and patents, PubCompare.ai ensures users can access the best Lingzhi products and procedures to enhance their research outcomes.
This intelligent comparison feature enables seamless, data-driven Lingzhi research.
Lingzhi, or Reishi as it is sometimes called, is a polypore fungus that belongs to the Ganodermataceae family.
It is commonly known by its Chinese name, Lingzhi, which translates to 'divine mushroom' or 'mushroom of immortality'.
This unique fungus has been utilized in traditional Chinese medicine for its potential to promote longevity, improve overall health, and support the immune system.
In addition to its traditional uses, Lingzhi has been the subject of extensive scientific research.
Researchers have explored the potential therapeutic properties of Lingzhi, including its antioxidant, anti-inflammatory, and immunomodulatory effects.
Studies have investigated the use of Lingzhi in the management of various health conditions, such as cancer, heart disease, and diabetes.
The PubCompare.ai platform harnesses the power of artificial intelligence to streamline Lingzhi research.
By analyzing data from academic literature, preprints, and patents, the platform identifies the most reliable and reproducible protocols for Lingzhi studies.
This feature empowers researchers to access the best Lingzhi products and procedures, ensuring their research outcomes are optimized and their Lingzhi experince is seamless.
Lingzhi, with its long history in traditional medicine and growing scientific interest, continues to captivate researchers and healthcare professionals alike.
The PubCompare.ai platform's AI-driven approach to Lingzhi research optimization ensures that users can navigate the complexities of this fascinating fungus with ease and confidence.