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Sustained release of naringin from silk-fibroin-nanohydroxyapatite scaffold for the enhancement of bone regeneration. Mater Today Bio 2022; 13:100206. [PMID: 35128373 PMCID: PMC8808263 DOI: 10.1016/j.mtbio.2022.100206] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 12/14/2022] Open
Abstract
Bone defects are a common challenge in the clinical setting. Bone tissue engineering (BTE) is an effective treatment for the clinical problem of large bone defects. In this study, we fabricated silk fibroin (SF)/hydroxyapatite (HAp) scaffolds inlaid with naringin poly lactic-co-glycolic acid (PLGA) microspheres, investigating the feasibility of their application in BTE. Naringin PLGA microspheres were manufactured and adhered to the SF/HAp scaffold. Bone mesenchymal stem cells (BMSCs) were inoculated onto the SF/HAp scaffold containing naringin PLGA microsphere to examine the biocompatibility of the SF/HAp scaffolds. A rabbit femoral distal bone defect model was used to evaluate the in vivo function of the SF/HAp scaffolds containing naringin-loaded PLGA microspheres. The current study demonstrated that SF/HAp scaffolds containing naringin-loaded PLGA microspheres show promise as osteo-modulatory biomaterials for bone regeneration.
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Key Words
- ALP, Alkaline phosphatase activity
- ANOVA, one-way analysis of variance
- BMSCs, Bone mesenchymal stem cells
- BP, biological process
- BTE, Bone tissue engineering
- Bone defect
- CC, cellular component
- CCK-8, Cell count kit-8
- DAVID, database for annotation, visualization, and integrated discovery
- GO, Gene ontology
- HAp, hydroxyapatite
- HUVEC, human umbilical endothelial cells
- Hydroxyapatite
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- MF, molecular function
- Microsphere
- Naringin
- PLGA
- PLGA, poly lactic-co-glycolic acid
- PVA, Polyvinyl alcohol
- RNA-Seq, RNA sequencing
- RT-PCR, real-time quantitative polymerase chain reaction
- SEM, scanning electron microscopy
- SF, silk fibroin
- Silk
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2
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Mendelian randomization analysis identified genes potentially pleiotropically associated with periodontitis. Saudi J Biol Sci 2021; 28:4089-4095. [PMID: 34220266 PMCID: PMC8241609 DOI: 10.1016/j.sjbs.2021.04.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 02/26/2021] [Accepted: 04/08/2021] [Indexed: 10/26/2022] Open
Abstract
OBJECTIVE To prioritize genes that were pleiotropically or potentially causally associated with periodontitis. METHODS We applied the summary data-based Mendelian randomization (SMR) method integrating genome-wide association study (GWAS) for periodontitis and expression quantitative trait loci (eQTL) data to identify genes that were pleiotropically associated with periodontitis. We performed separate SMR analysis using CAGE eQTL data and GTEx eQTL data. SMR analysis were done for participants of European and East Asian ancestries, separately. RESULTS We identified multiple genes showing pleiotropic association with periodontitis in participants of European ancestry and participants of East Asian ancestry. PDCD2 (corresponding probe: ILMN_1758915) was the top hit showing pleotropic association with periodontitis in the participants of European ancestry using CAGE eQTL data, and BX093763 (corresponding probe: ILMN_1899903) and AC104135.3 (corresponding probe: ENSG00000204792.2) were the top hits in the participants of East Asian ancestry using CAGE eQTL data and GTEx eQTL data, respectively. CONCLUSION We identified multiple genes that may be involved in the pathogenesis of periodontitis in participants of European ancestry and participants of East Asian ancestry. Our findings provided important leads to a better understanding of the mechanisms underlying periodontitis and revealed potential therapeutic targets for the effective treatment of periodontitis.
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Interpopulation differences of retroduplication variations (RDVs) in rice retrogenes and their phenotypic correlations. Comput Struct Biotechnol J 2021; 19:600-611. [PMID: 33510865 PMCID: PMC7811064 DOI: 10.1016/j.csbj.2020.12.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/29/2020] [Accepted: 12/31/2020] [Indexed: 11/21/2022] Open
Abstract
Retroduplication variation (RDV), a type of retrocopy polymorphism, is considered to have essential biological significance, but its effect on gene function and species phenotype is still poorly understood. To this end, we analyzed the retrocopies and RDVs in 3,010 rice genomes. We calculated the RDV frequencies in the genome of each rice population; detected the mutated, ancestral and expressed retrogenes in rice genomes; and analyzed their RDV influence on rice phenotypic traits. Collectively, 73 RDVs were identified, and 14 RDVs in ancestral retrogenes can significantly affect rice phenotypes. Our research reveals that RDV plays an important role in rice migration, domestication and evolution. We think that RDV is a good molecular breeding marker candidate. To our knowledge, this is the first study on the relationship between retrogene function, expression, RDV and species phenotype.
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Identification of potential therapeutic target of naringenin in breast cancer stem cells inhibition by bioinformatics and in vitro studies. Saudi Pharm J 2021; 29:12-26. [PMID: 33603536 PMCID: PMC7873751 DOI: 10.1016/j.jsps.2020.12.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 12/03/2020] [Indexed: 12/15/2022] Open
Abstract
Cancer therapy is a strategic measure in inhibiting breast cancer stem cell (BCSC) pathways. Naringenin, a citrus flavonoid, was found to increase breast cancer cells' sensitivity to chemotherapeutic agents. Bioinformatics study and 3D tumorsphere in vitro modeling in breast cancer (mammosphere) were used in this study, which aims to explore the potential therapeutic targets of naringenin (PTTNs) in inhibiting BCSCs. Bioinformatic analyses identified direct target proteins (DTPs), indirect target proteins (ITPs), naringenin-mediated proteins (NMPs), BCSC regulatory genes, and PTTNs. The PTTNs were further analyzed for gene ontology, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, protein-protein interaction (PPI) networks, and hub protein selection. Mammospheres were cultured in serum-free media. The effects of naringenin were measured by MTT-based cytotoxicity, mammosphere forming potential (MFP), colony formation, scratch wound-healing assay, and flow cytometry-based cell cycle analyses and apoptosis assays. Gene expression analysis was performed using real-time quantitative polymerase chain reaction (q-RT PCR). Bioinformatics analysis revealed p53 and estrogen receptor alpha (ERα) as PTTNs, and KEGG pathway enrichment analysis revealed that TGF-ß and Wnt/ß-catenin pathways are regulated by PTTNs. Naringenin demonstrated cytotoxicity and inhibited mammosphere and colony formation, migration, and epithelial to mesenchymal transition in the mammosphere. The mRNA of tumor suppressors P53 and ERα were downregulated in the mammosphere, but were significantly upregulated upon naringenin treatment. By modulating the P53 and ERα mRNA, naringenin has the potential of inhibiting BCSCs. Further studies on the molecular mechanism and formulation of naringenin in BCSCs would be beneficial for its development as a BCSC-targeting drug.
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Key Words
- BCSCs, Breast cancer stem cells
- Bioinformatics
- Breast cancer stem cells
- CSC, Cancer stem cell
- DAVID, Database for Annotation, Visualization, and Integrated Discovery
- DTPs, Direct target proteins
- DXR, Doxorubicin
- EGF, Epidermal growth factor
- EMT, Epithelial to mesenchymal transition
- ERα
- FITC, fluorescein isothiocyanate
- GO, Gene ontology
- ITPs, Indirect target proteins
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- MET, Metformin
- MFP, Mammosphere forming potential
- NAR, Naringenin
- NMPs, Naringenin-mediated proteins
- Naringenin
- P53
- PE, phycoerythrin
- PPI, Protein-protein interaction
- PTTN, Potential target of naringenin in inhibition of BCSCs
- ROS, Reactive oxygen species
- Targeted therapy
- q-RT PCR, Quantitative real-time polymerase chain reaction
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Bioinformatics analyses of significant genes, related pathways, and candidate diagnostic biomarkers and molecular targets in SARS-CoV-2/COVID-19. GENE REPORTS 2020; 21:100956. [PMID: 33553808 PMCID: PMC7854084 DOI: 10.1016/j.genrep.2020.100956] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/31/2020] [Indexed: 12/12/2022]
Abstract
Severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) infection is a leading cause of pneumonia and death. The aim of this investigation is to identify the key genes in SARS-CoV-2 infection and uncover their potential functions. We downloaded the expression profiling by high throughput sequencing of GSE152075 from the Gene Expression Omnibus database. Normalization of the data from primary SARS-CoV-2 infected samples and negative control samples in the database was conducted using R software. Then, joint analysis of the data was performed. Pathway and Gene ontology (GO) enrichment analyses were performed, and the protein-protein interaction (PPI) network, target gene - miRNA regulatory network, target gene - TF regulatory network of the differentially expressed genes (DEGs) were constructed using Cytoscape software. Identification of diagnostic biomarkers was conducted using receiver operating characteristic (ROC) curve analysis. 994 DEGs (496 up regulated and 498 down regulated genes) were identified. Pathway and GO enrichment analysis showed up and down regulated genes mainly enriched in the NOD-like receptor signaling pathway, Ribosome, response to external biotic stimulus and viral transcription in SARS-CoV-2 infection. Down and up regulated genes were selected to establish the PPI network, modules, target gene - miRNA regulatory network, target gene - TF regulatory network revealed that these genes were involved in adaptive immune system, fluid shear stress and atherosclerosis, influenza A and protein processing in endoplasmic reticulum. In total, ten genes (CBL, ISG15, NEDD4, PML, REL, CTNNB1, ERBB2, JUN, RPS8 and STUB1) were identified as good diagnostic biomarkers. In conclusion, the identified DEGs, hub genes and target genes contribute to the understanding of the molecular mechanisms underlying the advancement of SARS-CoV-2 infection and they may be used as diagnostic and molecular targets for the treatment of patients with SARS-CoV-2 infection in the future.
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Key Words
- Bioinformatics
- CBL, Cbl proto-oncogene
- DEGs, differentially expressed genes
- Diagnosis
- GO, Gene ontology
- ISG15, ISG15 ubiquitin like modifier
- Key genes
- NEDD4, NEDD4 E3 ubiquitin protein ligase
- PML, promyelocyticleukemia
- PPI, protein-protein interaction
- Pathways
- REL, REL proto-oncogene, NF-kB subunit
- ROC, receiver operating characteristic
- SARS-CoV-2 infection
- SARS-CoV-2, Severe acute respiratory syndrome corona virus 2
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Lingzhi and San-Miao-San with hyaluronic acid gel mitigate cartilage degeneration in anterior cruciate ligament transection induced osteoarthritis. J Orthop Translat 2020; 26:132-140. [PMID: 33437632 PMCID: PMC7773973 DOI: 10.1016/j.jot.2020.07.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/27/2020] [Accepted: 07/31/2020] [Indexed: 12/20/2022] Open
Abstract
Objective To investigate the mitigate efficacy of Chinese medicine Lingzhi (LZ) and San-Miao-San (SMS) combined with hyaluronic acid (HA)-gel in attenuating cartilage degeneration in traumatic osteoarthritis (OA). Methods The standardized surgery of anterior cruciate ligament transection (ACLT) was made from the medial compartment of right hind limbs of 8-week-old female SD rats and resulted in a traumatic OA. Rats (n = 5/group) were treated once intra-articular injection of 50 μl HA-gel, 50 μl HA-gel+50 μg LZ-SMS, 50 μl of saline+50 μg LZ-SMS and null (ACLT group) respectively, except sham group. Limbs were harvested for μCT scan and histopathological staining 3-month post-treatment. Inflammatory cytokines from plasma and synovial fluid were detected using Immunology Multiplex Assay kit. The putative targets of active compounds in LZ-SMS and known therapeutic targets for OA were combined to construct protein–protein interaction network. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was adopted to predict the potential targets and signaling pathway of LZ-SMS in OA through the tool of DAVID Bioinformatics. Results In vivo, HA-gel + LZ-SMS treatment resulted in a higher volume ratio of hyaline cartilage (HC)/calcified cartilage (CC) and HC/Sum (total volume of cartilage), compared to ACLT and HA-gel groups. In addition, histological results showed the elevated cartilage matrix, chondrogenic and osteoblastic signals in HA-gel + LZ-SMS treatment. Treatment also significantly altered subchondral bone (SCB) structure including an increase in BV/TV, Tb.Th, BMD, Conn.Dn, Tb.N, and DA, as well as a significant decrease in Tb.Sp and Po(tot), which implied a protective effect on maintaining the stabilization of tibial SCB microstructure. Furthermore, there was also a down-regulated inflammatory cytokines and upregulated anti-inflammatory cytokine IL-10 in HA+LZ-SMS group. Finally, 64 shared targets from 37 active compounds in LZ-SMS related to the core genes for the development of OA. LZ-SMS has a putative role in regulating inflammatory circumstance through influencing the MAPK signaling pathway. Conclusion Our study elucidated a protective effect of HA-gel + LZ-SMS in mitigating cartilage degradation and putative interaction with targets and signaling pathway for the development of traumatic OA. The translational potential of this article Our results provide a biological rationale for the use of LZ-SMS as a potential candidate for OA treatment.
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Key Words
- 3D, Three-dimensional
- AC, Articular cartilage
- ACLT, Anterior cruciate ligament transection
- Acan, Aggrecan
- Articular cartilage
- BMD, Bone mineral density
- BV/TV, Bone volume fraction
- CC, Calcified cartilage
- Conn.Dn, Connectivity density
- DA, Degree of anisotropy
- DL, Drug-likeness
- ECM, Extracellular matrix
- FDR, False discovery rate
- GO, Gene ontology
- HA, Hyaluronic acid
- HC, Hyaline cartilage
- Hyaluronic acid gel
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- LZ-SMS, Lingzhi-San-Miao-San
- Lingzhi and San-Miao-San
- MZ, Middle zone area of articular cartilage
- NC, Negative control
- OA, Osteoarthritis
- OB, Oral bioavailability
- OMIM, Online Mendelian Inheritance in Man
- Osteoarthritis
- PPI, Protein–protein interaction
- Po(tot), Total porosity
- ROI, Region of Interest
- SC, Superficial cartilage
- SCB, Subchondral bone
- SZ, Superficial zone of articular cartilage
- Subchondral trabecular bone
- Sum, Whole cartilage
- TCM, Traditional Chinese medicine
- TCMSP, Traditional Chinese Medicine Systems Pharmacology Database
- Tb.N, Trabecular number
- Tb.Pf, Trabecular bone pattern factor
- Tb.Sp, Trabecular separation
- Tb.Th, Trabecular thickness
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ceRNA network development and tumour-infiltrating immune cell analysis of metastatic breast cancer to bone. J Bone Oncol 2020; 24:100304. [PMID: 32760644 PMCID: PMC7393400 DOI: 10.1016/j.jbo.2020.100304] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/09/2020] [Accepted: 07/10/2020] [Indexed: 12/18/2022] Open
Abstract
PURPOSE Advanced breast cancer commonly metastasises to bone; however, the molecular mechanisms underlying the affinity for breast cancer cells to bone remains unclear. Thus, we developed nomograms based on a competing endogenous RNA (ceRNA) network and analysed tumour-infiltrating immune cells to elucidate the molecular pathways that may predict prognosis in patients with breast cancer. METHODS We obtained the RNA expression profile of 1091 primary breast cancer samples included in The Cancer Genome Atlas database, 58 of which were from patients with bone metastasis. We analysed the differential RNA expression patterns between breast cancer with and without bone metastasis and developed a ceRNA network. Cibersort was employed to differentiate between immune cell types based on tumour transcripts. Nomograms were then established based on the ceRNA network and immune cell analysis. The value of prognostic factors was evaluated by Kaplan-Meier survival analysis and a Cox proportional risk model. RESULTS We found significant differences in long non-coding RNAs (lncRNAs), 18 microRNAs (miRNAs), and 20 messenger RNAs (mRNAs) between breast cancer with and without bone metastasis, which were used to construct a ceRNA network. We found that the protein-coding genes GJB3, CAMMV, PTPRZ1, and FBN3 were significantly differentially expressed by Kaplan-Meier analysis. We also observed significant differences in the abundance of plasma cell and follicular helper T cell populations between the two groups. In addition, the proportion of mast cells, gamma delta T cells, and plasma cells differed depending on disease location and stage. Our analysis showed that a high proportion of follicular helper T cells and a low proportion of eosinophils promoted survival and that DLX6-AS1, Wnt6, and GABBR2 expression may be associated with bone metastasis in breast cancer. CONCLUSIONS We developed a bioinformatic tool for exploring the molecular mechanisms of bone metastasis in patients with breast cancer and identified factors that may predict the occurrence of bone metastasis.
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Key Words
- AIC, Akaike information criterion
- AUC, Area under curve
- Bone metastasis
- Breast cancer
- DE, Differentially expressed
- DEmRNA, differentially expressed messenger RNA
- EMT, epithelial-mesenchymal transition
- ER, estrogen receptor
- FPKM, fragments per kilobase per million mapped reads
- GO, Gene ontology
- HER2, human epidermal growth factor receptor 2
- Immune infiltration
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- Nomogram
- PCC, Pearson correlation coefficient
- Prognosis
- ROC curve, receiver operating characteristic curve
- Runx2, runt related transcription factor 2
- TCGA, The Cancer Genome Atlas
- TNM, Tumor, Node, Metastases
- ceRNA network
- ceRNA, competing endogenous RNA
- lncRNA, long non-coding RNA
- mRNA, messenger RNA
- miRNA, microRNA
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Iron deficiency triggered transcriptome changes in bread wheat. Comput Struct Biotechnol J 2020; 18:2709-2722. [PMID: 33101609 PMCID: PMC7550799 DOI: 10.1016/j.csbj.2020.09.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 09/07/2020] [Accepted: 09/07/2020] [Indexed: 11/21/2022] Open
Abstract
A series of complex transport, storage and regulation mechanisms control iron metabolism and thereby maintain iron homeostasis in plants. Despite several studies on iron deficiency responses in different plant species, these mechanisms remain unclear in the allohexaploid wheat, which is the most widely cultivated commercial crop. We used RNA sequencing to reveal transcriptomic changes in the wheat flag leaves and roots, when subjected to iron limited conditions. We identified 5969 and 2591 differentially expressed genes (DEGs) in the flag leaves and roots, respectively. Genes involved in the synthesis of iron ligands i.e., nicotianamine (NA) and deoxymugineic acid (DMA) were significantly up-regulated during iron deficiency. In total, 337 and 635 genes encoding transporters exhibited altered expression in roots and flag leaves, respectively. Several genes related to MAJOR FACILITATOR SUPERFAMILY (MFS), ATP-BINDING CASSETTE (ABC) transporter superfamily, NATURAL RESISTANCE ASSOCIATED MACROPHAGE PROTEIN (NRAMP) family and OLIGOPEPTIDE TRANSPORTER (OPT) family were regulated, indicating their important roles in combating iron deficiency stress. Among the regulatory factors, the genes encoding for transcription factors of BASIC HELIX-LOOP-HELIX (bHLH) family were highly up-regulated in both roots and the flag leaves. The jasmonate biosynthesis pathway was significantly altered but with notable expression differences between roots and flag leaves. Homoeologs expression and induction bias analysis revealed subgenome specific differential expression. Our findings provide an integrated overview on regulated molecular processes in response to iron deficiency stress in wheat. This information could potentially serve as a guideline for breeding iron deficiency stress tolerant crops as well as for designing appropriate wheat iron biofortification strategies.
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Key Words
- 3-HMA, 3-hydroxymugineic acid
- ABC, ATP-BINDING CASSETTE
- ACC, 1-aminocyclopropane-1-carboxylate
- AEC, AUXIN EFFLUX CARRIER
- AOC, ALLENE OXIDE CYCLASE
- AOS, ALLENE OXIDE SYNTHASE
- AQP, AQUAPORIN
- AVA, avenic acid
- DEGs, differentially expressed genes
- DMA, deoxymugineic acid
- DMAS, DEOXYMUGINEIC ACID SYNTHASE
- DPA, days post anthesis
- ERF, ETHYLENE-RESPONSIVE FACTOR
- FAD, FATTY ACID DESATURASE
- FDR, false discovery rate
- FIT, FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR
- FRO, FERRIC REDUCTASE OXIDASE
- GCN, gene co-expression network
- GO, Gene ontology
- GSH, GLUTATHIONE
- HC, high confidence
- HMA, HEAVY METAL-ASSOCIATED
- IDE, iron deficiency-responsive cis-acting element
- IDEF, IDE BINDING FACTOR
- IHW, independent hypothesis weighting
- ILR3, IAA‐LEUCINE RESISTANT3
- IREG/FPN, IRON REGULATED PROTEIN/FERROPORTIN
- IRT1, IRON-REGULATED TRANSPORTER
- Iron deficiency
- Iron, Fe
- JAs, jasmonates
- JMT, JASMONATE O-METHYLTRANSFERASE
- KAT, 3-KETOACYL-COA THIOLASE
- LOX, LIPOXYGENASE
- MA, mugineic acid
- MATE, MULTI ANTIMICROBIAL EXTRUSION PROTEIN
- MFS, MAJOR FACILITATOR SUPERFAMILY
- MRP, MULTIDRUG RESISTANCE PROTEIN
- MT, METALLOTHIONEIN
- NA, nicotianamine
- NAAT, NICOTIANAMINE AMINOTRANSFERASE
- NAC, NO APICAL MERISTEM (NAM)/ARABIDOPSIS TRANSCRIPTION ACTIVATION FACTOR (ATAF)/CUP-SHAPED COTYLEDON (CUC)
- NAS, NICOTIANAMINE SYNTHASE
- NRAMP, NATURAL RESISTANCE ASSOCIATED MACROPHAGE PROTEIN
- NRT1/PTR, NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER
- OPCL, 4-COUMARATE COA LIGASE
- OPR, 12-OXOPHYTODIENOATE REDUCTASE
- OPT, OLIGOPEPTIDE TRANSPORTER
- PDR, PLEIOTROPIC DRUG RESISTANCE
- PLA, PHOSPHOLIPASE A1
- PRI, POSITIVE REGULATOR OF IRON DEFICIENCY RESPONSE
- PSs, phytosiderophores
- PT, peptide transport
- PYE, POPEYE
- RNA sequencing
- SAM, S-adenosyl-L-methionine
- SAMS, S-ADENOSYL-L-METHIONINE SYNTHETASE
- SLC40A1, SOLUTE CARRIER FAMILY 40 MEMBER 1
- SWEET, SUGARS WILL EVENTUALLY BE EXPORTED TRANSPORTERS
- TOM, TRANSPORTER OF MUGINEIC ACID
- Transcriptomic profiles
- VIT, VACUOLAR IRON TRANSPORTER
- Wheat
- YSL, YELLOW STRIPE LIKE
- ZIFL, ZINC INDUCED FACILITATOR-LIKE
- ZIP, ZINC/IRON PERMEASE
- bHLH, BASIC HELIX-LOOP-HELIX
- bZIP, BASIC LEUCINE ZIPPER
- epiHDMA, 3-epihydroxy-2′-deoxymugineic acid
- epiHMA, 3-epihydroxymugineic acid
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An Evaluation of Machine Learning Approaches for the Prediction of Essential Genes in Eukaryotes Using Protein Sequence-Derived Features. Comput Struct Biotechnol J 2019; 17:785-796. [PMID: 31312416 PMCID: PMC6607062 DOI: 10.1016/j.csbj.2019.05.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/23/2019] [Accepted: 05/26/2019] [Indexed: 12/23/2022] Open
Abstract
The availability of whole-genome sequences and associated multi-omics data sets, combined with advances in gene knockout and knockdown methods, has enabled large-scale annotation and exploration of gene and protein functions in eukaryotes. Knowing which genes are essential for the survival of eukaryotic organisms is paramount for an understanding of the basic mechanisms of life, and could assist in identifying intervention targets in eukaryotic pathogens and cancer. Here, we studied essential gene orthologs among selected species of eukaryotes, and then employed a systematic machine-learning approach, using protein sequence-derived features and selection procedures, to investigate essential gene predictions within and among species. We showed that the numbers of essential gene orthologs comprise small fractions when compared with the total number of orthologs among the eukaryotic species studied. In addition, we demonstrated that machine-learning models trained with subsets of essentiality-related data performed better than random guessing of gene essentiality for a particular species. Consistent with our gene ortholog analysis, the predictions of essential genes among multiple (including distantly-related) species is possible, yet challenging, suggesting that most essential genes are unique to a species. The present work provides a foundation for the expansion of genome-wide essentiality investigations in eukaryotes using machine learning approaches.
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Key Words
- CRISPR, Clustered regularly interspaced short palindromic repeats
- Essential genes
- Essentiality prediction
- Eukaryotes
- GBM, Gradient boosting method
- GI, Genetic interaction
- GLM, Generalised linear model
- GO, Gene ontology
- ML, Machine-learning
- Machine-learning
- NN, Artificial neural network
- OGEE, Online GEne essentiality database
- PPI, Protein-protein interaction
- PR-AUC, Area under the precision-recall curve
- RF, Random Forest
- RNAi, RNA interference
- ROC-AUC, Area under the receiver operating characteristic curve
- SPLS, Sparse partial least squares
- SVM, Support-Vector machine
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De novo sequencing of Eucommia ulmoides flower bud transcriptomes for identification of genes related to floral development. GENOMICS DATA 2016; 9:105-10. [PMID: 27486566 PMCID: PMC4957572 DOI: 10.1016/j.gdata.2016.07.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 06/28/2016] [Accepted: 07/06/2016] [Indexed: 12/18/2022]
Abstract
Eucommia ulmoides Oliver is a woody perennial dioecious species native to China and has great economic value. However, little is known about flower bud development in this species. In this study, the transcriptomes of female and male flower buds were sequenced using the Illumina platform, a next-generation sequencing technology that provides cost-effective, highly efficient transcriptome profiling. In total, 11,558,188,080 clean reads were assembled into 75,065 unigenes with an average length of 1011 bp by de novo assembly using Trinity software. Through similarity comparisons with known protein databases, 47,071 unigenes were annotated, 146 of which were putatively related to the floral development of E. ulmoides. Fifteen of the 146 unigenes had significantly different expression levels between the two samples. Additionally, 24,346 simple sequence repeats were identified in 18,565 unigenes with 12,793 sequences suitable for the designed primers. In total, 67,447 and 58,236 single nucleotide polymorphisms were identified in male and female buds, respectively. This study provides a valuable resource for further conservation genetics and functional genomics research on E. ulmoides.
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Adaptation of the targeted capture Methyl-Seq platform for the mouse genome identifies novel tissue-specific DNA methylation patterns of genes involved in neurodevelopment. Epigenetics 2016; 10:581-96. [PMID: 25985232 DOI: 10.1080/15592294.2015.1045179] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Methyl-Seq was recently developed as a targeted approach to assess DNA methylation (DNAm) at a genome-wide level in human. We adapted it for mouse and sought to examine DNAm differences across liver and 2 brain regions: cortex and hippocampus. A custom hybridization array was designed to isolate 99 Mb of CpG islands, shores, shelves, and regulatory elements in the mouse genome. This was followed by bisulfite conversion and sequencing on the Illumina HiSeq2000. The majority of differentially methylated cytosines (DMCs) were present at greater than expected frequency in introns, intergenic regions, near CpG islands, and transcriptional enhancers. Liver-specific enhancers were observed to be methylated in cortex, while cortex specific enhancers were methylated in the liver. Interestingly, commonly shared enhancers were differentially methylated between the liver and cortex. Gene ontology and pathway analysis showed that genes that were hypomethylated in the cortex and hippocampus were enriched for neuronal components and neuronal function. In contrast, genes that were hypomethylated in the liver were enriched for cellular components important for liver function. Bisulfite-pyrosequencing validation of 75 DMCs from 19 different loci showed a correlation of r = 0.87 with Methyl-Seq data. We also identified genes involved in neurodevelopment that were not previously reported to be differentially methylated across brain regions. This platform constitutes a valuable tool for future genome-wide studies involving mouse models of disease.
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Key Words
- Apcdd1, Adenomatous Polyposis Coli Down-Regulated 1
- ChIP, Chromatin immunoprecipitation
- DMCs, Differentially methylated cytosines (DMCs)
- DMRs, Differentially methylated regions
- DNA methylation
- DNAm, DNA methylation
- FDR, False discovery rate
- GFAP, Glial fibrillary acidic protein
- GO, Gene ontology
- Gb, Gigabases
- H3K27ac, Histone 3 lysine 27 acetylation
- H3K4me1, Histone marks histone 3 lysine 4 monomethylation
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- MAP, Mitogen activated protein
- Msx1, msh homeobox1
- PAVIS, Peak Annotation and Visualization
- RV, Range of variation
- TFBS, Transcription factor binding sites
- UTR, Untranslated regions.
- brain
- epigenetics
- genome-wide
- methylation array
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Gene expression profiling data of Schizosaccharomyces pombe under nitrosative stress using differential display. Data Brief 2015; 6:101-11. [PMID: 26858975 PMCID: PMC4706557 DOI: 10.1016/j.dib.2015.11.047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 11/17/2015] [Accepted: 11/22/2015] [Indexed: 12/02/2022] Open
Abstract
Excess production of nitric oxide (NO) and reactive nitrogen intermediates (RNIs) causes nitrosative stress on cells. Schizosaccharomyces pombe was used as a model to study nitrosative stress response. In the present data article, we have used differential display to identify the differentially expressed genes in the fission yeast under nitrosative stress conditions. We have used pure NO donor compound detaNONOate at final concentrations of 0.1 mM and 1 mM to treat the cells for 15 min alongside control before studying their gene expression profiles. At both the treated conditions, we identified genes which were commonly repressed while several genes were induced upon both 0.1 mM and 1 mM treatments. The differentially expressed genes were further analyzed in DAVID and categorized into several different pathways.
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