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Integrated metallomic and metabolomic profiling of plasma and tissues provides deep insights into the protective effect of raw and salt-processed Achyranthes bidentata Blume extract in ovariectomia rats
پروفایل فلزی و متابولیکی یکپارچه پلاسما و بافتها ، بینش عمیقی در مورد اثر محافظت شده از عصاره خام و نمک فرآوری شده Ashyranthes bidentata Blume در تخمدان موش -2019 Ethnopharmacological relevance: Achyranthes bidentata Blume (AB) is a well-known traditional Chinese medicine
for treating osteoporosis and bone fracture. In the current, researches on pharmacological mechanism of AB
mostly focused on molecular pathways, knowledge about its metabolic signatures is largely unclear. This study
aims to develop an integrative metabolomics and metallomic approach for deciphering the biochemical basis of
anti-osteoporosis effects of raw and salt-processed AB.
Method: Gas chromatography–mass spectrometry (GC–MS) and inductively coupled plasma mass spectrometry
(ICP-MS) were combined for metabolomic and metallomic profiling of rats serum, liver and kidney derived from
the sham group, model group, E2, raw and salt-processed AB treated groups. Meanwhile, micro-CT and biomechanical
analysis were carried out to ensure the success of the osteoporosis model and to validate the antiosteoporosis
effect of raw and salt-processed AB. Partial least squares discriminant analysis (PLS-DA) was employed
to screen potential biomarkers and the MetaboAnalyst and KEGG PATHWAY Database were used to
investigate the metabolic pathway.
Results: Raw and salt-processed AB protected the rats against osteoporosis, as evidenced by the restoration of the
alkaline phosphatase activity, osteocalcin concentration, urine calcium/creatinine ratio and urine phosphorus/
creatinine ratio. The combination of PCA and PLS-DA revealed deviations in ninety-four differential biomarkers
between raw AB treated group and model group. The identified biomarkers were primarily engaged in the
metabolic pathways including galactose metabolism, urea cycle, arginine and proline metabolism, alanine
metabolism, lactose degradation, ammonia recycling and glycine and serine metabolism. The levels of these
biomarkers showed significant alterations and a tendency to be restored to normal values in raw and saltprocessed
AB treated osteoporosis rats. Of note, the levels of trace elements, such as Zn, Se, Mn, Cu and Fe, were
elevated after raw and salt-processed AB treatment. Finally, a correlation network diagram was constructed to
show the biomarkers perturbed by raw and salt-processed AB.
Conclusion: Our findings indicate that raw and salt-processed AB has positive effects on osteoporosis rats.
Meanwhile, metabolomic and metallomic method coupled with metabolites enrichment analysis and pattern
recognition serves as a useful tool for revealing the action mechanism of traditional Chinese medicine. Keywords: Anti-osteoporosis | Achyranthes bidentata Blume | GC-MS | ICP-MS | Pattern recognition |
مقاله انگلیسی |
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Glioma stages prediction based on machine learning algorithm combined with protein-protein interaction networks
پیش بینی مراحل گلیوما بر اساس الگوریتم یادگیری ماشین همراه با شبکه های تعامل پروتئین-پروتئین-2019 Background: Glioma is the most lethal nervous system cancer. Recent studies have made great efforts to study
the occurrence and development of glioma, but the molecular mechanisms are still unclear. This study was
designed to reveal the molecular mechanisms of glioma based on protein-protein interaction network combined
with machine learning methods. Key differentially expressed genes (DEGs) were screened and selected by using
the protein-protein interaction (PPI) networks.
Results: As a result, 19 genes between grade I and grade II, 21 genes between grade II and grade III, and 20 genes
between grade III and grade IV. Then, five machine learning methods were employed to predict the gliomas
stages based on the selected key genes. After comparison, Complement Naive Bayes classifier was employed to
build the prediction model for grade II-III with accuracy 72.8%. And Random forest was employed to build the
prediction model for grade I-II and grade III-VI with accuracy 97.1% and 83.2%, respectively. Finally, the selected
genes were analyzed by PPI networks, Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and
Genomes (KEGG) pathways, and the results improve our understanding of the biological functions of select DEGs
involved in glioma growth. We expect that the key genes expressed have a guiding significance for the occurrence
of gliomas or, at the very least, that they are useful for tumor researchers.
Conclusion: Machine learning combined with PPI networks, GO and KEGG analyses of selected DEGs improve
our understanding of the biological functions involved in glioma growth. Keywords: DEGs | Machine learning | PPI networks | GO | KEGG | SVM | ANN | Random forest | Couple naïve Bayes |
مقاله انگلیسی |
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Genome-wide analysis of Excretory/Secretory proteins in root-knot nematode, Meloidogyne incognita provides potential targets for parasite control
تحلیل گسترده ژنومی پروتئین های غضولاتی/ تراوشی در نماتود ریشه - گره، ملوئیدوژین اهداف بالقوه ای برای کنترل پارازیت فراهم می کند-2017 The root-knot nematode, Meloidogyne incognita causes significant damage to various economically
important crops. Infection is associated with secretion of effector proteins into host cytoplasm and
interference with host innate immunity. To combat this infection, the identification and functional
annotations of Excretory/Secretory (ES) proteins serve as a key to produce durable control measures. The
identification of ES proteins through experimental methods are expensive and time consuming while
bioinformatics approaches are cost-effective by prioritizing the experimental analysis of potential drug
targets for parasitic diseases. In this study, we predicted and functionally annotated the 1889 ES proteins
in M. incognita genome using integration of several bioinformatics tools. Of these 1889 ES proteins, 473
(25%) had orthologues in free living nematode Caenorhabditis elegans, 825(67.8%) in parasitic nematodes
whereas 561 (29.7%) appeared to be novel and M. incognita specific molecules. Of the C. elegans
homologues, 17 ES proteins had “loss of function phenotype” by RNA interference and could represent
potential drug targets for parasite intervention and control. We could functionally annotate 429 (22.7%)
ES proteins using Gene Ontology (GO) terms, 672 (35.5%) proteins to protein domains and established
pathway associations for 223 (11.8%) sequences using Kyoto Encyclopaedia of Genes and Genomes
(KEGG). The 162 (8.5%) ES proteins were also mapped to several important plant cell-wall degrading
CAZyme families including chitinase, cellulase, xylanase, pectate lyase and endo-b-1,4-xylanase. Our
comprehensive analysis of M. incognita secretome provides functional information for further
experimental study.
Keywords: Excretory/secretory proteins | Phytonematode | Host-pathogen interaction | Drug targets | Parasitism genes | Effector proteins |
مقاله انگلیسی |
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Genome-wide identification and characterization of conserved and novel microRNAs in grass carp (Ctenopharyngodon idella) by deep sequencing
شناسایی و تشخیص ژنوم وسیع میکرو RNA های نگهداری شده و نوین در توده علف توسط ترتیب گذاری عمیق-2017 MicroRNAs (miRNAs) are post-transcriptional regulators which bind to target to regulate protein
expression by repressing translation or promoting degradation of the target mRNA. Studies have shown
that deep sequencing is a powerful tool for the identification of miRNAs, and it is believed that may more
miRNAs remain to be discovered in grass carp. In the present study, a pool of equal amounts of RNA
obtained from 8 different adult grass carp tissues (spleen, liver, muscle, kidney, skin, testis, gut and heart)
was sequenced using deep sequencing technology. A total of 16.579.334 raw reads were yielded from the
pooled small RNA library. Using bioinformatics analysis, we identified 160 conserved miRNAs and 18
novel miRNAs in grass carp. Randomly selected 6 conserved and 2 novel miRNAs were confirmed their
expression by stem-loop qRT-PCR assay. Furthermore, the 1212 potential targets of these miRNAs were
predicted using miRNA target prediction tool. GO and KEGG pathway enrichment analyses indicated
relevant biological processes. Our study provides the first genome-wide investigation of miRNAs from 8
mixed tissues of grass carp, and the data obtained expand the known grass carp miRNA inventory and
provide a basis for further understanding functions of grass carp miRNAs.
Keywords: Grass carp | miRNA | Deep sequencing | Targets |
مقاله انگلیسی |
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Comprehensive comparison of two protein family of P-ATPases (13A1 and 13A3) in insects
مقایسه جامع دو P-ATPase خانواده پروتئین (13A1 و 13A3) در حشرات-2017 The P-type ATPases (P-ATPases) are present in all living cells where they mediate ion transport across membranes on the expense of ATP hydrolysis. Different ions which are transported by these pumps are protons like calcium, sodium, potassium, and heavy metals such as manganese, iron, copper, and zinc. Maintenance of the proper gradients for essential ions across cellular membranes makes P-ATPases crucial for cell survival. In this study, characterization of two families of P-ATPases including P-ATPase 13A1 and P-ATPase 13A3 protein was compared in two different insect species from different orders. According to the conserved motifs found with MEME, nine motifs were shared by insects of 13A1 family but eight in 13A3 family. Seven different insect species from 13A1 and five samples from 13A3 family were selected as the representative samples for functional and structural analyses. The structural and functional analyses were performed with ProtParam, SOPMA, SignalP 4.1, TMHMM 2.0, ProtScale and ProDom tools in the ExPASy database. The tertiary structure of Bombus terrestris as a sample of each family of insects were predicted by the Phyre2 and TM-score servers and their similarities were verified by SuperPose server. The tertiary structures were predicted via the “c3b9bA” model (PDB Accession Code: 3B9B) in P-ATPase 13A1 family and “c2zxeA” model (PDB Accession Code: 2ZXE) in P-ATPase 13A3 family. A phylogenetic tree was constructed with MEGA 6.06 software using the Neighbor-joining method. According to the results, there was a high identity of P-ATPase families so that they should be derived from a common ancestor however they belonged to separate groups. In protein–protein interaction analysis by STRING 10.0, six common enriched pathways of KEGG were identified in B. terrestris in both families. The obtained data provide a background for bioinformatic studies of the function and evolution of other insects and organisms.© 2017 Elsevier Ltd. All rights reserved. |
مقاله انگلیسی |