Shotgun based proteomics and peptidomics analysis were used to investigate the proteins and peptides in marine traditional Chinese medicine(TCM) Sepiae Endoconcha(cuttlebone). Peptides were extracted from cuttlebone by acidified methanol, and then strong cation exchange(SCX) resin was used to enrich those peptides. Also, proteins from cuttlebone were extracted and digested by trypsin. nano-LC Q Exactive Orbitrap mass spectrometry was used to analyze proteins and peptides from cuttlebone. As a result, a total of 16 proteins and 168 peptides were identified by protein database search, and 328 peptides were identified by De novo sequencing. The identified proteins were hemocyanin, enolase, myosin, actin, calmodulin, etc., and the identified peptides were derived from actin, histone, and tubulin. All these proteins and peptides were important components in cuttlebone, which would provide important theoretical and research basis for marine TCM cuttlebone investigations.
Cations ; Databases, Protein ; Mass Spectrometry ; Peptides ; Proteomics

Atherosclerosis is the main cause of stroke, and dyslipidemia is the most important risk factor for atherosclerosis. In this paper, pharmacophore and molecular docking models of eight key lipid-lowering targets, namely NPC1 L1, HMG-CoA reductase, SQS, MTP, CETP, PPARα, LXRα and LXRβ, were used to screen out the small molecular database of traditional Chinese medicine(TCM), which was made up of ingredients of thirteen Chinese herbal medicines contained in Xixian Tongshuan Preparation. The screening results indicated that the preparation could showed an effect in regulating lipid on target NPC1 L1, HMG-CoA reductase, LXRβ and SQS through four groups of potential active compounds, namely prupersin A in peach kernel and suffruticoside A in gastrodiaelata, limocitrin-β-D-glucoside in Ligusticum chuanxiong, 2'-(2,3-dihydroxybenzoyl)-sweroside in Pinellia ternate and quercitrin in Panax notoginseng, 4-tert-butyl-2-[(5-tert-butyl-2-hydroxy-phenyl)methoxy-methyl]-6-(hydroxymethyl)phenol in Gastrodia elata. Moreover, the properties and extraction process of the most potentialactive compounds were consistent with the preparation process of Xixian Tongshuan Capsules, which indicated that the capsule had more advantages than the pill in the existing two dosage forms of Xixian Tongshuan Preparation. This study analyzed the pharmacodynamic basis and mechanism of Xixian Tongshuan Capsules in regulating lipid for treating stroke, and provided evidence for its further research and clinical application.
Databases, Chemical ; Drugs, Chinese Herbal ; pharmacology ; Lipid Metabolism ; Lipids ; Medicine, Chinese Traditional ; Molecular Docking Simulation

In a population-based study with 4 years of follow up, we evaluated the prevalence of Coxiella burnetii in cattle on Ulleung Island, Korea. In this study, the rates of C. burnetii infection in cattle on Ulleung Island were determined by PCR and were found to be 0.3–1.0% in the period 2011–2014. All 17 C. burnetii partial 16S rRNA gene sequences from PCR-positive cattle were identical and 2 geographic representatives were included in our analysis. The nucleotide sequences of the 2 samples showed high (98.4–100%) identity with C. burnetii sequences obtained from the GenBank. In this long-term tracking study, the number of cattle positive for C. burnetii on Ulleung Island was low. To prevent the transmission of C. burnetii on Ulleung Island, control strategy should include biosecurity improvement in surveillance, livestock management, administering suitable tests before purchasing animals to detect C. burnetii shedders, and restricting movements between herds.
Animals ; Base Sequence ; Cattle ; Coxiella burnetii ; Coxiella ; Databases, Nucleic Acid ; Follow-Up Studies ; Genes, rRNA ; Korea ; Livestock ; Phylogeny ; Polymerase Chain Reaction ; Prevalence

Forensic science is an academic field that utilizes scientific knowledge and the conducting of research in legal procedures. Recently, legal science has been receiving more attention since the use of DNA identification started, especially in criminal procedures, in accordance with the development of human genetics. DNA identification has been used to identify criminals by analyzing humanoriginated biological materials obtained from crime scenes, and, more recently, the breadth and effectiveness of their use has been increasing with the operation of DNA databases. The Korean government regulates the operation and utilization of the DNA database through the “Act on Use and Protection of DNA Identification Information.” Meanwhile, the actual study of human genetics is regulated by the “Bioethics and Safety Act.” Professional areas, such as forensic science, are not areas where regulation by the laws is appropriate. However, the core part of behavior has to be ruled by the laws, considering the impact of scientific achievements on society and individuals when they are utilized. Since most scientific research and performance utilization belong in the scientific and technological domains, regulation through experts' autonomous guidelines is more appropriate. For the regulation of biomedical research through ethical guidelines, some requirements should be satisfied: the ethical guideline should be made by suitable professionals; the ethical guideline should be scientifically and ethically reliable; the ethical guideline should be enforced by a trustworthy institution; and most importantly, the scientist community should be trustworthy.
Crime ; Criminals ; Databases, Nucleic Acid ; DNA ; Forensic Sciences ; Genetics, Medical ; Humans ; Jurisprudence

Cryptosporidium is a common intestinal protozoan that can lead to diarrhea in humans and dogs. The predominant species of infection are C. hominis and C. parvum in humans, and C. canis in dogs. However, C. canis can infect immunocompromised humans. Considering the close contact with humans, dogs have the potential to be reservoirs for human cryptosporidiosis. Breeding kennels are the major supply source of puppies for pet shops. The present study is to determine the molecular prevalence and characteristics of Cryptosporidium spp. found in breeding kennel dogs. A total of 314 fecal samples were collected from young and adult dogs kept in 5 breeding kennels. A polymerase chain reaction targeting the small subunit rRNA gene was employed for the detection of Cryptosporidium spp. To determine the species, the DNA sequences were compared to GenBank data. Overall, 21.0% of the fecal samples were positive for Cryptosporidium spp. infection. Cryptosporidium spp. was detected in all 5 facilities. A sequencing analysis demonstrated that all isolates shared 99–100% similarity with C. canis. The results suggest that Cryptosporidium spp. infection is present at a high-level in breeding kennel dogs. However, because dominant species in this survey was C. canis, the importance of breeding kennel dogs as reservoirs for Cryptosporidium spp. transmission to humans is likely to be low in Japan.
Adult ; Animals ; Base Sequence ; Breeding ; Cryptosporidiosis ; Cryptosporidium ; Databases, Nucleic Acid ; Diarrhea ; Dogs ; Genes, rRNA ; Humans ; Japan ; Polymerase Chain Reaction ; Prevalence

Mitochondrial DNA sequence variability of Spirometra erinaceieuropaei in GenBank was observed by reinvestigation of mitochondrial cox1 and cytb sequences. The DNA sequences were analyzed in this study, comprising complete DNA sequences of cox1 (n=239) and cytb (n=213) genes. The 10 complete mitochondrial DNA sequences of Spirometra species were compared with those of Korea, China and Japan. The sequences were analyzed for nucleotide composition, conserved sites, variable sites, singleton sites and parsimony-informative sites. Phylogenetic analyses was done using neighbor joining, maximum parsimony, Bayesian inference and maximum-likelihood on cox1 and cytb sequences of Spirometra species. These polymorphic sites identified 148 (cox1) and 83 (cytb) haplotypes within 239 and 213 isolates from 3 Asian countries. Phylogenetic tree topologies were presented high-level confidence values for the 2 major branches of 2 Spirometra species containing S. erinaceieuropaei and S. decipiens, and S. decipiens sub-clades including all sequences registered as S. erinaceieuropaei in cox1 and cytb genes. These results indicated that mitochondrial haplotypes of S. erinaceieuropaei and S. decipiens were found in the 3 Asian countries.
Asian Continental Ancestry Group ; Base Sequence ; China ; Databases, Nucleic Acid ; DNA, Mitochondrial ; Haplotypes ; Humans ; Japan ; Korea ; Mitochondria ; Spirometra ; Trees

We analyzed Clonorchis sinensis ancient DNA (aDNA) acquired from the specimens of the Joseon mummies. The target regions were cytochrome C oxidase subunit 1 (CO1), internal transcribed spacer 1 (ITS1), nicotinamide adenine dinucleotide hydrogen (NADH) dehydrogenase subunits 2 (NAD2) and 5 (NAD5). The sequences of C. sinensis aDNA was completely or almost identical to modern C. sinensis sequences in GenBank. We also found that ITS1, NAD2 and NAD5 could be good markers for molecular diagnosis between C. sinensis and the other trematode parasite species. The current result could improve our knowledge about genetic history of C. sinensis.
Clonorchis sinensis ; Cytochromes c ; Cytochromes ; Databases, Nucleic Acid ; Diagnosis ; DNA ; Electron Transport Complex IV ; Hydrogen ; Mummies ; NAD ; Niacinamide ; Oxidoreductases ; Parasites ; Republic of Korea

In this paper,the case reports on rug-induced liver injury( ADR cases) related to Gukang Capsules containing Psoralea corylifolia( Buguzhi,BGZ) were collected from the adverse reaction monitoring database from January 1,2012 to December 31,2016,and the in-patients cases with drug-induced liver injury admitted to a tertiary Class A liver disease hospital from January 1,2010 to December 31,2016 were also collected. These collected cases were re-evaluated and analyzed. 110 cases with liver injury related to this preparation were collected from adverse reaction monitoring database,and 55 cases of them received the preparation alone,mainly for fracture treatment( 52. 74%). Ninty one cases( 82. 72%) met the standard of the biochemical diagnostic criteria for drug-induced liver injury. 89. 01% of patients were over the age of 41 and women accounted for 60. 9%. The time from administration to liver injury was 1-208 days,with the median of 29 d. The dose of the preparation was 2. 4-4. 8 g per day,with a cumulative dose ranging from 3. 6-699. 6 g. The recovery and improvement rate reached 96. 70% after positive treatment. Seven inpatient cases related to the preparation were collected in a tertiary Class A liver disease hospital,6 females and 1 male. All of them were over 40 years old. Two cases reached the " suspicious diagnosis" standard and 5 cases reached the " clinical diagnosis" standard in Guidelines for the diagnosis and treatment of herb-induced liver injury. Six patients had a good prognosis effect,but another one had liver failure. This preparation is commonly used in fracture,osteoarthritis and other diseases,with remarkable curative effect. However,ADR cases and hospital cases all indicated the risk of liver injury. There was no significant correlation between the time and dose of drug use and the occurrence of liver injury.The induced-liver injury may have immunological heterogeneity,thus regular monitoring of liver function should be taken during clinical use.
Adult ; Chemical and Drug Induced Liver Injury ; Databases, Factual ; Drugs, Chinese Herbal ; Female ; Humans ; Male

The aim of this paper was to screen the active targets of Schizonepetae Herba and Saposhnikoviae Radix in the treatment of ulcerative colitis by means of network pharmacology,and to investigate their mechanism of action. The effective components of Schizonepetae Herba and Saposhnikoviae Radix were screened out by traditional Chinese medicine systematic pharmacological( TCMSP)database,with oral bioavilability( OB) ≥30% and drug-like( DL) ≥18% selected as the thresholds. Target PPI network was built between the main components and their corresponding targets. One hundred and eighty-two human genes corresponding to the medicine target sites were obtained from Uniprot database; 3 874 genes corresponding to ulcerative colitis were obtained from Genecard database.A total of 115 intersection genes were screened from disease genes and medicine genes,and the PPI interaction analysis was conducted by using String tool. Disease-target PPI network was drawn by using Cytoscape software,and component-target-disease network was constructed. One hundred and eight nodes and 1 882 connections were found,and then Cytoscape software was used to merge the networks and filter the core network for gene GO function analysis and KEGG pathway enrichment analysis. The mechanism of Schizonepetae Herba and Saposhnikoviae Radix was then verified by animal experiment. Gene GO functional analysis suggested that biological process,molecular functions and cell components were involved,and it was found that ulcerative colitis might be related to transcription factor activity,and cytokine receptor binding,etc. Gene KEGG pathway enrichment analysis showed that the mechanism of ulcerative colitis might be associated with TNF and Toll-like receptors( TLRs) signaling pathway-mediated cytoinflammatory factors interleukin-1( IL-1) and interleukin-6( IL6). The possible mechanism of the effective components of Schizonepetae Herba and Saposhnikoviae Radix in treating ulcerative colitis might be related to intervening the cytokine receptor binding of TNF and TLRs signaling pathways,reducing the transcription of nuclear factor-kappaB( NF-κB),and inhibiting the secretion of intestinal inflammatory factors IL-1 and IL-6.
Animals ; Apiaceae/chemistry* ; Colitis, Ulcerative/drug therapy* ; Databases, Genetic ; Drugs, Chinese Herbal/therapeutic use* ; Humans ; Interleukins/metabolism* ; Lamiaceae/chemistry* ; Medicine, Chinese Traditional ; Phytotherapy ; Plant Roots/chemistry* ; Protein Interaction Mapping ; Signal Transduction ; Software ; Toll-Like Receptors/metabolism*

Molecular identification of human externally visible characteristic （EVC）, which is also called forensic DNA phenotyping （FDP）, can serve as a "molecular witness" when the routine investigations can not determine the identity of a criminal and the DNA database find no match after comparison. FDP could assist in investigation of cases by inferring the externally visible phenotypic characteristics from DNA obtained from the biological materials left at crime scenes, or unknown corpses. In the last few years, studies on the selection of EVC related molecular markers have been reported frequently and some of the EVCs could already be inferred with a certain accuracy, such as hair color and iris color. Further fundamental research on molecular genetics of human external phenotypic characteristics, as well as the continuous innovation on molecular biological technology would promote the rapid development of DNA molecular identification of human phenotypic characteristics.
DNA/genetics* ; Databases, Nucleic Acid ; Eye Color/genetics* ; Forensic Anthropology/trends* ; Forensic Genetics/trends* ; Hair Color/genetics* ; Humans ; Phenotype ; Physical Appearance, Body/genetics* ; Skin Pigmentation/genetics*