Establishment of Molecular Biological Method for Identification of Bacteria by 16S rDNA and gyrB Gene

[Objectives]The paper was to establish a molecular biological method for identification of bacterial strains.[Methods]The thalli of standard bacterial strains existing in the laboratory were collected and genomic DNA was extracted for amplification of 16S rDNA and gyrB gene.The 16S rDNA and gyrB gene sequences were obtained after sequencing.Sequences were aligned and analyzed via EzBioCloud and NCBI database,and phylogenetic trees were constructed to determine the species relationship of strains.Meantime,they were compared with known strains.[Results]This method could identify 5 standard strains accurately to the species level.The 16S rDNA and gyrB gene sequences were aligned and analyzed in EzBioCloud database and NCBI database.The strain with the max score was consistent with the known strain.And the query cover and ident were both above 99%.[Conclusions]The established molecular biological method for identification of bacterial strains by 16S rDNA and gyrB gene has good accuracy,which effectively solves the problem that the laboratory identification of bacteria relies on traditional methods and the accuracy can not be guaranteed,and further improves the identification ability of laboratory bacterial strains.

Selection and Molecular Biological Identification of a Strain of Bacillus sp. Inhibiting the Growth of Saprolegnia ferax

Based on the theory of biological control of Saprolegnia ferax,antagonism test of nine strains of Bacillus sp. to S. ferax JL was carried out. Bacillus sp.BA1 was screened to have significantly inhibitory effects on the growth of S. ferax JL( P 【 0. 05). Then,the effects of Bacillus sp. BA1 on different sources of S. ferax were carried out. Results showed that BA1 also had significantly inhibitory effects on S. ferax 6#,10# and S2( P 【 0. 05). Sequence of 16 S r DNA of BA1 was analyzed; and homologous alignment analysis showed that BA1 had more than 99% similarity with Bacillus cereus. Therefore,it could be concluded that strain BA1 was B. cereus,which significantly inhibited the growth of S. ferax and could be used as the biological control agent for S. ferax diseases in aquaculture.

Exploring the molecular biological mechanism of Shugan Jianpi Decoction in the treatment of depression-related breast cancer based on network pharmacology

Objective:To explore the molecular biological mechanism of Shugan Jianpi Decoction in treating depression-related breast cancer based on network pharmacology.Methods:The active compounds of Shugan Jianpi Decoction were explored to obtain their drug targets,and the venny network,"TCM-component-target"network,PPI network,"pathway-gene"network,GO and KEGG enrichment results were constructed using relevant softwares.Results:A total of 121 active ingredients,250 genes,2357 GO functions and 184 KEGG pathways were obtained.Conclusion:The active ingredients of Shugan Jianpi Decoction are quercetinll、kaempferol、luteolin、naringenin.The key targets are MAPK1,MAPK3,RELA,and AKT1.GO functions include cellular response to hormone stimulus、cellular response to lipid、cellular response to oxidative stress and so on.KEGG mainly involves PI3K-Akt,microRNAs,and FoxO signaling pathways.This study preliminarily explores the molecular biological mechanism of Shugan Jianpi Decoction in the treatment of depression-related breast cancer,and speculates that it mainly acts by arresting the cell cycle,inhibiting cancer cell proliferation,mediating cancer cell apoptosis,and preventing its recurrence and metastasis,which provides new evidence and new direction for subsequent clinical application and experimental research.

FROM MOLECULAR RESPONSE TO CELL RESPONSE-Approaching the complexity of biological systems

I. THE COMPLEXITY OFBIOLOGICAL RESPONSESFor an organism, to be living or notdepends on its response to foreign matters.Facing the increasing amount and diversi-ty of chemicals, natural and synthetic, tounderstand the principles of the biologicalresponses becomes extremely importantin pursuing the way of rational utiliza-tion and governing the foreign matters.However, most biological responses aretoo complex to explore their nature. Forinstance, the risk to human beings andorganisms related to the application ofrare earths in agriculture, forestation, fish-ery and husbandry has been argued

Proteomic signatures of infiltrative gastric cancer by proteomic and bioinformatic analysis

BACKGROUND Proteomic signatures of Ming's infiltrative gastric cancer(IGC)remain unknown.AIM To elucidate the molecular characteristics of IGC at the proteomics level.METHODS Twelve pairs of IGC and adjacent normal tissues were collected and their proteomes were analyzed by high performance liquid chromatography tandem mass spectrometry.The identified peptides were sequenced de novo and matched against the SwissProt database using Maxquant software.The differentially expressed proteins(DEPs)were screened using|log2(Fold change)|>1 and P-adj<0.01 as the thresholds.The expression levels of selected proteins were verified by Western blotting.The interaction network of the DEPs was constructed with the STRING database and visualized using Cytoscape with cytoHubba software.The DEPs were functionally annotated using clusterProfiler,STRING and DAVID for Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathways.P<0.05 was considered statistically significant.RESULTS A total of 7361 DEPs were identified,of which 94 were significantly up-regulated and 223 were significantly down-regulated in IGC relative to normal gastric tissues.The top 10 up-regulated proteins were MRTO4,BOP1,PES1,WDR12,BRIX1,NOP2,POLR1C,NOC2L,MYBBP1A and TSR1,and the top 10 down-regulated proteins were NDUFS8,NDUFS6,NDUFA8,NDUFA5,NDUFC2,NDUFB8,NDUFB5,NDUFB9,UQCRC2 and UQCRC1.The up-regulated proteins were enriched for 9 biological processes including DNA replication,ribosome biogenesis and initiation of DNA replication,and the cellular component MCM complex.Among the down-regulated proteins,17 biological processes were enriched,including glucose metabolism,pyruvic acid metabolism and fatty acidβ-oxidation.In addition,the mitochondrial inner membrane,mitochondrial matrix and mitochondrial proton transport ATP synthase complex were among the 6 enriched cellular components,and 11 molecular functions including reduced nicotinamide adenine dinucleotide dehydrogenase activity,acyl-CoA dehydrogenase activity and nicotinamide adenine dinucleotide binding were also enriched.The significant KEGG pathways for the up-regulated proteins were DNA replication,cell cycle and mismatch repair,whereas 18 pathways including oxidative phosphorylation,fatty acid degradation and phenylalanine metabolism were significantly enriched among the down-regulated proteins.CONCLUSION The proteins involved in cell cycle regulation,DNA replication and mismatch repair,and metabolism were significantly altered in IGC,and the proteomic profile may enable the discovery of novel biomarkers.

Classification of musical hallucinations and the characters along with neural-molecular mechanisms of musical hallucinations associated with psychiatric disorders

BACKGROUND Musical hallucinations(MH)involve the false perception of music in the absence of external stimuli which links with different etiologies.The pathomechanisms of MH encompass various conditions.The etiological classification of MH is of particular importance and offers valuable insights to understand MH,and further to develop the effective treatment of MH.Over the recent decades,more MH cases have been reported,revealing newly identified medical and psychiatric causes of MH.Functional imaging studies reveal that MH activates a wide array of brain regions.An up-to-date analysis on MH,especially on MH comorbid psychiatric conditions is warranted.AIM To propose a new classification of MH;to study the age and gender differences of MH in mental disorders;and neuropathology of MH.METHODS Literatures searches were conducted using keywords such as“music hallucination,”“music hallucination and mental illness,”“music hallucination and gender difference,”and“music hallucination and psychiatric disease”in the databases of PubMed,Google Scholar,and Web of Science.MH cases were collected and categorized based on their etiologies.The t-test and ANOVA were employed(P<0.05)to compare the age differences of MH different etiological groups.Function neuroimaging studies of neural networks regulating MH and their possible molecular mechanisms were discussed.RESULTS Among the 357 yielded publications,294 MH cases were collected.The average age of MH cases was 67.9 years,with a predominance of females(66.8%females vs 33.2%males).MH was classified into eight groups based on their etiological mechanisms.Statistical analysis of MH cases indicates varying associations with psychiatric diagnoses.CONCLUSION We carried out a more comprehensive review of MH studies.For the first time according to our knowledge,we demonstrated the psychiatric conditions linked and/or associated with MH from statistical,biological and molecular point of view.

水乳型磷酸铝除锈防锈性能及成膜机理研究

研究了水乳型磷酸铝的防锈作用和防锈性能 .根据系统研究结果 ,认为磷酸铝含量大于 4 0 %时 ,防锈膜与基底钢铁制件结合牢固、平整、光洁 。

Isolation and Identification of a High-pathogenicity Strepto- coccus suis Serotype 7 Strain

In order to diagnose the diseased pigs in a certain large pig farm in Binzhou City, Shandong Province, the dead piglets with joint swelling were subjected to necroscopy, and the pathogenic bacterium was isolated and identified. One Gram-positive Streptococcus was isolated. The strain was subjected to characteristic culture, microscopic examination and molecular biological identification, and resistance detection, animal regression experiment and mouse pathogenicity test were carried out. The results showed that the isolate was identified to be Streptococcus suis serotype 7, which was resistant to multiple drugs; and the pathogenicity test showed that the strain had high pathogenicity to pigs, resulting in neurosis on partial pigs, and the strain had no pathogenicity to Kunming and BALB/c mice but certain pathogenicity to CD1 mice.

Identification of Mulberry Endophytic Fungus Macrophomina phaseolina Strain

An endophytic fungus MOD-1 was isolated from the roots of mulberry trees,and was identified as Macrophomina phaseolina by morphology and molecular biology.The 5.8 S rDNA/ITS region sequence of the strain has been registered in GeneBank with the accession number of EU250575.

Biological effect and molecular mechanism study of biomaterials based on proteomic research

Along with the role transformation of biomaterials from bioinert substitute to regenerative inducer, the biological effect and mechanism of material-organism interaction become more important. Since most of animal tests and cellular experiments stay on the phenomenon description instead of mechanism interpretation, the development of proteomics technologies provides a golden opportunity to uncover the molecular interaction mechanism between biomaterial-organism on whole scale. This review summarizes current application of proteomics in biological effect and mechanism study of biomaterials, and discusses the development and challenges for future studies.

Using Gamma-Radiation for Drug Releasing from MWNT Vehicle

A drug delivery system via multi-walled carbon nanotube （MWNT） vehicle was synthesized in aqueous solution. MWNTs were first noncovalently functionalized with chitosan oligomers （CS） with a molecule weight of 4000-6000, making MWNTs water-soluble, and then a cancer ancillary drug tea polyphenols （TP） was conjugated mainly via the hydrogen bond between CS and TP molecules, making MWNTs efficient vehicle for drug delivering. The release of drug molecules can be realized by pH variation and γ-radiation, leading to new methods for controlling drug release from carbon nanotubes carrier. Due to the high penetrability of γ-rays, γ-radiation shows up new opportunities in controlled drug release, possibly facilitating the future cancer treatment in vivo.

Potent protection of Danshensu (β-3, 4-dihydroxyphenyl-lactic acid) against excitotoxic effects of maternal intragastric administration of monosodium glutamate at a late stage of pregnancy on developing mouse fetal brain

Recent studies have demonstrated that ferulic acid[3-（4-hydroxy-3-methoxyphenyl）-2-propenoic acid]and sodium ferulate produce protective effects against glutamate-induced neurotoxicity in adult mice.Danshensu（β-3,4-dihydroxyphenyl-lactic acid）has a similar molecular structure and pharmacological action to caffeic acid.This study aimed to validate the protection conferred by Danshensu against excitotoxic effects of maternal intragastric administration of monosodium glutamate at late stages of pregnancy in the developing mouse fetal brain.Behavioral tests,as well as histopathological and immunohistochemical examination of hippocampi were performed in filial mice.Results revealed that maternal intragastric administration of excessive monosodium glutamate（1.0,2.0,4.0 g/kg body weight）at a late stage of pregnancy resulted in a series of behavioral disorders（hyperactivity,lesions of learning and memory,and disturbance in cooperation of movement ability under high-altitude stress）,histopathological impairment（neuronal edema,degeneration,necrosis,and hyperplasia）and molecular cellular biological changes（upregulated expression of N-methyI-D-aspartate receptor type 1 and neuropeptide Y in the hippocampal region of the brain of the filial mice from mothers treated with monosodium glutamate）.Simultaneous administration of sodium Danshensu partially reversed the effects of monosodium glutamate on the above mentioned phenomena.These findings indicate that sodium Danshensu exhibits obvious protective effects on the excitotoxicity of monosodium glutamate.

Further Discussion on Polaron Existence in Dry DNA

We study the interaction between holes and molecular vibrations on dry DNA by using the extended Firsov＇s model. The ground state energy, calculated by using two Hilbert spaces, Fock state space and coherent state space, is confirmed. The polaron binding energy, defined with the ground state energy, is 0.014eV, much less than the thermal energy 0.026eV at room temperature 300K, which means that polarons are difficult to form self-trapping at room temperature and Anderson localization will prevent a metallic state on dry DNA. The results are consistent with the available experiments.

A Quasi-One-Dimensional Model for a Chain of Water Molecules on the Nanometer Scale

Water confined into the interior channels of narrow carbon nanotubes or transmembrane proteins can form collectively oriented molecular chains held together by tight hydrogen bonds. We develop a quasi-one-dimensional model for a chain of water molecules which interact with each other via the Coulomb and power-like repulsive interactions. We explore the equilibrium property of the water chain and derive an exact analytical expression for the total interaction energy of the water chain, denoted by W（0）int. It is found that W（0）int is minimal when the distance between the two neighboring water molecules in a hydrogen-bonded chain is equal to 0.265 nm. The model is expected to be useful for studying analytically the properties of single-file water molecules inside water channels, such as the concerted motion of water molecules.

Conventional and microwave irradiated synthesis,biological activity evaluation and molecular docking studies of highly substituted piperazine-azole hybrids

Azole derivatives（3,6） obtained starting from 1-（2-methoxyphenyl） piperazine were converted to the corresponding Mannich bases containing β-lactame or flouroquinolone core via a one pot three component reaction.The synthesis of conazole analogues was carried out starting from triazoles by three steps.Reactions were carried out under conventional and microwave mediated conditions.All the newly synthesized compounds were screened for their antimicrobial,enzyme inhibition and antioxidant activity,and most of them displayed good-moderate activity.Binding affinities and non-covalent interactions between enzyme-ligand complexes were predicted with molecular docking method at molecular level.Docking results complemented well the experimental results on α-glucosidase and urease inhibitory effects of the compounds.Higher binding affinities and much more interaction networks were observed for active compounds in contrary to inactive ones.It was predicted with the docking studies that triazole and anisole moieties in the structure of the synthesized compounds contributed to the stabilization of corresponding enzymes through noncovalent interactions.

Current molecular biologic techniques for characterizing environmental microbial community

Microbes are vital to the earth because of their enormous numbers and instinct function maintaining the natural balance. Since the microbiology was applied in environmental science and engineering more than a century ago, researchers desire for more and more information concerning the microbial spatio-temporal variations in almost every fields from contaminated soil to wastewater treatment plant （WWTP）. For the past 30 years, molecular biologic techniques explored for environ- mental microbial community （EMC） have spanned a broad range of approaches to facilitate the researches with the assistance of computer science： faster, more accurate and more sensitive. In this feature article, we outlined several current and emerging molecular biologic techniques applied in detection of EMC, and presented and assessed in detail the application of three promising tools.

Effect of different molecular weight organic components on the increase of microbial growth potential of secondary effluent by ozonation

Ozonation has been widely applied in advanced wastewater treatment. In this study, the effect of ozonation on assimilable organic carbon （AOC） levels in secondary effluents was investigated, and AOC variation of different molecular weight （MW） organic components was analyzed. Although the removal efflciencies were 47%-76% and 94%-100% for UV2s4 and color at ozone dosage of 10 mg/L, dissolved organic carbon （DOC） in secondary effluents was hardly removed by ozonation. The AOC levels increased by 70%-780% at an ozone dosage range of 1-10 mg/L. AOC increased significantly in the instantaneous ozone demand phase, and the increase in AOC was correlated to the decrease in UV254 during ozonation. The results of MW distribution showed that, ozonation led to the transformation of larger molecules into smaller ones, but the increase in low MW （〈1 kDa） fraction did not contribute much to AOC production. The change of high MW （〉100 kDa and 10-100 kDa） fractions itself during ozonation was the main reason for the increase of AOC levels. Furthermore, the oxidation of organic matters with high MWs （〉 100 kDa and 10-100 kDa） resulted in more AOC production than those with low MWs （1-10 kDa and 〈1 kDa）. The results indicated that removing large molecules in secondary effluents could limit the increase of AOC during ozonation.

Influences and mechanisms of nanofullerene on the horizontal transfer of plasmid-encoded antibiotic resistance genes between E.coli strains

The spread and development of antibiotic resistance globally have led to severe public health problems.It has been shown that some non-antibiotic substances can also promote the diffusion and spread of antibiotic resistance genes(ARGs).Nanofullerene(nC60)is a type of nanomaterial widely used around the world,and some studies have discovered both the biological toxicity and environmental toxicity of nC6O .In this study,cellular and molecular biology techniques were employed to investigate the influences of nC6O at sub-minimum inhibitory concentrations(sub-MICs)on the conjugation of ARGs between the E.coli strains.Compared with the control group,nC6O significantly increased the conjugation rates of ARGs by 1.32-10.82 folds within the concentration range of 7.03-1800μg/L.This study further explored the mechanism of this phenomenon,finding that sub-MICs of nC6O could induce the production of reactive oxygen species(ROS),trigger SOSresponse and oxidative stress,affect the expression of outer membrane proteins(OMPs)genes,increase membrane permeability,and thus promote the occurrence of conjugation.This research enriches our understanding of the environmental toxicity of nC6O,raises our risk awareness toward nC6O ,and may promote the more rational employment of nC6O materials.