Isolation and Identification of Staphylococcus chromogenes and 3 D Structural Analysis of the katA Gene

[Objective]Staphylococcus arthritis became an increasingly significant health problem in intensive chicken farming in China.[Method]In this study,a bacteria strain was isolated from the broiler chicken suffering from arthritis and named as the strain Gg1.[Result]It was then identified as Staphylococcus chromogenes by the biochemical tests and phylogenetic tree analysis based on 16S rDNA sequence.Furthermore,the catalase（katA）gene was amplified by PCR using the designed primers,and the expected fragment was 1 232 bp long encoding a protein of 410 amino acids that shares the conserved motifs including catalase,heme-binding ligand and active center motif.Six phosphorylation sites（Ser95,Thr96,Ser241,Ser242,Thr281,Ser338）,four conserved residues（Ser95,His216,Tyr281,Asp341）and two active sites（His56,Asn129）were demonstrated by multiple sequence alignment and homology comparisons.The homology modeling of 3D structure of katA protein was done by SWISSMODEL server based on the template retrieved from the catalase（PDB：2ISA_A）of Vibrio salmonicida.The katA protein represents a four-domain globular protein,the quality and reliability of the resulting protein structure was further verified by Ramachandran plot.[Conclusion]To our knowledge,this is the first report of S.chromogenes linked to arthritis in chicken and the bioinformatic characterization of its katA gene.

Isolation and Identification of Porcine Epidemic Diarrhea Virus(PEDV) HLJ Strain with IPEC-J2 Cells and Phylogenetic Analysis of Its S Gene

Porcine epidemic diarrhea(PED)is caused by porcine epidemic diarrhea virus(PEDV),and is characterized by vomiting,diarrhea and dehydration of suckling pigs from 80% to 100% morbidity and 50% to 90% mortality,and resulted in tremendous economic losses to swine industry.The PEDV mainly infects small intestine of pigs,resulting in vacuolar degeneration and necrosis of mucosal epithelium.The IPEC-J2 is a pig intestine epithelial cell line,which is similar to the intestinal environment of piglets,can be used to isolate and identify the PEDV field isolates.In this study,it appeared the PEDV typical postmortem changes and histopathological lesion of degeneration and destruction of small intestine in infected piglets,and IHC identified that the PEDV distributed in the mucosa and submucosa of small intestine mostly.Furthermore,the PEDV HLJ strain was successfully isolated and characterized in the IPEC-J2 cells,and indicated that the IPEC-J2 cell line was sensitive to isolate and adapt the PEDV field strain,and could be utilized to multiply the PEDV rapidly.The S gene analysis indicated that the PEDV HLJ strain was the prevailed virus,belonged to Group 1 with attenuated virulent DR13,SC1402 and J-S2/2015 strains isolated in South Korea and China from 2014 to 2015.This study had important theoretical and practical significances on analyzing genetic variation of the PEDV,understanding the pathogenic characteristics of the virus and developing new vaccines for the PED.

Isolation and identification of Rhodosporidium diobovatum DS-0205 from deep-sea sediment of eastern Pacific Ocean

A facultative heterotrophic strain （DS-0205） was isolated from a deep-sea sediment sample collected at a depth of 5.2 km in the eastern Pacific Ocean, China. Strain DS-0205 is motile helmet-like single cell or pairs, forming hemisphere with the center sunken of variable size. It has a widespread carbon source and nitrogen source, including agarose, citric acid, salicin, D-glucitol nitrate, sodium nitrite and cthylamine, tt can grow in the following environment： temperature 4-37℃, pH 2.0-12.0, tolerance to NaCl≤15%. Two phylogenetic trees, one based on the ITS and 5.8S rRNA sequences and the other based on the 18S rRNA sequences, unite strain DS-0205（=JCM 0205） to the type strain of Rhodosporidium diobovatum JCM 3787 through a considerable evolutionary distance. These results suggest that strain DS-0205 is a new strain of the Rhodosporidium diobovatum.

Isolation and Identification of Porcine Circovirus Type 2 in Taizhou

In September 2011, an infectious disease suspected to be postweaning multisystemic wasting syndrome （PMWS） broke out in some pig farm in Taizhou. The inguinal lymph node, liver and lung tissues were collected and grinded into tissue suspension. The suspension was subjected to PCR detection, and the positive product was sequenced. The suspension of positive samples was filtered with 0.22 μm filter membrane, and the filtrate was inoculated onto PK15 cells. After five generations of blind passages, the cell viral liquid was collected and extracted for DNA, which was subjected to PCR detection and indirect immunofluorescence. The results showed that the isolate was porcine circovirus type 2 （PCV2） and designated as TAIZ110926. The target sequence was committed to NCBI with a serial number： KF039888.

Isolation,Identification and Susceptibility Analysis of Bacillus pyocyaners from a Canine Pyometra

In order to clarify the causes of the fester disease in companion animals,this study involved isolation,identification and drug susceptibility analysis of pathogenic bacteria from the uterus of an 11-year-old female dog who was admitted to the veterinary hospital of Tianjin Agricultural University.According to the results of colony morphology,smear staining microscopy,physiological and biochemical reaction and 16 S rRNA gene analysis,the bacteria was identified as a Bacillus pyocyaners.The susceptibility analysis showed that the isolate is highly sensitive to aztreonam,cefdinir,cefotaxime,cefepime,ceftazidime,ofloxacin,streptomycin,kanamycin,piperacillin and tobramycin.Moreover,the isolate is moderately sensitive to ceftriaxone,cefuroxime and cefoxitin,but resistant to ampicillin,cefazolin,cefazine and medemycin.The research results provide references for controlling infection caused by B.pyocyaners.

Molecular Identification of Gallibacterium from Hen and Analysis of Its 16S rRNA Gene

Two strains of Gallibacterium, isolated from one laying hen flock in Zhengzhou City of Henan Province, were identified by the morphological observation, genus -specific PCR, and analysis of 16S rRNA gene, which was used to generate the phylogenetic tree, with the 21 members of the 12 genera belonging to Pasteurellaceae to analyze the homology. Two strains were named Yu-ZZ-HL-I-SLG and Yu-ZZ-HL-II-GZ. The comparative result of the 16S rDNA sequence shows that the 2 isolated strains are identical in sequence; the highest identity （99.9%） was observed between the isolated strain and one of the strains of Gallibacterium anatis （AF22.8002）, the homologies between the isolated strain and 3 strains of gallibacterium accessed in NCBI （AF22.8016, Gallibacterium genomosp. 1, AF228017, Gallibacterium genomosp. 2, AF22.8018, Gal- libacterium genomosp. 1 ） were above 97.1%, higher than that of the isolated strain and the other strains of the other 11 genera which were between 90.7% -93.2%. It can be seen from the phylogenetic tree that the 2 isolated strains and the other 4 strain of gallibacterium fell into the same branch, furthermore the 2 isolated strains and the strain of Gallibacterium anatis locate in an internal branch, indicating that the 2 isolated strains belong to Gallibacterium anatis.

Amino acid identification and sequence analysis of peptides by reaction mass spectrometry

Fast atom bombardment mass spectrometry (FAB-MS) is applied to distinguish N- terminal series ions from C-terminal series ions of a peptide by on-probe acetylation, it provides valuable information about the sequence of an unknown peptide. The FAB mass spectra contain a number of characteristic ions at low-mass region in addition to the sequence ions at high-mass region. It was found that the ions below m/z 200 are characteristic of the amino acid composition of the peptide, from which the amino acid composition of the peptide could be estimated. Additionally, mixture analysis is also discussed.

Isolation,identification,and antagonism protein analysis of B34 against Thanatephorus cuc-umeris

A strain B34 against Thanatephorus cucumeris was screened from rice plants. Lab and field experiments showed that the control effects of this fungal strain were better than that of Jinggangmycin on PDA plate. Based on the chemical components of cell wall and physiological and biochemical characters of B34, the fungal was named as Pseudomonas aureofaciens. It was a new antagonistic strain against Thanatephorus cucumeris.

Identification and Antibacterial Activity Study of a Terrestrial Strain of Brevibacterium aureus 431

This study isolated and purified strain 431 from an animal probiotic product.Through staining and microscopic examination,colony morphology analysis,biochemical reaction tests,and 16S rDNA sequence alignment,the strain was identified and named Brevibacterium aureus 431.The study focused on the production of biosurfactants by strain 431,and antibacterial activity tests were conducted on the strain and its secondary metabolites.The results showed that strain 431 exhibited no resistance to 10 commonly used drugs,and its concentrated secondary metabolites were highly sensitive to the indicator bacterium Escherichia coli.Oral administration of strain 431 to BALB/c mice resulted in normal mental state,diet,and bowel movements,with no signs of illness or death,indicating that strain 431 is highly safe and non-pathogenic to mice.The study suggests that Brevibacterium aureus 431 has significant research value as a new source of actinomycetes and that its secondary metabolites have potential application value in the development of antibacterial drugs.

Isolation of Swine Corynebacteria and Analysis of 16S rDNA Gene

A strain of gram-positive bacillus was isolated from suppurative lung organs of nursery pigs in a pig farm, which was further characterized by morphological observation, cultivation test, biochemical test, drug sensitivity test, pathogenicity test and 16S rDNA gene cloning and sequence analysis. The results showed that the isolate grew well in rabbit blood agar plate and horse serum tryptone soybean agar （TSA） plate under aerobic condition, which could lead to mortality of mice and were susceptible to cephalosporin antibiotics and fluoroquinolone antibiotics. Phylogenetic analysis showed that the isolate had close genetic evolutionary relationships with Corynebacterium bacteria, and the sequence of 16S rRNA gene shared the homology of 91.7% -98.3% with the representative strain of coryne- bacteria, indicating the isolated strain was eorynebactefium.

Isolation, Molecular and Phylogenetic Analysis of Porcine Encephalomyocarditis Virus Strain HLJ in China

Encephalomyocarditis virus(EMCV)is a positive single-stranded small RNA virus without envelope,which can infect a variety of mammals.Swines are the most susceptible animals,which can cause acute myocarditis and respiratory failure in piglets and reproductive failure in pregnant sows.Diseases caused by EMCV have a wide range of effects on the global swine industry.In this study,a strain of EMCV was isolated from a swine aborted fetus in northeast China.It was identified by reverse transcriptase polymerase chain reaction(RT-PCR),electron microscopic observation and indirect immunofluorescence assay.The subsequent results showed that the virus titer of HLJ strain grew to 8.3 lgTCID50 on baby hamster kidney 21(BHK-21)cells.And HLJ strain caused the specific cytopathic effect(CPE)on BHK-21 cells and severe pathological changes in mice.Complete genome sequencing and multiple sequence alignment showed that the homology between HLJ strain and other isolates worldwide was 71.5%-99.7%.Phylogenetic analysis showed that EMCV isolates fell into five clusters:lineageⅠ,Ⅱ,Ⅲ,ⅣandⅤ,based on the nucleotide sequences of the entire open reading frame(ORF)and VP1 gene.HLJ isolate was grouped into lineage I.The analyses of amino acid mutation sites of VP1 protein showed that the amino acids at positions 20 and 54 in VP1 junction were unique to HLJ strain.The isolation of HLJ strain enriched the epidemiological database of EMCV.

Identification,Isolation and Genomic Characterization of Porcine Astrovirus in Shandong Province,China in 2021-2023

[Objective]The paper was to identify,isolate,and characterize porcine astrovirus in Shandong Province between 2021 and 2023.[Method]A total of 1025 samples of porcine diarrhea samples were collected from various regions of Shandong Province between January 2021 and October 2023.The samples were tested by RT-PCR,followed by sequencing and phylogenetic analyses of the polymerase.[Result]The total positive rate of PAstV was 34.6%(355/1025).The respective proportions of individuals infected with PAstV-1,PAstV-2,PAstV-4 and PAstV-5 were 25.4%(90/355),28.2%(100/355),35.2%(125/355)and 22.5%(80/355),respectively.Additionally,mixed infection was observed.Meanwhile,849 samples of healthy pigs were tested by RT-PCR,and the results demonstrated that the total positive rate of PAstV was 8.13%(69/849).Of these,the proportion of PAstV-1,PAstV-2 and PAstV-4 infection was 27.5%(19/69),37.7%(26/69)and 40.6%(28/69),and a mixed infection also existed.Further sequencing and characterization of some the selected isolates revealed low sequence identities(56.2%)with known PAstV strains,indicating the presence of novel types or genotypes of PAstVs.Furthermore,the isolation conditions of porcine astrovirus were optimized,resulting in the purification of a pure PAstV-4 strain(designated PAstV-4-GRF1).The virus was found to exhibit typical astroviral morphology,with nucleotide identity ranging from 89.9 to 95.4%with previously published PAstV-4 strains.Then,macrovirus transcriptome sequencing showed that 88.30%of the CRF1 samples were mammalian astroviruses.By species classification,PAstV 4 and PAstV 2 accounted for 21.79%and 0.32%,respectively.Phylogenetic tree analysis showed that the c15050 fragment was identical to the GRF-1 sequencing fragment of the isolated strain,and exhibited the highest homology with the Hunan PAstV-4 sequence MK460231 in China.[Conclusion]As the inaugural isolated PAstV-4 strain,it furnishes pivotal materialfor the investigation ofthe biological and pathogenic properties of this virus as well as for the prospectivedevelopment of relevant biological and diagnostic reagents.

16S rRNA Cloning and Identification of a Strain Isolated from Intestinal Tract of Rex Rabbit

This study was conducted to identify bacterial strain HeNan-001 isolated from intestinal tract of healthy rex rabbit. The strain was identified by gram staining, and OD600 values at different culture time were measured to develop a bacterial growth curve. The metabolic pathways of the bacterium using sugar in fermentation was identified with biochemical tubes. Total RNA of the strain was extracted, and total eDNA was obtained by Oligo （dT） method. Primers were designed using Primer 5.0 hip-software according to the 16S rRNA sequence published in GenBank, through cloning, ligation to vector PMD18T, construction of PMD18T/16S rRNA vector and transformation into DHSα, plasmid was extracted and sequenced, and the sequencing result was compared with sequences in NCBI followed by drawing of phylogenetic tree. The strain was verified to be double-stranded gram-positive cocci, which could ferment glucose, mannose, maltose and sorbitol, producing acids production, but failed to ferment sucrose, serum inulin and β-galactosidase. The phylogenetie tree analysis showed that the isolated bacterium shared the highest homology with an India isolate, and belongs to diplostreptococcus. This study provides significance experimental data and theoretical guidance for further development and utilization of the bacterial strain.

Modeling and parameter identification of amplitude- and frequency-dependent rubber isolator

A model to describe the hysteresis damping characteristic of rubber material was presented.It consists of a parallel spring and damper,whose coefficients change with the vibration amplitude and frequency.In order to acquire these relations,force decomposition was carried out according to some sine vibration measurement data of nonlinear forces changing with the deformation of the rubber material.The nonlinear force is decomposed into a spring force and a damper force,which are represented by the amplitude-and frequency-dependent spring and damper coefficients,respectively.Repeating this step for different measurements gives different coefficients corresponding to different amplitudes and frequencies.Then,the application of a parameter identification method provides the requested approximation functions over amplitude and frequency.Using those formulae,as an example,the dynamic characteristic of a hollow shaft system supported by rubber rings was analyzed and the acceleration response curve in the centroid position was calculated.Comparisons with the sine vibration experiments of the real system show a maximal inaccuracy of 8.5%.Application of this model and procedure can simplify the modeling and analysis of mechanical systems including rubber materials.

Association between childhood obesity and gut microbiota:16S rRNA gene sequencing-based cohort study

BACKGROUND This study aimed to identify characteristic gut genera in obese and normal-weight children(8-12 years old)using 16S rDNA sequencing.The research aimed to provide insights for mechanistic studies and prevention strategies for childhood obesity.Thirty normal-weight and thirty age-and sex-matched obese children were included.Questionnaires and body measurements were collected,and fecal samples underwent 16S rDNA sequencing.Significant differences in body mass index(BMI)and body-fat percentage were observed between the groups.Analysis of gut microbiota diversity revealed lowerα-diversity in obese children.Differences in gut microbiota composition were found between the two groups.Prevotella and Firmicutes were more abundant in the obese group,while Bacteroides and Sanguibacteroides were more prevalent in the control group.AIM To identify the characteristic gut genera in obese and normal-weight children(8-12-year-old)using 16S rDNA sequencing,and provide a basis for subsequent mechanistic studies and prevention strategies for childhood obesity.METHODS Thirty each normal-weight,1:1 matched for age and sex,and obese children,with an obese status from 2020 to 2022,were included in the control and obese groups,respectively.Basic information was collected through questionnaires and body measurements were obtained from both obese and normal-weight children.Fecal samples were collected from both groups and subjected to 16S rDNA sequencing using an Illumina MiSeq sequencing platform for gut microbiota diversity analysis.RESULTS Significant differences in BMI and body-fat percentage were observed between the two groups.The Ace and Chao1 indices were significantly lower in the obese group than those in the control group,whereas differences were not significant in the Shannon and Simpson indices.Kruskal-Wallis tests indicated significant differences in unweighted and weighted UniFrac distances between the gut microbiota of normal-weight and obese children(P<0.01),suggesting substantial disparities in both the species and quantity of gut microbiota between the two groups.Prevotella,Firmicutes,Bacteroides,and Sanguibacteroides were more abundant in the obese and control groups,respectively.Heatmap results demonstrated significant differences in the gut microbiota composition between obese and normal-weight children.CONCLUSION Obese children exhibited lowerα-diversity in their gut microbiota than did the normal-weight children.Significant differences were observed in the composition of gut microbiota between obese and normal-weight children.

Parameter Identification of Rubber Isolators Using Frequency-Dependent Spring and Damper Coefficients

A model to describe the hysteresis damper character of rubber material is presented in this paper. It consists of a parallel spring and damper, whose coefficients change with vibration frequencies. In order to acquire these relations, the force decomposition is carried out according to some sine vibration measurement data about nonlinear forces changing with deformations of the rubber material. The nonlinear force is decomposed into a spring force and a damper force, which are represented by a frcquency-dependent spring and damper coefficient, respectively. Repeating this step for different measurements will give different coefficients corresponding to different frequencies. Then, application of a parameter identification method will provide the requested functions over frequency. Using those formulae, as an example, the dynamic character of a hollow shaft system supported by rubber rings is analyzed and the acceleration response curve in the centroid position is calculated. Comparisons with sine vibration experiments of the real system show a maximal inaccuracy of 8. 8 %. Application of this model and procedure can simplify the modeling and analysis of mechanical systems including rubber materials.

Monitoring and Identification of the Seismically Isolated “Our Lady of Tears” Shrine in Syracuse

This paper describes the installation and management of the monitoring system of the “Our Lady of Tears Shrine” in Syracuse, whose dome is an imposing r.c. and prestressed r.c. structure of about 22,000 ton that was seismically isolated by flat sliding devices with hysteretic dampers. The monitoring system, representing an upgrading and improvement of an old system never made working, has some innovative features, because it allows to manage with the same dedicated hardware and software both the slow (thermal variations, relative humidity, wind direction and velocity) and the fast acquisitions (dynamic vibrations by wind and earthquake). The monitoring system was inserted among those structures maintained and controlled by the Seismic Observatory of Structures of the National Department of Civil Protection. Some records of low magnitude earthquakes allowed to validate the correct behaviour of the whole structure, as well as to make a dynamic identification of the complex construction and to calibrate a detailed finite element model of the Sanctuary, thus predicting isolators’ behaviour under design earthquake.

Characterizations and Analysis of the Mold from Animal Specimens in Shenzhen Museum

Biological specimens play an important role in cultural exchange, science popularization, scientific research and economic window, but the preparation and preservation technology system of biological specimens is relatively unsafe and inefficient. Mold grows seriously on animal specimens, which is not only harmful to human beings’ health and environment, but also is one of the factors that restricts the development of the natural history museums where these specimens are kept. This paper identified the mold species of animal specimens by PCR with ITS primers, bio-micro-scopic observation, sequencing and phylogenetic tree analysis. The results showed the mold of animal specimens mainly belonged to Aspergillus and Neurospora. This study established the foundations of controlling and restoring the mold that infected animal specimens and guided a new methodology of preparation and environmental friendly exhibition for animal specimens.

Gait Recognition by Cross Wavelet Transform and Graph Model

In this paper, a multi-view gait based human recognition system using the fusion of two kinds of features is proposed.We use cross wavelet transform to extract dynamic feature and bipartite graph model to extract static feature which are coefficients of quadrature mirror filter(QMF)-graph wavelet filter bank. Feature fusion is done after normalization. For normalization of features, min-max rule is used and mean-variance method is used to find weights for normalized features. Euclidean distance between each feature vector and center of the cluster which is obtained by k-means clustering is used as similarity measure in Bayesian framework. Experiments performed on widely used CASIA B gait database show that, the fusion of these two feature sets preserve discriminant information. We report 99.90 % average recognition rate.

Purification and Partial Characterization of an Antibacterial Protein Tz1

A strain (T3) of Bacillus has been screened from paddy field. It secretes large amount of antibacterialproteins which show a strong inhibiting activity against several pathogens of rice. This paper presentsa systematic study of the inhibition spectrum and characteristics of T3 proteins. Total proteins wereprecipitated with ammonium sulfate at 70% saturation from cell-free culture. One of the proteins(Tzl) was purified from the crude extracts with Sephadex G-100, DEAE52 and FPLC Superose 12columns. A single band was demonstrated in both 15% SDS-PAGE and IEF, with an apparent MWof 6,9 kd and a pI of 7.8. Its amino acid composition was analyzed and part of its sequence,determined.