ABSTRACT
Serratia ureilytica KML.E1 was recovered from a disused tungsten mine in Hong Kong and can tolerate copper(II) concentrations up to 90 mM. Its complete genome, a single chromosome of 5,094,661 bp (59.68% G+ C), was established through hybrid assembly.
ABSTRACT
The endophytic strain Gluconobacter frateurii ML.ISBL3 was isolated from aerial roots of Syngonium podophyllum in Hong Kong. Its complete genome, established through hybrid assembly, comprises a single chromosome of 3,309,710 bp (56.30% G+C).
ABSTRACT
The endophytic strain Klebsiella variicola subsp. variicola ML.9ba2 was isolated from aerial roots of Philodendron erubescens in Hong Kong. Its complete genome of 5,682,083 bp (57.29% G+C), comprising a single chromosome and an IncF plasmid, was established through hybrid assembly.
ABSTRACT
The C1-metabolizing strain Enterobacter roggenkampii RX.G5M56 was isolated from a freshwater stream in Hong Kong. Its complete genome, a single chromosome of 4,772,201 bp (GC content of 56.05%), was established through hybrid assembly.
ABSTRACT
The cellulolytic strain Klebsiella sp. CTHL.F3a was isolated from kimchi (Korean fermented cabbage/vegetables). Its complete genome sequence (6,146,223 bp, GC content of 55.21%), comprising a chromosome and a single plasmid, was established through hybrid assembly.
ABSTRACT
Stenotrophomonas maltophilia is a widely distributed, Gram-negative bacillus that is increasingly identified as a multidrug-resistant opportunistic pathogen of concern. Here, we report the draft genome sequences of nine strains that were isolated from a freshwater catchment area in Hong Kong, corresponding to four different monophyletic lineages within the species.
ABSTRACT
Staphylococcus arlettae is commonly found on the skin of animals. Here, we describe the complete genome sequence of S. arlettae AHKW2e (2,649,260 bp; GC content, 33.6%), isolated from a dog's paws in Hong Kong, established through hybrid assembly and representing the second complete genome sequence of this species.
ABSTRACT
Klebsiella quasipneumoniae MMCC7 is a multidrug- and heavy metal-resistant strain isolated from the feces of a pet shop eclectus parrot in Hong Kong. The complete genome, a single chromosome and circular plasmid (5,382,488 bp; G+C content, 57.79%), was determined by hybrid assembly.
ABSTRACT
The enterobacterium genus Kluyvera is widely distributed in the environment and a rare source of infection in humans. Kluyvera sp. strain CRP was isolated from feces of a healthy, captive Chinese red panda (Ailurus fulgens), and its complete genome (5,157,963 bp, 54.80% GC content) was established through hybrid assembly.
ABSTRACT
Micrococcus luteus strain CW.Ay was isolated from indoor air in Hong Kong. The complete genome (2,543,764 bp; GC content, 72.93%) was established by hybrid assembly and comprised a linear plasmid and a single chromosome featuring many genes to account for its broad distribution in very diverse habitats.
ABSTRACT
Acinetobacter pittii is widespread in the environment, and the Acinetobacter calcoaceticus-baumannii complex, to which it belongs, is a major cause of hospital-acquired pneumonia and bacteremia. A. pitti BHS4 was isolated from an air-conditioning unit in Hong Kong and its complete genome sequence (3,901,980 bp; GC content, 38.79%) established through hybrid assembly.
ABSTRACT
Kosakonia cowanii is a Gram-negative, motile, facultative anaerobic enterobacterium that is found in soil, water, and sewage. K. cowanii SMBL-WEM22 is a halotolerant strain that was isolated from seawater in Hong Kong. The complete genome of SMBL-WEM22 (5,037,617 bp, with a GC content of 55.02%) was determined by hybrid assembly of short- and long-read DNA sequences.
Subject(s)
Food Contamination , Kidney/drug effects , Kidney/embryology , Milk , Triazines/toxicity , Animals , Cells, Cultured , Female , Fetus/drug effects , Humans , In Vitro Techniques , Kidney Calculi/chemically induced , Maternal-Fetal Exchange , Mice , Nephritis/chemically induced , Pregnancy , Prenatal Exposure Delayed Effects , Triazines/metabolismABSTRACT
In various practical applications, nanomaterials typically have functionalized surfaces. Yet, the studies of toxicity and antibacterial activity of functionalized nanoparticles are scarce. We investigated the effect of surface modifications on antibacterial activity of ZnO under ambient illumination, and we found that nanoparticles coated with different surface modifying reagents could exhibit higher or lower toxicity compared to bare ZnO, depending on the surface modifying reagent used. Different surface modifying reagent molecules resulted in differences in the release of Zn(2+) ions and the production of reactive oxygen species (ROS). However, the antibacterial activity did not correlate with the ROS levels or the Zn(2+) ion release. One of the surface-modified ZnO samples exhibited significantly lower Zn(2+) ion release while at the same time exhibiting improved antibacterial activity. In all cases, damage of the cell wall membranes and/or changes in the membrane permeability have been observed, together with the changes in ATR-FTIR spectra indicating differences in protein conformation. Mechanisms of antibacterial activity are discussed.
Subject(s)
Anti-Bacterial Agents/chemistry , Anti-Bacterial Agents/pharmacology , Nanoparticles/chemistry , Zinc Oxide/chemistry , Zinc Oxide/pharmacology , Bacillus/drug effects , Bacterial Infections/prevention & control , Enterococcus faecalis/drug effects , Escherichia coli/drug effects , Humans , Lighting , Nanoparticles/ultrastructure , Reactive Oxygen Species/metabolism , Surface PropertiesSubject(s)
Peptidyl-Dipeptidase A/genetics , Peptidyl-Dipeptidase A/metabolism , Severe Acute Respiratory Syndrome/virology , Severe acute respiratory syndrome-related coronavirus/pathogenicity , Vesiculovirus/pathogenicity , Virus Attachment , Angiotensin-Converting Enzyme 2 , Animals , Cats , Cells, Cultured , Chickens , Chinchilla , Chiroptera , Cricetinae , Disease Susceptibility/virology , Dogs , Genetic Vectors , Guinea Pigs , Host Specificity , Humans , Membrane Glycoproteins/metabolism , Membrane Proteins/metabolism , Mesocricetus , Mice , Phodopus , Rabbits , Rats , Rats, Sprague-Dawley , Severe acute respiratory syndrome-related coronavirus/physiology , Sequence Analysis, DNA , Severe Acute Respiratory Syndrome/transmission , Spike Glycoprotein, Coronavirus , Sus scrofa , Vesiculovirus/physiology , Viral Envelope Proteins/metabolism , ViverridaeABSTRACT
Porcine reproductive and respiratory syndrome (PRRS) is a swine disease of major economic importance that causes reproductive and respiratory problems in pigs. PRRSV strains are divided into European (Type 1) and North-American (Type 2) genotypes. Within the European PRRSV genotype, three subtypes have been delineated. Full genome sequences for North American and European subtype 1 strains have been described. Here, the first complete genomic characterization of a European subtype 3 strain (Lena) is described. Amplification of Orf1a and Orf1b fragments was achieved using a set of degenerate oligonucleotides. Using RT-PCR with Lena-specific primers, the full length sequence (15001 nt) was obtained. Alignment of Lena with European subtype 1 reference strain Lelystad showed variation over the entire length (84% identity/89% similarity at amino acid level) with the most variation in Orf1a (Nsp2/NSP2) with a deletion of 29 amino acids. Phylogenetic relationships using different Orfs supported Lena's genetic distinction from European subtype 1 strains. The availability of the European subtype 3 PRRSV full genome may be important for the understanding of PRRSV evolution and the more pronounced pathogenic nature of Lena.
Subject(s)
Genome, Viral , Porcine Reproductive and Respiratory Syndrome/virology , Porcine respiratory and reproductive syndrome virus/genetics , Porcine respiratory and reproductive syndrome virus/isolation & purification , Animals , Europe , Molecular Sequence Data , Open Reading Frames , Phylogeny , Porcine respiratory and reproductive syndrome virus/classification , SwineABSTRACT
This note describes the development of nine polymorphic microsatellite loci in the limpet Cellana grata to investigate population structure and cohort variation in this species. The number of alleles ranged from seven to 22 and observed heterozygosity ranged from 0.62 to 0.95. Deviation from the Hardy-Weinberg equilibrium was detected in two loci, both as a result of heterozygote deficiency. Null alleles were detected in one of these loci. These genetic markers will be used to investigate the genetic structure of C. grata populations, as well as variation among cohorts of this common intertidal species.
ABSTRACT
The human genome has linkage disequilibrium (LD) blocks, within which single-nucleotide polymorphisms show strong association with each other. We examined data from the International HapMap Project to define LD blocks and to detect DNA sequence features inside of them. We used permutation tests to determine the empirical significance of the association of LD blocks with genes and Alu repeats. Very large LD blocks (>200 kb) have significantly higher gene coverage and Alu frequency than the outcome obtained from permutation-based simulation, whereas there was no significant positive correlation between gene density and block size. We also observed a reduced frequency of Alu repeats at the gaps between large LD blocks, indicating that their enrichment in large LD blocks does not introduce recombination hotspots that would cause these gaps.
Subject(s)
Alu Elements , Genome, Human , Linkage Disequilibrium , Databases, Nucleic Acid , Genetics, Population , Humans , Models, Genetic , Polymorphism, Single Nucleotide , Recombination, GeneticABSTRACT
The human genome has linkage disequilibrium (LD) blocks, within which single-nucleotide polymorphisms show strong association with each other. We examined data from the International HapMap Project to define LD blocks and to detect DNA sequence features inside of them. We used permutation tests to determine the empirical significance of the association of LD blocks with genes and Alu repeats. Very large LD blocks (>200 kb) have significantly higher gene coverage and Alu frequency than the outcome obtained from permutation-based simulation, whereas there was no significant positive correlation between gene density and block size. We also observed a reduced frequency of Alu repeats at the gaps between large LD blocks, indicating that their enrichment in large LD blocks does not introduce recombination hotspots that would cause these gaps.
Subject(s)
Humans , Alu Elements , Genome, Human , Linkage Disequilibrium , Databases, Nucleic Acid , Genetics, Population , Models, Genetic , Polymorphism, Single Nucleotide , Recombination, GeneticABSTRACT
The main objective of this paper is to review the chemical and genetic methods used in authentication of ginseng, especially the recent advances in microsatellite genotyping and its application to the authentication of other traditional Chinese medicines (TCM). The standardization and modernization of TCM hinge on the authentication of their botanical identities. Analysis of well-characterized marker compounds is now the most popular method for identifying the herbal materials and quality control of TCM, eg, ginsenoside profiling for authentication of Panax species. However, in many herbal species the chemical composition of the plant changes with the external environment and processing conditions, which lowers the reliability of these authentication methods. In the light of the advances in molecular biotechnology in the past few decades, genetic tools are now considered to provide more standardized and reliable methods for authentication of herbal materials at the DNA level. These genetic tools include random amplified polymorphic DNA (RAPD), DNA fingerprinting using multi-loci probes, restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP), and microsatellite marker technology. The practicality of these methods varies in terms of their sensitivity, reliability, reproducibility, and running cost. Using ginseng as an example, we reviewed the advantages and limitations of these molecular techniques in TCM authentication. We have developed a set of microsatellite markers from American ginseng that are able to differentiate Panax ginseng and Panax quinquetolius with the resolution down to farm level, ie, confirmation of its botanical identity and origin. Compared with other molecular techniques, microsatellite marker technology is more robust, accurate, reproducible, reliable, and sensitive. This is essential for large-scale TCM authentication centers.