Complete genome sequence of Gluconobacter frateurii ML.ISBL3, an endophytic strain isolated from aerial roots of Syngonium podophyllum.

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).

Complete genome sequence of Klebsiella variicola subsp. variicola ML.9ba2, an endophytic strain isolated from aerial roots of Philodendron erubescens.

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.

Complete genome sequence of Serratia ureilytica KML.E1, a copper-tolerant strain isolated from a disused tungsten mine.

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.

Complete Genome Sequence of Enterobacter roggenkampii RX.G5M56, a C1-Metabolizing Strain from a Freshwater Stream in Hong Kong.

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.

Antibacterial activity of ZnO nanoparticles with a modified surface under ambient illumination.

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.

Complete genome characterization of a East European Type 1 subtype 3 porcine reproductive and respiratory syndrome virus.

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.

Characterization of chicken visfatin gene: cDNA cloning, tissue distribution, and promoter analysis.

Here we report the cloning and characterization of chicken visfatin (also called pre-B cell enhancing factor; PBEF, or nicotinamide phosphoribosyltransferase; Nampt) gene. Sequence analyses revealed that the coding region of visfatin is 1,482 bp in length and encodes a protein of 493 amino acids, which shares high amino acid sequence identity not only to visfatin of human (94%), rat (94%), carp (89%), and zebrafish (89%), but also to Nampt of sponge (58%) and cyanobacterium (48%). The reverse transcription PCR assay and Northern-blot analysis demonstrated that visfatin was widely expressed in all chicken tissues examined. Using a dual luciferase reporter system, we further demonstrated that the cloned 1,372-bp fragment upstream of the putative translation start site (ATG) displayed the maximal promoter activity in cultured CHO, DF-1, and HEK293 cells, whereas the removal of its 5'-region (1,075 bp) or 3'-region (297 bp) could only partially reduce its promoter activity, implying that visfatin gene transcription was likely controlled by multiple promoters near the translation start site. Taken together, results from present study will contribute to our better understanding of the expression and roles of visfatin gene in chickens.

Draft Genome Sequences of Nine Stenotrophomonas maltophilia Isolates from a Freshwater Catchment Area in Hong Kong.

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.

Complete Genome Sequence of Klebsiella sp. CTHL.F3a, a Cellulolytic Strain Isolated from Korean Kimchi.

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.

Complete Genome Sequence of Kluyvera sp. CRP, a Cellulolytic Strain Isolated from Red Panda Feces (Ailurus fulgens).

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.

Complete Genome Sequence of Klebsiella quasipneumoniae MMCC7, Isolated from an Eclectus Parrot (Eclectus roratus).

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.

Complete Genome Sequence of Staphylococcus arlettae AHKW2e, Isolated from a Dog's Paws in Hong Kong.

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.

Complete Genome Sequence of Micrococcus luteus Strain CW.Ay, Isolated from Indoor Air in a Hong Kong School.

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.

Complete Genome Sequence of SMBL-WEM22, a Halotolerant Strain of Kosakonia cowanii Isolated from Hong Kong Seawater.

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.

Complete Genome Sequence of Acinetobacter pittii BHS4, Isolated from Air-Conditioning Condensate in Hong Kong.

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.

SARS coronavirus and apoptosis.

1. The adenovirus-mediated overexpression of SARS coronavirus (SARS-CoV) spike protein (S) and its C-terminal domain (S2) induce apoptosis in Vero E6 cells. 2. Such apoptosis in Vero E6 cells is time- and dose-dependent. 3. The adenovirus-mediated overexpression of SARS-CoV N-terminal domain (S1) and other structural proteins, including E,M and N protein, do not induce apoptosis.

Cloning, tissue distribution, and functional characterization of chicken glucagon receptor.

Glucagon has been reported to play an important role in hepatic glucose metabolism of vertebrates including birds. However, the molecular mechanism of its actions in birds remains largely unknown. In present study, the full-length cDNA of chicken glucagon receptor (GCGR) was first cloned from brain tissue using reverse transcription-PCR. This putative chicken GCGR (named cGCGR-s) is 496 amino acids (AA) long and shares high AA sequence identity with that of human (70%), rat (69%), mouse (69%), and Xenopus (64%), and a comparatively lower identity with goldfish (53%). In addition, a full-length cDNA encoding a novel glucagon receptor variant (named cGCGR-v1) of 554 AA was identified in this study. Sequence analysis revealed that this receptor variant arises from the retention of intron 4 (174 bp) and thus causes a 58-AA insertion at the large N-terminal extracellular domain. Using the pGL3-CRE-luciferase reporter system, we demonstrated that human glucagon could potently activate chicken GCGR-s and GCGR-v1 expressed in Chinese hamster ovary cells, confirming that both cGCGR-s and cGCGR-v1 are functional and able to couple to the intracellular cyclic adenosine mono-phosphate-protein kinase A signaling pathway. Using a reverse transcription-PCR assay, we further examined the expression of glucagon receptor in adult chicken tissues, including different regions of the brain. Glucagon receptor was shown to be highly expressed in liver and moderately or weakly expressed in other tissues examined. In the central nervous system, the greatest expression was consistently detected in the hypothalamus. Taken together, our data not only suggest that glucagon receptor plays a critical role in mediating the actions of glucagon in liver, but also imply that glucagon may have important roles in nonhepatic tissues, such as in the hypothalamus of brain in chickens.

Cloning and characterization of chicken growth hormone binding protein (cGHBP).

Growth hormone (GH) is indispensable for the growth of animals and its biological activity is mediated by binding to the growth hormone receptor (GHR) [Harvey S, Scanes CG, Daughaday WH. Growth hormone. Boca Raton: CRC Press; 1995]. GHR is a transmembrane protein responsible for signal transduction upon GH binding. GH also binds to the growth hormone binding protein (GHBP) which is the soluble form of GHR extracellular domain existing in circulation. Actions of GHBP include prolongation of GH bioavailability and prevention of GH signaling system from over-stimulation. To date, little is known about the mechanisms generating the chicken GHBP (cGHBP). Elucidating the genomic structure of cGHR will provide insights into such underlying mechanisms. Using polymerase chain reaction and library screening methods, we have characterized the genomic organization of chicken GHR (cGHR). The full-length coding region of the cGHR transcript is composed of eight exons (exons 2-10), lacking a human homolog exon 3 and spans at least 71 kb on the genome. A novel transcript of size 1.2kb was isolated from chicken liver total RNA using 5' and 3' rapid cDNA ends amplification (RACE). It was generated by utilizing a previously unknown polyadenylation signal located at the intron 6. Semi-quantitative reverse transcription polymerase chain reaction showed that this transcript is widely expressed in a variety of tissues. This transcript has an open reading frame comprising 203 amino acids. In vitro binding assay using ELISA demonstrated that Escherichia coli expressed recombinant protein encoded by this transcript was able to bind with chicken GH. Hence, this transcript is a potential candidate for cGHBP.

Increased gene coverage and Alu frequency in large linkage disequilibrium blocks of the human genome.

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.