Permanent Genetic Resources added to Molecular Ecology Resources Database 1 April 2010 - 31 May 2010.

This article documents the addition of 396 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Anthocidaris crassispina, Aphis glycines, Argyrosomus regius, Astrocaryum sciophilum, Dasypus novemcinctus, Delomys sublineatus, Dermatemys mawii, Fundulus heteroclitus, Homalaspis plana, Jumellea rossii, Khaya senegalensis, Mugil cephalus, Neoceratitis cyanescens, Phalacrocorax aristotelis, Phytophthora infestans, Piper cordulatum, Pterocarpus indicus, Rana dalmatina, Rosa pulverulenta, Saxifraga oppositifolia, Scomber colias, Semecarpus kathalekanensis, Stichopus monotuberculatus, Striga hermonthica, Tarentola boettgeri and Thermophis baileyi. These loci were cross-tested on the following species: Aphis gossypii, Sooretamys angouya, Euryoryzomys russatus, Fundulus notatus, Fundulus olivaceus, Fundulus catenatus, Fundulus majalis, Jumellea fragrans, Jumellea triquetra Jumellea recta, Jumellea stenophylla, Liza richardsonii, Piper marginatum, Piper aequale, Piper darienensis, Piper dilatatum, Rana temporaria, Rana iberica, Rana pyrenaica, Semecarpus anacardium, Semecarpus auriculata, Semecarpus travancorica, Spondias acuminata, Holigarna grahamii, Holigarna beddomii, Mangifera indica, Anacardium occidentale, Tarentola delalandii, Tarentola caboverdianus and Thermophis zhaoermii.

Chemical composition of gas- and aerosol-phase products from the photooxidation of naphthalene.

The current work focuses on the detailed evolution of the chemical composition of both the gas- and aerosol-phase constituents produced from the OH-initiated photooxidation of naphthalene under low- and high-NO(x) conditions. Under high-NO(x) conditions ring-opening products are the primary gas-phase products, suggesting that the mechanism involves dissociation of alkoxy radicals (RO) formed through an RO(2) + NO pathway, or a bicyclic peroxy mechanism. In contrast to the high-NO(x) chemistry, ring-retaining compounds appear to dominate the low-NO(x) gas-phase products owing to the RO(2) + HO(2) pathway. We are able to chemically characterize 53-68% of the secondary organic aerosol (SOA) mass. Atomic oxygen-to-carbon (O/C), hydrogen-to-carbon (H/C), and nitrogen-to-carbon (N/C) ratios measured in bulk samples by high-resolution electrospray ionization time-of-flight mass spectrometry (HR-ESI-TOFMS) are the same as the ratios observed with online high-resolution time-of-flight aerosol mass spectrometry (HR-ToF-AMS), suggesting that the chemical compositions and oxidation levels found in the chemically-characterized fraction of the particle phase are representative of the bulk aerosol. Oligomers, organosulfates (R-OSO(3)), and other high-molecular-weight (MW) products are not observed in either the low- or high-NO(x) SOA; however, in the presence of neutral ammonium sulfate seed aerosol, an organic sulfonic acid (R-SO(3)), characterized as hydroxybenzene sulfonic acid, is observed in naphthalene SOA produced under both high- and low-NO(x) conditions. Acidic compounds and organic peroxides are found to account for a large fraction of the chemically characterized high- and low-NO(x) SOA. We propose that the major gas- and aerosol-phase products observed are generated through the formation and further reaction of 2-formylcinnamaldehyde or a bicyclic peroxy intermediate. The chemical similarity between the laboratory SOA and ambient aerosol collected from Birmingham, Alabama (AL) and Pasadena, California (CA) confirm the importance of PAH oxidation in the formation of aerosol within the urban atmosphere.

Isolation and characterization of microsatellite markers from the limpet Cellana grata.

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.

Molecular epidemiology of the novel coronavirus that causes severe acute respiratory syndrome.

BACKGROUND: Severe acute respiratory syndrome (SARS) is a newly emerged disease caused by a novel coronavirus (SARS-CoV), which spread globally in early 2003, affecting over 30 countries. We have used molecular epidemiology to define the patterns of spread of the virus in Hong Kong and beyond. METHODS: The case definition of SARS was based on that recommended by WHO. We genetically sequenced the gene for the S1 unit of the viral spike protein of viruses from patients with SARS in Hong Kong (138) and Guangdong (three) in February to April, 2003. We undertook phylogenetic comparisons with 27 other sequences available from public databases (Genbank). FINDINGS: Most of the Hong Kong viruses (139/142), including those from a large outbreak in an apartment block, clustered closely together with the isolate from a single index case (HKU-33) who came from Guangdong to Hong Kong in late February. Three other isolates were genetically distinct from HKU-33 in Hong Kong during February, but none of these contributed substantially to the subsequent local outbreak. Viruses identified in Guangdong and Beijing were genetically more diverse. INTERPRETATION: The molecular epidemiological evidence suggests that most SARS-CoV from the outbreak in Hong Kong, as well as the viruses from Canada, Vietnam, and Singapore, are genetically closely linked. Three viruses found in Hong Kong in February were phylogenetically distinct from the major cluster, which suggests that several introductions of the virus had occurred, but that only one was associated with the subsequent outbreak in Hong Kong, which in turn spread globally.

The complete genome sequence of severe acute respiratory syndrome coronavirus strain HKU-39849 (HK-39).

The complete genomic nucleotide sequence (29.7kb) of a Hong Kong severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) strain HK-39 is determined. Phylogenetic analysis of the genomic sequence reveals it to be a distinct member of the Coronaviridae family. 5' RACE assay confirms the presence of at least six subgenomic transcripts all containing the predicted intergenic sequences. Five open reading frames (ORFs), namely ORF1a, 1b, S, M, and N, are found to be homologues to other CoV members, and three more unknown ORFs (X1, X2, and X3) are unparalleled in all other known CoV species. Optimal alignment and computer analysis of the homologous ORFs has predicted the characteristic structural and functional domains on the putative genes. The overall nucleotides conservation of the homologous ORFs is low (<5%) compared with other known CoVs, implying that HK-39 is a newly emergent SARS-CoV phylogenetically distant from other known members. SimPlot analysis supports this finding, and also suggests that this novel virus is not a product of a recent recombinant from any of the known characterized CoVs. Together, these results confirm that HK-39 is a novel and distinct member of the Coronaviridae family, with unknown origin. The completion of the genomic sequence of the virus will assist in tracing its origin.

The hygroscopic properties of dicarboxylic and multifunctional acids: measurements and UNIFAC predictions.

The role of water-soluble organic compounds on the hygroscopic properties of atmospheric aerosols has recently been the subject of many studies. In particular, low molecular weight dicarboxylic acids and some multifunctional organic acids have been found or are expected to exist in atmospheric aerosols in urban, semiurban, rural, and remote sites. Unlike for their inorganic counterparts, the hygroscopic properties of organic acids have not been well characterized. In this study, the hygroscopic properties of selected water-soluble dicarboxylic acids (oxalic acid, malonic acid, succinic acid, and glutaric acid) and multifunctional acids (citric acid, DL-malic acid, and L-(+)-tartaric acid) were studied using single droplets levitated in an electrodynamic balance at 25 degrees C. The water activities of bulk samples of dilute solutions were also measured. Solute evaporation was observed in the dicarboxylic acids but not in the multifunctional acids. Oxalic acid, succinic acid, and glutaric acid droplets crystallize upon evaporation of water, but, except for glutaric acid droplets, do not deliquesce even at 90% relative humidity (RH). Mass transfer limitation of the deliquescence process was observed in glutaric acid. Neither crystallization nor deliquescence was observed in malonic acid, citric acid, DL-malic acid, or L-(+)-tartaric acid. Malonic acid and these three hydroxy-carboxylic acids absorb water even at RH much lower than their respective deliquescence RH. The growth factor (Gf), defined as the ratio of the particle diameter at RH = 10% to that at RH = 90%, of oxalic acid and succinic acid was close to unity, indicating no hygroscopicity in this range. The remaining acids (malonic acid, glutaric acid, citric acid, malic acid, and tartaric acid) showed roughly similar hygroscopicity of a Gf of 1.30-1.53, which is similar to that of "more hygroscopic" aerosols in field measurements reported in the literature. A generalized equation for these four acids, Gf = (1-aw)-0.163, was developed to represent the hygroscopicity of these acids. Water activity predictions from calculations using the UNIFAC model were found to agree with the measured water activity data to within 40% for most of the acids but the deviations were as large as about 100% for malic acid and tartaric acid. We modified the functional group interaction parameters of the COOH(-H20, OH-H20, and OH-COOH pairs by fitting the UNIFAC model with the measured data. The modified UNIFAC model improves the agreement of predictions and measurements to within 38% for all the acids studied.

Differential expression of amino acid transport systems A and ASC during erythroleukemia cell differentiation.

The human erythroleukemic cell K-562 serves as an in vitro model to study changes in cell surface antigens and mechanisms regulating globin gene expression associated with in vivo erythropoiesis. In this report we have examined the regulation of amino acid transport systems, in particular, systems A and ASC, during differentiation of erythroleukemic cells. For additional comparison we examined the uptake of leucine, 3-aminoendobicyclo-(3,2,1)-octane-3-carboxylic acid (BCO), arginine, and glutamate. Hexamethylene-bis-acetamide (HMBA), dimethyl sulfoxide, and butyrate induce cell differentiation with a block in G1-G0 phase of the cell cycle. These agents caused a significant downregulation of 2-(methylamino)isobutyric acid uptake by system A. In contrast, the Na(+)-dependent threonine uptake by system ASC remained unaltered. The uptake of leucine, BCO, arginine, and glutamate by as yet unidentified systems was, however, stimulated after HMBA treatment. Hemin, a potent inducer of hemoglobin synthesis in K-562 cells, does not block cell cycle events and, interestingly, had no significant effect on both systems A and ASC. These differences in inducer actions suggest that system A activity may be related to specific stages of cell differentiation and perhaps to other cellular signals.