1 2 3 4 5 6 7 8 9 10 11 12 13 ... |Next
Stenotrophomonas panacihumi sp. nov., isolated from soil of a ginseng field.
J Microbiol. 2010 Feb;48(1):30-5
Authors: Yi H, Srinivasan S, Kim MK
The study isolated a Gram-negative, rod-shaped, non-motile bacterium from the soil of a ginseng field in Daejeon, South Korea and characterized it to determine its taxonomic position. Phylogenetic analysis, based on the 16S rRNA gene sequence, revealed that strain MK06(T) belongs to the family Xanthomonadacea, and showed the highest degree of sequence similarity to Stenotrophomonas rhizophila e-p10(T) (98.6%), Xanthomonas campestris LMG 568T (98.0%), Stenotrophomonas maltophilia ATCC 1d3637(T) (97.3%), and Stenotrophomonas humi R-32729(T) (96.9%). Chemotaxonomic data revealed that strain MK06(T) possesses ubiquinone Q-8 as the predominant respiratory lipoquinone, which is common in the genus Stenotrophomonas, and that the predominant fatty acids were 15:0 iso (41.1%), 15:0 anteiso (12.6%), and 17:1 iso omega9c (8.6%). The results of physiological and biochemical tests clearly demonstrated that strain MK06(T) represents a distinct species and supported its affiliation with the genus Stenotrophomonas. Based on these data, MK06(T) (KCTC, 22893(T); JCM, 16536(T); KEMB, 9004-002(T)) should be classified as the type strain for a novel species, for which we propose the name Stenotrophomonas panacihumi sp. nov.
PMID: 20221726 [PubMed - in process]
Acinetobacter brisouii sp. nov., isolated from a wetland in Korea.
J Microbiol. 2010 Feb;48(1):36-9
Authors: Anandham R, Weon HY, Kim SJ, Kim YS, Kim BY, Kwon SW
A bacterial strain 5YN5-8(T) was isolated from peat layer on Yongneup in Korea. Cells of strain 5YN5-8(T) were strictly aerobic, Gram-negative, coccobacilli, non-spore forming, and non-motile. The isolate exhibited optimal growth at 28 degrees C, pH 7.0, and 0-1% NaCl. Results of 16S rRNA gene sequence analyses indicated a close relationship of this isolate to Acinetobacter calcoaceticus (97.8% similarity for strain DSM 30006(T)). It also exhibited 94.4-97.8% 16S rRNA gene sequence similarities to the validly published Acinetobacter species. The value for DNA-DNA hybridization between strain 5YN5-8(T) and other members of the genus Acinetobacter ranged from 16 to 28%. Predominant cellular fatty acids were C(18:1) omega9c, summed feature 4 containing C(15:0) iso 2-OH and/or C(16:1) omega7c, and C(16:0). The DNA G+C content was 43.9 mol%. Phylogenetic, phenotypic, and chemotaxonomic data accumulated in this study revealed that the isolate could be classified in a novel species of the genus Acinetobacter. The name Acinetobacter brisouii sp. nov. is proposed for the novel species, with 5YN5-8(T) (=KACC 11602(T) = DSM 18516(T)) as the type strain.
PMID: 20221727 [PubMed - in process]
Tentaculate fossils from the cambrian of Canada (british columbia) and china (yunnan) interpreted as primitive deuterostomes.
PLoS One. 2010;5(3):e9586
Authors: Caron JB, Conway Morris S, Shu D
Molecular and morphological evidence unite the hemichordates and echinoderms as the Ambulacraria, but their earliest history remains almost entirely conjectural. This is on account of the morphological disparity of the ambulacrarians and a paucity of obvious stem-groups. We describe here a new taxon Herpetogaster collinsi gen. et sp. nov. from the Burgess Shale (Middle Cambrian) Lagersttte. This soft-bodied vermiform animal has a pair of elongate dendritic oral tentacles, a flexible stolon with an attachment disc, and a re-curved trunk with at least 13 segments that is directed dextrally. A differentiated but un-looped gut is enclosed in a sac suspended by mesenteries. It consists of a short pharynx, a conspicuous lenticular stomach, followed by a narrow intestine sub-equal in length. This new taxon, together with the Lower Cambrian Phlogites and more intriguingly the hitherto enigmatic discoidal eldoniids (Cambrian-Devonian), form a distinctive clade (herein the cambroernids). Although one hypothesis of their relationships would look to the lophotrochozoans (specifically the entoprocts), we suggest that the evidence is more consistent with their being primitive deuterostomes, with specific comparisons being made to the pterobranch hemichordates and pre-radial echinoderms. On this basis some of the earliest ambulacrarians are interpreted as soft-bodied animals with a muscular stalk, and possessing prominent tentacles.
PMID: 20221405 [PubMed - in process]
A time line of the environmental genetics of the haptophytes.
Mol Biol Evol. 2010 Jan;27(1):161-76
Authors: Liu H, Aris-Brosou S, Probert I, de Vargas C
The use of genomic data and the rise of phylogenomics have radically changed our view of the eukaryotic tree of life at a high taxonomic level by identifying 4-6 "supergroups." Yet, our understanding of the evolution of key innovations within each of these supergroups is limited because of poor species sampling relative to the massive diversity encompassed by each supergroup. Here we apply a multigene approach that incorporates a wide taxonomic diversity to infer the time line of the emergence of strategic evolutionary transitions in the haptophytes, a group of ecologically and biogeochemically significant marine protists that belong to the Chromalveolata supergroup. Four genes (SSU, LSU, tufA, and rbcL) were extensively analyzed under several Bayesian models to assess the robustness of the phylogeny, particularly with respect to 1) data partitioning; 2) the origin of the genes (host vs. endosymbiont); 3) across-site rate variation; and 4) across-lineage rate variation. We show with a relaxed clock analysis that the origin of haptophytes dates back to 824 million years ago (Ma) (95% highest probability density 1,031-637 Ma). Our dating results show that the ability to calcify evolved earlier than previously thought, between 329 and 291 Ma, in the Carboniferous period and that the transition from mixotrophy to autotrophy occurred during the same time period. Although these two transitions precede a habitat change of major diversities from coastal/neritic waters to the pelagic realm (291-243 Ma, around the Permian/Triassic boundary event), the emergence of calcification, full autotrophy, and oceanic lifestyle seem mutually independent.
PMID: 19762334 [PubMed - indexed for MEDLINE]
Molecular cloning of pigeon UDP-galactose:beta-D-galactoside alpha1,4-galactosyltransferase and UDP-galactose:beta-D-galactoside beta1,4-galactosyltransferase, two novel enzymes catalyzing the formation of Gal alpha1-4Gal beta1-4Gal beta1-4GlcNAc sequence.
J Biol Chem. 2010 Feb 19;285(8):5178-87
Authors: Suzuki N, Yamamoto K
We previously found that pigeon IgG possesses unique N-glycan structures that contain the Gal alpha1-4Gal beta1-4Gal beta1-4GlcNAc sequence at their nonreducing termini. This sequence is most likely produced by putative alpha1,4- and beta1,4-galactosyltransferases (GalTs), which are responsible for the biosynthesis of the Gal alpha1-4Gal and Gal beta1-4Gal sequences on the N-glycans, respectively. Because no such glycan structures have been found in mammalian glycoproteins, the biosynthetic enzymes that produce these glycans are likely to have distinct substrate specificities from the known mammalian GalTs. To study these enzymes, we cloned the pigeon liver cDNAs encoding alpha4GalT and beta4GalT by expression cloning and characterized these enzymes using the recombinant proteins. The deduced amino acid sequence of pigeon alpha4GalT has 58.2% identity to human alpha4GalT and 68.0 and 66.6% identity to putative alpha4GalTs from chicken and zebra finch, respectively. Unlike human and putative chicken alpha4GalTs, which possess globotriosylceramide synthase activity, pigeon alpha4GalT preferred to catalyze formation of the Gal alpha1-4Gal sequence on glycoproteins. In contrast, the sequence of pigeon beta4GalT revealed a type II transmembrane protein consisting of 438 amino acid residues, with no significant homology to the glycosyltransferases so far identified from mammals and chicken. However, hypothetical proteins from zebra finch (78.8% identity), frogs (58.9-60.4%), zebrafish (37.1-43.0%), and spotted green pufferfish (43.3%) were similar to pigeon beta4GalT, suggesting that the pigeon beta4GalT gene was inherited from the common ancestors of these vertebrates. The sequence analysis revealed that pigeon beta4GalT and its homologs form a new family of glycosyltransferases.
PMID: 19959475 [PubMed - indexed for MEDLINE]
Variations of thiaminase I activity pH dependencies among typical Great Lakes forage fish and Paenibacillus thiaminolyticus.
J Aquat Anim Health. 2009 Dec;21(4):207-16
Authors: Zajicek JL, Brown L, Brown SB, Honeyfield DC, Fitzsimons JD, Tillitt DE
The source of thiaminase in the Great Lakes food web remains unknown. Biochemical characterization of the thiaminase I activities observed in forage fish was undertaken to provide insights into potential thiaminase sources and to optimize catalytic assay conditions. We measured the thiaminase I activities of crude extracts from five forage fish species and one strain of Paenibacillus thiaminolyticus over a range of pH values. The clupeids, alewife Alosa pseudoharengus and gizzard shad Dorosoma cepedianum, had very similar thiaminase I pH dependencies, with optimal activity ranges (> or = 90% of maximum activity) between pH 4.6 and 5.5. Rainbow smelt Osmerus mordax and spottail shiner Notropis hudsonius had optimal activity ranges between pH 5.5-6.6. The thiaminase I activity pH dependence profile of P. thiaminolyticus had an optimal activity range between pH 5.4 and 6.3, which was similar to the optimal range for rainbow smelt and spottail shiners. Incubation of P. thiaminolyticus extracts with extracts from bloater Coregonus hoyi (normally, bloaters have little or no detectable thiaminase I activity) did not significantly alter the pH dependence profile of P. thiaminolyticus-derived thiaminase I, such that it continued to resemble that of the rainbow smelt and spottail shiner, with an apparent optimal activity range between pH 5.7 and 6.6. These data are consistent with the hypothesis of a bacterial source for thiaminase I in the nonclupeid species of forage fish; however, the data also suggest different sources of thiaminase I enzymes in the clupeid species.
PMID: 20218495 [PubMed - in process]
Quantitative polymerase chain reaction (PCR) assays for a bacterial thiaminase I gene and the thiaminase-producing bacterium Paenibacillus thiaminolyticus.
J Aquat Anim Health. 2009 Dec;21(4):229-38
Authors: Richter CA, Wright-Osment MK, Zajicek JL, Honeyfield DC, Tillitt DE
The thiaminase I enzyme produced by the gram-positive bacterium Paenibacillus thiaminolyticus isolated from the viscera of Lake Michigan alewives Alosa pseudoharengus is currently the only defined source of the thiaminase activity linked to thiamine (vitamin B1) deficiency in early mortality syndrome (EMS) in the larvae of Great Lakes salmonines. Diets of alewife or isolated strains of P. thiaminolyticus mixed in a semipurified diet and fed to lake trout Salvelinus namaycush have been shown to produce EMS in fry. We utilized quantitative polymerase chain reaction (Q-PCR) to aid in studies of the sources of P. thiaminolyticus and thiaminase I. Quantitative PCR assays were established to detect the thiaminase I gene of P. thiaminolyticus, the 16S rRNA gene from most species of bacteria, and the 16S rRNA gene specifically from P. thiaminolyticus and a few closely related taxa. The Q-PCR assays are linear over at least six orders of magnitude and can detect the thiaminase I gene of P. thiaminolyticus from as few as 1,000 P. thiaminolyticus cells/g of sample or the Paenibacillus 16S rRNA gene from as few as 100 P. thiaminolyticus cells/g of sample. The initial results from alewife viscera samples with high thiaminase activity yielded unexpectedly low densities of P. thiaminolyticus cells; Paenibacillus thiaminolyticus was detectable in 2 of 6 alewife viscera tested at densities on the order of 100 cells/g out of 100,000,000 total bacterial cells/g. The low numbers of P. thiaminolyticus detected suggest that alewives contain additional non-P. thiaminolyticus sources of thiaminase activity.
PMID: 20218497 [PubMed - in process]
Recombinant Expression of an Alkali Stable GH10 Xylanase from Paenibacillus barcinonensis.
J Agric Food Chem. 2010 Mar 10;
Authors: Valenzuela SV, Díaz P, Javier Pastor FI
Xylanase A from Paenibacillus barcinonensis, a new species isolated from a rice field, has been cloned and expressed in Escherichia coli. Purified recombinant xylanase showed high activity on xylans from hardwoods and cereals, and exhibited K(m) and V(max) of 2.93 mg/mL and 50.67 U/mg on birchwood xylan. Xylanase A was highly active at 60 degrees C in alkaline pH values up to 9.5 and remained stable for at least 3 h in alkaline conditions. The amino acid sequence deduced from xynA revealed that it is a single domain xylanase belonging to the GH10 family. Thin layer chromatography analysis showed that the enzyme released a mixture of hydrolysis products including substituted xylooligomers from cereal arabinoxylans, while xylose, xylobiose, and aldotetraouronic acid were the main products released from glucuronoxylan from birchwood. The enzyme released a complex mixture of xylooligomers for acetylated xylan from eucalyptus, revealing its potential to depolymerize this widely used resource in the pulp and paper industry.
PMID: 20218604 [PubMed - as supplied by publisher]
Parasitoid Wasps: From Natural History to Genomic Studies.
Curr Biol. 2010 Mar 9;20(5):R242-R244
Authors: Wurm Y, Keller L
The sequencing of three Nasonia genomes provides new insights on the molecular signature associated with parasitoid lifestyle, allows comparison with the social honey bee, and enables the identification of genes underlying between-species and sex-specific differences.
PMID: 20219176 [PubMed - as supplied by publisher]
The role of radial oxygen loss and root anatomy on zinc uptake and tolerance in mangrove seedlings.
Environ Pollut. 2010 Mar 8;
Authors: Cheng H, Liu Y, Tam NF, Wang X, Li SY, Chen GZ, Ye ZH
Root anatomy, radial oxygen loss (ROL) and zinc (Zn) uptake and tolerance in mangrove plants were investigated using seedlings of Aegiceras corniculatum, Bruguiera gymnorrhiza and Rhizophora stylosa. The results revealed that B. gymnorrhiza, which possessed the 'tightest barrier' in ROL spatial patterns among the three species studied, took up the least Zn and showed the highest Zn tolerance. Furthermore, zinc significantly decreased the ROL of all three plants by inhibition of root permeability, which included an obvious thickening of outer cortex and significant increases of lignification in cell walls. The results of SEM X-ray microanalysis further confirmed that such an inducible, low permeability of roots was likely an adaptive strategy to metal stress by direct prevention of excessive Zn entering into the root. The present study proposes new evidence of structural adaptive strategy on metal tolerance by mangrove seedlings.
PMID: 20219275 [PubMed - as supplied by publisher]
Synthesis of biodiesel from a model waste oil feedstock using a carbon-based solid acid catalyst: Reaction and separation.
Bioresour Technol. 2010 Mar 8;
Authors: Shu Q, Nawaz Z, Gao J, Liao Y, Zhang Q, Wang D, Wang J
A solid acid catalyst that can keep high activity and stability is necessary when low cost feedstocks are utilized for biodiesel synthesis because the reaction medium contains a large amount of water. Three solid acid catalysts were prepared by the sulfonation of carbonized vegetable oil asphalt and petroleum asphalt. The structure of these catalysts was characterized by a variety of techniques. A new process that used the coupling of the reaction and separation was employed, which greatly improved the conversion of cottonseed oil (triglyceride) and free fatty acids (FFA) when a model waste oil feedstock was used. The vegetable oil asphalt-based catalyst showed the highest catalytic activity. This was due to the high density and stability of its acid sites, its loose irregular network, its hydrophobicity that prevented the hydration of -OH species, and large pores that provided more acid sites for the reactants.
PMID: 20219353 [PubMed - as supplied by publisher]
Femtosecond primary charge separation in Synechocystis sp. PCC 6803 photosystem I.
Biochim Biophys Acta. 2010 Feb 25;
Authors: Shelaev IV, Gostev FE, Mamedov MD, Sarkisov OM, Nadtochenko VA, Shuvalov VA, Semenov AY
The ultrafast (<100fs) conversion of delocalized exciton into charge-separated state between the primary donor P700 (bleaching at 705nm) and the primary acceptor A(0) (bleaching at 690nm) in photosystem I (PS I) complexes from Synechocystis sp. PCC 6803 was observed. The data were obtained by application of pump-probe technique with 20-fs low-energy pump pulses centered at 720nm. The earliest absorbance changes (close to zero delay) with a bleaching at 690nm are similar to the product of the absorption spectrum of PS I complex and the laser pulse spectrum, which represents the efficiency spectrum of the light absorption by PS I upon femtosecond excitation centered at 720nm. During the first approximately 60fs the energy transfer from the chlorophyll (Chl) species bleaching at 690nm to the Chl bleaching at 705nm occurs, resulting in almost equal bleaching of the two forms with the formation of delocalized exciton between 690-nm and 705-nm Chls. Within the next approximately 40fs the formation of a new broad band centered at approximately 660nm (attributed to the appearance of Chl anion radical) is observed. This band decays with time constant simultaneously with an electron transfer to A(1) (phylloquinone). The subtraction of kinetic difference absorption spectra of the closed (state P700(+)A(0)A(1)) PS I RC from that of the open (state P700A(0)A(1)) RC reveals the pure spectrum of the P700(+)A(0)(-) ion-radical pair. The experimental data were analyzed using a simple kinetic scheme: [Formula: see text] , and a global fitting procedure based on the singular value decomposition analysis. The calculated kinetics of transitions between intermediate states and their spectra were similar to the kinetics recorded at 694 and 705nm and the experimental spectra obtained by subtraction of the spectra of closed reaction centers (RCs) from the spectra of open RCs. As a result, we found that the main events in RCs of PS I under our experimental conditions include very fast (<100fs) charge separation with the formation of the P700(+)A(0)(-)A(1) state in approximately one half of the RCs, the approximately 5-ps energy transfer from antenna Chl* to P700A(0)A(1) in the remaining RCs, and approximately 25-ps formation of the secondary radical pair P700(+)A(0)A(1)(-).
PMID: 20219440 [PubMed - as supplied by publisher]
Insect Multicopper Oxidases: Diversity, Properties, and Physiological Roles.
Insect Biochem Mol Biol. 2010 Feb 25;
Authors: Dittmer NT, Kanost MR
Multicopper oxidases (MCOs) are a group of related proteins that are ubiquitous in nature. They perform a wide variety of functions including pigmentation, lignin synthesis and degradation, iron homeostasis, and morphogenesis. The laccases of fungi are intensely studied for their biotechnological potential as a more environmentally friendly alternative to harsh or toxic chemicals used for certain industrial applications. Research into insect MCOs has recently attracted renewed interest as it is evident that they have diverse roles in insect physiology. MCO mRNA or enzymatic activity has been detected in extracts from epidermis, midgut, Malpighian tubules, salivary glands, and reproductive tissues. Genome sequencing has allowed for the identification of MCO genes and revealed that the number of genes can vary between species. The function of one of the genes, MCO2, has been demonstrated to be a laccase-type phenoloxidase critical for cuticle sclerotization. However, the enzymatic properties and physiological functions of the remaining MCOs remain to be elucidated. A better understanding of the roles MCOs play in insect biology may help to develop new control measures of pest species.
PMID: 20219675 [PubMed - as supplied by publisher]
MHC gene copy number variation in Tasmanian devils: implications for the spread of a contagious cancer.
Proc Biol Sci. 2010 Mar 10;
Authors: Siddle HV, Marzec J, Cheng Y, Jones M, Belov K
Tasmanian devils face extinction owing to the emergence of a contagious cancer. Devil facial tumour disease (DFTD) is a clonal cancer spread owing to a lack of major histocompatibility complex (MHC) barriers in Tasmanian devil populations. We present a comprehensive screen of MHC diversity in devils and identify 25 MHC types and 53 novel sequences, but conclude that overall levels of MHC diversity at the sequence level are low. The majority of MHC Class I variation can be explained by allelic copy number variation with two to seven sequence variants identified per individual. MHC sequences are divided into two distinct groups based on sequence similarity. DFTD cells and most devils have sequences from both groups. Twenty per cent of individuals have a restricted MHC repertoire and contain only group I or only group II sequences. Counterintuitively, we postulate that the immune system of individuals with a restricted MHC repertoire may recognize foreign MHC antigens on the surface of the DFTD cell. The implication of these results for management of DFTD and this endangered species are discussed.
PMID: 20219742 [PubMed - as supplied by publisher]
Solving the Problem of Ambiguous Paralogy for Marker Loci: Microsatellite Markers with Diploid Inheritance in Allohexaploid Mercurialis annua (Euphorbiaceae).
J Hered. 2010 Mar 10;
Authors: Korbecka G, Rymer PD, Harris SA, Pannell JR
Mercurialis annua is a wind-pollinated annual showing a remarkable sexual-system variation, with hexaploid populations being either monoecious or androdioecious. Hexaploid M. annua is most likely a product of hybridization between diploid M. huetii and tetraploid M. annua; therefore, we developed microsatellite loci by isolating simple sequence repeat (SSR) sequences from the diploid progenitor, cross-amplification tests in M. huetii/M. annua species complex followed by selection of loci amplifying only in M. huetii and hexaploid M. annua, and testing polymorphism in 1 hexaploid population. This protocol resulted in 10 unlinked, polymorphic loci amplifying 4-10 alleles per locus. Due to specific amplification of the diploid part of the genome originating from M. huetii, these loci produce codominantly scored, diploid data for allohexaploid species, thereby simplifying data collection and subsequent analyses. Sequencing of the hexaploid polymerase chain reaction product for all 10 loci and aligning it with M. huetii SSR library sequence confirmed orthology of the characterized loci. Inheritance tests in 4 hexaploid crosses confirmed diploid Mendelian segregation of the new loci.
PMID: 20219887 [PubMed - as supplied by publisher]
New polymorphic microsatellite markers able to distinguish among Candida parapsilosis sensu stricto isolates.
J Clin Microbiol. 2010 Mar 10;
Authors: Sabino R, Sampaio P, Rosado L, Stevens DA, Clemons KV, Pais C
Among the Candida species causing bloodstream infections, C. parapsilosis is one of the most frequently isolated. The objective of this work was the identification of new microsatellite loci able to distinguish among C. parapsilosis isolates. DNA sequences with trinucleotide repeats were selected from the C. parapsilosis genome database. PCR primer sets flanking the microsatellite repeats were designed and tested in 20 independent isolates. Based on the amplification efficiency, specificity, and observed polymorphism, four of the sequences were selected for strain typing. Two hundred and thirty three independent C. parapsilosis sensu stricto isolates were genotyped using these markers. The polymorphic loci exhibited from 20 to 42 alleles and 39 to 92 genotypes. In a multiplex analysis, 192 genotypes were obtained and the combined discriminatory power of the four microsatellites was 0.99. Reproducibility was demonstrated by submission of subcultures of 4 isolates each in triplicate, interspersed with unique numbers among a group of 30 isolates, for blind testing. Comparison of the genotypes obtained by microsatellite analysis and those obtained by RAPD, RFLP and ITS grouping was performed and showed that the microsatellite method could distinguish individual isolates; none of the other methods could do this. Related species C. orthopsilosis and C. metapsilosis were not confused with C. parapsilosis sensu stricto. These new microsatellites are a valuable tool to differentiate C. parapsilosis sensu stricto strains, vital in epidemiology to answer questions of strain relatedness and determine pathways of transmission.
PMID: 20220157 [PubMed - as supplied by publisher]
Evaluation of an immunochromatographic test (ICT) for the rapid and reliable serodiagnosis of human tularemia and the detection of F. tularensis-specific antibodies in serum from different mammalian species.
Authors: Splettstoesser W, Guglielmo-Viret V, Seibold E, Thullier P
Tularemia is a highly contagious infectious zoonosis caused by the bacterial agent Francisella (F.) tularensis. Serology is still considered to be a cornerstone in tularemia diagnosis due to the low sensitivity of bacterial culture and the lack of standardization in PCR methodology for the direct identification of the pathogen. We have developed a novel immunochromatographic test (ICT) to efficiently detect F. tularensis-specific antibodies in sera from humans and other mammalian species (non-human primate, pig, rabbit). This new tool requires none or minimal laboratory equipment and results are obtained within 15 minutes. When compared to the method of microagglutination, which was shown to be more specific than the enzyme-linked immunosorbent assay (ELISA), the ICT had a sensitivity of 98.3% (58 positive sera tested) and a specificity of 96.5% (58 negative sera tested) on human sera. On animal sera, the overall sensitivity was 100% (22 positive sera tested) and specificity was also 100% (70 negative sera tested). This rapid test preferentially detects IgG antibodies which may occur early in the course of human tularemia, but further evaluation with human sera is important to prove that the ICT can be a valuable field test to support a presumptive diagnosis of tularemia. The ICT can also be a useful tool to monitor successful vaccination with subunit vaccines or live vaccine strains containing LPS (e.g. LVS) and to detect seropositive individuals or animals in outbreak situations or in the context of epidemiologic surveillance programs in endemic areas as recently recommended by the World Health Organization.
PMID: 20220165 [PubMed - as supplied by publisher]
Detection of multiple Bartonella species in digestive and reproductive tissues of fleas collected from sympatric mammals.
ISME J. 2010 Mar 11;
Authors: Brinkerhoff RJ, Kabeya H, Inoue K, Bai Y, Maruyama S
At least 12 species in the genus Bartonella are zoonotic pathogens that may be transmitted among mammalian hosts by fleas or other arthropods. Apparent host specificity by some Bartonella species to mammalian hosts has been observed, and the detection of multiple Bartonella species in mammalian fleas suggests that fleas take bloodmeals from a variety of host species. However, many flea species are observed to parasitize a narrow host range. Therefore, we suspect that fleas may acquire Bartonella by a mechanism other than ingesting infectious blood. We found that detection of multiple Bartonella genotypes and species is apparently common in fleas and that the majority of fleas tested (5/9) carried Bartonella species atypical of their hosts. We also detected Bartonella DNA in flea reproductive tissues, suggesting that vertical transmission of this organism in vectors is possible, potentially leading to the accumulation of Bartonella diversity over time within fleas.The ISME Journal advance online publication, 11 March 2010; doi:10.1038/ismej.2010.22.
PMID: 20220787 [PubMed - as supplied by publisher]
Systematic planning of genome-scale experiments in poorly studied species.
PLoS Comput Biol. 2010;6(3):e1000698
Authors: Guan Y, Dunham M, Caudy A, Troyanskaya O
Genome-scale datasets have been used extensively in model organisms to screen for specific candidates or to predict functions for uncharacterized genes. However, despite the availability of extensive knowledge in model organisms, the planning of genome-scale experiments in poorly studied species is still based on the intuition of experts or heuristic trials. We propose that computational and systematic approaches can be applied to drive the experiment planning process in poorly studied species based on available data and knowledge in closely related model organisms. In this paper, we suggest a computational strategy for recommending genome-scale experiments based on their capability to interrogate diverse biological processes to enable protein function assignment. To this end, we use the data-rich functional genomics compendium of the model organism to quantify the accuracy of each dataset in predicting each specific biological process and the overlap in such coverage between different datasets. Our approach uses an optimized combination of these quantifications to recommend an ordered list of experiments for accurately annotating most proteins in the poorly studied related organisms to most biological processes, as well as a set of experiments that target each specific biological process. The effectiveness of this experiment- planning system is demonstrated for two related yeast species: the model organism Saccharomyces cerevisiae and the comparatively poorly studied Saccharomyces bayanus. Our system recommended a set of S. bayanus experiments based on an S. cerevisiae microarray data compendium. In silico evaluations estimate that less than 10% of the experiments could achieve similar functional coverage to the whole microarray compendium. This estimation was confirmed by performing the recommended experiments in S. bayanus, therefore significantly reducing the labor devoted to characterize the poorly studied genome. This experiment-planning framework could readily be adapted to the design of other types of large-scale experiments as well as other groups of organisms.
PMID: 20221257 [PubMed - in process]
Year-round tracking of small trans-saharan migrants using light-level geolocators.
PLoS One. 2010;5(3):e9566
Authors: Bchler E, Hahn S, Schaub M, Arlettaz R, Jenni L, Fox JW, Afanasyev V, Liechti F
Since 1899 ringing (or banding) remained the most important source of information about migration routes, stopover sites and wintering grounds for birds that are too small to carry satellite-based tracking systems. Despite the large quantity of migrating birds ringed in their breeding areas in Europe, the number of ring recoveries from sub-Saharan Africa is very low and therefore the whereabouts of most small bird species outside the breeding season remain a mystery. With new miniaturized light-level geolocators it is now possible to look beyond the limits of ring recovery data. Here we show for the first time year round tracks of a near passerine trans-Saharan migrant, the European Hoopoe (Upupa epops epops). Three birds wintered in the Sahel zone of Western Africa where they remained stationary for most of the time. One bird chose a south-easterly route following the Italian peninsula. Birds from the same breeding population used different migration routes and wintering sites, suggesting a low level of migratory connectivity between breeding and wintering areas. Our tracking of a near passerine bird, the European Hoopoe, with light-level geolocators opens a new chapter in the research of Palaearctic-African bird migration as this new tool revolutionizes our ability to discover migration routes, stopover sites and wintering grounds of small birds.
PMID: 20221266 [PubMed - in process]
Detoxification of Multiple Heavy Metals by a Half-Molecule ABC Transporter, HMT-1, and Coelomocytes of Caenorhabditis elegans.
PLoS One. 2010;5(3):e9564
Authors: Schwartz MS, Benci JL, Selote DS, Sharma AK, Chen AG, Dang H, Fares H, Vatamaniuk OK
BACKGROUND: Developing methods for protecting organisms in metal-polluted environments is contingent upon our understanding of cellular detoxification mechanisms. In this regard, half-molecule ATP-binding cassette (ABC) transporters of the HMT-1 subfamily are required for cadmium (Cd) detoxification. HMTs have conserved structural architecture that distinguishes them from other ABC transporters and allows the identification of homologs in genomes of different species including humans. We recently discovered that HMT-1 from the simple, unicellular organism, Schizosaccharomyces pombe, SpHMT1, acts independently of phytochelatin synthase (PCS) and detoxifies Cd, but not other heavy metals. Whether HMTs from multicellular organisms confer tolerance only to Cd or also to other heavy metals is not known. METHODOLOGY/PRINCIPAL FINDINGS: Using molecular genetics approaches and functional in vivo assays we showed that HMT-1 from a multicellular organism, Caenorhabditis elegans, functions distinctly from its S. pombe counterpart in that in addition to Cd it confers tolerance to arsenic (As) and copper (Cu) while acting independently of pcs-1. Further investigation of hmt-1 and pcs-1 revealed that these genes are expressed in different cell types, supporting the notion that hmt-1 and pcs-1 operate in distinct detoxification pathways. Interestingly, pcs-1 and hmt-1 are co-expressed in highly endocytic C. elegans cells with unknown function, the coelomocytes. By analyzing heavy metal and oxidative stress sensitivities of the coelomocyte-deficient C. elegans strain we discovered that coelomocytes are essential mainly for detoxification of heavy metals, but not of oxidative stress, a by-product of heavy metal toxicity. CONCLUSIONS/SIGNIFICANCE: We established that HMT-1 from the multicellular organism confers tolerance to multiple heavy metals and is expressed in liver-like cells, the coelomocytes, as well as head neurons and intestinal cells, which are cell types that are affected by heavy metal poisoning in humans. We also showed that coelomocytes are involved in detoxification of heavy metals. Therefore, the HMT-1-dependent detoxification pathway and coelomocytes of C. elegans emerge as novel models for studies of heavy metal-promoted diseases.
PMID: 20221439 [PubMed - in process]
Paraoxonase 1, Quorum Sensing, and P. aeruginosa Infection: A Novel Model.
Adv Exp Med Biol. 2010;660:183-93
Authors: Estin ML, Stoltz DA, Zabner J
Pseudomonas aeruginosa is a Gram-negative bacterium which exacts a heavy burden on immunocompromised patients, but is non-pathogenic in a healthy host. Using small signaling molecules called acyl-homoserine lactones (AHLs), populations of P. aeruginosa can coordinate phenotypic changes, including biofilm formation and virulence factor secretion. This concentration-dependent process is called quorum sensing (QS). Interference with QS has been identified as a potential source of new treatments for P. aeruginosa infection. The human enzyme paraoxonase 1 (PON1) degrades AHL molecules, and is a promising candidate for QS interference therapy. Although paraoxonase orthologs exist in many species, genetic redundancy in humans and other mammals has made studying the specific effects of PON1 quite difficult. Arthropods, however, do not express any PON homologs. We generated a novel model to study the specific effects of PON1 by transgenically expressing human PON1 in Drosophila melanogaster. Using this model, we showed that P. aeruginosa infection lethality is QS-dependent, and that expression of PON1 has a protective effect. This work demonstrates the value of a D. melanogaster model for investigating the specific functions of members of the paraoxonase family in vivo, and suggests that PON1 plays a role in innateimmunity.
PMID: 20221881 [PubMed - in process]
A research team led by the University of Colorado at Boulder has discovered a previously unknown cellular "switch" that may provide researchers with a new means of triggering programmed cell death, findings with implications for treating cancer.
The series for UBC's Celebrate Research Week continues today with an entry from Dr. Brian Klinkenberg today's photograph by him via Flickr) and graduate student Claire Wooten. Lindsay writes the introduction:
Dr. Brian Klinkenberg is a professor in the UBC Department of Geography where his research focuses on advanced spatial analysis with respect to physical, health and social sciences (and the intersection of these disciplines). Dr. Klinkenberg is also the editor and project coordinator of E-Flora BC / E-Fauna BC.
Dr. Klinkenberg writes: Understanding the spatial aspects of plant dynamics is a critical part of landscape ecology today. Recently in my lab our focus on spatial analysis has led us to explore the decline of yellow-cedar in BC (see gallery link at bottom of page). Exploring the spatial occurrences on these species in the landscape has led to key insights into distributions and biogeographic changes.
Claire Wooten (graduate student) and Dr. Klinkenberg co-wrote the following about yellow-cedar die-off:
For over two decades, the phenomenon of yellow-cedar decline has perplexed researchers. Yellow-cedar (Chamaecyparis nootkatensis) (D. Don) Spach), which ranges from southern Oregon to Prince William Sound, Alaska, was known to be declining on over 200,000 ha of undisturbed forest in southeast Alaska (Snyder et al. 2008). During an aerial survey in 2004, numerous large areas of dead and dying yellow-cedar were found in coastal locations in B.C., and the nature of the dieback was found to be consistent with the phenomenon in southeast Alaska (Hennon et al. 2005).
Research into the decline of this long-lived species began in the early 1980s and a sequence of symptoms was identified. The initial symptom was determined to be fine root death, followed by death of small-diameter roots (Hennon et al. 2006) (PDF). As the roots start to die, the trees develop thin off-colour crowns and necrotic lesions spread from larger roots up the bole (Hennon et al. 2006). The natural resistance of yellow cedar heartwood to decay allows dead trees to remain standing for 80 to 100 years after death. By examining the standing snags it was possible to establish that the decline of yellow-cedars began in about 1880-1900 (Hennon & Shaw, 1997).
Investigations initially focused on finding a biotic cause of the decline, but one by one the suspected agents were ruled out (Hennon et al. 1990). Attention then shifted to abiotic factors potentially associated with the decline--an association with wet, poorly drained soils was found. However the relationship with soil drainage is inconsistent, with limited decline occurring on wet sites at higher elevations (Hennon et al. 2006). Air and soil temperature were determined to be stronger risk factors than poorly drained soils (D'Amore & Hennon, 2006).
These clues led researchers to propose a new, complex hypothesis to explain yellow-cedar decline. According to Hennon et al. (2006), saturated soils create open, exposed canopies which experience soil warming early in the spring. This warming triggers the yellow-cedars to lose their cold tolerance, making them more susceptible to freezing injury. Snow appears to protect yellow-cedar against this freezing injury by preventing soil warming. However, the end of the Little Ice Age, which coincided with the onset of decline, has led to a reduction in snowpack at lower elevations (Hennon et al. 2006). This shift in climate may represent the environmental trigger responsible for the decline and suggests that the dieback may expand if warming trends continue (Hennon et al. 2006).
Our research questions are being addressed through a combination of remote sensing and GIS techniques. Spatial patterns of biophysical factors (e.g. elevation, slope, aspect) are being used in our assessment of the relations between the distribution of decline and the environmental predictors.
The high value of yellow-cedar wood and the desire to conserve species diversity means that a management strategy incorporating the influence of a warming climate is required. Ultimately, this research may provide insight into the devastating effects that climate change can have on a forest ecosystem.
Dr. Klinkenberg also adds an additional note regarding the name of this species:
There has been much debate over the taxonomic status of yellow-cedar following the discovery of a closely related tree species in northern Vietnam, Xanthocyparis vietnamensis Farjon & Hiep. Whether yellow-cedar is transferred to this newly established genus as Xanthocyparis nootkatensis or the older Callitropsis nootkatensis (D.Don) Örest name is adopted, will be determined at the next International Botanical Congress in 2011 (Mill & Farjon, 2006).
References
D'Amore, D. and Hennon, P.E. 2006. Evaluation of soil saturation, soil chemistry, and early spring soil and air temperatures as risk factors in yellow-cedar decline. Global Change Biology. 12: 524-545
Hennon, P.E., D'Amore, D., Wittwer, D., Johnson, A., Schaberg, P., Hawley, G., Beier, C., Sink, S. and Juday, G. 2006. Climate warming, reduced snow, and freezing injury could explain the demise of yellow-cedar in southeast Alaska, USA. World Resource Review. 18(2): 427-450.
Hennon, P.E., D'Amore, D., Zeglen, S. and Grainger, M. 2005. Yellow-cedar decline in the North Coast Forest District of British Columbia. Res. Note RN-549. Portland, OR: U.S. Dep. Agric., Pacific Northwest Research Station. pp.20.
Hennon, P.E. and Shaw, C.G. III. 1997. The enigma of yellow-cedar decline - What is killing these long-lived, defensive trees? Journal of Forestry. 95(12): 4-10.
Mill, R. R. And Farjon, A. 2006. Proposal to conserve the name Xanthocyparis against Callitropsis Oerst. (Cupressaceeae). Taxon. 55(1): 229-231.
Snyder, C., Schultz, M.E. and Lundquist, J. (Compilers) 2008. Forest health conditions in Alaska - 2007: a forest health protection report. Gen. Tech. Rep. R10-PR-18. Anchorage, AL: U.S. Dep. Agric., Forest Service, Alaska Region.
MIAMI--Malaria continues to be a global scourge, sickening some 300 million to 500 million people annually. Most of the resulting one million to three million malaria deaths occur in regions where it is highly endemic, such as sub-Saharan Africa and parts of south Asia. [More]
