|
| | 1. |
2011 May 15 |
Evaluation of CA 242 as a Tumor Marker in Gallbladder Cancer.
Rana S, Dutta U, Kochhar R, Rana SV, Gupta R, Pal R, Jain K, Srinivasan R, Nagi B, Nain CK, Singh K
J Gastrointest Cancer. 2011 May 15; [Epub ahead of print]
Abstract
PURPOSE: Gallbladder and pancreas share common embryological origin, and malignancies of these organs may share common tumor antigens. CA 242 is a tumor marker for pancreatic cancer, but has not been studied in gallbladder cancer (GBC). We measured serum CA 242 levels in patients with GBC and compared it with those in patients with gallstones (GS) and healthy volunteers. METHODS: We enrolled consecutive patients with GBC (cases), GS (disease controls), and healthy volunteers (healthy controls). Serum CA 242, CEA, and CA 19-9 levels were measured using ELISA. Receiver operator curve was plotted for all the three markers. RESULTS: We studied 117 patients with GBC, 58 with GS, and 10 healthy volunteers. Among patients with GBC, 81 (69%) also had GB calculi. Patients with GBC more often had elevated CA 242 levels (64%) compared to those with GS (17%; p < 0.001) and healthy controls (0%; p < 0.001). The median levels of CA 242 was higher in the GBC group (59 [199] U/ml) compared to the GS group (10 [13] U/ml; p < 0.001) and the control group (3 [14.5] U/ml; p < 0.001). The sensitivity, specificity, positive predictive value (PPV), and negative predictive values of CA 242 for diagnosis of GBC were 64%, 83%, 88%, and 53%, respectively. At a cutoff of 45 U/ml, the specificity and PPV increased to 100%. CA 242 had higher AOC (0.759) compared to CEA (0.528) and CA 19-9 (0.430). CONCLUSIONS: CA 242 is a promising tumor marker for GBC and performs better than CEA and CA 19-9.
[Pubmed: 21573879]
| | 2. |
2011 Oct 5 |
The genomic response to courtship song stimulation in female Drosophila melanogaster.
Immonen E, Ritchie MG
Proc Biol Sci. 2011 Oct 5; [Epub ahead of print]
Abstract
Courtship behaviour involves a complex exchange of signals and responses. These are usually studied at the phenotypic level, and genetic or transcriptional responses to courtship are still poorly understood. Here, we examine the gene-expression changes in Drosophila melanogaster females in response to one of the key male courtship signals in mate recognition, song produced by male wing vibration. Using long oligonucleotide microarrays, we identified several genes that responded differentially to the presence or absence of acoustic courtship stimulus. These changes were modest in both the number of genes involved and fold-changes, but notably dominated by antennal signalling genes involved in olfaction as well as neuropeptides and immune response genes. Second, we compared the expression patterns of females stimulated with synthetic song typical of either conspecific or heterospecific (Drosophila simulans) males. In this case, antennal olfactory signalling and innate immunity genes were also enriched among the differentially expressed genes. We confirmed and investigated the time course of expression differences of two identified immunity genes using real-time quantitative PCR. Our results provide novel insight into specific molecular changes in females in response to courtship song stimulation. These may be involved in both signal perception and interpretation and some may anticipate molecular interactions that occur between the sexes after mating.
[Pubmed: 21976688]
| | 3. |
2011 Aug 24 |
Defence strategies against a parasitoid wasp in Drosophila: fight or flight?
Lefèvre T, de Roode JC, Kacsoh BZ, Schlenke TA
Biol Lett. 2011 Aug 24; [Epub ahead of print]
Abstract
Hosts may defend themselves against parasitism through a wide variety of defence mechanisms, but due to finite resources, investment in one defence mechanism may trade-off with investment in another mechanism. We studied resistance strategies against the parasitoid wasp Leptopilina boulardi in two Drosophila species. We found that D. melanogaster had significantly lower physiological resistance against L. boulardi than D. simulans, and hypothesized that D. melanogaster might instead invest more heavily in other forms of defence, such as behavioural defence. We found that when given a choice between clean oviposition sites and sites infested with wasps, both D. melanogaster and D. simulans detected and avoided infested sites, which presumably limits later exposure of their offspring to infection. Unlike D. simulans, however, D. melanogaster laid significantly fewer eggs than controls in the forced presence of wasps. Our findings suggest that D. melanogaster relies more heavily on behavioural avoidance as defence against wasp parasitism than D. simulans, and that this may compensate for a lack of physiological defence.
[Pubmed: 21865240]
| | 4. |
2011 Dec 1 |
Rapid functional divergence of a newly evolved polyubiquitin gene in Drosophila and its role in the trade-off between male fecundity and lifespan.
Zhan Z, Ding Y, Zhao R, Zhang Y, Yu H, Zhou Q, Yang S, Xiang H, Wang W
Mol. Biol. Evol. 2011 Dec 1; [Epub ahead of print]
Abstract
The cost of reproduction is a pivotal trade-off with various biological processes during the evolution of organisms. However, the genes and molecular mechanisms underlying the evolution of balancing reproductive capacity and its cost are still largely unknown. Here, we present a comprehensive study on the evolution, expression and biological functions of a newly evolved pair of X-linked polyubiquitin tandemly duplicated genes, CG32744 and CG11700, of which the duplication event occurred in Drosophila melanogaster lineage after the split from D. simulans clade. We found that CG32744 retains conserved polyubiquitin-coding sequences across Drosophila species and is ubiquitously expressed, while CG11700 has accumulated numerous amino acid changes and shows a male-specific expression pattern. Null mutants of CG11700 have a higher male fecundity but shorter lifespan while its overexpression decreases male fecundity. In contrast, the null mutants of the peptide-conserved CG32744 do not exhibit such phenotypes. These results suggest that CG11700 might have experienced neofunctionalization and evolved important functions in the trade-off between male fecundity and lifespan, and that CG32744 likely has retained the ancestral function.
[Pubmed: 22135190]
| | 5. |
2011 Nov 9 |
Coagulase-negative staphylococci from non-mastitic bovine mammary gland: characterization of Staphylococcus chromogenes and Staphylococcus haemolyticus by antibiotic susceptibility testing and pulsed-field gel electrophoresis.
Pate M, Zdovc I, Avberšek J, Ocepek M, Pengov A, Podpečan O
J. Dairy Res. 2011 Nov 9;:1-6. Epub 2011 Nov 9.
Abstract
During routine microbiological examination of milk samples from dairy cows without clinical signs of mastitis, quarter milk samples of 231 dairy cows from 12 herds were investigated for the presence of coagulase-negative staphylococci (CNS). The isolates were identified on the basis of colony morphology, Gram staining, catalase and coagulase test and the commercial kit, API Staph. CNS was detected in 29% (67/231) of the cows. A total of seven CNS species were identified with the most prevalent being Staphylococcus (Staph.) chromogenes (30%) and Staph. haemolyticus (28·8%), followed by Staph. simulans (11·2%), Staph. xylosus (11·2%), Staph. epidermidis (7·5%), Staph. hyicus (6·3%) and Staph. sciuri (5%). The predominant species, Staph. chromogenes and Staph. haemolyticus, were further characterized by antibiotic susceptibility testing using the agar disc diffusion method (Kirby-Bauer) and by pulsed-field gel electrophoresis (PFGE). Considerable resistance to ampicillin and penicillin was observed in both species. Isolates with identical or highly similar PFGE profiles were detected at the herd level despite a marked heterogeneity seen for both species. On the basis of somatic cell count, absence of clinical signs of inflammation and heterogeneity of genotypes, we assume that CNS isolated in this study could not be considered as important causative agents of the bovine mammary gland inflammation.
[Pubmed: 22067091]
| | 6. |
2011 Dec 24 |
Nain-e Havandi Andrographis paniculata present yesterday, absent today: a plenary review on underutilized herb of Iran's pharmaceutical plants.
Valdiani A, Kadir MA, Tan SG, Talei D, Abdullah MP, Nikzad S
Mol Biol Rep. 2011 Dec 24; [Epub ahead of print]
Abstract
Nain-e Havandi (Andrographis paniculata Nees.) (AP) is an annual herbaceous plant belonging to the family Acanthacea. Only a few species of Andrographis genus out of 28 are medicinally concerned of which AP is the most important. Knowledge about the arrival of AP to Iran is extremely lacking but most probably it has been imported from India. However, evidence implies the familiarity of Iran's folkloric medicine with this plant, but it has been disappeared from contemporary medicine for unknown reasons. Presence of active ingredients from diterpenoids group such as andrographolide, neoandrographolide and 14-deoxy-11,12-didehydroandrographolide has given incredible unique medicinal properties to the plant. Traditionally, Nain-e Havandi has been used in the role of a non-farm plant as a remedy for skin problems, flu, respiratory disease, and snakebite in East and Southeast Asia for centuries. Recently, it has been utilized as a treatment for HIV, hepatitis, diabetes, cancer and kidney disorders. Intensive cultivation of the herb started only in the past decade in countries such as China, India, Thailand, Indonesia, West Indies, Mauritius and to some extent, in Malaysia. Availability of different ecological zones in Iran complies with reestablishment of AP in tropical and temperate regions of the country. This is killing two birds with one stone, supporting the conservational and economic aspects.
[Pubmed: 22198549]
| | 7. |
2012 May |
A single amino acid determines the toxicity of Ginkgo biloba extracts
Thompson, McGonigle, Duke, Johnston, Lummis
FASEB J 2012 May;26(5):1884-1891.
Abstract
Ginkgo biloba extracts are currently used for a wide range of health-related conditions. Some of the medical benefits of these extracts are controversial, but their lack of toxicity in humans is not in doubt. These extracts are, however, highly toxic to insects. Their active components (ginkgolides and bilobalide) have structures similar to the convulsant picrotoxin, a GABAA receptor antagonist, so their lack of toxicity in mammals is puzzling. Here, we show that the different compositions of insect and vertebrate GABA receptor pores are responsible for the differing toxicities. Insect GABA receptors contain Ala at their 2′ position in the pore. Substitution with Val, which is the equivalent residue in vertebrate GABAA receptor α-subunits, decreases ginkgolide potency by up to 10,000-fold. The reverse mutation in vertebrate GABAA α1 subunits increased the sensitivity of α1β2 and α1β2γ2 receptors to ginkgolides. Mutant cycle analysis demonstrates a strong interaction between the ginkgolides and the 2′ residue, a result supported by in silico docking of compounds into a model of the pore. We conclude that the insecticidal activity of G. biloba extracts can be attributed to their effects at insect GABA receptors, and the presence of a Val at the 2′ position in vertebrate GABAA receptors explains why these compounds are not similarly toxic to humans.—Thompson, A. J., McGonigle, I., Duke, R., Johnston, G. A. R., Lummis, S. C. R. A single amino acid determines the toxicity of Ginkgo biloba extracts.
[Pubmed: 22253475]
| | 8. |
2012 May 4 |
A Cytochrome P450 Conserved in Insects Is Involved in Cuticle Formation
Sztal, Chung, Berger, Currie, Batterham, Daborn
PLoS One 2012 May 4;7(5). published online before print
Abstract
The sequencing of numerous insect genomes has revealed dynamic changes in the number and identity of cytochrome P450 genes in different insects. In the evolutionary sense, the rapid birth and death of many P450 genes is observed, with only a small number of P450 genes showing orthology between insects with sequenced genomes. It is likely that these conserved P450s function in conserved pathways. In this study, we demonstrate the P450 gene, Cyp301a1, present in all insect genomes sequenced to date, affects the formation of the adult cuticle in Drosophila melanogaster. A Cyp301a1 piggyBac insertion mutant and RNAi of Cyp301a1 both show a similar cuticle malformation phenotype, which can be reduced by 20-hydroxyecdysone, suggesting that Cyp301a1 is an important gene involved in the formation of the adult cuticle and may be involved in ecdysone regulation in this tissue.
[Pubmed: 22574182]
| | 9. |
2012 May 3 |
Biological diversity of the Minnesota caddisflies (Insecta, Trichoptera)
Houghton
Zookeys 2012 May 3;(189):1-389. published online before print
Abstract
The caddisfly fauna of Minnesota contains at least 277 species within 21 families and 75 genera. These species are based on examination of 312,884 specimens from 2,166 collections of 937 Minnesota aquatic habitats from 1890 to 2007. Included in these totals is my own quantitative sampling of 4 representative habitat types: small streams, medium rivers, large rivers, and lakes, from each of the 58 major Minnesota watersheds from June through September during 1999–2001. All species are illustrated herein, and their known Minnesota abundances, distributions, adult flight periodicities, and habitat affinities presented. Four species: Lepidostoma griseum (Lepidostomatidae), Psilotreta indecisa (Odontoceridae), and Phryganea sayi and Ptilostomis angustipennis (Phryganeidae) are added to the known fauna. An additional 31 dubious species records are removed for various reasons. Of the 5 determined caddisfly regions of the state, species richness per watershed was highest in the Lake Superior and Northern Regions, intermediate in the Southeastern, and lowest in the Northwestern and Southern. Of the 48 individual collections that yielded >40 species, all but 1 were from the Northern Region. Many species, especially within the families Limnephilidae and Phryganeidae, have appeared to decrease in distribution and abundance during the past 75 years, particularly those once common within the Northwestern and Southern Regions. Many species now appear regionally extirpated, and a few have disappeared from the entire state. The loss of species in the Northwestern and Southern Regions, and probably elsewhere, is almost certainly related to the conversion of many habitats to large-scale agriculture during the mid-20th century.
[Pubmed: 22615539]
| | 10. |
2012 May 22 |
Salivary Gland Transcriptomes and Proteomes of Phlebotomus tobbi and Phlebotomus sergenti, Vectors of Leishmaniasis
Rohoušová, Subrahmanyam, Volfová, Mu, Volf, Valenzuela, Jochim
PLoS Negl Trop Dis 2012 May 22;6(5). published online before print
Abstract
Phlebotomus tobbi is a vector of Leishmania infantum, and P. sergenti is a vector of Leishmania tropica. Le. infantum and Le. tropica typically cause visceral or cutaneous leishmaniasis, respectively, but Le. infantum strains transmitted by P. tobbi can cause cutaneous disease. To better understand the components and possible implications of sand fly saliva in leishmaniasis, the transcriptomes of the salivary glands (SGs) of these two sand fly species were sequenced, characterized and compared.
[Pubmed: 22629480]
| | 11. |
2012 May 21 |
HeT-A_pi1, a piRNA Target Sequence in the Drosophila Telomeric Retrotransposon HeT-A, Is Extremely Conserved across Copies and Species
Petit, Piñeyro, López-Panadès, Casacuberta, Navarro
PLoS One 2012 May 21;7(5). published online before print
Abstract
The maintenance of the telomeres in Drosophila species depends on the transposition of the non-LTR retrotransposons HeT-A, TAHRE and TART. HeT-A and TART elements have been found in all studied species of Drosophila suggesting that their function has been maintained for more than 60 million years. Of the three elements, HeT-A is by far the main component of D. melanogaster telomeres and, unexpectedly for an element with an essential role in telomere elongation, the conservation of the nucleotide sequence of HeT-A is very low. In order to better understand the function of this telomeric retrotransposon, we studied the degree of conservation along HeT-A copies. We identified a small sequence within the 3′ UTR of the element that is extremely conserved among copies of the element both, within D. melanogaster and related species from the melanogaster group. The sequence corresponds to a piRNA target in D. melanogaster that we named HeT-A_pi1. Comparison with piRNA target sequences from other Drosophila retrotransposons showed that HeT-A_pi1 is the piRNA target in the Drosophila genome with the highest degree of conservation among species from the melanogaster group. The high conservation of this piRNA target in contrast with the surrounding sequence, suggests an important function of the HeT-A_pi1 sequence in the co-evolution of the HeT-A retrotransposon and the Drosophila genome.
[Pubmed: 22629389]
| | 12. |
2012 May 30 |
A DNA Barcode Library for North American Ephemeroptera: Progress and Prospects
Webb, Jacobus, Funk, Zhou, Kondratieff, Geraci, DeWalt, Baird, Richard, Phillips, Hebert
PLoS One 2012 May 30;7(5). published online before print
Abstract
DNA barcoding of aquatic macroinvertebrates holds much promise as a tool for taxonomic research and for providing the reliable identifications needed for water quality assessment programs. A prerequisite for identification using barcodes is a reliable reference library. We gathered 4165 sequences from the barcode region of the mitochondrial cytochrome c oxidase subunit I gene representing 264 nominal and 90 provisional species of mayflies (Insecta: Ephemeroptera) from Canada, Mexico, and the United States. No species shared barcode sequences and all can be identified with barcodes with the possible exception of some Caenis. Minimum interspecific distances ranged from 0.3–24.7% (mean: 12.5%), while the average intraspecific divergence was 1.97%. The latter value was inflated by the presence of very high divergences in some taxa. In fact, nearly 20% of the species included two or three haplotype clusters showing greater than 5.0% sequence divergence and some values are as high as 26.7%. Many of the species with high divergences are polyphyletic and likely represent species complexes. Indeed, many of these polyphyletic species have numerous synonyms and individuals in some barcode clusters show morphological attributes characteristic of the synonymized species. In light of our findings, it is imperative that type or topotype specimens be sequenced to correctly associate barcode clusters with morphological species concepts and to determine the status of currently synonymized species.
[Pubmed: 22666447]
| | 13. |
2012 May 25 |
Identification, Expression and Target Gene Analyses of MicroRNAs in Spodoptera litura
Rao, He, Liu, Zheng, Huang, Feng
PLoS One 2012 May 25;7(5). published online before print
Abstract
MicroRNAs (miRNAs) are small RNAs widely present in animals and plants and involved in post-transcriptional regulation of gene transcripts. In this study we identified and validated 58 miRNAs from an EST dataset of Spodoptera litura based on the computational and experimental analysis of sequence conservation and secondary structure of miRNA by comparing the miRNA sequences in the miRbase. RT-PCR was conducted to examine the expression of these miRNAs and stem-loop RT-PCR assay was performed to examine expression of 11 mature miRNAs (out of the 58 putative miRNA) that showed significant changes in different tissues and stages of the insect development. One hundred twenty eight possible target genes against the 11 miRNAs were predicted by using computational methods. Binding of one miRNA (sli-miR-928b) with the three possible target mRNAs was confirmed by Southern blotting, implying its possible function in regulation of the target genes.
[Pubmed: 22662202]
| | 14. |
2012 May 23 |
Expansion and Evolution of the X-Linked Testis Specific Multigene Families in the melanogaster Species Subgroup
Kogan, Usakin, Ryazansky, Gvozdev
PLoS One 2012 May 23;7(5). published online before print
Abstract
The testis specific X-linked genes whose evolution is traced here in the melanogaster species subgroup are thought to undergo fast rate of diversification. The CK2ßtes and NACβtes gene families encode the diverged regulatory β-subunits of protein kinase CK2 and the homologs of β-subunit of nascent peptide associated complex, respectively. We annotated the CK2βtes-like genes related to CK2ßtes family in the D. simulans and D. sechellia genomes. The ancestor CK2βtes-like genes preserved in D. simulans and D. sechellia are considered to be intermediates in the emergence of the D. melanogaster specific Stellate genes related to the CK2ßtes family. The CK2ßtes-like genes are more similar to the unique autosomal CK2ßtes gene than to Stellates, taking into account their peculiarities of polymorphism. The formation of a variant the CK2ßtes gene Stellate in D. melanogaster as a result of illegitimate recombination between a NACßtes promoter and a distinct polymorphic variant of CK2ßtes-like ancestor copy was traced. We found a close nonrandom proximity between the dispersed defective copies of DINE-1 transposons, the members of Helitron family, and the CK2βtes and NACβtes genes, suggesting an involvement of DINE-1 elements in duplication and amplification of these genes.
[Pubmed: 22649555]
| | 15. |
2012 Apr 20 |
High-Throughput PCR Assays To Monitor Wolbachia Infection in the Dengue Mosquito (Aedes aegypti) and Drosophila simulans.
Lee SF, White VL, Weeks AR, Hoffmann AA, Endersby NM
Appl. Environ. Microbiol. 2012 Jul;78(13):4740-3. Epub 2012 Apr 20.
Abstract
We have developed and validated two new fluorescence-based PCR assays to detect the Wolbachia wMel strain in Aedes aegypti and the wRi and wAu strains in Drosophila simulans. The new assays are accurate, informative, and cost-efficient for large-scale Wolbachia screening.
[Pubmed: 22522691]
| | 16. |
2012 May 25 |
Evolution of Eye Morphology and Rhodopsin Expression in the Drosophila melanogaster Species Subgroup
Posnien, Hopfen, Hilbrant, Ramos-Womack, Murat, Schönauer, Herbert, Nunes, Arif, Breuker, Schlötterer, Mitteroecker, McGregor
PLoS One 2012 May 25;7(5). published online before print
Abstract
A striking diversity of compound eye size and shape has evolved among insects. The number of ommatidia and their size are major determinants of the visual sensitivity and acuity of the compound eye. Each ommatidium is composed of eight photoreceptor cells that facilitate the discrimination of different colours via the expression of various light sensitive Rhodopsin proteins. It follows that variation in eye size, shape, and opsin composition is likely to directly influence vision. We analyzed variation in these three traits in D. melanogaster, D. simulans and D. mauritiana. We show that D. mauritiana generally has larger eyes than its sibling species, which is due to a combination of larger ommatidia and more ommatidia. In addition, intra- and inter-specific differences in eye size among D. simulans and D. melanogaster strains are mainly caused by variation in ommatidia number. By applying a geometric morphometrics approach to assess whether the formation of larger eyes influences other parts of the head capsule, we found that an increase in eye size is associated with a reduction in the adjacent face cuticle. Our shape analysis also demonstrates that D. mauritiana eyes are specifically enlarged in the dorsal region. Intriguingly, this dorsal enlargement is associated with enhanced expression of rhodopsin 3 in D. mauritiana. In summary, our data suggests that the morphology and functional properties of the compound eyes vary considerably within and among these closely related Drosophila species and may be part of coordinated morphological changes affecting the head capsule.
[Pubmed: 22662147]
| | 17. |
2012 Jun 1 |
Type-I Prenyl Protease Function Is Required in the Male Germline of Drosophila
melanogaster
Adolphsen, Amell, Havko, Kevorkian, Mears, Neher, Schwarz, Schulze
G3 (Bethesda) 2012 Jun 1;2(6):629-642. published online before print
Abstract
Many proteins require the addition of a hydrophobic prenyl anchor (prenylation) for proper trafficking and localization in the cell. Prenyl proteases play critical roles in modifying proteins for membrane anchorage. The type I prenyl protease has a defined function in yeast (Ste24p/Afc1p) where it modifies a mating pheromone, and in humans (Zmpste24) where it has been implicated in a disease of premature aging. Despite these apparently very different biological processes, the type I prenyl protease gene is highly conserved, encoded by a single gene in a wide range of animal and plant groups. A notable exception is Drosophila melanogaster, where the gene encoding the type I prenyl protease has undergone an unprecedented series of duplications in the genome, resulting in five distinct paralogs, three of which are organized in a tandem array, and demonstrate high conservation, particularly in the vicinity of the active site of the enzyme. We have undertaken targeted deletion to remove the three tandem paralogs from the genome. The result is a male fertility defect, manifesting late in spermatogenesis. Our results also show that the ancestral type I prenyl protease gene in Drosophila is under strong purifying selection, while the more recent replicates are evolving rapidly. Our rescue data support a role for the rapidly evolving tandem paralogs in the male germline. We propose that potential targets for the male-specific type I prenyl proteases include proteins involved in the very dramatic cytoskeletal remodeling events required for spermatid maturation.
[Pubmed: 22690372]
| | 18. |
2012 Jun |
Limits to the Rate of Adaptive Substitution in Sexual Populations
Weissman, Barton
PLoS Genet 2012 Jun;8(6).
Abstract
In large populations, many beneficial mutations may be simultaneously available and may compete with one another, slowing adaptation. By finding the probability of fixation of a favorable allele in a simple model of a haploid sexual population, we find limits to the rate of adaptive substitution, , that depend on simple parameter combinations. When variance in fitness is low and linkage is loose, the baseline rate of substitution is , where is the population size, is the rate of beneficial mutations per genome, and is their mean selective advantage. Heritable variance in log fitness due to unlinked loci reduces by under polygamy and under monogamy. With a linear genetic map of length Morgans, interference is yet stronger. We use a scaling argument to show that the density of adaptive substitutions depends on , , , and only through the baseline density: . Under the approximation that the interference due to different sweeps adds up, we show that , implying that interference prevents the rate of adaptive substitution from exceeding one per centimorgan per 200 generations. Simulations and numerical calculations confirm the scaling argument and confirm the additive approximation for ; for higher , the rate of adaptation grows above , but only very slowly. We also consider the effect of sweeps on neutral diversity and show that, while even occasional sweeps can greatly reduce neutral diversity, this effect saturates as sweeps become more common—diversity can be maintained even in populations experiencing very strong interference. Our results indicate that for some organisms the rate of adaptive substitution may be primarily recombination-limited, depending only weakly on the mutation supply and the strength of selection.
[Pubmed: 22685419]
| | 19. |
2012 Jul |
Characterization of the n-3 polyunsaturated fatty acid enrichment in laying hens fed an extruded flax enrichment source.
Nain S, Renema RA, Korver DR, Zuidhof MJ
Poult. Sci. 2012 Jul;91(7):1720-32.
Abstract
The time required to reach a plateau of n-3 polyunsaturated fatty acid (PUFA) concentration in plasma and egg yolk and dynamics of the enrichment process were examined in laying hens. A group of 75 Lohmann White Leghorn layers (65 wk) were fed one of 3 diets: control, moderate, or high n-3 PUFA-enriched diet for 18 d. Diets provided similar ME and CP and contained 0, 7.5%, or 15% LinPRO (source of n-3 PUFA), respectively. Prior to dietary treatment, baseline values were established for the BW, fatty acid composition in egg yolk on a whole-egg basis, and in plasma. These measurements were repeated at 6, 12, and 18 d of feeding. Enzymatic conversion rates of linolenic acid (LNA) to long-chain fatty acids were calculated. Data were analyzed with Proc Mixed of SAS, and broken stick analysis was used to determine n-3 PUFA plateau using the NLIN procedure of SAS (P < 0.05). The total egg yolk n-3 PUFA reached a plateau of 343.7 mg/egg and 272.9 mg/egg after 6.6 and 5.9 d on the high and moderate diets, respectively. In blood plasma, the n-3 PUFA concentrations reached saturation in 7.2 d with 0.93 mg/mL and 0.67 mg/mL on high and moderate diets, respectively. The transfer efficiency of total n-3 PUFA from the diet to the egg yolk was calculated as 55.6% in control birds, 30.5% in moderate birds, and 22.2% in high birds, demonstrating reduced transfer efficiency of n-3 PUFA as inclusion in the feed increases. Final egg yolk n-3 PUFA concentrations had a CV of 16.5% compared with 28.5% for plasma. After 12 d, the long-chain n-3 PUFA [eicosapentaenoic acid (EPA), docosapentaenoic acid (DPA), and docosahexaenoic acid (DHA)] were significantly higher in egg yolk from hens on the moderate and high enriched diets compared with those from hens fed the control diet, whereas in plasma values did not differ. Broken stick analysis of egg enrichment indicated that high birds reached the target threshold of 300 mg of total n-3 PUFA/egg in 5 d. A significant increase in EPA, DPA, and DHA and reduction in arachidonic acid content in egg yolks from hens fed enriched diets compared with the control diet confirms competition for enzymes during postabsorptive modification of these fatty acids. This work contributes to the understanding of individual hen effects on n-3 PUFA absorption and the effect of level of dietary enrichment with an extruded flax product on final yolk n-3 PUFA concentration.
[Pubmed: 22700520]
| | 20. |
2012 Feb 28 |
Is the biofilm formation and slime producing ability of coagulase-negative staphylococci associated with the persistence and severity of intramammary infection?
Simojoki H, Hyvönen P, Plumed Ferrer C, Taponen S, Pyörälä S
Vet. Microbiol. 2012 Aug 17;158(3-4):344-52. Epub 2012 Feb 28.
Abstract
Biofilm and slime formation assists bacteria in avoiding the host immune defence and antimicrobial therapy. It is suspected to affect the severity or persistence of mastitis caused by coagulase-negative staphylococci (CNS), which are a common cause of bovine mastitis. The phenotypic biofilm formation ability of 244 CNS isolates (199 isolates from bovine mastitis and 52 type and reference strains) was investigated with a tissue culture plate (TCP) assay and fluorescent in situ hybridization (FISH). Slime production of the strains was assessed using Congo red agar (CRA) plates. Additionally, genes encoding the adhesion proteins MSCRAMM (microbial surface components recognizing adhesive matrix molecules) and biofilm-associated proteins (bap) were detected. The severity of intramammary infection (IMI) in mastitis from which the isolates originated was measured with milk N-acetyl-β-d-glucosaminidase (NAGase) activity. One-third of isolates from mastitis produced biofilm when analysed with TCP or FISH. The kappa test value, measuring the agreement between two tests, differed between CNS species. Slime production was less frequent for isolates of the common mastitis species Staphylococcus chromogenes (0.2% of isolates produced slime) and Staphylococcus simulans (3.5%) compared to Staphylococcus epidermidis (40%). No association was found between the phenotypic ability to form biofilm and the persistence of IMI or severity of mastitis. Slime production was rare in isolates originating from IMI. Only 12.7% of isolates from persistent IMI and 1.8% of isolates from spontaneously eliminated IMI produced slime. The eno gene encoding laminin-binding protein was most frequently detected among the isolates from mastitis, 75% of them having this gene. Only a few other MSCRAMM genes were detected.
[Pubmed: 22424866]
| | 21. |
2012 |
An IMS/ATP Assay for the Detection of Mycobacterium tuberculosis in Urine
Hunter, Lim
Tuberc Res Treat 2012;2012.
Abstract
Background. Although sputum smears are the gold standard for diagnosis of tuberculosis, sensitivity in HIV/TB coinfection cases is low, indicating a need for alternative methods. Urine is being increasingly evaluated. Materials and Methods. A novel method for detecting Mycobacterium tuberculosis (MTB) in synthetic urine using a combined IMS/ATP assay was evaluated. Preliminary work established standard ATP conditions and the sensitivity and specificity of the MTB antibody. Eighty-four blinded samples in four replicate assays were evaluated for the presence of MTB using labeled immunomagnetic beads for capture. Beads were separated, washed, and resuspended in broth and added to a microtiter plate. Bioluminescent output was measured and signal-to-noise ratios were calculated. All samples were plated on Middlebrook 7H10 agar or trypticase soy agar to determine limit of detection and recoveries. Results and Conclusions. MTB was distinguished from common bacteriuria isolates and other nontarget bacteria by its ATP results. IMS/ATP successfully detected 19 of 28 samples of MTB in synthetic urine with a limit of detection of 104 CFU/ml. Sensitivity and specificity were 67.9% and 82.1%, respectively. This assay offers a possible rapid screening method for HIV-positive patients with suspected coinfection to improve MTB diagnosis.
[Pubmed: 22655193]
| | 22. |
2012 Jun 4 |
Intraspecific Crossability in Andrographis paniculata Nees: A Barrier against Breeding of the Species
Valdiani, Abdul Kadir, Said Saad, Talei, Omidvar, Hua
ScientificWorldJournal 2012 Jun 4;2012. published online before print
Abstract
The ambiguity of crossability in Andrographis paniculata (AP) was pointed out in the present research. Accordingly, the effects of different style length and crossing time on intraspecific crossability of seven AP accessions in 21 possible combinations were investigated. The best results came out between 08:00 to 11:00 h for manual out-crossing of AP, while the time from 12:00 to 18:00 h showed a decreasing trend. Moreover, 12 mm style length was found as the most proper phenological stage in terms of stigmatic receptivity to perform out-crossing in this plant. All in all, AP behaved unlikely in each combination, and a significant difference was observed in crossability of AP accessions (P < 0.01). The lowest and highest crossability rate was found in hybrids 21 (11261NS × 11344K) and 27 (11322PA × 11350T) with 0.25% and 13.33%, respectively. Furthermore, a significant negative relationship between style length and crossibility (r2 = 0.762∗∗) was recorded in this research. As a final conclusion, crossing time and proper style length can improve the intraspecific crossability in the species, considerably. Despite all the mentioned contrivances, we still believe that a genetic incongruity should be involved as an additional obstacle in crossability of those combinations that failed or responded deficiently to outcrossing.
[Pubmed: 22701352]
| | 23. |
2012 Jun |
Phylogenomic Analysis Reveals Dynamic Evolutionary History of the Drosophila Heterochromatin Protein 1 (HP1) Gene Family
Levine, McCoy, Vermaak, Lee, Hiatt, Matsen, Malik
PLoS Genet 2012 Jun;8(6).
Abstract
Heterochromatin is the gene-poor, satellite-rich eukaryotic genome compartment that supports many essential cellular processes. The functional diversity of proteins that bind and often epigenetically define heterochromatic DNA sequence reflects the diverse functions supported by this enigmatic genome compartment. Moreover, heterogeneous signatures of selection at chromosomal proteins often mirror the heterogeneity of evolutionary forces that act on heterochromatic DNA. To identify new such surrogates for dissecting heterochromatin function and evolution, we conducted a comprehensive phylogenomic analysis of the Heterochromatin Protein 1 gene family across 40 million years of Drosophila evolution. Our study expands this gene family from 5 genes to at least 26 genes, including several uncharacterized genes in Drosophila melanogaster. The 21 newly defined HP1s introduce unprecedented structural diversity, lineage-restriction, and germline-biased expression patterns into the HP1 family. We find little evidence of positive selection at these HP1 genes in both population genetic and molecular evolution analyses. Instead, we find that dynamic evolution occurs via prolific gene gains and losses. Despite this dynamic gene turnover, the number of HP1 genes is relatively constant across species. We propose that karyotype evolution drives at least some HP1 gene turnover. For example, the loss of the male germline-restricted HP1E in the obscura group coincides with one episode of dramatic karyotypic evolution, including the gain of a neo-Y in this lineage. This expanded compendium of ovary- and testis-restricted HP1 genes revealed by our study, together with correlated gain/loss dynamics and chromosome fission/fusion events, will guide functional analyses of novel roles supported by germline chromatin.
[Pubmed: 22737079]
| | 24. |
2012 Jun 22 |
Petunia Floral Defensins with Unique Prodomains as Novel Candidates for Development of Fusarium Wilt Resistance in Transgenic Banana Plants
Ghag, Shekhawat, Ganapathi
PLoS One 2012 Jun 22;7(6). published online before print
Abstract
Antimicrobial peptides are a potent group of defense active molecules that have been utilized in developing resistance against a multitude of plant pathogens. Floral defensins constitute a group of cysteine-rich peptides showing potent growth inhibition of pathogenic filamentous fungi especially Fusarium oxysporum in vitro. Full length genes coding for two Petunia floral defensins, PhDef1 and PhDef2 having unique C- terminal 31 and 27 amino acid long predicted prodomains, were overexpressed in transgenic banana plants using embryogenic cells as explants for Agrobacterium–mediated genetic transformation. High level constitutive expression of these defensins in elite banana cv. Rasthali led to significant resistance against infection of Fusarium oxysporum f. sp. cubense as shown by in vitro and ex vivo bioassay studies. Transgenic banana lines expressing either of the two defensins were clearly less chlorotic and had significantly less infestation and discoloration in the vital corm region of the plant as compared to untransformed controls. Transgenic banana plants expressing high level of full-length PhDef1 and PhDef2 were phenotypically normal and no stunting was observed. In conclusion, our results suggest that high-level constitutive expression of floral defensins having distinctive prodomains is an efficient strategy for development of fungal resistance in economically important fruit crops like banana.
[Pubmed: 22745785]
| | 25. |
2012 Jun |
Incompatibility and Competitive Exclusion of Genomic Segments between Sibling Drosophila Species
Fang, Yukilevich, Chen, Turissini, Zeng, Boussy, Wu
PLoS Genet 2012 Jun;8(6).
Abstract
The extent and nature of genetic incompatibilities between incipient races and sibling species is of fundamental importance to our view of speciation. However, with the exception of hybrid inviability and sterility factors, little is known about the extent of other, more subtle genetic incompatibilities between incipient species. Here we experimentally demonstrate the prevalence of such genetic incompatibilities between two young allopatric sibling species, Drosophila simulans and D. sechellia. Our experiments took advantage of 12 introgression lines that carried random introgressed D. sechellia segments in different parts of the D. simulans genome. First, we found that these introgression lines did not show any measurable sterility or inviability effects. To study if these sechellia introgressions in a simulans background contained other fitness consequences, we competed and genetically tracked the marked alleles within each introgression against the wild-type alleles for 20 generations. Strikingly, all marked D. sechellia introgression alleles rapidly decreased in frequency in only 6 to 7 generations. We then developed computer simulations to model our competition results. These simulations indicated that selection against D. sechellia introgression alleles was high (average s = 0.43) and that the marker alleles and the incompatible alleles did not separate in 78% of the introgressions. The latter result likely implies that most introgressions contain multiple genetic incompatibilities. Thus, this study reveals that, even at early stages of speciation, many parts of the genome diverge to a point where introducing foreign elements has detrimental fitness consequences, but which cannot be seen using standard sterility and inviability assays.
[Pubmed: 22761593]
| | 26. |
2012 |
The Distribution of eIF4E-Family Members across Insecta
Tettweiler, Kowanda, Lasko, Sonenberg, Hernández
Comp Funct Genomics 2012;2012.
Abstract
Insects are part of the earliest faunas that invaded terrestrial environments and are the first organisms that evolved controlled flight. Nowadays, insects are the most diverse animal group on the planet and comprise the majority of extant animal species described. Moreover, they have a huge impact in the biosphere as well as in all aspects of human life and economy; therefore understanding all aspects of insect biology is of great importance. In insects, as in all cells, translation is a fundamental process for gene expression. However, translation in insects has been mostly studied only in the model organism Drosophila melanogaster. We used all publicly available genomic sequences to investigate in insects the distribution of the genes encoding the cap-binding protein eIF4E, a protein that plays a crucial role in eukaryotic translation. We found that there is a diversity of multiple ortholog genes encoding eIF4E isoforms within the genus Drosophila. In striking contrast, insects outside this genus contain only a single eIF4E gene, related to D. melanogaster eIF4E-1. We also found that all insect species here analyzed contain only one Class II gene, termed 4E-HP. We discuss the possible evolutionary causes originating the multiplicity of eIF4E genes within the genus Drosophila.
[Pubmed: 22745595]
| | 27. |
2012 Jun |
Gustatory Perception and Fat Body Energy Metabolism Are Jointly Affected by Vitellogenin and Juvenile Hormone in Honey Bees
Wang, Brent, Fennern, Amdam
PLoS Genet 2012 Jun;8(6).
Abstract
Honey bees (Apis mellifera) provide a system for studying social and food-related behavior. A caste of workers performs age-related tasks: young bees (nurses) usually feed the brood and other adult bees inside the nest, while older bees (foragers) forage outside for pollen, a protein/lipid source, or nectar, a carbohydrate source. The workers' transition from nursing to foraging and their foraging preferences correlate with differences in gustatory perception, metabolic gene expression, and endocrine physiology including the endocrine factors vitellogenin (Vg) and juvenile hormone (JH). However, the understanding of connections among social behavior, energy metabolism, and endocrine factors is incomplete. We used RNA interference (RNAi) to perturb the gene network of Vg and JH to learn more about these connections through effects on gustation, gene transcripts, and physiology. The RNAi perturbation was achieved by single and double knockdown of the genes ultraspiracle (usp) and vg, which encode a putative JH receptor and Vg, respectively. The double knockdown enhanced gustatory perception and elevated hemolymph glucose, trehalose, and JH. We also observed transcriptional responses in insulin like peptide 1 (ilp1), the adipokinetic hormone receptor (AKHR), and cGMP-dependent protein kinase (PKG, or “foraging gene” Amfor). Our study demonstrates that the Vg–JH regulatory module controls changes in carbohydrate metabolism, but not lipid metabolism, when worker bees shift from nursing to foraging. The module is also placed upstream of ilp1, AKHR, and PKG for the first time. As insulin, adipokinetic hormone (AKH), and PKG pathways influence metabolism and gustation in many animals, we propose that honey bees have conserved pathways in carbohydrate metabolism and conserved connections between energy metabolism and gustatory perception. Thus, perhaps the bee can make general contributions to the understanding of food-related behavior and metabolic disorders.
[Pubmed: 22761585]
| | 28. |
2012 Jun 29 |
Diversifying Selection Underlies the Origin of Allozyme Polymorphism at the Phosphoglucose Isomerase Locus in Tigriopus californicus
Schoville, Flowers, Burton
PLoS One 2012 Jun 29;7(6). published online before print
Abstract
The marine copepod Tigriopus californicus lives in intertidal rock pools along the Pacific coast, where it exhibits strong, temporally stable population genetic structure. Previous allozyme surveys have found high frequency private alleles among neighboring subpopulations, indicating that there is limited genetic exchange between populations. Here we evaluate the factors responsible for the diversification and maintenance of alleles at the phosphoglucose isomerase (Pgi) locus by evaluating patterns of nucleotide variation underlying previously identified allozyme polymorphism. Copepods were sampled from eleven sites throughout California and Baja California, revealing deep genetic structure among populations as well as genetic variability within populations. Evidence of recombination is limited to the sample from Pescadero and there is no support for linkage disequilibrium across the Pgi locus. Neutrality tests and codon-based models of substitution suggest the action of natural selection due to elevated non-synonymous substitutions at a small number of sites in Pgi. Two sites are identified as the charge-changing residues underlying allozyme polymorphisms in T. californicus. A reanalysis of allozyme variation at several focal populations, spanning a period of 26 years and over 200 generations, shows that Pgi alleles are maintained without notable frequency changes. Our data suggest that diversifying selection accounted for the origin of Pgi allozymes, while McDonald-Kreitman tests and the temporal stability of private allozyme alleles suggests that balancing selection may be involved in the maintenance of amino acid polymorphisms within populations.
[Pubmed: 22768211]
| | 29. |
2012 May 16 |
Diversity and Biosynthetic Potential of Culturable Actinomycetes Associated with Marine Sponges in the China Seas
Xi, Ruan, Huang
Int J Mol Sci 2012 May 16;13(5):5917-5932. published online before print
Abstract
The diversity and secondary metabolite potential of culturable actinomycetes associated with eight different marine sponges collected from the South China Sea and the Yellow sea were investigated. A total of 327 strains were isolated and 108 representative isolates were selected for phylogenetic analysis. Ten families and 13 genera of Actinomycetales were detected, among which five genera represent first records isolated from marine sponges. Oligotrophic medium M5 (water agar) proved to be efficient for selective isolation, and “Micromonospora–Streptomyces” was proposed as the major distribution group of sponge-associated actinomycetes from the China Seas. Ten isolates are likely to represent novel species. Sponge Hymeniacidon perleve was found to contain the highest genus diversity (seven genera) of actinomycetes. Housekeeping gene phylogenetic analyses of the isolates indicated one ubiquitous Micromonospora species, one unique Streptomyces species and one unique Verrucosispora phylogroup. Of the isolates, 27.5% displayed antimicrobial activity, and 91% contained polyketide synthase and/or nonribosomal peptide synthetase genes, indicating that these isolates had a high potential to produce secondary metabolites. The isolates from sponge Axinella sp. contained the highest presence of both antimicrobial activity and NRPS genes, while those from isolation medium DNBA showed the highest presence of antimicrobial activity and PKS I genes.
[Pubmed: 22754340]
| | 30. |
2012 Jul 11 |
No Effect of Wolbachia on Resistance to Intracellular Infection by Pathogenic Bacteria in Drosophila melanogaster
Rottschaefer, Lazzaro
PLoS One 2012 Jul 11;7(7). published online before print
Abstract
Multiple studies have shown that infection with the endosymbiotic bacterium Wolbachia pipientis confers Drosophila melanogaster and other insects with resistance to infection by RNA viruses. Studies investigating whether Wolbachia infection induces the immune system or confers protection against secondary bacterial infection have not shown any effect. These studies, however, have emphasized resistance against extracellular pathogens. Since Wolbachia lives inside the host cell, we hypothesized that Wolbachia might confer resistance to pathogens that establish infection by invading host cells. We therefore tested whether Wolbachia-infected D. melanogaster are protected against infection by the intracellular pathogenic bacteria Listeria monocytogenes and Salmonella typhimurium, as well as the extracellular pathogenic bacterium Providencia rettgeri. We evaluated the ability of flies infected with Wolbachia to suppress secondary infection by pathogenic bacteria relative to genetically matched controls that had been cured of Wolbachia by treatment with tetracycline. We found no evidence that Wolbachia alters host ability to suppress proliferation of any of the three pathogenic bacteria. Our results indicate that Wolbachia-induced antiviral protection does not result from a generalized response to intracellular pathogens.
[Pubmed: 22808174]
| | 31. |
2012 Jul 11 |
Volatile Drosophila Cuticular Pheromones Are Affected by Social but Not Sexual Experience
Farine, Ferveur, Everaerts
PLoS One 2012 Jul 11;7(7). published online before print
Abstract
Recognition of conspecifics and mates is based on a variety of sensory cues that are specific to the species, sex and social status of each individual. The courtship and mating activity of Drosophila melanogaster flies is thought to depend on the olfactory perception of a male-specific volatile pheromone, cis-vaccenyl acetate (cVA), and the gustatory perception of cuticular hydrocarbons (CHs), some of which are sexually dimorphic. Using two complementary sampling methods (headspace Solid Phase Micro-Extraction [SPME] and solvent extraction) coupled with GC-MS analysis, we measured the dispersion of pheromonal CHs in the air and on the substrate around the fly. We also followed the variations in CHs that were induced by social and sexual interactions. We found that all CHs present on the fly body were deposited as a thin layer on the substrate, whereas only a few of these molecules were also detected in the air. Moreover, social experience during early adult development and in mature flies strongly affected male volatile CHs but not cVA, whereas sexual interaction only had a moderate influence on dispersed CHs. Our study suggests that, in addition to their role as contact cues, CHs can influence fly behavior at a distance and that volatile, deposited and body pheromonal CHs participate in a three-step recognition of the chemical identity and social status of insects.
[Pubmed: 22808151]
| | 32. |
2012 Jul 11 |
Physiological and Biochemical Aspects of the Resistance of Banana Plants to Fusarium Wilt Potentiated by Silicon.
Fortunato A, Rodrigues F, Nascimento K
Phytopathology. 2012 Jul 11; [Epub ahead of print]
Abstract
This study evaluated the physiological and biochemical mechanisms feasibly involved with an increase in resistance of banana plants against Fusarium wilt, caused by Fusarium oxysporum f.sp. cubense (Foc), by silicon (Si). Plants from the Grand Nain (resistant to Foc) and "Maçã" (susceptible to Foc) cultivars were grown in plastic pots amended with 0 (-Si) or 0.39 g Si (+Si) per kg of soil and inoculated with the race 1 of Foc. The relative lesion length (RLL) and the asymptomatic fungal colonization on tissue (AFCT) were evaluated at 40 days after plants inoculation. Root samples were collected at different times after inoculation with Foc to determine the concentrations of lipid peroxidation (expressed as equivalents of malondialdehyde - MDA), hydrogen peroxide (H2O2), pigments (chlorophyll a, chlorophyll b, total chlorophyll, and carotenoids), total soluble phenolics (TSP) and lignin-thioglycolic acid (LTGA) derivatives, the activities of the enzymes phenylalanine ammonia-lyases (PAL), peroxidases (POX), polyphenoloxidases (PPO), β-1,3-glucanases (GLU), and chitinases (CHI), and Si concentration on roots. Root Si concentration was significantly increased by 35.3% for the +Si treatment compared with the -Si treatment. For cultivar Grand Nain, the root Si concentration was significantly increased by 12.8% compared to cultivar "Maçã". Plants from cultivar Grand Nain and "Maçã" in the +Si treatment showed significant reductions of 40.0 and 57.2%, respectively, for RLL compared with the -Si treatment. For the AFCT, there was a significant reduction of 18.5% in the +Si treatment compared with the -Si treatment. The concentration of malondialdehyde significantly decreased for plants from cultivars Grand Nain and "Maçã" supplied with Si compared to the -Si treatment while the concentrations of H2O2 on roots and pigments on leaves significantly increased. The concentrations of TSP and LTGA derivatives as well as the PAL, PPO, POX, GLU, and CHI activities significantly increased on roots of plants from cultivars Grand Nain and "Maçã" from the +Si treatment compared to the -Si treatment. Results of this study suggest that Fusarium wilt intensity on roots of banana plants supplied with Si decreased due to an increase in the concentrations of H2O2, TSP, and LTGA derivatives and greater activities of PAL, PPO, POX, GLU, and CHI in a scenario where the damage to root tissue during the course of infection by Foc was minimal.
[Pubmed: 22784251]
| | 33. |
2012 Jul 6 |
Complex patterns of local adaptation in heat tolerance in Drosophila simulans from eastern Australia.
van Heerwaarden B, Lee RF, Wegener B, Weeks AR, Sgró CM
J Evol Biol. 2012 Jul 6; [Epub ahead of print]
Abstract
Latitudinal clines are considered a powerful means of investigating evolutionary responses to climatic selection in nature. However, most clinal studies of climatic adaptation in Drosophila have involved species that contain cosmopolitan inversion polymorphisms that show clinal patterns themselves, making it difficult to determine whether the traits or inversions are under selection. Further, although climatic selection is unlikely to act on only one life stage in metamorphic organisms, a few studies have examined clinal patterns across life stages. Finally, clinal patterns of heat tolerance may also depend on the assay used. To unravel these potentially confounding effects on clinal patterns of thermal tolerance, we examined adult and larval heat tolerance traits in populations of Drosophila simulans from eastern Australia using static and dynamic (ramping 0.06 °C min(-1) ) assays. We also used microsatellites markers to clarify whether demographic factors or selection are responsible for population differentiation along clines. Significant cubic clinal patterns were observed for adult static basal, hardened and dynamic heat knockdown time and static basal heat survival in larvae. In contrast, static, hardened larval heat survival increased linearly with latitude whereas no clinal association was found for larval ramping survival. Significant associations between adult and larval traits and climatic variables, and low population differentiation at microsatellite loci, suggest a role for climatic selection, rather than demographic processes, in generating these clinal patterns. Our results suggest that adaptation to thermal stress may be species and life-stage specific, complicating our efforts to understand the evolutionary responses to selection for increasing thermotolerance.
[Pubmed: 22775577]
| | 34. |
2012 Jun 20 |
Lung Infection Caused by Mycobacterium riyadhense Confused with Mycobacterium tuberculosis: The First Case in Korea.
Choi JI, Lim JH, Kim SR, Lee SH, Park JS, Seo KW, Jeon JB, Jeong J
Ann Lab Med. 2012 Jul;32(4):298-303. Epub 2012 Jun 20.
Abstract
A slowly growing, non-chromogenic mycobacterial strain was isolated from sputum and bronchial lavage fluid samples of a patient presenting with productive cough, blood-tinged sputum, low-grade fever, and weakness. A positive acid-fast bacilli sputum smear result prompted the initiation of an anti-tuberculosis regimen. Multiplex real-time PCR showed a negative result for Mycobacterium tuberculosis complex and a positive result for nontuberculous mycobacteria. The DNA chip test confirmed this organism as a member of the genus Mycobacterium, but could not specify the species. Interestingly, the mycolic acid patterns obtained by HPLC nearly overlapped with those of M. simulans. The sequences of the Mycobacterium 16S rRNA gene and 16S-23S internal transcribed spacer region were unique and were found to have 100% similarity with those of M. riyadhense. After a review of the literature, we report this case as the first Korean case of M. riyadhense lung infection.
[Pubmed: 22779073]
| | 35. |
2012 Jun 26 |
Bioaugmented composting of Jatropha de-oiled cake and vegetable waste under aerobic and partial anaerobic conditions.
Chaturvedi S, Kumar A, Singh B, Nain L, Joshi M, Satya S
J Basic Microbiol. 2012 Jun 26; [Epub ahead of print]
Abstract
This study was conducted to assess the effect of microbial inoculation in Jatropha cake composting with different vegetable waste. The microbial inoculums composed of fungal strains (Aspergillus awamori, Aspergillus nidulans, Trichoderma viride, Phanerochaete chrysosporium) and bacterial inoculums (Pseudomonas striata as phosphorus solublizer and Azotobacter chroococcum as nitrogen fixer) were added to the compost mixture after the thermophilic phase was over for bioaugmenting of Jatropha cake under aerobic and partial anaerobic conditions. Addition of both fungal and bacterial inoculum with mixed substrate (Jatropha cake + vegetable waste) during composting (aerobic and partial anaerobic) showed, better results as compared to compost with only fungal inoculants. Increased enzymatic activity initially, during composting (like dehydrogenase, alkaline phosphatase activity and FDA) proved role of inoculated microbes in rapid decomposition. Analysis of compost (with both bacterial and fungal inoculum) showed presence of high humus (12.7%), humic acid (0.5%), fulvic acid (5.68%), soluble protein content and low C/N ratio. Decreased in concentration of extractable metals (Cu, Fe and Mn) were recorded at maturity in all the substrate composts. The C/N ratio was significantly correlated to parameters like humic acid, humus, fulvic acid, protein and also microbial activity parameters. We conclude that the composting of de-oiled Jatropha cake with different vegetables waste could be feasible and sustainable approach in recycling of agricultural and industrial residues in huge quantities. (© 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim).
[Pubmed: 22736484]
| | 36. |
2012 Jun 21 |
Clinical presentation of celiac disease among pediatric compared to adolescent and adult patients.
Kochhar R, Jain K, Thapa BR, Rawal P, Khaliq A, Kochhar R, Bhadada S, Vaiphei K, Varma S, Dutta U, Nain CK, Prasad KK, Singh K
Indian J Gastroenterol. 2012 Jun 21; [Epub ahead of print]
Abstract
BACKGROUND: Celiac disease (CD) is being increasingly recognized in adults though a majority of patients continue to be diagnosed in childhood. AIM: To compare the clinical presentation and profile of newly diagnosed pediatric and adolescent/adult CD patients. MATERIALS AND METHODS: Retrospective analysis of patients diagnosed with CD between year 1997 and 2007 in the pediatric group, and between year 2000 and 2007 in the adolescent/adult group was done for clinical presentation, endoscopic findings and duodenal histology. RESULTS: A total of 434 children and 298 adults were studied. The mean age of diagnosis was 6.5 ± 2.5 years (1-11 years) in children and 29.3 ± 13.3 years (6-73 years) in adolescent/adults. The mean duration of symptoms before diagnosis was 3.5 ± 2.5 years in children and 4.9 ± 4.6 years in the latter. Diarrhea as the presenting symptom was seen in 74 % of children and 58.7 % of adolescent/adults. Anemia (on investigations) was seen in 84 % of children and 94 % of adolescent/adults. CONCLUSIONS: Pediatric patients of CD present more often with typical features than adults. Atypical presentations are more common in adults and the latent period for diagnosis is also longer in adolescent/adults. There is a need for increasing awareness about CD, both among pediatricians and physicians caring for adult patients.
[Pubmed: 22717947]
| | 37. |
2012 Jun 13 |
Fine-scale genetic analysis of species-specific female preference in Drosophila simulans.
Laturney M, Moehring AJ
J Evol Biol. 2012 Jun 13; [Epub ahead of print]
Abstract
Behavioural differences are thought to be the first components to contribute to species isolation, yet the precise genetic basis of behavioural isolation remains poorly understood. Here, we used a combination of behaviour assays and genetic mapping to provide the first refined map locating candidate genes for interspecific female preference isolating Drosophila simulans from D. melanogaster. First, we tested whether two genes identified as affecting D. melanogaster female intraspecific mate choice also affect interspecific mate choice; neither of these genes was found to contribute to species-specific female preference. Next, we used deficiency mapping to locate genes on the right arm of the third chromosome for species-specific female preference and identified five small significant regions that contain candidate genes contributing to behavioural isolation. All five regions were located in areas that would have low interspecific recombination, which mirrors the results of other behavioural isolation studies that used quantitative trait locus (QTL) mapping, but without the potential concern of bias towards regions of low recombination that QTL mapping may have. As this model system may be refined to the individual gene level using the same methodology, this initial map we provide may potentially serve as a ready template for the identification and characterization of the first behavioural isolation genes.
[Pubmed: 22694106]
| | 38. |
2012 Jun 6 |
Anti-staphylococcal activities of lysostaphin and LytM catalytic domain.
Sabala I, Jonsson IM, Tarkowski A, Bochtler M
BMC Microbiol. 2012 Jun 6;12(1):97. Epub 2012 Jun 6.
Abstract
ABSTRACT: BACKGROUND: Lysostaphin and the catalytic domain of LytM cleave pentaglycine crossbridges ofStaphylococcus aureus peptidoglycan. The bacteriocin lysostaphin is secreted byStaphylococcus simulans biovar staphylolyticus and directed against the cell walls ofcompeting S. aureus. LytM is produced by S. aureus as a latent autolysin and can beactivated in vitro by the removal of an N-terminal domain and occluding region. RESULTS: We compared the efficacies of the lysostaphin and LytM catalytic domains using a newlydeveloped model of chronic S. aureus infected eczema. Lysostaphin was effective, like inother models. In contrast, LytM was not significantly better than control. The differenttreatment outcomes could be correlated with in vitro properties of the proteins, including proteolytic stability, affinity to cell wall components other than peptidoglycan, and sensitivityto the ionic milieu. CONCLUSIONS: Although lysostaphin and LytM cleave the same peptide bond in the peptidoglycan, the twoenzymes have very different environmental requirements what is reflected in their contrastingperformance in mouse eczema model.
[Pubmed: 22672475]
| | 39. |
2012 Jun 6 |
Genome sequencing reveals complex speciation in the Drosophila simulans clade.
Garrigan D, Kingan SB, Geneva AJ, Andolfatto P, Clark AG, Thornton KR, Presgraves DC
Genome Res. 2012 Jun 6; [Epub ahead of print]
Abstract
The three species of the Drosophila simulans clade-the cosmopolitan species, D. simulans, and the two island endemic species, D. mauritiana and D. sechellia-are important models in speciation genetics, but some details of their phylogenetic and speciation history remain unresolved. The order and timing of speciation are disputed, and the existence, magnitude, and timing of gene flow among the three species remain unclear. Here we report on the analysis of a whole-genome four-species sequence alignment that includes all three D. simulans clade species as well as the D. melanogaster reference sequence. The alignment comprises novel, paired short-read sequence data from a single highly inbred line each from D. simulans, D. mauritiana, and D. sechellia. We are unable to reject a species phylogeny with a basal polytomy; the estimated age of the polytomy is 242,000 yr before the present. However, we also find that up to 4.6% of autosomal and 2.2% of X-linked regions have evolutionary histories consistent with recent gene flow between the mainland species (D. simulans) and the two island endemic species (D. mauritiana and D. sechellia). Our findings thus show that gene flow has occurred throughout the genomes of the D. simulans clade species despite considerable geographic, ecological, and intrinsic reproductive isolation. Last, our analysis of lineage-specific changes confirms that the D. sechellia genome has experienced a significant excess of slightly deleterious changes and a dearth of presumed favorable changes. The relatively reduced efficacy of natural selection in D. sechellia is consistent with its derived, persistently reduced historical effective population size.
[Pubmed: 22534282]
| | 40. |
2012 Jun 6 |
Major role of positive selection in the evolution of conservative segments of Drosophila proteins.
Bazykin GA, Kondrashov AS
Proc Biol Sci. 2012 Jun 6; [Epub ahead of print]
Abstract
Slow evolution of conservative segments of coding and non-coding DNA is caused by the action of negative selection, which removes new mutations. However, the mode of selection that affects the few substitutions that do occur within such segments remains unclear. Here, we show that the fraction of allele replacements that were driven by positive selection, and the strength of this selection, is the highest within the conservative segments of Drosophila protein-coding genes. The McDonald-Kreitman test, applied to the data on variation in Drosophila melanogaster and in Drosophila simulans, indicates that within the most conservative protein segments, approximately 72 per cent (approx. 80%) of allele replacements were driven by positive selection, as opposed to only approximately 44 per cent (approx. 53%) at rapidly evolving segments. Data on multiple non-synonymous substitutions at a codon lead to the same conclusion and additionally indicate that positive selection driving allele replacements at conservative sites is the strongest, as it accelerates evolution by a factor of approximately 40, as opposed to a factor of approximately 5 at rapidly evolving sites. Thus, random drift plays only a minor role in the evolution of conservative DNA segments, and those relatively rare allele replacements that occur within such segments are mostly driven by substantial positive selection.
[Pubmed: 22673359]
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