Dicarboximide resistance in field isolates of Alternaria alternata is mediated by a mutation in a two-component histidine kinase gene

Isolates of Alternaria alternata collected from a field site which had previously been treated with the dicarboximide fungicide iprodione were found to demonstrate a high level of resistance to iprodione and the phenylpyrrole fungicide, fludioxonil in plate assays. In order to determine the genetic basis for this fungicide resistance a partial length clone of a two-component histidine kinase (HK) was isolated from genomic DNA of a fungicide-sensitive A. alternata isolate using degenerate primers by PCR. Analysis of the AaHK1 gene structure indicates the presence of six 90 amino acid repeat domains upstream of a kinase domain as found in the homologous HK genes from other fungal species. Comparison of nucleic acid sequences from the fungicide-sensitive and fungicide-resistant A. alternata isolates confirmed the presence of mutations leading to premature termination of the translated HK protein. The possible role of the two-component HK in the development of dicarboximide resistance in A. alternata is discussed.     

LoFreq: a sequence-quality aware,ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets

The study of cell-population heterogeneity in a range of biological systems, from viruses to bacterial isolates to tumor samples, has been transformed by recent advances in sequencing throughput. While the high-coverage afforded can be used, in principle, to identify very rare variants in a population, existing ad hoc approaches frequently fail to distinguish true variants from sequencing errors. We report a method (LoFreq) that models sequencing run-specific error rates to accurately call variants occurring in <0.05% of a population. Using simulated and real datasets (viral, bacterial and human), we show that LoFreq has near-perfect specificity, with significantly improved sensitivity compared with existing methods and can efficiently analyze deep Illumina sequencing datasets without resorting to approximations or heuristics. We also present experimental validation for LoFreq on two different platforms (Fluidigm and Sequenom) and its application to call rare somatic variants from exome sequencing datasets for gastric cancer. Source code and executables for LoFreq are freely available at http://sourceforge.net/projects/lofreq/.     

Multifunctional 0D–2D Ni2P Nanocrystals–Black Phosphorus Heterostructure

0D transition metal phosphides (TMPs) nanocrystals (NCs)–2D ultrathin black phosphorus (BP) heterostructure (Ni₂P@BP) have been synthesized via a facile sonication‐assisted exfoliation followed by a solvothermal process. Compared with the bare BP, the specially designed Ni₂P@BP architecture can enhance the electrical conductivity (from 2.12 × 10² to 6.25 × 10⁴ S m^–1), tune the charge carrier concentration (from 1.25 × 10¹⁷ to 1.37 × 10²⁰ cm^–3), and reduce the thermal conductivity (from 44.5 to 7.69 W m^–1 K^–1) at 300 K, which can be considered for multiple applications. As a result, the Ni₂P@BP exhibits excellent Li storage properties and high hydrogen evolution reaction electrocatalytic activities. The Ni₂P@BP shows improved Li diffusion kinetics (e.g., the Li ions diffusion coefficient increases from 1.14 × 10^–14 cm² s^–1 for pure BP nanosheets to 8.02 × 10^–13 cm² s^–1 for Ni₂P@BP). In addition, the Ni₂P@BP electrode sustains hydrogen production with almost unchanged activity over 3000 cycles, which indicates its good chemical stability when operating under strong reducing environment.     

Antimicrobial activity of honey from the stingless bee Trigona carbonaria determined by agar diffusion,agar dilution,broth microdilution and time‐kill methodology

Aims: The aim of this study was to determine the spectrum of antimicrobial activity of 11 samples of stingless bee honey compared to medicinal, table and artificial honeys. Methods and Results: Activity was assessed by agar diffusion, agar dilution, broth microdilution and time‐kill viability assays. By agar dilution, minimum inhibitory concentration (MIC) ranges were 4% to >10% (w/v) for Gram‐positive bacteria, 6% to >16% (w/v) for Gram‐negative bacteria and 6% to >10% (w/v) for Candida spp. By broth microdilution, all organisms with the exception of Candida albicans and Candida glabrata were inhibited at ≤32% (w/v). Geometric MIC (w/v) means for stingless bee honeys ranged from 7·1% to 16·0% and were 11·7% for medicinal honey and 26·5% for table honey. Treatment of organisms with 20% (w/v) stingless bee honey for 60 min resulted in decreases of 1–3 log for Staphylococcus aureus, >3 log for Pseudomonas aeruginosa and <1 log for C. albicans. Similar treatment with each control honey resulted in decreases of <1 log for all organisms. Conclusions: Stingless bee honey has broad‐spectrum antibacterial activity although activity against Candida was limited. Stingless bee honey samples varied in activity and the basis for this remains to be determined. Significance and Impact of the Study: Stingless bee honey had similar activity to medicinal honey and may therefore have a role as a medicinal agent.     

X-linked megalocornea caused by mutations in CHRDL1 identifies an essential role for ventroptin in anterior segment development

X-linked megalocornea (MGC1) is an ocular anterior segment disorder characterized by an increased cornea diameter and deep anterior chamber evident at birth and later onset of mosaic corneal degeneration (shagreen), arcus juvenilis, and presenile cataracts. We identified copy-number variation, frameshift, missense, splice-site and nonsense mutations in the Chordin-like 1 gene (CHRDL1) on Xq23 as the cause of the condition in seven MGC1 families. CHRDL1 encodes ventroptin, a bone morphogenic protein antagonist with a proposed role in specification of topographic retinotectal projections. Electrophysiological evaluation revealed mild generalized cone system dysfunction and, in one patient, an interhemispheric asymmetry in visual evoked potentials. We show that CHRDL1 is expressed in the developing human cornea and anterior segment in addition to the retina. We explored the impact of loss of ventroptin function on brain function and morphology in vivo. CHRDL1 is differentially expressed in the human fetal brain, and there is high expression in cerebellum and neocortex. We show that MGC1 patients have a superior cognitive ability despite a striking focal loss of myelination of white matter. Our findings reveal an unexpected requirement for ventroptin during anterior segment development and the consequences of a lack of function in the retina and brain.     

Replication and Meta-Analysis of GWAS Identified Susceptibility Loci in Kawasaki Disease Confirm the Importance of B Lymphoid Tyrosine Kinase (BLK) in Disease Susceptibility

The BLK and CD40 loci have been associated with Kawasaki disease (KD) in two genome-wide association studies (GWAS) conducted in a Taiwanese population of Han Chinese ancestry (Taiwanese) and in Japanese cohorts. Here we build on these findings with replication studies of the BLK and CD40 loci in populations of Korean and European descent. The BLK region was significantly associated with KD susceptibility in both populations. Within the BLK gene the rs2736340-located linkage disequilibrium (LD ) comprising the promoter and first intron was strongly associated with KD, with the combined results of Asian studies including Taiwanese, Japanese, and Korean populations (2,539 KD patients and 7,021 controls) providing very compelling evidence of association (rs2736340, OR = 1.498, 1.354–1.657; P = 4.74×10⁻³¹). We determined the percentage of B cells present in the peripheral blood mononuclear cell (PBMC) population and the expression of BLK in the peripheral blood leukocytes (leukocytes) of KD patients during the acute and convalescent stages. The percentage of B cells in the PBMC population and the expression of BLK in leukocytes were induced in patients in the acute stage of KD. In B cell lines derived from KD patients, and in purified B cells from KD patients obtained during the acute stage, those with the risk allele of rs2736340 expressed significantly lower levels of BLK. These results suggest that peripheral B cells play a pathogenic role during the acute stage of KD. Decreased BLK expression in peripheral blood B cells may alter B cell function and predispose individuals to KD. These associative data suggest a role for B cells during acute KD. Understanding the functional implications may facilitate the development of B cell-mediated therapy for KD.     

An assessment of orchids’ diversity in Penang Hill,Penang, Malaysia after 115 years

A comprehensive study on the orchid diversity in Penang Hill, Penang, Malaysia was conducted from 2004 to 2008 with the objective to evaluate the presence of orchid species listed by Curtis (J Strait Br R Asiat Soc 25:67–173, 1894) after more than 100 years. A total of 85 species were identified during this study, of which 52 are epiphytic or lithophytic and 33 are terrestrial orchids. This study identified 57 species or 64.8% were the same as those recorded by Curtis (1894), and 78 species or 66.1% of Turner’s (Gardens’ Bull Singap 47(2):599–620, 1995) checklist of 118 species for the state of Penang including 18 species which were not recorded by Curtis (1894) and the current study but are actually collected from Penang Hill. A comparison table of the current findings against Curtis (1894) and Turner (1995) is provided which shows only 56 species were the same in all three studies. The preferred account for comparison was Curtis’ (1894) list as his report was specifically for the areas around Penang Island especially Penang Hill, Georgetown and Ayer Itam areas. Our study reveals that about 50% of Curtis’ collection localities have been converted to residential areas and agricultural land, and this probably explains the decreasing numbers of species found in the current study especially for the terrestrial species as epiphytic species have better adaptation capabilities towards environmental changes. Seven species were identified as new records to Penang Hill as they were not recorded by Curtis (1894). None of the three species recorded as endemic to Penang by Turner (1995) was recollected during the current study, of which only Zeuxine rupestris was in Curtis’ (1894) list. Overall, we concluded that Penang hill harbours at least 136 species of orchids of which 78 species or 57.4% were recollected in this study. This also indicates that this area is still suitable for orchid growth even though it is surrounded by rapid development and mass conversion of forested land into fruit orchards and residential area. The designation of Penang Hill as a Permanent Forest Reserve would better guarantee the survival of some orchid species unless human interventions and climatic changes occur.     

Impact of Measurement Error on Testing Genetic Association with Quantitative Traits

Measurement error of a phenotypic trait reduces the power to detect genetic associations. We examined the impact of sample size, allele frequency and effect size in presence of measurement error for quantitative traits. The statistical power to detect genetic association with phenotype mean and variability was investigated analytically. The non-centrality parameter for a non-central F distribution was derived and verified using computer simulations. We obtained equivalent formulas for the cost of phenotype measurement error. Effects of differences in measurements were examined in a genome-wide association study (GWAS) of two grading scales for cataract and a replication study of genetic variants influencing blood pressure. The mean absolute difference between the analytic power and simulation power for comparison of phenotypic means and variances was less than 0.005, and the absolute difference did not exceed 0.02. To maintain the same power, a one standard deviation (SD) in measurement error of a standard normal distributed trait required a one-fold increase in sample size for comparison of means, and a three-fold increase in sample size for comparison of variances. GWAS results revealed almost no overlap in the significant SNPs (p<10⁻⁵) for the two cataract grading scales while replication results in genetic variants of blood pressure displayed no significant differences between averaged blood pressure measurements and single blood pressure measurements. We have developed a framework for researchers to quantify power in the presence of measurement error, which will be applicable to studies of phenotypes in which the measurement is highly variable.