Search

Context High levels of exchangeable sodium or potassium in soils can lead to issues such as dispersion and deterioration of soil structure, reduced hydraulic conductivity and inadequate aeration. Gypsum is the most common soil amendment used to treat these issues but current methods to determine application rates (e.g. based on exchangeable sodium percentage or addition of dissolved calcium to diluted soil extracts) have limitations. Aim The aim of this study was to develop a simple soil incubation test to determine gypsum rates that are sufficient to eliminate soil dispersion. Methods Accurately weighed amounts of gypsum (to represent rates between 0 and 10 t ha−1) were mixed with soil (n = 8, three replicates) in small columns (50 mL plastic syringe-valve) and incubated under wet conditions for different periods. The turbidity, electrical conductivity, pH and cation concentrations in the column leachate were measured. Key results As gypsum rate increased, turbidity in the leachate decreased and this relationship was fitted with a natural logarithm function for each soil (average R2 = 0.71). A desired leachate turbidity target of ≤10 NTU was used in the equation to estimate the gypsum rate when dispersion was overcome for each soil. Testing suggested that a 1-day soil incubation time was sufficient. Conclusions Advantages of this new method include (a) non-reliance on exchangeable cation measurements, (b) direct relationship of the turbidity measure with soil dispersion and (c) the influence of soil salinity on dispersion being implicitly considered. Implications This method should provide improved decision support for management of dispersive soils.

Leaf blight caused by Calonectria species is a major constraint to Eucalyptus trees in China. Calonectria leaf disease on Eucalyptus planted in China was first reported in HaiNan Island in 1985. No systematic investigation or identification of Calonectria species associated with diseased Eucalyptus in HaiNan Island have been performed to date. In order to comprehensively understand the species diversity, distribution, and pathogenicity of Calonectria associated with diseased Eucalyptus trees in HaiNan Island, 400 Calonectria isolates were obtained from 278 diseased Eucalyptus trees planted in 17 sites in five counties/regions. All 400 isolates were identified based on DNA sequence comparisons of the translation elongation factor 1-alpha (tef1), β-tubulin (tub2), calmodulin (cmdA), and histone H3 (his3) gene regions as well as a combination of morphological characteristics. Seven species, namely C. acaciicola (198 isolates, 49.5%), C. pseudoreteaudii (161 isolates, 40.25%), C. reteaudii (29 isolates, 7.25%), C. hawksworthii (6 isolates, 1.5%), C. hongkongensis (4 isolates, 1%), C. auriculiformis (1 isolate, 0.25%) and C. chinensis (1 isolate, 0.25%), were identified. This is the first report of C. acaciicola in China. Calonectria acaciicola, C. pseudoreteaudii, and C. reteaudii belong to the C. reteaudii species complex and were the dominant species collected, accounting for 97% of all the isolates obtained. Overlap in vesicle shape, macroconidia size, and macroconidia septa number existed among these three species in the C. reteaudii species complex. The geographical regions significantly influenced the distribution of C. acaciicola and C. pseudoreteaudii. Representative isolates of C. acaciicola, C. pseudoreteaudii, C. reteaudii and C. hawksworthii produced abundant macroconidia were used in conidial suspension inoculation on Eucalyptus seedlings. Inoculation showed that all four of the tested Calonectria species were highly pathogenic to the two tested Eucalyptus genotypes. The tolerances of two Eucalyptus genotypes were significantly different. This study conducted the first systematic investigation and identification of Calonectria species associated with Eucalyptus leaf blight in HaiNan Island and advanced the concept of selection of disease resistant Eucalyptus genotypes for managing Eucalyptus leaf blight caused by Calonectria species in China.

Stroke was the third leading cause of global disability-adjusted life years and its treatment drugs were limited. Researchers still need to find reliable diagnostic biomarkers and therapeutic targets. This study aimed to explore hub genes associated with ischemic stroke (IS) through bioinformatics analysis and identify its potential diagnostic biomarkers and therapeutic targets. The microarray data sets of GSE58294 and GSE16561 related to IS were downloaded from the Gene Expression Omnibus (GEO) database. Weighted co-expression network analysis (WGCNA) and differential expression analysis were integrated to find overlapping genes, and then hub genes were screened by Least absolute shrinkage and selection operator (LASSO) regression. NetworkAnalyst database was used to construct the TF-gene network and miRNA-TF regulatory network of the hub genes. DGIdb and CMap databases were used to predict targeted drugs and small molecule compounds. Through the Comprehensive analysis of GSE58294 and GSE16561, 10 hub genes were screened by LASSO regression, namely ARG1, LY96, ABCA1, SLC22A4, CD163, TPM2, SLC25A42, ID3, FAM102A and CD79B. NetworkAnalyst database analysis showed that ABCA1 was the hub gene most regulated by miRNA and TF. TRRUST and NetworkAnalyst databases showed that SP1 (P=0.0246) was a key transcription factor for hub genes. Finally, DGIdb database analysis identified 7 therapeutic drugs targeted with ABCA1 and SLC22A4, and 4 small molecule compounds targeted with ID3 and SLC22A4 were obtained from CMap database. We identified IS-related diagnostic biomarkers and therapeutic drugs, which can provide new insights for the diagnosis and treatment of IS.

Stroke is the third leading cause of disability-adjusted life years worldwide, and drugs available for its treatment are limited. This study aimed to explore high-confidence candidate genes associated with ischemic stroke (IS) through bioinformatics analysis and identify potential diagnostic biomarkers and gene-drug interactions. Weighted gene coexpression network analysis (WGCNA) and differentially expressed genes (DEGs) were integrated to identify overlapping genes. Then, high-confidence candidate genes were screened by least absolute shrinkage and selection operator (LASSO) regression. Receiver operating characteristic (ROC) curves were used to evaluate the diagnostic value of high-confidence candidate genes as biomarkers for IS. The NetworkAnalyst database was used to construct the TF-gene network and miRNA-TF regulatory network of the high-confidence candidate genes. The DGIdb database was used to identified gene-drug interactions. Through the comprehensive analysis of GSE58294 and GSE16561, 10 high-confidence candidate genes were identified by LASSO regression: ARG1, LY96, ABCA1, SLC22A4, CD163, TPM2, SLC25A42, ID3, FAM102A and CD79B. FAM102A had the highest diagnostic value, and the area under curve (AUC), sensitivity and specificity values were 0.974, 0.919 and 0.936, respectively. The HPA database demonstrated that 10 high-confidence candidate genes were expressed in the brain and blood in normal humans. Finally, DGIdb database analysis identified 8 gene-drug interactions. We identified IS-related diagnostic biomarkers and gene-drug interactions that potentially provide new insights into the diagnosis and treatment of IS.

Histone deacetylases (HDACs) regulate gene transcription, and play a critical role in plant growth, development and stress responses. HD2 proteins are plant specific histone deacetylases. In woody plants, functions of HD2s are not known. In this study, we cloned an HD2 gene PtHDT902 from Populus trichocarpa and investigated its sequence, expression, subcellular localization, and functions in root development and salt stress responses. Our findings indicated that PtHDT902 was a nuclear protein and its expression was regulated by abiotic stresses. The over-expression of PtHDT902 in both Arabidopsis and poplar increased the expression levels of gibberellin (GA) biosynthetic genes. The expression of PtHDT902 in Arabidopsis enhanced primary root growth, and its over-expression in poplar inhibited adventitious root formation. These phenotypes resulted from over-expression of PtHDT902 were consistent with the GA-overproduction phenotypes. In addition, the poplar plants over-expressing PtHDT902 exhibited lower tolerance to salt than non-transgenic plants. These findings indicated that PtHDT902 worked as an important regulator in adventitious root formation and salt stress tolerance in poplar.

Sodicity, where a high proportion of cation exchange sites are occupied by monovalent Na+ ions relative to divalent cations Ca2+ and Mg2+, is a widespread and serious problem globally as this can result in soil dispersion, low hydraulic conductivity and poor aeration. It has been increasingly recognized that the presence of potassium (K+) can also be a contributor to soil structural stability problems. The aim of this research was to investigate the long term (>15 years) effects of irrigating treated winery wastewater on soil structural stability, for which K+ comprises a high proportion of total cation concentrations, at a vineyard trial site in the Barossa Valley, Australia. Analysis of the long-term soil dataset was undertaken along with laboratory experiments to determine the current or future impacts of high exchangeable K+ on soil hydraulic conductivity and dispersion. Field results showed build-up of K+ in subsoils and a corresponding decline in Mg2+. This appears due to the higher selectivity and exchange of K+ relative to Na+, and higher K/Na ratio in the wastewater. The potential dispersibility of the subsoils was demonstrated via a high turbidity of soil suspensions and high values of the Emerson Dispersion Index. Declining relative hydraulic conductivity occurred for subsoils leached with winery wastewater followed by low ionic strength water. Flocculation measurements were performed in which aliquots of CaCl2 were added to determine the amount of Ca2+ needed to overcome dispersion. We conclude that the long-term use of winery wastewater irrigation has potential to negatively impact soil structural stability via increasing exchangeable K+. Further field research is required but Ca or Mg based amendments could be used to reduce dispersion risks.

Dysplastic nevi (DN) is a strong risk factor for cutaneous malignant melanoma (CMM), and it frequently occurs in melanoma-prone families. To identify genetic variants for DN, we genotyped 677 tagSNPs in 38 melanoma candidate genes that are involved in pigmentation, DNA repair, cell cycle control, and melanocyte proliferation pathways in a total of 504 individuals (310 with DN, 194 without DN) from 53 melanoma-prone families (23 CDKN2A mutation positive and 30 negative). Conditional logistic regression, conditioning on families, was used to estimate the association between DN and each single-nucleotide polymorphism (SNP) separately, adjusted for age, sex, CMM, and CDKN2A status. P-values for SNPs in the same gene were combined to yield gene-specific P-values. Two genes, CDK6 (cyclin-dependent kinase 6) and XRCC1, were significantly associated with DN after Bonferroni correction for multiple testing (P=0.0001 and 0.00025, respectively), whereas neither gene was significantly associated with CMM. Associations for CDK6 SNPs were stronger in CDKN2A mutation–positive families (rs2079147, Pinteraction=0.0033), whereas XRCC1 SNPs had similar effects in mutation-positive and -negative families. The association for one of the associated SNPs in XRCC1 (rs25487) was replicated in two independent data sets (random-effect meta-analysis: P

Selenium (Se) is an essential trace element in vivo involved in the defense against oxidative stress. Se deficiency is associated with many human diseases. The bioactivity of Se is dose- and species-dependent. Silkworm pupa has been reported to accumulate Se mainly in proteins. Thus the characterization of major Se-containing proteins is very important in the application of Se-rich silkworm pupas in food and drugs. In this study, crude proteins were extracted from Se-rich silkworm pupas, followed by DEAE-Sepharose and Sephedex G-75 chromatography. Se content was measured after each step to determine the highest Se-containing fraction for the next step of separation. The proteins obtained were analyzed using SDS-PAGE, followed by in-gel digestion with trypsin, and were characterized by MALDI-TOF MS and ESI-MS/MS. These data showed two proteins mainly accumulated Se in the silkworm pupas. Those two proteins were proven by mass spectrometry to be arylphorin and sex-specific storage-protein 2 precursor (SP-2), respectively. Both of them belong to the storage proteins of amino acids during metamorphosis and the non-feeding pupal stage. The results suggest that Se could be enriched by storage proteins and be supplied to silkworm pupas in accompany with amino acids for the synthesis of new Se-containing proteins and peptides.

Summary Choosing an appropriate single-marker association test is critical to the success of case-control genetic association studies. An ideal single-marker analysis should have robust performance across a wide range of potential disease risk models. MAX was designed specifically to achieve such robustness. In this work, we derived the power calculation formula for MAX and conducted a comprehensive power comparison between MAX and two other commonly used single-marker tests, the one-degree-of-freedom (1-df) Cochran-Armitage trend test and the 2-df Pearson χ2 test. We used a single-marker disease risk model and a two-marker haplotype risk model to explore the performances of the above three tests. We found that each test has its own “sweet” spots. Among the three tests considered, MAX appears to have the most robust performance.

Alzheimer disease (AD) is a devastating neurodegenerative disease affecting more than five million Americans. In this study, we have used updated genetic linkage data from chromosome 10 in combination with expression data from serial analysis of gene expression to choose a new set of thirteen candidate genes for genetic analysis in late onset Alzheimer disease (LOAD). Results in this study identify the KIAA1462 locus as a candidate locus for LOAD in APOE4 carriers. Two genes exist at this locus, KIAA1462, a gene associated with coronary artery disease, and "rokimi", encoding an untranslated spliced RNA The genetic architecture at this locus suggests that the gene product important in this association is either "rokimi", or a different isoform of KIAA1462 than the isoform that is important in cardiovascular disease. Expression data suggests that isoform f of KIAA1462 is a more attractive candidate for association with LOAD in APOE4 carriers than "rokimi" which had no detectable expression in brain. © 2013 Murdock et al.

Chromosome 9p21 has been implicated in the pathogenesis of cutaneous malignant melanoma (CMM). In addition to CDKN2A, the major known high-risk susceptibility gene for CMM, recent studies suggest that other 9p21 genes may be involved in melanoma/nevi development. To identify 9p21 variants that influence susceptibility to CMM and number of nevi in CMM-prone families with and without CDKN2A mutations, we analyzed 562 individuals (183 CMM) from 53 families (23 CDKN2A+, 30 CDKN2A-) for 233 tagging SNPs in 21 genes at 9p21. Single SNP- and gene-based regression analyses were used to assess the risk of CMM, nevi count, skin complexion, and tanning ability associated with these SNPs and genes. We found that SNP rs7023329 in the MTAP gene was associated with number of nevi (P (trend) = 0.003) confirming a recent finding by a genome-wide association study. In addition, three SNPs in the ACO1 gene, rs7855483 (P (trend) = 0.002), rs17288067 (P (trend) = 0.0009), and rs10813813 (P (trend) = 0.005), showed the strongest associations with CMM risk. None of the examined 9p21 SNPs was associated with skin complexion, whereas two SNPs, rs10964862 in IFNW1 (P (trend) = 0.003), and rs13290968 in TUSC1 (P (trend) = 0.0006), were associated with tanning ability. Gene-based analyses suggested that the ACO1 gene was significantly associated with CMM (P = 0.0004); genes IFNW1 (P = 0.002) and ACO1 (P = 0.0002) were significantly associated with tanning ability. Our findings are consistent with recent proposals that additional 9p21 genes may contribute to CMM susceptibility in CMM-prone families. These genetic variants may, at least partially, exert their effects through nevi and tanning ability.

Although several genes (including a strong effect in the human leukocyte antigen (HLA) region) and some environmental factors have been implicated to cause susceptibility to rheumatoid arthritis (RA), the etiology of the disease is not completely understood. The ability to screen the entire genome for association to complex diseases has great potential for identifying gene effects. However, the efficiency of gene detection in this situation may be improved by methods specifically designed for high-dimensional data. The aim of this study was to compare how three different statistical approaches, multifactor dimensionality reduction (MDR), random forests (RF), and an omnibus approach, worked in identifying gene effects (including gene-gene interaction) associated with RA. We developed a test set of genes based on previous linkage and association findings and tested all three methods. In the presence of the HLA shared-epitope factor, other genes showed weaker effects. All three methods detected SNPs in PTPN22 and TRAF1-C5 as being important. But we did not detect any new genes in this study. We conclude that the three high-dimensional methods are useful as an initial screening for gene associations to identify promising genes for further modeling and additional replication studies.

Interest is increasing in epistasis as a possible source of the unexplained variance missed by genome-wide association studies. The Genetic Analysis Workshop 16 Group 9 participants evaluated a wide variety of classical and novel analytical methods for detecting epistasis, in both the statistical and machine learning paradigms, applied to both real and simulated data. Because the magnitude of epistasis is clearly relative to scale of penetrance, and therefore to some extent, to the choice of model framework, it is not surprising that strong interactions under one model might be minimized or even disappear entirely under a different modeling framework.

SNP rs498055 in the predicted gene LOC439999 on chromosome 10 was recently identified as being strongly associated with late-onset Alzheimer disease (LOAD). This SNP falls within a chromosomal region that has engendered continued interest generated from both preliminary genetic linkage and candidate gene studies. To independently evaluate this interesting candidate SNP we examined four independent datasets, three family-based and one case-control. All the cases were late-onset AD Caucasian patients with minimum age at onsetor= 60 years. None of the three family samples or the combined family-based dataset showed association in either allelic or genotypic family-based association tests at p0.05. Both original and OSA two-point LOD scores were calculated. However, there was no evidence indicating linkage no matter what covariates were applied (the highest LOD score was 0.82). The case-control dataset did not demonstrate any association between this SNP and AD (all p-values0.52). Our results do not confirm the previous association, but are consistent with a more recent negative association result that used family-based association tests to examine the effect of this SNP in two family datasets. Thus we conclude that rs498055 is not associated with an increased risk of LOAD.

The availability of large amounts of genomic DNA (gDNA) is the limiting factor for many of the molecular biology assays in genetic epidemiologic studies. Whole-genome amplification using multiple displacement amplification is used to amplify a representative sample of gDNA from small amounts of gDNA to optimize gDNA yield. We collected oral rinse DNA samples through the mail from 3,377 women enrolled in a population-based U.S. breast cancer case-control study and did whole-genome amplification by multiple displacement amplification. Genotyping was done for 66 single nucleotide polymorphisms (SNP) in 18 candidate susceptibility genes using amplified DNA with genomic replicates included for quality control. The concordance rates (percentages of agreement) in 95 quality control replicates of gDNA and amplified DNA for 66 SNPs ranged from 88% to 100% (median, 97%). The average allelic error rate was 0.9%. However, in further analyses based on the full control series (n = 1,492), >60% of the SNPs failed tests for Hardy-Weinberg equilibrium (P < 0.05), with evidence of heterozygote loss in the great majority. Even eliminating the 9% of samples with lower quality or input DNA, tests for Hardy-Weinberg equilibrium indicated persistent allele bias in nearly a third of the SNPs. Whole-genome amplification may introduce substantial allele amplification bias in gDNA collected using a common protocol in population-based epidemiologic studies. (Cancer Epidemiol Biomarkers Prev 2007;16(8):1610–4)

With the exception of ApoE (APOE), no universally accepted genetic association has been identified with late-onset Alzheimer disease (AD). A broad region of chromosome 10 has engendered continued interest generated from both preliminary genetic linkage and candidate gene studies. To better examine this region, we combined unbiased genetic linkage with candidate gene association studies. We genotyped 36 SNPs evenly spaced across 80.2 Mb in a family-based data set containing 1,337 discordant sibling pairs in 567 multiplex families to narrow the peak region of linkage using both covariate and subset analyses. Simultaneously, we examined five functional candidate genes (VR22, LRRTM3, PLAU, TNFRSF6, and IDE) that also fell within the broad area of linkage. A total of 50 SNPs were genotyped across the genes in the family-based data set and an independent case–control data set containing 483 cases and 879 controls. Of the 50 SNPs in the five candidate genes, 22 gave nominally significant association results in at least one data set, with at least one positive SNP in each gene. SNPs rs2441718 and rs2456737 in VR22 (67.8 Mb) showed association in both family-based and case–control data sets (both P=0.03). A two-point logarithmic odds (LOD) score of 2.69 was obtained at SNP rs1890739 (45.1 Mb, P=0.03 in 21% of the families) when the families were ordered from low to high by ApoE LOD score using ordered subset analysis (OSA). These data continue to support a role for chromosome 10 loci in AD. However, the candidate gene and linkage analysis results did not converge, suggesting that there is more extensive heterogeneity on chromosome 10 than previously appreciated. Hum Mutat 28(11),1065–1073, 2007. Published 2007 Wiley-Liss, Inc.

Up to now, most researchers have been paying attention to the negative transfer of mother tongue to second language writing. Few studies, if any, have touched upon the positive transfer. Therefore, the purpose of this study is to investigate the positive transfer of Chinese to 26 first-year university students’ English writing holistically and segmentally in the use of words, grammar, coherence, and content and organization. The result of the Pearson correlation coefficient turned out to be 0.43 at the 5% significance level, indicating a positive relationship between the Chinese writing and the English writing. The questionnaires have also confirmed the result of the correlation analysis. In particular, the positive transfer of Chinese seems to be more apparent in the content and organization of the English writing, followed by coherence and use of words. Thus, it can be concluded that the positive transfer of mother tongue can facilitate English writing.