Expression of the legume symbiotic lectin genes psl and gs52 promotes rhizobial colonization of roots in rice

Transgenic rice (Oryza sativa L. cv. Murasaki) carrying genes encoding pea (Pisum sativum) lectin (PSL) or wild-soybean (Glycine soja) lectin-nucleotide phosphohydrolase (GS52) were inoculated with Rhizobium leguminosarum bv. viciae or Bradyrhizobium japonicum USDA110, respectively, as well as with Rhizobium sp. NGR234, and root colonization was assessed in comparison to comparably inoculated control plants. The data showed that expression of PSL and GS52 significantly promoted rhizobial colonization of root epidermal cells including root hairs in rice. In addition, in the case of R. leguminosarum bv. viciae and B. japonicum USDA110 colonization of the psl and gs52 transgenic rice plants, respectively, the bacterial cells were found to preferentially home towards and aggregate maximally at the root hair tip regions rather than on the root hair "stalks". The above data suggest that the lectins PSL and GS52, which participate in rhizobial recognition by root epidermal cells in pea and soybean, respectively, are also able to facilitate rhizobial attachment and colonization of the epidermal cells in rice roots. Moreover, aggregation of R. leguminosarum bv. viciae and B. japonicum USDA110 cells preferentially at root hair tip regions suggest that similar to legumes, the PSL and GS52 lectins are targeted to the root hair tips in transgenic rice, enabling higher bacterial attachment/colonization at the tip region. Rhizobial colonization at root hair tips in the psl and gs52 rice plants frequently led to the localized dissolution of the cell wall creating perforations at the tip region. It is likely that the presence of lectins, such as PSL and GS52 leads to structural modifications in cell wall organization of the root hair/epidermal cells, making them prone to localized dissolution by the hydrolytic activity of compatible rhizobia to permit invasion of the root cells. © 2005 Elsevier Ireland Ltd. All rights reserved

Genome-wide meta-analysis of common variant differences between men and women

The male-to-female sex ratio at birth is constant across world populations with an average of 1.06 (106 male to 100 female live births) for populations of European descent. The sex ratio is considered to be affected by numerous biological and environmental factors and to have a heritable component. The aim of this study was to investigate the presence of common allele modest effects at autosomal and chromosome X variants that could explain the observed sex ratio at birth. We conducted a large-scale genome-wide association scan (GWAS) meta-analysis across 51 studies, comprising overall 114 863 individuals (61 094 women and 53 769 men) of European ancestry and 2 623 828 common (minor allele frequency >0.05) single-nucleotide polymorphisms (SNPs). Allele frequencies were compared between men and women for directly-typed and imputed variants within each study. Forward-time simulations for unlinked, neutral, autosomal, common loci were performed under the demographic model for European populations with a fixed sex ratio and a random mating scheme to assess the probability of detecting significant allele frequency differences. We do not detect any genome-wide significant (P < 5 × 10−8) common SNP differences between men and women in this well-powered meta-analysis. The simulated data provided results entirely consistent with these findings. This large-scale investigation across ∼115 000 individuals shows no detectable contribution from common genetic variants to the observed skew in the sex ratio. The absence of sex-specific differences is useful in guiding genetic association study design, for example when using mixed controls for sex-biased trait

The genetic architecture of type 2 diabetes

The genetic architecture of common traits, including the number, frequency, and effect sizes of inherited variants that contribute to individual risk, has been long debated. Genome-wide association studies have identified scores of common variants associated with type 2 diabetes, but in aggregate, these explain only a fraction of heritability. To test the hypothesis that lower-frequency variants explain much of the remainder, the GoT2D and T2D-GENES consortia performed whole genome sequencing in 2,657 Europeans with and without diabetes, and exome sequencing in a total of 12,940 subjects from five ancestral groups. To increase statistical power, we expanded sample size via genotyping and imputation in a further 111,548 subjects. Variants associated with type 2 diabetes after sequencing were overwhelmingly common and most fell within regions previously identified by genome-wide association studies. Comprehensive enumeration of sequence variation is necessary to identify functional alleles that provide important clues to disease pathophysiology, but large-scale sequencing does not support a major role for lower-frequency variants in predisposition to type 2 diabetes

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Rising rural body-mass index is the main driver of the global obesity epidemic in adults

Body-mass index (BMI) has increased steadily in most countries in parallel with a rise in the proportion of the population who live in cities 1,2 . This has led to a widely reported view that urbanization is one of the most important drivers of the global rise in obesity 3�6 . Here we use 2,009 population-based studies, with measurements of height and weight in more than 112 million adults, to report national, regional and global trends in mean BMI segregated by place of residence (a rural or urban area) from 1985 to 2017. We show that, contrary to the dominant paradigm, more than 55 of the global rise in mean BMI from 1985 to 2017�and more than 80 in some low- and middle-income regions�was due to increases in BMI in rural areas. This large contribution stems from the fact that, with the exception of women in sub-Saharan Africa, BMI is increasing at the same rate or faster in rural areas than in cities in low- and middle-income regions. These trends have in turn resulted in a closing�and in some countries reversal�of the gap in BMI between urban and rural areas in low- and middle-income countries, especially for women. In high-income and industrialized countries, we noted a persistently higher rural BMI, especially for women. There is an urgent need for an integrated approach to rural nutrition that enhances financial and physical access to healthy foods, to avoid replacing the rural undernutrition disadvantage in poor countries with a more general malnutrition disadvantage that entails excessive consumption of low-quality calories. © 2019, The Author(s)

Addressing quality issues of historical GIS data: An example of Republican Beijing

This article addresses several issues related to historical GIS data using a project studying the social culture of Republican Beijing as an illustration. For large-scale historical GIS projects, certain data layers or themes are fundamental to and provide the context for various types of investigation. We suggested that these data may be regarded as framework data, similar to the concept of the core dataset identified in the US National Spatial Data Infrastructure (NSDI) framework, but in a GIS project context. Due to various reasons, most historical GIS data always invite concerns about their quality. We discussed how typical spatial data quality concepts are partially applicable to historical GIS data. We also highlighted the data quality aspects that are more significant to historical than contemporary GIS data. Compiling high-quality historical GIS data is challenging. We used the data layer of temple locations as an example to illustrate the process of using a set of principles to resolve the inconsistencies of data from multiple sources to deal with location accuracy and data completeness problems. Two common but related quality concerns of historical GIS data are their relatively low spatial resolution and imprecise locations. The original population dataset of Republican Beijing suffers from these two issues. Using ancillary data, more precise population locations and population distribution at a higher resolution were estimated. Compilation of historical GIS data requires fusing data of different sources in order to enhance the quality of the data. © 2012 Taylor and Francis Group, LLC