Pastures to woodlands: changes in soil microbial communities and carbon following reforestation

Reforestation of agricultural lands has the potential to sequester C, while providing other environmentalbenefits. It is well established that reforestation can have a profound impact on soil physicochemicalproperties but the associated changes to soil microbial communities are poorly understood. Therefore,the objective of this study was to quantify changes in soil physicochemical properties and microbialcommunities in soils collected from reforested pastures and compare then to remnant vegetation and un-reforested pastures. To address this aim, we collected soil from two locations (pasture and its adjacentreforested zone, or pasture and its adjacent remnant vegetation) on each of ten separate farms thatcovered the range of planting ages (0–30 years and remnant vegetation) in a temperate region ofsoutheastern Australia. Soils were analysed for a range of physicochemical properties (including C andnutrients), and microbial biomass and community composition (PLFA profiles). Soil C:N ratios increasedwith age of tree planting, and soil C concentration was highest in the remnant woodlands. Reforestationhad no clear impact on soil microbial biomass or fungal:bacterial ratios (based on PLFA’s). Reforestationwas associated with significant changes in the molecular composition of the soil microbial community atmany farms but similar changes were found within a pasture. These results indicate that reforestation ofpastures can result in changes in soil properties within a few decades, but that soil microbial communitycomposition can vary as much spatially within pastures as it does after reforestation.T.R. Cavagnaro, S.C. Cunningham, S. Fitzpatric

Can sexual selection drive female life histories? A comparative study on Galliform birds

Sexual selection is an important driver of many of the most spectacular morphological traits that we find in the animal kingdom (for example see Andersson, 1994). As such, sexual selection is most often emphasized as

Being (im)polite: A forensic linguistic approach to interpreting a hate speech case

In a hate speech case a court might have to determine whether a person’s words were hurtful or harmful. Would it be possible to determine whether words are hurtful or harmful by using linguistics? This article offers a linguistic perspective on a court’s interpretation of the Equality Act in a hate speech case and focuses on speech acts and politeness. If the speech acts of a verbal exchange are studied and the levels of politeness are gauged, a court would be able to affi rm the hurtfulness or harmfulness of the speaker’s words. The article begins with a brief discussion on the potential role of the linguist in a courtroom; this is followed by a summary of the facts of the case. Then the court case is analysed and discussed in terms of speech acts and politeness. By employing principles in pragmatics the author reaches the same conclusion as the court.Afrikaans and Theory of Literatur

The development of children's comprehension and appreciation of riddles

Humor appreciation and understanding is important for children’s social relationships. The current study examined the associations between riddle comprehension, riddle appreciation, and smiling/laughter in children from a wide age-range aged 4 to 11 years old, as well as how cognitive processing style relates to riddle comprehension. Style was distinguished between local and global language processing at the sentence level. The results showed that only children above the age of 8 years old showed a reliable relationship between humor comprehension and smiling/laughter. These findings show that laughter should not be taken as an automatic indicator of explicit understanding. In addition, higher vocabulary ability was independently associated with better humor comprehension. This demonstrates a separable role language proficiency in humor comprehension and suggests avenues for future research in atypical populations known to have difficulties in this area

A multi-centred randomised trial of radical surgery versus adjuvant chemoradiotherapy after local excision for early rectal cancer

Background: Rectal cancer surgery is accompanied with high morbidity and poor long term functional outcome. Screening programs have shown a shift towards more early staged cancers. Patients with early rectal cancer can potentially benefit significantly from rectal preserving therapy. For the earliest stage cancers, local excision is sufficient when the risk of lymph node disease and subsequent recurrence is below 5 %. However, the majority of early cancers are associated with an intermediate risk of lymph node involvement (5-20 %) suggesting that local excision alone is not sufficient, while completion radical surgery, which is currently standard of care, could be a substantial overtreatment for this group of patients. Methods/Study design: In this multicentre randomised trial, patients with an intermediate risk T1-2 rectal cancer, that has been locally excised using an endoluminal technique, will be randomized between adjuvant chemo-radiotherapylimited to the mesorectum and standard completion total mesorectal excision (TME). To strictly monitor the risk of locoregional recurrence in the experimental arm and enable early salvage surgery, there will be additional follow up with frequent MRI and endoscopy. The primary outcome of the study is three-year local recurrence rate. Secondary outcomes are morbidity, disease free and overall survival, stoma rate, functional outcomes, health related quality of life and costs. The design is a non inferiority study with a total sample size of 302 patients. Discussion: The results of the TESAR trial will potentially demonstrate that adjuvant chemoradiotherapy is an oncological safe treatment option in patients who are confronted with the difficult clinical dilemma of a radically removed intermediate risk early rectal cancer by polypectomy or transanal surgery that is conventionally treated with subsequent radical surgery. Preserving the rectum using adjuvant radiotherapy is expected to significantly improve morbidity, function and quality of life if compared to completion TME surgery. Trial registration:NCT02371304, registration date: February 2015

Meta-analysis of genome-wide association studies identifies common susceptibility polymorphisms for colorectal and endometrial cancer near SH2B3 and TSHZ1

High-risk mutations in several genes predispose to both colorectal cancer (CRC) and endometrial cancer (EC). We therefore hypothesised that some lower-risk genetic variants might also predispose to both CRC and EC. Using CRC and EC genome-wide association series, totalling 13,265 cancer cases and 40,245 controls, we found that the protective allele [G] at one previously-identified CRC polymorphism, rs2736100 near TERT, was associated with EC risk (odds ratio (OR) = 1.08, P = 0.000167); this polymorphism influences the risk of several other cancers. A further CRC polymorphism near TERC also showed evidence of association with EC (OR = 0.92; P = 0.03). Overall, however, there was no good evidence that the set of CRC polymorphisms was associated with EC risk, and neither of two previously-reported EC polymorphisms was associated with CRC risk. A combined analysis revealed one genome-wide significant polymorphism, rs3184504, on chromosome 12q24 (OR = 1.10, P = 7.23 × 10−9) with shared effects on CRC and EC risk. This polymorphism, a missense variant in the gene SH2B3, is also associated with haematological and autoimmune disorders, suggesting that it influences cancer risk through the immune response. Another polymorphism, rs12970291 near gene TSHZ1, was associated with both CRC and EC (OR = 1.26, P = 4.82 × 10−8), with the alleles showing opposite effects on the risks of the two cancers

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved

Fine-Scale Mapping of the 4q24 Locus Identifies Two Independent Loci Associated with Breast Cancer Risk

Background: A recent association study identified a common variant (rs9790517) at 4q24 to be associated with breast cancer risk. Independent association signals and potential functional variants in this locus have not been explored. Methods: We conducted a fine-mapping analysis in 55,540 breast cancer cases and 51,168 controls from the Breast Cancer Association Consortium. Results: Conditional analyses identified two independent association signals among women of European ancestry, represented by rs9790517 [conditional P = 2.51 × 10−4; OR, 1.04; 95% confidence interval (CI), 1.02–1.07] and rs77928427 (P = 1.86 × 10−4; OR, 1.04; 95% CI, 1.02–1.07). Functional annotation using data from the Encyclopedia of DNA Elements (ENCODE) project revealed two putative functional variants, rs62331150 and rs73838678 in linkage disequilibrium (LD) with rs9790517 (r2 ≥ 0.90) residing in the active promoter or enhancer, respectively, of the nearest gene, TET2. Both variants are located in DNase I hypersensitivity and transcription factor–binding sites. Using data from both The Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC), we showed that rs62331150 was associated with level of expression of TET2 in breast normal and tumor tissue. Conclusion: Our study identified two independent association signals at 4q24 in relation to breast cancer risk and suggested that observed association in this locus may be mediated through the regulation of TET2. Impact: Fine-mapping study with large sample size warranted for identification of independent loci for breast cancer risk