Threshold Responses to Soil Moisture Deficit by Trees and Soil in Tropical Rain Forests: Insights from Field Experiments

Many tropical rain forest regions are at risk of increased future drought. The net effects of drought on forest ecosystem functioning will be substantial if important ecological thresholds are passed. However, understanding and predicting these effects is challenging using observational studies alone. Field-based rainfall exclusion (canopy throughfall exclusion; TFE) experiments can offer mechanistic insight into the response to extended or severe drought and can be used to help improve model-based simulations, which are currently inadequate. Only eight TFE experiments have been reported for tropical rain forests. We examine them, synthesizing key results and focusing on two processes that have shown threshold behavior in response to drought: (1) tree mortality and (2) the efflux of carbon dioxdie from soil, soil respiration. We show that: (a) where tested using large-scale field experiments, tropical rain forest tree mortality is resistant to long-term soil moisture deficit up to a threshold of 50% of the water that is extractable by vegetation from the soil, but high mortality occurs beyond this value, with evidence from one site of increased autotrophic respiration, and (b) soil respiration reaches its peak value in response to soil moisture at significantly higher soil moisture content for clay-rich soils than for clay-poor soils. This first synthesis of tropical TFE experiments offers the hypothesis that low soil moisture-related thresholds for key stress responses in soil and vegetation may prove to be widely applicable across tropical rain forests despite the diversity of these forests

Evidence for Antisense Transcription Associated with MicroRNA Target mRNAs in Arabidopsis

Antisense transcription is a pervasive phenomenon, but its source and functional significance is largely unknown. We took an expression-based approach to explore microRNA (miRNA)-related antisense transcription by computational analyses of published whole-genome tiling microarray transcriptome and deep sequencing small RNA (smRNA) data. Statistical support for greater abundance of antisense transcription signatures and smRNAs was observed for miRNA targets than for paralogous genes with no miRNA cleavage site. Antisense smRNAs were also found associated with MIRNA genes. This suggests that miRNA-associated “transitivity” (production of small interfering RNAs through antisense transcription) is more common than previously reported. High-resolution (3 nt) custom tiling microarray transcriptome analysis was performed with probes 400 bp 5′ upstream and 3′ downstream of the miRNA cleavage sites (direction relative to the mRNA) for 22 select miRNA target genes. We hybridized RNAs labeled from the smRNA pathway mutants, including hen1-1, dcl1-7, hyl1-2, rdr6-15, and sgs3-14. Results showed that antisense transcripts associated with miRNA targets were mainly elevated in hen1-1 and sgs3-14 to a lesser extent, and somewhat reduced in dcl11-7, hyl11-2, or rdr6-15 mutants. This was corroborated by semi-quantitative reverse transcription PCR; however, a direct correlation of antisense transcript abundance in MIR164 gene knockouts was not observed. Our overall analysis reveals a more widespread role for miRNA-associated transitivity with implications for functions of antisense transcription in gene regulation. HEN1 and SGS3 may be links for miRNA target entry into different RNA processing pathways

A glacial cryptic refuge in south-east Australia: human occupation and mobility from 36 000 years ago in the Sydney Basin, New South Wales

Excavations across a source-bordering dune overlooking the Hawkesbury River in north-west Sydney, Australia, suggest initial occupation of the region by at least 36 ka, with variable but uninterrupted use until the early Holocene; following abandonment, the site was then re-occupied by ∼3 ka. Along with a handful of other sites, the results provide the earliest reliable evidence of permanent regional populations within south-eastern Australia, and support a model in which early colonizers followed the coastal fringe with forays along the main river systems. The evidence is consistent with the demographic model of Williams, 2013 (Proceedings of the Royal Society Series B 280: 20130486), which suggested low, but established regional populations before the Last Glacial Maximum (LGM), a population nadir following the LGM and increasing use of the region from ∼12 to 8 ka. The site exhibits increased use at the onset and peak of the LGM, and provides an example of a cryptic refuge as defined by Smith, 2013 (The Archaeology of Australia's Deserts. Cambridge University Press: New York). Specifically, changing artefact densities and attributes show the site was used repeatedly, but for shorter periods through this time, and suggest it formed one of a series of key localities in a point-to-point (rather than home-base) subsistence strategy. This strategy was maintained until the site's abandonment in the early Holocene, despite changing population and climatic conditions through the Terminal Pleistocene

Use of bacterial whole-genome sequencing to investigate local persistence and spread in bovine tuberculosis

Mycobacterium bovis is the causal agent of bovine tuberculosis, one of the most important diseases currently facing the UK cattle industry. Here, we use high-density whole genome sequencing (WGS) in a defined sub-population of M. bovis in 145 cattle across 66 herd breakdowns to gain insights into local spread and persistence. We show that despite low divergence among isolates, WGS can in principle expose contributions of under-sampled host populations to M. bovis transmission. However, we demonstrate that in our data such a signal is due to molecular type switching, which had been previously undocumented for M. bovis. Isolates from farms with a known history of direct cattle movement between them did not show a statistical signal of higher genetic similarity. Despite an overall signal of genetic isolation by distance, genetic distances also showed no apparent relationship with spatial distance among affected farms over distances <5 km. Using simulations, we find that even over the brief evolutionary timescale covered by our data, Bayesian phylogeographic approaches are feasible. Applying such approaches showed that M. bovis dispersal in this system is heterogeneous but slow overall, averaging 2 km/year. These results confirm that widespread application of WGS to M. bovis will bring novel and important insights into the dynamics of M. bovis spread and persistence, but that the current questions most pertinent to control will be best addressed using approaches that more directly integrate WGS with additional epidemiological data

Gc (vitamin D-binding protein) binds the 33.5 K tryptic fragment of actin

Limited proteolysis of G-actin was performed with trypsin and chymotrypsin to compare the binding sites for Gc and DNase. DNase I bound to the N-terminal area corresponding to the major cleavage site on G-actin (residues 62–68) and inhibited proteolysis, but did not bind the 33.5K C-terminal fragment (G-actin 33.5) generated. In contrast, Gc did not exert any inhibitory effect upon proteolysis of the intact native G-actin 42.0 molecule, although its presence protected G-actin 33.5 from further proteolysis. This was shown by gel filtration to be due to the formation of complexes between Gc and G-actin 33.5