Seeing red: the origin of grain pigmentation in US weedy rice

Weedy forms of crop species infest agricultural fields worldwide and are a leading cause of crop losses, yet little is known about how these weeds evolve. Red rice (Oryza sativa), a major weed of cultivated rice fields in the US, is recognized by the dark‐pigmented grain that gives it its common name. Studies using neutral molecular markers have indicated a close relationship between US red rice and domesticated rice, suggesting that the weed may have originated through reversion of domesticated rice to a feral form. We have tested this reversion hypothesis by examining molecular variation at Rc, the regulatory gene responsible for grain pigmentation differences between domesticated and wild rice. Loss‐of‐function mutations at Rc account for the absence of proanthocyanidin pigments in cultivated rice grains, and the major rc domestication allele has been shown to be capable of spontaneous reversion to a functional form through additional mutations at the Rc locus. Using a diverse sample of 156 weedy, domesticated and wild Oryzas, we analysed DNA sequence variation at Rc and its surrounding 4 Mb genomic region. We find that reversion of domestication alleles does not account for the pigmented grains of weed accessions; moreover, we find that haplotypes characterizing the weed are either absent or very rare in cultivated rice. Sequences from genomic regions flanking Rc are consistent with a genomic footprint of the rc selective sweep in cultivated rice, and they are compatible with a close relationship of red rice to Asian Oryzas that have never been cultivated in the US.     

不同耕作方式对内蒙古旱作农田土壤侵蚀的影响

研究黄河流域内蒙古黄土高原丘陵区农田土壤侵蚀状况,对本区域生态农业建设具有重要的意义。试验于2006年在内蒙古呼和浩特市清水河县进行,设免耕(NT)、免耕覆盖(NS)和传统耕作(CT)3种耕作处理方式,种植作物为胡麻和燕麦,观测了全年降雨量和地表水径流量及土壤流失量。结果表明:免耕覆盖及免耕能显著减少降雨对土壤的侵蚀,与传统耕作相比,免耕覆盖处理的燕麦地地表水径流量和土壤的流失量分别减少21.9%和88.3%;3种耕作方式的土壤侵蚀量均受到坡度的影响,并随着坡度的增大而增大,相同环境条件下,不同作物存在一定差异;通过对3种耕作方式下,胡麻和燕麦田土壤侵蚀量与降雨量的关系符合幂函数,且拟合优度良好,均>0.9。     

Carbon exchange of a mature,naturally regenerated pine forest in north Florida

We used eddy covariance and biomass measurements to quantify the carbon (C) dynamics of a naturally regenerated longleaf pine/slash pine flatwoods ecosystem in north Florida for 4 years, July 2000 to June 2002 and 2004 to 2005, to quantify how forest type, silvicultural intensity and environment influence stand‐level C balance. Precipitation over the study periods ranged from extreme drought (July 2000–June 2002) to above‐average precipitation (2004 and 2005). After photosynthetic photon flux density (PPFD), vapor pressure deficit (VPD) >1.5 kPa and air temperature <10 °C were important constraints on daytime half‐hourly net CO₂ exchange (NEE_day) and reduced the magnitude of midday CO₂ exchange by >5 μmol CO₂ m^?2 s^?1. Analysis of water use efficiency indicated that stomatal closure at VPD>1.5 kPa moderated transpiration similarly in both drought and wet years. Night‐time exchange (NEE_night) was an exponential function of air temperature, with rates further modulated by soil moisture. Estimated annual net ecosystem production (NEP) was remarkably consistent among the four measurement years (range: 158–192 g C m^?2 yr^?1). In comparison, annual ecosystem C assimilation estimates from biomass measurements between 2000 and 2002 ranged from 77 to 136 g C m^?2 yr^?1. Understory fluxes accounted for approximately 25–35% of above‐canopy NEE over 24‐h periods, and 85% and 27% of whole‐ecosystem fluxes during night and midday (11:00–15:00 hours) periods, respectively. Concurrent measurements of a nearby intensively managed slash pine plantation showed that annual NEP was three to four times greater than that of the Austin Cary Memorial Forest, highlighting the importance of silviculture and management in regulating stand‐level C budgets.     

Potential effects of climate change on DOC release from three different soil types on the Northern Pennines UK: examination using field manipulation experiments

Three field manipulation experiments were carried out during 1993–1995 on the Northern Pennines to investigate the influences of temperature, solar radiation and rainfall on the release of dissolved organic carbon (DOC) from vegetated soil cores using zero‐tension lysimeters. The cores were manipulated by being translocated to four sites down a climatic gradient, by artificial soil heating or being exposed to double normal rainfall. In each experiment three soil types, a brown earth, a micropodzol and a peaty gley, with differing organic matter content and distribution within the profile, were studied. DOC data, expressed as mg C m^?2 day^?1, were analysed following log₁₀ transformation, by a repeated measures analysis of variance procedure, using climatic variables measured concurrently with sampling, and 1 and 2 months before sampling. DOC release was dominated by rainfall but was also associated with solar radiation and temperature. With each of the three climatic variables, rainfall, solar radiation and temperature, both positive and negative effects on DOC release have been found significant, indicating that the concurrent and delayed effects of the same variable may be different. DOC release was positively related with all three soils to concurrent rainfall, indicating rainfall's primary leaching action. DOC release was also negatively related to rainfall of the previous month indicating that its action depletes the leachable pool of DOC in the soil. DOC release was positively associated with solar radiation 2 months earlier, indicating that DOC's main source is that of primary production; DOC peaks closely followed peaks of annual primary production. DOC release was linked with temperature, the strongest association being with temperature 2 months earlier, indicating that temperature effects both primary production and DOC regeneration via organic matter decomposition. A conceptual model, relating our findings to those processes known to govern DOC release from soils, has been presented.     

Localization of 5''-Ribonucleotide Phosphohydrolase in Regenerating (and Normal) Limb Tissues of the Adult Newt Notophthalmus viridescens

The regenerating forelimb of the adult newt, Notophthalmus viridescens was investigated for 5'-nucleotidase (5' ribonucleotide phosphohydrolase, 3.1.3.5) acitivity. The newt's humeri were surgically removed, and after a twenty-one-day recovery period, the forelimbs amputated above the elbows. Regenerates were sampled at predetermined times for specific phases in the progress of regeneration, frozen, sectioned in a cryostat, and the sections fixed in 10% cold formol calcium. The Wachstein and Meisel [25] lead procedure at neutral pH was used predominately in these experiments, although tests were also conducted with Gomori's [14] calcium, Allen's [21] highly alkaline procedures. The substrates used to obtain specific enzyme reactions were adenine, cytosine, guanine, uracil and inosine 5'-monophosphate nucleotides. Sodium beta-glycerophosphate served as a non-specific phosphomonoesterase substrate, distilled water replaced substrate, and inhibitors such as zinc and cyanide ions were used as control measures to assist in increasing the precision in interpreting the results obtained. The most reactive 5'-nucleotidase (5'-Nase) loci were in the walls of the blood vascular system, mysial and neural sheaths, dermis, and periosteum: the principal cells involved were macrophages, endothelium of blood vessels, and fibrocytes of connective tissues. A moderate enzyme response was elicited from secretory cells of some of the subcutaneous glands, hypertrophied chondrocytes and osteogenic centers, chondrocytes in the articular regions and within red blood cells and leucocytes. Normal, injured and degenerating, or regenerating striated muscle and nerve fibers were judged unreactive for 5'-Nase. The epidermis and wound epithelium displayed negative responses for 5'-Nase. Cells forming the regeneration blastema were 5'-Nase reactive during the early formative phase, but with growth and development of the blastema into bulb and conic forms, these cells did not respond for this enzyme-activity. One suggestion offered is that the absence of 5'-Nase in cells of the blastema may be related to the lack of an adequate blood-vascular supply. Several functions of 5'-Nase in normal and regenerating tissues are discussed. A basic conclusion reached is that 5'-nucleotidase hydrolyses may be more involved in fundamental anabolic than in catabolic metabolism.     

The Diffusion of KCI from Micro-electrodes

The diffusion of salt from the tips of 3 M KCI filled micro-electrodesis measured. The leakage of KCI in 3 min is found to be 5.70x 10^–12–1.08 x 10^–11 mol for tips of 0.2–0.6µm diameter, and 2.70 x 10^–11 mol for tips of 0.6–1.0µm diameter. The observed leakages compare with estimatesbased on the diffusion coefficient of KCI and micro-electrodegeometry. The results confirm that the use of 3 M KCI in micro-electrodesmay lead to serious contamination of impaled cells providedthe electrode tips remain unoccluded.     

Ocean acidification and warming will lower coral reef resilience

Ocean warming and acidification from increasing levels of atmospheric CO₂ represent major global threats to coral reefs, and are in many regions exacerbated by local‐scale disturbances such as overfishing and nutrient enrichment. Our understanding of global threats and local‐scale disturbances on reefs is growing, but their relative contribution to reef resilience and vulnerability in the future is unclear. Here, we analyse quantitatively how different combinations of CO₂ and fishing pressure on herbivores will affect the ecological resilience of a simplified benthic reef community, as defined by its capacity to maintain and recover to coral‐dominated states. We use a dynamic community model integrated with the growth and mortality responses for branching corals (Acropora) and fleshy macroalgae (Lobophora). We operationalize the resilience framework by parameterizing the response function for coral growth (calcification) by ocean acidification and warming, coral bleaching and mortality by warming, macroalgal mortality by herbivore grazing and macroalgal growth via nutrient loading. The model was run for changes in sea surface temperature and water chemistry predicted by the rise in atmospheric CO₂ projected from the IPCC's fossil‐fuel intensive A1FI scenario during this century. Results demonstrated that severe acidification and warming alone can lower reef resilience (via impairment of coral growth and increased coral mortality) even under high grazing intensity and low nutrients. Further, the threshold at which herbivore overfishing (reduced grazing) leads to a coral–algal phase shift was lowered by acidification and warming. These analyses support two important conclusions: Firstly, reefs already subjected to herbivore overfishing and nutrification are likely to be more vulnerable to increasing CO₂. Secondly, under CO₂ regimes above 450–500 ppm, management of local‐scale disturbances will become critical to keeping reefs within an Acropora‐rich domain.     

The mole nose instructs the brain

Star-nosed moles normally have 11 mobile appendages, or rays, extending from each side of the nose. In cytochrome oxidase preparations, each ray is visible in primary somatosensory cortex as a dark band separated by light septa. When a single mole was found with 12 rays on each side of the nose, primary somatosensory cortex had 12 bands. We take this as further evidence that morphological features of somatosensory cortex are determined by the periphery.     

Proximal Femoral Density Patterns are Consistent with Bicentric Joint Loads

We developed an alternate method for density-based load estimation and applied it to estimate hip joint load distributions for two femora. Two-dimensional finite element models were constructed from single energy quantitative computed tomography (QCT) data. Load estimation was performed using five loading regions on the femoral head. Within each loading region, individual nodal loads, normal to the local surface, were supplied as input to the load estimation. An optimization procedure independently adjusted individual nodal load magnitudes in each region, and the magnitudes of muscle forces on the greater trochanter, such that the applied tissue stimulus approached the reference stimulus throughout the model. Dominant estimated load resultant directions were generally consistent with published experimental data for loads during gait. The estimated loads also suggested that loads near the extremes of the articulating surface may be important (even required) for development and maintenance of normal bone architecture. Estimated load distributions within nearly all regions predicted bicentric loading patterns, which are consistent with observations of hip joint incongruity. Remodeling simulations with the estimated loads predicted density distributions with features qualitatively similar to the QCT data sets. This study illustrates how applications of density-based bone load estimation can improve understanding of dominant loading patterns in other bones and joints. The prediction of bicentric loading suggests a very fine level of local adaptation to details of joint loading.     

Quantitative biochronology of Devonian ammonoids from Morocco and proposals for a refined unitary association method

Monnet, C., Klug, C., Goudemand, N., De Baets, K. & Bucher, H. 2011: Quantitative biochronology of Devonian ammonoids from Morocco and proposals for a refined unitary association method. Lethaia, Vol. 44, pp. 469–489. Based on a rich dataset, the biostratigraphy of the late Emsian and the Eifelian (Early–Middle Devonian) ammonoids from the Moroccan Tafilalt is re‐evaluated. We processed this dataset (comprising 53 species from 15 sections) with the unitary association method (UAM), by means of the UA‐graph freeware. This led to the construction of a sequence of 17 UAs (maximal sets of actually or virtually coexisting taxa), which are grouped into 10 laterally reproducible association zones. This biostratigraphical subdivision of this interval is in some parts finer than the classically used empirical stratigraphical scheme and than a previous graphic correlation analysis. It enabled us to measure regional ammonoid diversity of this interval in detail. The UAM is a powerful biochronological method, which benefits from complementary tools to analyse conflicting inter‐taxon stratigraphical relationships inherent to complex biostratigraphical datasets. In cases of under‐constrained superpositional relationships between the taxa, the UAM can yield results, which are not parsimonious in terms of reconstructed virtual coexistences. We suggest several additions to complement the algorithmic steps of the method. The most important is the exhaustive or heuristic reconstruction of possible solutions resolving the observed biostratigraphical contradictions (conflicting inter‐taxon superpositional relationships and cycles between maximal cliques) and the selection among the solutions of the most‐parsimonious one(s) in terms of reconstructed virtual coexistences. Multiple equivalent results may then be processed with standard consensus techniques. Finally, the robustness of the results can be tested by bootstrapping methods to provide confidence estimates on the ranges and associations of studied taxa. □Ammonites, Anti‐Atlas, biostratigraphy, correlation, zonation, diversity.