Simultaneous fine mapping of closely linked epistatic quantitative trait loci using combined linkage disequilibrium and linkage with a general pedigree

Causal mutations and their intra- and inter-locus interactions play a critical role in complex trait variation. It is often not easy to detect epistatic quantitative trait loci (QTL) due to complicated population structure requirements for detecting epistatic effects in linkage analysis studies and due to main effects often being hidden by interaction effects. Mapping their positions is even harder when they are closely linked. The data structure requirement may be overcome when information on linkage disequilibrium is used. We present an approach using a mixed linear model nested in an empirical Bayesian approach, which simultaneously takes into account additive, dominance and epistatic effects due to multiple QTL. The covariance structure used in the mixed linear model is based on combined linkage disequilibrium and linkage information. In a simulation study where there are complex epistatic interactions between QTL, it is possible to simultaneously map interacting QTL into a small region using the proposed approach. The estimated variance components are accurate and less biased with the proposed approach compared with traditional models.     

Organic geochemical changes in Pliocene sediments of ODP Site 1083 (Benguela Upwelling System)

The intensification of the Northern Hemisphere Glaciation (INHG) was a major event in the development of the current climate state, and as one of the most productive regions in the world's oceans, the behaviour of the Benguela Upwelling System (BUS) following the INHG is of wide interest. To investigate post-INHG changes in productivity and organic matter accumulation, total organic carbon and biomarker accumulation rates were determined for sediments from ODP Site 1083 and compared to alkenone-derived sea surface temperatures and nitrogen isotopic compositions. These data indicate that the interval between 2.6 and 2.4 Ma was characterized by dramatic changes in upwelling intensity and organic carbon export on the northern edge of the modern BUS. The upwelling is reflected by significant changes in alkenone-derived SST estimates between glacial and interglacial intervals, with a total variability of 16 °C. The studied interval is also characterized by large changes in organic matter export as reflected by changes in TOC and biomarker accumulation rates, which show maxima during OIS 98 and during the transition from OIS 97 to 96. Intervals of elevated TOC are also characterized by elevated concentrations of sedimentary microbial biomarkers and lower %CaCO₃, suggesting that enhanced delivery of labile organic matter to the seafloor resulted in enhanced remineralisation with released CO₂ being consumed by CaCO₃ dissolution. However, in apparent contrast to recent Pleistocene sediments at the same site, organic matter export after the INHG was not solely driven by upwelling intensity. Of the three Pliocene glacial–interglacial cycles examined (OIS 101 to 96), each is unique with respect to the timing and magnitude of changes in organic matter accumulation. Each is also characterized by different algal assemblages as inferred from biomarker distributions, with OIS 97 and 96 particularly dominated by diatoms. We suggest that these differences reflect the important but evolving role of Southern Ocean waters in the Pliocene BUS: nutrient depletion of SO waters occurred during parts of Pliocene glacial intervals such that even intense upwelling did not persistently result in enhanced organic matter accumulation rates.     

N-ras mutations in human cutaneous melanoma from sun-exposed body sites.

In 7 of 37 patients with cutaneous melanoma, mutations in the N-ras gene were found. The primary tumors of these seven patients were exclusively localized on body sites continuously exposed to sunlight. Moreover, the ras mutations were all at or near dipyrimidine sites known to be targets of UV damage. Two primary tumors were biclonal with respect to ras mutation. An active role for UV irradiation in induction of the mutations is suggested.     

The New Face of Debt-Peonage in the Bolivian Amazon: Social Networks and Bargaining Instruments

The debt-peonage system is an agreement between patrons and laborers in different economic activities worldwide. A common feature is social exploitation of laborers that generate profits to the patrons. In recent literature it has been argued that debt-peonage can be an economically sound arrangement that secures the needs of actors. The paper evaluates to what extent traditionally strong debt-peonage in forest-dwelling communities in the Bolivian Amazon, has developed in a way that better secures the needs and economic interest of multiple actors. Case studies in sixteen communities yielded qualitative information on debt relations between peasants, traders and former patrons. Debt-peonage changed from a mechanism to provide and keep workforce indebted to new social relationships, equitable commercial links, opportunity to access work capital and production chain diversification. This rapid shift was caused by important changes in land and forest regulations.     

Precession-forced changes in South West African vegetation during Marine Isotope Stages 101–100 (2.56–2.51 Ma)

The intensification of Northern Hemisphere Glaciation (iNHG) is one of the critical climate thresholds in the Cenozoic. This study focuses on marine sediments recovered from Marine Isotope Stages 101/100 at the Ocean Drilling Program Site 1083 to assesses the impact of the iNHG on continental southern African vegetation through n-alkane (straight-chain hydrocarbon) abundance and δ¹³C values. The n-alkane abundance data yield a convoluted signal due to the number of controlling factors such as the source area, transportation routes and vegetation type. The C₃₁ n-alkane δ¹³C values, however, exhibit a cyclic pattern with a periodicity of c. 20 ka, and are not correlated to the abundance data. It is inferred that the signal does not represent a change in the geographical source of n-alkanes. Instead, we suggest that the variations are caused by water-stress-induced changes in either carbon isotope fractionation during C₃ photosynthesis or subtle changes in the proportion of C₃ and C₄ plants. These changes, unlike variations in oceanographic proxies, closely track precessional forcing factors and are independent of the prevailing obliquity-forced glacial/interglacial cycles. We conclude that the varying monsoon strength, rather than pCO₂ or temperature change, forced changes in southern African vegetation during this period.     

Serological evidence for Encephalitozoon cuniculi infection (nosemiasis) in gnotobiotic guineapigs

Encephalitozoon cuniculi infection (nosemiasis) was serologically diagnosed in hysterectomy-derived gnotobiotically reared guineapigs. The probability of vertical transplacental transmission is discussed.