Haplotype phasing after joint estimation of recombination and linkage disequilibrium in breeding populations

A novel method for haplotype phasing in families after joint estimation of recombination fraction and linkage disequilibrium is developed. Results from Monte Carlo computer simulations show that the newly developed E.M. algorithm is accurate if true recombination fraction is 0 even for single families of relatively small sizes. Estimates of recombination fraction and linkage disequilibrium were 0.00 （SD 0.00） and 0.19 （SD 0.03） for simulated recombination fraction and linkage disequilibrium of 0.00 and 0.20, respectively. A genome fragmentation phasing strategy was developed and used for phasing haplotypes in a sire and 36 progeny using the 50 k Illumina BeadChip by： a） estimation of the recombination fraction and LD in consecutive SNPs using family information, b） linkage analyses between fragments, c） phasing of haplotypes in parents and progeny and in following generations. Homozygous SNPs in progeny allowed determination of paternal fragment inheritance, and deduction of SNP sequence information of haplotypes from dams. The strategy also allowed detection of genotyping errors. A total of 613 recombination events were detected after linkage analysis was carried out between fragments. Hot and cold spots were identified at the individual （sire level）. SNPs for which the sire and calf were heterozygotes became informative （over 90%） after the phasing of haplotypes. Average of regions of identity between half-sibs when comparing its maternal inherited haplotypes （with at least 20 SNP） in common was 0.11 with a maximum of 0.29 and a minimum of 0.05. A Monte-Carlo simulation of BTA1 with the same linkage disequilibrium structure and genetic linkage as the cattle family yielded a 99.98 and 99.94% of correct phases for informative SNPs in sire and calves, respectively.     

Antiplatelet and Anticoagulant Effects of Diterpenes Isolated from the Marine Alga,Dictyota menstrualis

Cardiovascular diseases represent a major cause of disability and death worldwide. Therapeutics are available, but they often have unsatisfactory results and may produce side effects. Alternative treatments based on the use of natural products have been extensively investigated, because of their low toxicity and side effects. Marine organisms are prime candidates for such products, as they are sources of numerous and complex substances with ecological and pharmacological effects. In this work, we investigated, through in vitro experiments, the effects of three diterpenes (pachydictyol A, isopachydictyol A and dichotomanol) from the Brazilian marine alga, Dictyota menstrualis, on platelet aggregation and plasma coagulation. Results showed that dichotomanol inhibited ADP- or collagen-induced aggregation of platelet-rich plasma (PRP), but failed to inhibit washed platelets (WP). In contrast, pachydictyol A and isopachydictyol A failed to inhibit the aggregation of PRP, but inhibited WP aggregation induced by collagen or thrombin. These diterpenes also inhibited coagulation analyzed by the prothrombin time and activated partial thromboplastin time and on commercial fibrinogen. Moreover, diterpenes inhibited the catalytic activity of thrombin. Theoretical studies using the Osiris Property Explorer software showed that diterpenes have low theoretical toxicity profiles and a drug-score similar to commercial anticoagulant drugs. In conclusion, these diterpenes are promising candidates for use in anticoagulant therapy, and this study also highlights the biotechnological potential of oceans and the importance of bioprospecting to develop medicines.     

Metal Pools, Fluxes, and Budgets in an Acidified Forested Catchment on the Precambrian Shield, Central Ontario, Canada

Atmospheric emissions of metals have decreased in North America; yet, metals remain an environmental concern due to their environmental persistence and toxicity to biota. In this study, pools and mass budgets were calculated for 15 metals in an acidified forested catchment in Central Ontario. Metals that were enriched in bulk deposition over background average values (As, Cd, Pb, Zn) were generally enriched in the forest floor and upper lake sediment. While the metal pool in vegetation is small compared with the soil pool, internal cycling of metals via litterfall is comparable to atmospheric deposition, soil water, and stream fluxes. Partitioning coefficients calculated from metal concentrations in soil water and bulk soil suggest that Cd, Mn, Ni, and Zn are the most mobile. The mineral soil and lake sediments were sinks for most metals, while the wetland was a source of metals during the study year, which was a drought year. Overall, lithogenic metals (Al, Ba, Co, Fe, Mn, Rb, Sr, Zn) primarily from a weathering source generally exhibited net export from the catchment, while metals contained in atmospheric pollution (As, Cd, Cr, Cu, Ni, Pb, V) exhibited net retention. Despite the acidified nature of the catchment, it functions to retain many pollutant metals.     

Role of topography, canopy structure, and floristics in nest-site selection and nesting success of canopy songbirds

Although oaks (Quercus spp.) have historically dominated many forests in eastern North America, forest composition is changing due to anthropogenic impacts on disturbance regimes. Silvicultural practices, such as partial harvesting, are one component of management to promote oak regeneration. From 2007 to 2009 our research examined nest-site selection and nesting success for a guild of five canopy songbirds in upland mixed-oak forests in southeastern Ohio, USA. We monitored >700 nests across three state forests in both open canopy shelterwood stands harvested to approximately 50% stocking, and closed-canopy mature second-growth. Habitat attributes, including topography, canopy structure, and floristics, were measured at nest sites and random plots ?100 m from nests representing microhabitat available within the territory. Canopy songbirds selected specific topographic microclimates: Eastern Wood-pewees (Contopus virens) nested on xeric ridgetops, Blue-gray Gnatcachers (Polioptila caerulea) favored valleys, and Cerulean Warblers (Dendroica cerulea) preferred productive northeast-facing slopes. Nest sites differed among species in terms of concealment, nest support, topographic position on the slope, and basal area of trees >38 cm dbh. Four of the five focal species selected Quercus alba as the nest substrate more than twice as much as available, and three species avoided Quercus rubra. Daily survival rates of nests were negatively associated with basal area of red oak species (both Quercus velutina and Q. rubra) for several species individually and across the canopy-nesting guild. Additional factors related to success included time of season for Eastern Wood-pewees, nest age for Cerulean Warblers, and concealment and size of the support branch for Scarlet Tanagers (Piranga olivacea). In the long-term management for oak regeneration could benefit canopy songbirds, but our results indicate that white oaks, especially Q. alba, may be preferable to red oak species.     

Evaluation of brief dietary questions to estimate vegetable and fruit consumption - using serum carotenoids and red-cell folate

OBJECTIVE: To evaluate responses to self-administered brief questions regarding consumption of vegetables and fruit by comparison with blood levels of serum carotenoids and red-cell folate. DESIGN: A cross-sectional study in which participants reported their usual intake of fruit and vegetables in servings per day, and serum levels of five carotenoids (alpha-carotene, beta-carotene, beta-cryptoxanthin, lutein/zeaxanthin and lycopene) and red-cell folate were measured. Serum carotenoid levels were determined by high-performance liquid chromatography, and red-cell folate by an automated immunoassay system. SETTINGS AND SUBJECTS: Between October and December 2000, a sample of 1598 adults aged 25 years and over, from six randomly selected urban centres in Queensland, Australia, were examined as part of a national study conducted to determine the prevalence of diabetes and associated cardiovascular risk factors. RESULTS: Statistically significant (P<0.01) associations with vegetable and fruit intake (categorised into groups: /=4 servings per day) were observed for alpha-carotene, beta-carotene, beta-cryptoxanthin, lutein/zeaxanthin and red-cell folate. The mean level of these carotenoids and of red-cell folate increased with increasing frequency of reported servings of vegetables and fruit, both before and after adjusting for potential confounding factors. A significant association with lycopene was observed only for vegetable intake before adjusting for confounders. CONCLUSIONS: These data indicate that brief questions may be a simple and valuable tool for monitoring vegetable and fruit intake in this population.     

Changes in photosynthesis and antioxidant metabolism of cotton (Gossypium hirsutum L.) plants in response to manganese stress

ABSTRACT

This study aimed to assess the physiological and biochemical responses of cotton plants to manganese (Mn²⁺) nutrition. Four cotton genotypes (G1 – TMG 47; G2 – FM 975 WS; G3 – TMG 11 WS and G4 – IMA 8405 GLT) were grown in nutrient solution under two Mn²⁺ concentrations (2 and 200 µmol L^?1) for 10 days. No visible symptoms of Mn²⁺ toxicity were observed in the genotypes tested. All genotypes showed a marked increase in leaf chlorophylls, pheophytins, carotenoids, sucrose and total sugars concentration in response to high Mn²⁺ in a nutrient solution. However, the net photosynthetic rate, stomatal conductance, internal carbon dioxide concentration and transpiration decreased in genotypes G1 and G2 growing under 200 µmol L^?1. Antioxidant enzymes such as superoxide dismutase (SOD), ascorbate peroxidase (APX) and glutathione reductase (GR) activities increased in genotypes G1, G3 and G4. Cotton genotypes showed an increased leaf antioxidant and sugar metabolism as a possible strategy to mitigate oxidative stress. The decrease in the net photosynthetic rate and stomatal conductance; the increased antioxidant enzymes activities (SOD, APX and GR); and the increase in leaf sucrose and total sugar concentration were the main physiological and biochemical responses in cotton plants to Mn²⁺ stress.     

Crossing the thresholds: human ecology and historical patterns of landscape degradation

In discussions of landscape sensitivity, human activities have generally been regarded as external forces contributing to landscape change, with a focus on the impacts of cultivation methods, fertiliser practices, grazing pressures and atmospheric pollution. However, there has been comparatively little study undertaken that integrates physical and social systems in a historic context to explain the basis of human activity in sensitive landscapes. Where such attempts have been made, the manner of common land management has figured prominently, with ‘tragedy of the commons’ concepts used to explain land degradation and to provide a foundation for policy response. This has also been the case in Southern Iceland and in this paper we assess the extent to which common land domestic grazing pressures were the primary external force causing soil erosion and land degradation during the period of occupation from ca. 874 AD. We first provide field observation of soil erosion, temporally defined by tephrochronology, to highlight the extent of land degradation during this period. The ‘tragedy of the commons’ explanation of degradation is then assessed by evaluating historic documentary sources, and by environmental reconstruction and modeling of historic grazing pressures. These analyses indicate that regulatory mechanisms were in place to prevent overgrazing from at least the 1200s AD and suggest that there was sufficient biomass to support the numbers of domestic livestock indicated from historic sources. We suggest that failure to remove domestic livestock before the end of the growing season and an absence of shepherding were more likely to contribute to land degradation than absolute numbers. Lack of appropriate regulation of domestic livestock on common grazing areas can be attributed to limited cultural knowledge of changing and rapidly fluctuating environmental conditions.     

Yeast Rtt109 promotes genome stability by acetylating histone H3 on lysine 56

Posttranslational modifications of the histone octamer play important roles in regulating responses to DNA damage. Here, we reveal that Saccharomyces cerevisiae Rtt109p promotes genome stability and resistance to DNA-damaging agents, and that it does this by functionally cooperating with the histone chaperone Asf1p to maintain normal chromatin structure. Furthermore, we show that, as for Asf1p, Rtt109p is required for histone H3 acetylation on lysine 56 (K56) in vivo. Moreover, we show that Rtt109p directly catalyzes this modification in vitro in a manner that is stimulated by Asf1p. These data establish Rtt109p as a member of a new class of histone acetyltransferases and show that its actions are critical for cell survival in the presence of DNA damage during S phase.     

A transient rise in tropical sea surface temperature during the Paleocene-Eocene thermal maximum

The Paleocene-Eocene Thermal Maximum (PETM) has been attributed to a rapid rise in greenhouse gas levels. If so, warming should have occurred at all latitudes, although amplified toward the poles. Existing records reveal an increase in high-latitude sea surface temperatures (SSTs) (8 degrees to 10 degrees C) and in bottom water temperatures (4 degrees to 5 degrees C). To date, however, the character of the tropical SST response during this event remains unconstrained. Here we address this deficiency by using paired oxygen isotope and minor element (magnesium/calcium) ratios of planktonic foraminifera from a tropical Pacific core to estimate changes in SST. Using mixed-layer foraminifera, we found that the combined proxies imply a 4 degrees to 5 degrees C rise in Pacific SST during the PETM. These results would necessitate a rise in atmospheric pCO2 to levels three to four times as high as those estimated for the late Paleocene.     

Comparison of cardiac output determined by arterial pulse pressure waveform analysis method (FloTrac/Vigileo) versus lithium dilution method in anesthetized dogs

Objective – To compare the determination of cardiac output (CO) via arterial pulse pressure waveform analysis (FloTrac/Vigileo) versus lithium dilution method. Design – Prospective study. Setting – University teaching hospital. Animals – Six adult dogs. Interventions – Dogs were instrumented for CO determinations using lithium dilution (LiDCO) and FloTrac/Vigileo methods. Direct blood pressure, heart rate, arterial blood gases, and end‐tidal isoflurane (ETIso) and CO₂ concentrations were measured throughout the study while CO was manipulated with different depth of anesthesia and rapid administration of isotonic crystalloids at 60 mL/kg/h. Measurements and Main Results – Baseline CO measurements were obtained at 1.3% ETIso and were lowered by 3% ETIso. Measurements were obtained in duplicate or triplicate with LiDCO and averaged for comparison with corresponding values measured continuously with the FloTrac/Vigileo method. For 30 comparisons between methods, a mean bias of ?100 mL/kg/min and 95% limits of agreement between ?311 and +112 mL/kg/min (212 mL/kg/min) was determined. The mean (mL/kg/min) of the differences of LiDCO?Vigileo=62.0402+?0.8383 × Vigileo, and the correlation coefficient (r) between the 2 methods 0.70 for all CO determinations. The repeatability coefficients for the individual LiDCO and FloTrac/Vigileo methods were 187 and 400 mL/kg/min, respectively. Mean LiDCO and FloTrac/Vigileo values from all measurements were 145 ± 68 mL/kg/min (range, 64–354) and 244 ± 144 mL/kg/min (range, 89–624), respectively. The overall mean relative error was 48 ± 14%. Conclusion – The FloTrac/Vigileo overestimated CO values compared with LiDCO and the relative error was high, which makes this method unreliable for use in dogs.