Multigenome DNA sequence conservation identifies Hox cis-regulatory elements

To learn how well ungapped sequence comparisons of multiple species can predict cis-regulatory elements in Caenorhabditis elegans, we made such predictions across the large, complex ceh-13/lin-39 locus and tested them transgenically. We also examined how prediction quality varied with different genomes and parameters in our comparisons. Specifically, we sequenced ∼0.5% of the C. brenneri and C. sp. 3 PS1010 genomes, and compared five Caenorhabditis genomes (C. elegans, C. briggsae, C. brenneri, C. remanei, and C. sp. 3 PS1010) to find regulatory elements in 22.8 kb of noncoding sequence from the ceh-13/lin-39 Hox subcluster. We developed the MUSSA program to find ungapped DNA sequences with N-way transitive conservation, applied it to the ceh-13/lin-39 locus, and transgenically assayed 21 regions with both high and low degrees of conservation. This identified 10 functional regulatory elements whose activities matched known ceh-13/lin-39 expression, with 100% specificity and a 77% recovery rate. One element was so well conserved that a similar mouse Hox cluster sequence recapitulated the native nematode expression pattern when tested in worms. Our findings suggest that ungapped sequence comparisons can predict regulatory elements genome-wide

Agronomic Characteristics, Malt Quality, and Disease Resistance of Barley Germplasm Lines with Partial Fusarium Head Blight Resistance

Fusarium head blight (FHB), incited by Fusarium graminearum Schwabe, has caused devastating losses in both yield and quality of barley (Hordeum vulgare L.) produced in the northern Great Plains from 1993 to 2003. Thirty-five barley germplasmlines with partial resistance to FHB have been identified in exotic and unadapted germplasm lines. Little is known about their agronomic characteristics, malt quality, and reaction to other diseases as compared to adapted cultivars. This information is needed so barley breeders can make informed decisions when planning crosses involving the resistant germplasm lines. The objective of this study was to compare the agronomic performance, malt quality, and disease reaction of barley germplasm lines with partial FHB resistance to cultivars grown in the northern Great Plains. Agronomic and malting data were collected on the 35 germplasm lines and five check cultivars grown in five environments in North Dakota from 1998 to 2000. Data for FHB severity and deoxynivalenol (DON, a mycotoxin produced by F. graminearum) accumulation were obtained for the same 40 entries grown in FHB-epidemic nurseries in North Dakota from 1997 to 1999. Seedling responses to foliar pathogens common in the northern Great Plains were determined in the greenhouse during fall 1997. None of the FHB-resistant barley germplasm lines had acceptable malt quality for all traits. Kernel plumpness, grain protein concentration, and malt extract were the traits impacted most severely. The FHB-resistant barley germplasm lines headed significantly later than the adapted barley cultivars. Most FHB-resistant germplasm lines were susceptible to the common foliar diseases of the northern Great Plains. At least four cycles of breeding will probably be necessary to develop FHB-resistant germplasm lines acceptable to producers and the malting and brewing industry

Heritability of Fusarium Head Blight Resistance and Deoxynivalenol Accumulation from Barley Accession CIho 4196

Fusarium head blight (FHB), incited by Fusarium graminearum Schwabe [telomorph Gibberella zea (Schwein)], has caused devastating losses to yield and quality of barley (Hordeum vulgare L.) produced in the upper U.S. Midwest from 1993 to 2000. Design of an efficient breeding strategy for developing FHB resistant cultivars is dependent on knowing (i) the heritability of FHB resistance and accumulation of deoxynivalenol (DON), a mycotoxin contaminant produced by F. graminearum and (ii) the correlated response of other traits during selection for reduced FHB. We conducted field studies in FHB disease nurseries using F4:5 and F4:6 families from the cross between the FHB susceptible six-rowed cultivar Foster and the resistant two-rowed accession CIho 4196 to gain knowledge in the areas listed above. Heritability of FHB severity and DON accumulation was 0.65 and 0.46, respectively. A moderately strong positive association between FHB severity and DON accumulation was observed (r = 0.62). FHB severity and DON accumulation were negatively associated with plant height, days to heading, spike angle, and spike density. The selection differentials calculated between the top F4:6 families selected for low FHB severity and the unselected F4:5 families were moderately high for FHB severity, DON accumulation, and days to heading. Less than 14% of the selected lines had six-rowed spikes. No difference in plant height was observed between the selected and unselected families. Thus, development of FHB resistant lines with acceptable DON accumulation and days to heading is obtainable. However, because no lines were as short as Foster, development of FHB resistant plants with acceptable plant height from a cross using CIho 4196 as a parent will be difficult

An Improved Analysis of Forest Carbon Dynamics using Data Assimilation

There are two broad approaches to quantifying landscape C dynamics - by measuring changes in C stocks over time, or by measuring fluxes of C directly. However, these data may be patchy, and have gaps or biases. An alternative approach to generating C budgets has been to use process-based models, constructed to simulate the key processes involved in C exchange. However, the process of model building is arguably subjective, and parameters may be poorly defined. This paper demonstrates why data assimilation (DA) techniques - which combine stock and flux observations with a dynamic model - improve estimates of, and provide insights into, ecosystem carbon (C) exchanges. We use an ensemble Kalman filter (EnKF) to link a series of measurements with a simple box model of C transformations. Measurements were collected at a young ponderosa pine stand in central Oregon over a 3-year period, and include eddy flux and soil C02 efflux data, litterfall collections, stem surveys, root and soil cores, and leaf area index data. The simple C model is a mass balance model with nine unknown parameters, tracking changes in C storage among five pools; foliar, wood and fine root pools in vegetation, and also fresh litter and soil organic matter (SOM) plus coarse woody debris pools. We nested the EnKF within an optimization routine to generate estimates from the data of the unknown parameters and the five initial conditions for the pools. The efficacy of the DA process can be judged by comparing the probability distributions of estimates produced with the EnKF analysis vs. those produced with reduced data or model alone. Using the model alone, estimated net ecosystem exchange of C (NEE)= -251 f 197g Cm-2 over the 3 years, compared with an estimate of -419 f 29gCm-2 when all observations were assimilated into the model. The uncertainty on daily measurements of NEE via eddy fluxes was estimated at 0.5gCm-2 day-1, but the uncertainty on assimilated estimates averaged 0.47 g Cm-2 day-1, and only exceeded 0.5gC m-2 day-1 on days where neither eddy flux nor soil efflux data were available. In generating C budgets, the assimilation process reduced the uncertainties associated with using data or model alone and the forecasts of NEE were statistically unbiased estimates. The results of the analysis emphasize the importance of time series as constraints. Occasional, rare measurements of stocks have limited use in constraining the estimates of other components of the C cycle. Long time series are particularly crucial for improving the analysis of pools with long time constants, such as SOM, woody biomass, and woody debris. Long-running forest stem surveys, and tree ring data, offer a rich resource that could be assimilated to provide an important constraint on C cycling of slow pools. For extending estimates of NEE across regions, DA can play a further important role, by assimilating remote-sensing data into the analysis of C cycles. We show, via sensitivity analysis, how assimilating an estimate of photosynthesis - which might be provided indirectly by remotely sensed data - improves the analysis of NEE

Ion-neutral sympathetic cooling in a hybrid linear rf Paul and magneto-optical trap

Long range polarization forces between ions and neutral atoms result in large elastic scattering cross sections, e.g., 10^6 a.u. for Na+ on Na or Ca+ on Na at cold and ultracold temperatures. This suggests that a hybrid ion-neutral trap should offer a general means for significant sympathetic cooling of atomic or molecular ions. We present SIMION 7.0 simulation results concerning the advantages and limitations of sympathetic cooling within a hybrid trap apparatus, consisting of a linear rf Paul trap concentric with a Na magneto-optical trap (MOT). This paper explores the impact of various heating mechanisms on the hybrid system and how parameters related to the MOT, Paul trap, number of ions, and ion species affect the efficiency of the sympathetic cooling

Zero-Mode Dynamics of String Webs

At sufficiently low energy the dynamics of a string web is dominated by zero modes involving rigid motion of the internal strings. The dimension of the associated moduli space equals the maximal number of internal faces in the web. The generic web moduli space has boundaries and multiple branches, and for webs with three or more faces the geometry is curved. Webs can also be studied in a lift to M-theory, where a string web is replaced by a membrane wrapped on a holomorphic curve in spacetime. In this case the moduli space is complexified and admits a Kaehler metric.Comment: LaTeX, 17 pages, 5 eps figures; v2: references adde

A Review of Weight Control Strategies and Their Effects on the Regulation of Hormonal Balance

The estimated prevalence of obesity in the USA is 72.5 million adults with costs attributed to obesity more than 147 billion dollars per year. Though caloric restriction has been used extensively in weight control studies, short-term success has been difficult to achieve, with long-term success of weight control being even more elusive. Therefore, novel approaches are needed to control the rates of obesity that are occurring globally. The purpose of this paper is to provide a synopsis of how exercise, sleep, psychological stress, and meal frequency and composition affect levels of ghrelin, cortisol, insulin GLP-1, and leptin and weight control. We will provide information regarding how hormones respond to various lifestyle factors which may affect appetite control, hunger, satiety, and weight control

Effects of Capsaicin and Evodiamine Ingestion on Energy Expenditure and Fat Oxidation at Rest and After Moderately-Intense Exercise in Young Men

Capsaicin and evodiamine are two thermogenic agents each recognized for their ability to stimulate the sympathetic nervous system and are thus found in many dietary supplements. Therefore, the purpose of this study was to observe the effects that capsaicin and evodiamine have on hemodynamics, energy expenditure, and markers of lipid oxidation while at rest and after a single bout of moderate-intensity exercise in young men. In a randomized, cross-over design, 11 men orally ingested 500 mg of capsaicin, evodiamine, or placebo while at rest after 30 minutes of resting energy expenditure assessment using open-circuit spirometry. After an additional 30 minutes of rest after supplement ingestion, resting energy expenditure was assessed again for 30 minutes. After the second resting energy expenditure assessment, treadmill exercise was performed until expending approximately 500 kilocalories (~30 minutes) at 65% peak oxygen consumption. Energy expenditure was assessed for another 30 minutes into the post-exercise period. Heart rate and blood pressure, core temperature, and venous blood samples were obtained 30 minutes before and one hour after supplement ingestion (i.e. immediately pre-exercise), and immediately after and 45 minutes post-exercise. Markers of lipid oxidation (serum glycerol, free fatty acids, serum glucose, epinephrine, and norepinephrine) were determined spectrophotometrically and with ELISA. Two-way analyses of variance (ANOVA) were performed for each dependent variable (p ≤ 0.05). Significant main effects for Time existed for hemodynamics, energy expenditure, serum catecholamines and markers of fat oxidation immediately following exercise (p \u3c 0.05). However, no significant Supplement x Time interactions were noted for any criterion variable (p \u3e 0.05), suggesting no preferential difference between supplements. Neither capsaicin nor evodiamine, at a single dose of 500 mg, are effective at inducing thermogenesis and increasing fat oxidation at rest or during exercise in young men