Secondary structure of β-hydroxydecanoyl thiol ester dehydrase, a 39-kDa protein, derived from Hα, Cα, Cβ and CO signal assignments and the Chemical Shift Index: Comparison with the crystal structure

Summary Nearly complete backbone ¹H, ¹⁵N and ¹³C signal assignments are reported for -hydroxydecanoyl thiol ester dehydrase, a 39-kDa homodimer containing 342 amino acids. Although ¹⁵N relaxation data show that the protein has a rotational correlation time of 18 ns, assignments were derived from triple-resonance experiments recorded at 500 MHz and pH 6.8, without deuteration. The Chemical Shift Index, CSI, identified two long helices and numerous -strands in dehydrase. The CSI predictions are in close agreement with the secondary structure identified in the recently derived crystal structure, particularly when one takes account of the numerous bulges in the -strands. The assignment of dehydrase and a large deuterated protein [Yamazaki et al. (1994) J. Am. Chem. Soc., 116, 11655–11666] suggest that assignment of 40–60 kDa proteins is feasible. Hence, further progress in understanding the chemical shift/structure relationship could open the way to determine the structures of such large proteins. Supplementary Material is available on request, comprising Table S1 listing the spectral parameters; Table S2 listing the assignments; Fig. S1 showing the 2D ¹H–¹⁵N HSQC spectrum; Fig. S2 showing sequential NOEs, secondary shifts, H-exchange and ³J_HN data; and Fig. S3 showing plots of the H, C, CO and C Chemical Shift Indexes.To whom correspondence should be addressed.     

Quantifying change in distributions: a new departure index that detects,measures and describes change in distributions from population structures,size-classes and other ordered data

Many statistics are available to compare distributions. Some are limited to nominal data while others, such as skew, Kullback-Leibler, Kolmogorov-Smirnov and the Gini coefficient, are useful for providing information about ordered distributions. While many of these tests are useful for determining properties of data in histograms, there has not been a test until now that allows for the detection of differences between distributions, describes the difference and is sensitive to the location of the departures. Such a test could be critical for comparing pre-and post-event distributions, such as a change in the distribution of biomass due to fire, for example, or for comparing data from different locations, such as soil size distributions, and even for evaluating economic disparity or examining differences in age demographics. We present a new statistic, a departure index, which allows a test distribution to be compared with any reference distribution. The resulting index contains information about the location, magnitude and direction of departure from the reference distribution to the test distribution. The departure index in turn provides a standardized response range that allows for a comparison of results from different analyses. A case study of actual fire data demonstrates the sensitivity and range of the test.     

High-moisture diet for laboratory rats: complete blood counts, serum biochemical values, and intestinal enzyme activity.

Rats were fed an irradiated high-moisture diet (KSC-25) with or without access to a water bottle. Physiologic values were compared between these two groups and a group of rats fed a purified diet. Hematologic and serum biochemical values, urine specific gravity, and intestinal enzyme activities were determined from samples collected from the three groups of rats. Sprague Dawley rats (n = 32) fed the irradiated high-moisture diet with or without a water bottle were the test animals. Rats (n = 16) fed an irradiated purified diet and water provided via a water bottle were the control group. The purified diet formulation modified AIN-76A, is a commonly used purified diet for laboratory rodents. All rats remained alert and healthy throughout the study. A comparison of the physiologic values of rats in this study with reported normal values indicated that all of the rats in the study were in good health. Significant differences (P less than 0.05) of the physiologic values from each rat group are reported.     

High-moisture diet for laboratory rats: nutrient analysis, growth, and organ weights.

A diet (KSC-25) to be sterilized by irradiation was formulated to contain 66% moisture and to provide the required nutrients for growing rats. Analyses of the irradiated dry diet provided data to evaluate its nutrient content. The diet was evaluated for its ability to supply all nutrients, including water, required by immature rats. Sixteen Sprague-Dawley rats were fed the high-moisture diet with or without access to a water bottle. Rats (n = 16) fed an irradiated purified diet in a meal form with access to a water bottle were the control animals. Feed efficiency, food and water consumption, and growth rate data were collected during the 28-day study. Organ weights were collected on day 28. The test diet met or exceeded the National Research Council (NRC) estimated nutritional requirements for immature laboratory rats. The 66% moisture KSC-25 diet provided all nutrients, including water, required by weanling male Sprague-Dawley rats for growth equivalent to the established purified diet.     

The Biogeochemistry of Carbon at Hubbard Brook

The biogeochemical behavior of carbon in the forested watersheds of the Hubbard Brook Experimental Forest (HBEF) was analyzed in long-term studies. The largest pools of C in the reference watershed (W6) reside in mineral soil organic matter (43% of total ecosystem C) and living biomass (40.5%), with the remainder in surface detritus (14.5%). Repeated sampling indicated that none of these pools was changing significantly in the late-1990s, although high spatial variability precluded the detection of small changes in the soil organic matter pools, which are large; hence, net ecosystem productivity (NEP) in this 2nd growth forest was near zero (± about 20 g C/m²-yr) and probably similar in magnitude to fluvial export of organic C. Aboveground net primary productivity (ANPP) of the forest declined by 24% between the late-1950s (462 g C/m²-yr) and the late-1990s (354 g C/m²-yr), illustrating age-related decline in forest NPP, effects of multiple stresses and unusual tree mortality, or both. Application of the simulation model PnET-II predicted 14% higher ANPP than was observed for 1996–1997, probably reflecting some unknown stresses. Fine litterfall flux (171 g C/m²-yr) has not changed much since the late-1960s. Because of high annual variation, C flux in woody litterfall (including tree mortality) was not tightly constrained but averaged about 90 g C/m²-yr. Carbon flux to soil organic matter in root turnover (128 g C/m²-yr) was only about half as large as aboveground detritus. Balancing the soil C budget requires that large amounts of C (80 g C/m²-yr) were transported from roots to rhizosphere carbon flux. Total soil respiration (TSR) ranged from 540 to 800 g C/m²-yr across eight stands and decreased with increasing elevation within the northern hardwood forest near W6. The watershed-wide TSR was estimated as 660 g C/m²-yr. Empirical measurements indicated that 58% of TSR occurred in the surface organic horizons and that root respiration comprised about 40% of TSR, most of the rest being microbial. Carbon flux directly associated with other heterotrophs in the HBEF was minor; for example, we estimated respiration of soil microarthropods, rodents, birds and moose at about 3, 5, 1 and 0.8 g C/m²-yr, respectively, or in total less than 2% of NPP. Hence, the effects of other heterotrophs on C flux were primarily indirect, with the exception of occasional irruptions of folivorous insects. Hydrologic fluxes of C were significant in the watershed C budget, especially in comparison with NEP. Although atmospheric inputs (1.7 g C/m²-yr) and streamflow outputs (2.7 g C/m²-yr) were small, larger quantities of C were transported within the ecosystem and a more substantial fraction of dissolved C was transported from the soil as inorganic C and evaded from the stream as CO₂ (4.0 g C/m²-yr). Carbon pools and fluxes change rapidly in response to catastrophic disturbances such as forest harvest or major windthrow events. These changes are dominated by living vegetation and dead wood pools, including roots. If biomass removal does not accompany large-scale disturbance, the ecosystem is a large net source of C to the atmosphere (500–1200 g C/m²-yr) for about a decade following disturbance and becomes a net sink about 15–20 years after disturbance; it remains a net sink of about 200–300 g C/m²-yr for about 40 years before rapidly approaching steady state. Shifts in NPP and NEP associated with common small-scale or diffuse forest disturbances (e.g., forest declines, pathogen irruptions, ice storms) are brief and much less dramatic. Spatial and temporal patterns in C pools and fluxes in the mature forest at the HBEF reflect variation in environmental factors. Temperature and growing-season length undoubtedly constrain C fluxes at the HBEF; however, temperature effects on leaf respiration may largely offset the effects of growing season length on photosynthesis. Occasional severe droughts also affect C flux by reducing both photosynthesis and soil respiration. In younger stands nutrient availability strongly limits NPP, but the role of soil nutrient availability in limiting C flux in the mature forest is not known. A portion of the elevational variation of ANPP within the HBEF probably is associated with soil resource limitation; moreover, sites on more fertile soils exhibit 20–25% higher biomass and ANPP than the forest-wide average. Several prominent biotic influences on C pools and fluxes also are clear. Biomass and NPP of both the young and mature forest depend upon tree species composition as well as environment. Similarly, litter decay differs among tree species and forest types, and forest floor C accumulation is twice as great in the spruce–fir–birch forests at higher elevations than in the northern hardwood forests, partly because of inherently slow litter decay and partly because of cold temperatures. This contributes to spatial patterns in soil solution and streamwater dissolved organic carbon across the Hubbard Brook Valley. Wood decay varies markedly both among species and within species because of biochemical differences and probably differences in the decay fungi colonizing wood. Although C biogeochemistry at the HBEF is representative of mountainous terrain in the region, other sites will depart from the patterns described at the HBEF, due to differences in site history, especially agricultural use and fires during earlier logging periods. Our understanding of the C cycle in northern hardwood forests is most limited in the area of soil pool size changes, woody litter deposition and rhizosphere C flux processes.     

Synchrony of Seed Dispersal, Hydrology and Local Climate in a Semi-arid River Reach in California

The temporal availability of propagules is a critical factor in sustaining pioneer riparian tree populations along snowmelt-driven rivers because seedling establishment is strongly linked to seasonal hydrology. River regulation in semi-arid regions threatens to decouple seed development and dispersal from the discharge regime to which they evolved. Using the lower Tuolumne River as a model system, we quantified and modeled propagule availability for Populus fremontii (POFR), Salix gooddingii (SAGO), and Salix exigua (SAEX), the tree and shrub species that dominate near-channel riparian stands in the San Joaquin Basin, CA. A degree-day model was fit to field data of seasonal seed density and local temperature from three sites in 2002–2004 to predict the onset of the peak dispersal period. To evaluate historical synchrony of seed dispersal and seasonal river hydrology, we compared peak spring runoff timing to modeled peak seed release periods for the last 75 years. The peak seed release period began on May 15 for POFR (range April 23–June 10), May 30 for SAGO (range May 19–June 11) and May 31 for SAEX (range May 8–June 30). Degree-day models for the onset of seed release reduced prediction error by 40–67% over day-of-year means; the models predicted best the interannual, versus site-to-site, variation in timing. The historical analysis suggests that POFR seed release coincided with peak runoff in almost all years, whereas SAGO and SAEX dispersal occurred during the spring flood recession. The degree-day modeling approach reduce uncertainty in dispersal timing and shows potential for guiding flow releases on regulated rivers to increase riparian tree recruitment at the lowest water cost.     

Vegetation composition,structure, and biomass of two unpolluted watersheds in the Cordillera de Piuchué, Chiloé Island,Chile

Research in pristine forests provides a necessary reference of energy and nutrient cycling in absence of anthropogenic influence. Therefore two unpolluted watersheds in the Cordillera de Piuchué of southern Chile (42 °30 S) were chosen for detailed ecosystem analysis. The goals of this study were to quantify the distribution of the living biomass in the research watershed and to document topographic gradients in the vegetation. Across a small spatial gradient from ravine bottom to ridgetop (approximately 60 m in elevation and < 300 m in length) in the Cordillera de Piuchué watersheds, there were significant shifts in vegetation composition, structure, and biomass. Based on sampling in 18, 100 m² plots, we identified three distinct community associations: a Fitzroya forest at the bottom of the watershed, a mid-slope Pilgerodendron-Tepualia transition zone, and a ridgetop moorland community. The Fitzroya forest was dominated by a cohort of approximately 400 year-old Fitzroya cupressoides trees. Both tree basal area (138 m²/ha) and total live biomass (656 Mg ha^–1) reached a maximum in this vegetation type. The Pilgerodendron-Tepualia forest consisted of smaller, shorter, and younger trees with dominance shared by Pilgerodendron uviferum, Tepualia stipularis, and to a lesser extent, F. cupressoides. Basal area and biomass were half that of the Fitzroya forest (69.5 m² ha^–1; 350 Mg ha^–1) but tree density was 65% greater. The moorland can best be described as an open community of mosses and cushion plants that included low stature individuals of P. uviferum, F. cupressoides, and T. stipularis. The size and age structure of F. cupressoides in the bottomland forest suggest that the current cohort of adult trees was established following a catastrophic disturbance and that F. cupressoides is unable to regenerate under its own canopy. In contrast, the size structure of the tree populations in the Pilgerodendron-Tepualia zone indicates that all the constituent tree species, except F. cupressoides, are able to reproduce at least at some microsites in the understory. The watershed-level means for live biomass were 306 Mg ha^–1 of aboveground tree biomass, 25 Mg ha^–1 of large root biomass (diameter ge 1 cm), and 46 Mg ha^–1 of small root biomass (diameter < 1 cm).     

Response of biomass,hydrology and biogeochemistry to alternative approaches of cutting a northern forest: model comparisons

Biogeochemistry - The biogeochemical model, PnET-BGC, was modified and parameterized using field data from an experimental whole-tree harvest of watershed (W5) in 1983–1984 at the Hubbard...