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.     

A target function for quaternary structural refinement from small angle scattering and NMR orientational restraints

We present a novel target function based on atomic coordinates that permits quaternary structural refinement of multi-domain protein–protein or protein–RNA complexes. It requires that the high-resolution structures of the individual domains are known and that small angle scattering (SAS) data as well as NMR orientational restraints from residual dipolar couplings (RDCs) of the complex are available. We show that, when used in combination, the translational and rotational restraints contained in SAS intensities and RDCs, respectively, define a target potential function that permits to determine the overall topology of complexes made up of domains with low internal symmetry. We apply the target function on a modestly anisotropic model system, the Barnase/Barstar complex, and discuss factors that influence the structural refinement such as data errors and the geometrical properties of the individual domains.     

Oligomeric structure of LOV domains in Arabidopsis phototropin

Oligomeric structures of the four LOV domains in Arabidopsis phototropin1 (phot1) and 2 (phot2) were studied using crosslinking. Both LOV1 domains of phot1 and phot2 form a dimer independently on the light conditions, suggesting that the LOV1 domain can be a stable dimerization site of phot in vivo. In contrast, phot1-LOV2 is in a monomer-dimer equilibrium and phot2-LOV2 exists as a monomer in the dark. Blue light-induced a slight increase in the monomer population in phot1-LOV2, suggesting a possible blue light-inducible dissociation of dimers. Furthermore, blue light caused a band shift of the phot2-LOV2 monomer. CD spectra revealed the unfolding of helices and the formation of strand structures. Both light-induced changes were reversible in the dark.

Structured summary

MINT-6823377, MINT-6823391:PHOT1 (uniprotkb:O48963) and PHOT1 (uniprotkb: O48963) bind (MI:0407) by cross-linking studies (MI:0030)MINT-6823495, MINT-6823508:PHOT2 (uniprotkb:P93025) and PHOT2 (uniprotkb:P93025) bind (MI:0407) by cross-linking studies (MI:0030)     

Interactome modeling

A long-term goal of the field of interactome modeling is to understand how global and local properties of complex macromolecular networks impact on observable biological properties, and how changes in such properties can lead to human diseases. The information available at this stage of development of the field provides strong evidence for the existence of such interesting global and local properties, but also demonstrates that many more datasets will be needed to provide accurate models with increasingly predictive capacity. This review focuses on an early attempt at mapping a multicellular interactome network and on the lessons learned from that attempt.     

Blastocladiella emersonii expresses a centrin similar to Chlamydomonas reinhardtii isoform not found in late-diverging fungi

Centrins are members of the calcium-binding EF-hand protein superfamily which can be divided into two subfamilies, probably associated with different functions: one related to Chlamydomonas reinhardtii centrin, CrCenp, and the other, represented by Saccharomyces cerevisiae isoform, ScCdc31p. ESTs encoding the two isoforms (BeCen1 and BeCen3) from the chytridiomycete Blastocladiella emersonii were isolated, and expression of the CrCenp-type centrin, BeCen1, was analyzed throughout the fungus life cycle. Becen1 mRNA levels increase transiently during sporulation and protein levels present a similar pattern. Immunolocalization studies seem to localize BeCen1 at the basal body zone and in the cytoplasm surrounding the nuclear cap, a zoospore organelle.     

Adhesion,proliferation, and adipogenesis in primary rat cell cultures: effects of collagenous substrata,fibronectin, and serum

Summary The effects of collagenous substrata, fibronectin, and fetal bovine serum on the adhesion, proliferation, and adipogenesis of rat stromal-vascular cells are reported. There was no effect on initial stromal-vascular cell-attachment by fetal bovine serum or fibronectin. The number of cells attached to a hydrated collagen-gel was almost twice (P<0.04) the number attached to dried collagen-gel or dried denatured collagen-gel. Total number of cells after 5 days in culture was similar among the collagenous substrata and among the treatments with or without fibronectin in the growth media. Total number of cells increased significantly (P<0.02) with 10% FBS. Adipocytic formation was inhibited by hydrated collagen-gel (P<0.02) compared to dried collagen-gel or dried, denatured collagenous substrata. An interaction occurred between dried, denatured gel and fetal bovine serum so that total formation of adipocytes increased by increasing the level of fetal bovine serum (P<0.07). Adipocytic formation was inhibited by hydrated collagen-gel at all levels of fetal bovine serum. The percentage of cells that converted to adipocytes was significantly lower (P<0.01) on hydrated collagen-gel compared to dried, denatured or dried collagen-gel. Percentage of conversion was not significantly different among levels of fetal bovine serum, although this percentage increased as fetal bovine serum level increased. Adipocytic conversion was not different between fibronectin-treated or untreated cells. Morphology of stromal vascular cells was similar on dried collagen and dried, denatured collagen-gel, but tended to remain bipolar on hydrated collagen-gel. These studies indicate that fetal bovine serum in combination with the extracellular matrix (dried, denatured collagen) increased the differentiation of rat stromal-vascular cells into adipocytes, and that hydrated collagen inhibited differentiation.     

Evaluation of swimming performance for fish passage of longnose dace Rhinichthys cataractae using an experimental flume

The swimming performance of longnose dace Rhinichthys cataractae, the most widely distributed minnow (Cyprinidae) in North America, was assessed in relation to potential passage barriers. The study estimated passage success, maximum ascent distances and maximum sprint speed in an open‐channel flume over a range of water velocities and temperatures (10·7, 15·3 and 19·3° C). Rhinichthys cataractae had high passage success (95%) in a 9·2 m flume section at mean test velocities of 39 and 64 cm s^–1, but success rate dropped to 66% at 78 cm s^–1. Only 20% of fish were able to ascend a 2·7 m section with a mean velocity of 122 cm s^–1. Rhinichthys cataractae actively selected low‐velocity pathways located along the bottom and corners of the flume at all test velocities and adopted position‐holding behaviour at higher water velocities. Mean volitional sprint speed was 174 cm s^–1 when fish volitionally sprinted in areas of high water velocities. Swimming performance generally increased with water temperature and fish length. Based on these results, fishways with mean velocities <64 cm s^–1 should allow passage of most R. cataractae. Water velocities >100 cm s^–1 within structures should be limited to short distance (<1 m) and structures with velocities ≥158 cm s^–1 would probably represent movement barriers. Study results highlighted the advantages of evaluating a multitude of swimming performance metrics in an open‐channel flume, which can simulate the hydraulic features of fishways and allow for behavioural observations that can facilitate the design of effective passage structures.     

Measurement of two-bond JCOHα coupling constants in proteins uniformly enriched with13C

Summary A simple E.COSY type technique is described for measurement of two-bond J_COH coupling constants in proteins that are uniformly enriched with¹³C. The method has been used to measure²J_COH for 132 residues in the proteins calmodulin and staphylococcal nuclease having non-overlapping H–C correlations. Measured²J_COH coupling constants fall in the 0 to –9.5 Hz range. A separate experiment, measuring the accuracy of these values, indicates a root-mean-square error of 1 Hz. Comparison of the J couplings with the dihedral back bone angles from crystallographic studies confirms a weak but statistically significant correlation between the dihedral angle and the magnitude of²J_COH, but also indicates that parameters other than have a significant effect on the value of the coupling.