Pasture degradation in the central Amazon: linking changes in carbon and nutrient cycling with remote sensing

The majority of deforested land in the Amazon Basin has become cattle pasture, making forest‐to‐pasture conversion an important contributor to the carbon (C) and climate dynamics of the region. However, our understanding of biogeochemical dynamics in pasturelands remains poor, especially when attempting to scale up predictions of C cycle changes. A wide range of pasture ages, soil types, management strategies, and climates make remote sensing the only realistic means to regionalize our understanding of pasture biogeochemistry and C cycling over such an enormous geographic area. However, the use of remote sensing has been impeded by a lack of effective links between variables that can be observed from satellites (e.g. live and senescent biomass) and variables that cannot be observed, but which may drive key changes in C storage and trace gas fluxes (e.g. soil nutrient status). We studied patterns in canopy biophysical–biochemical properties and soil biogeochemical processes along pasture age gradients on two important soil types in the central Amazon. Our goals were to (1) improve our understanding of the plot‐scale biogeochemical dynamics of this land‐use change, (2) evaluate the effects of pasture development on two contrasting soil types (clayey Oxisols and sandy Entisols), and (3) attempt to use remotely sensed variables to scale up the site‐specific variability in biogeochemical conditions of pasturelands. The biogeochemical analyses showed that (1) aboveground and soil C stocks decreased with pasture age on both clayey and sandy soils, (2) declines in plant biomass were well correlated with declines in soil C and with available phosphorus (P) and calcium (Ca), and (3) despite low initial values for total and available soil P, ecosystem P stocks declined further with pasture age, as did a number of other nutrients. Spectral mixture analysis of Landsat imagery provided estimates of photosynthetic vegetation (PV) and non‐photosynthetic vegetation (NPV) that were highly correlated with field measurements of these variables and plant biomass. In turn, the remotely sensed sum PV+NPV was well correlated with the changes in soil organic carbon and nitrogen, and available P and Ca. These results suggest that remote sensing can be an excellent indicator of not only pasture area, but of pasture condition and C storage, thereby greatly improving regional estimates of the environmental consequences of such land‐use change.     

The interplay between hMLH1 and hMRE11: role in MMR and the effect of hMLH1 mutations

Our previous studies indicate that hMRE11 plays a role in MMR, and this function of hMRE11 is most likely mediated by the hMLH1-hMRE11 interaction. Here, we explored the functional implications of the hMLH1-hMRE11 interaction in MMR and the effects of hMLH1 mutations on their interaction. Our in vitro MMR assay demonstrated that the dominant-negative hMRE11^452-634 mutant peptide (i.e., harboring only the hMLH1-interacting domain) imparted a significant reduction in both 3′ excision and 3′-directed MMR activities. Furthermore, the expression of hMRE11^452-634, and to a lesser extent hMRE11^1-634 (ATLD1), impaired G2/M checkpoint control in response to MNU and cisplatin treatments, rendering cells resistant to killings by these two anticancer drugs. Analysis of 38 hMLH1 missense mutations showed that the majority of mutations caused significant (>50%) reductions in their interaction with hMRE11, suggesting a potential link between aberrant protein interaction and the pathogenic effects of hMLH1 variants.     

Dissolved Organic Carbon in Terrestrial Ecosystems: Synthesis and a Model

The movement of dissolved organic carbon (DOC) through soils is an important process for the transport of carbon within ecosystems and the formation of soil organic matter. In some cases, DOC fluxes may also contribute to the carbon balance of terrestrial ecosystems; in most ecosystems, they are an important source of energy, carbon, and nutrient transfers from terrestrial to aquatic ecosystems. Despite their importance for terrestrial and aquatic biogeochemistry, these fluxes are rarely represented in conceptual or numerical models of terrestrial biogeochemistry. In part, this is due to the lack of a comprehensive understanding of the suite of processes that control DOC dynamics in soils. In this article, we synthesize information on the geochemical and biological factors that control DOC fluxes through soils. We focus on conceptual issues and quantitative evaluations of key process rates to present a general numerical model of DOC dynamics. We then test the sensitivity of the model to variation in the controlling parameters to highlight both the significance of DOC fluxes to terrestrial carbon processes and the key uncertainties that require additional experiments and data. Simulation model results indicate the importance of representing both root carbon inputs and soluble carbon fluxes to predict the quantity and distribution of soil carbon in soil layers. For a test case in a temperate forest, DOC contributed 25% of the total soil profile carbon, whereas roots provided the remainder. The analysis also shows that physical factors—most notably, sorption dynamics and hydrology—play the dominant role in regulating DOC losses from terrestrial ecosystems but that interactions between hydrology and microbial–DOC relationships are important in regulating the fluxes of DOC in the litter and surface soil horizons. The model also indicates that DOC fluxes to deeper soil layers can support a large fraction (up to 30%) of microbial activity below 40 cm. Received 14 January 2000; accepted 6 September 2000     

胰岛细胞抗体分型与胰岛细胞凋亡的实验研究

研究通过大量临床糖尿病病人胰岛细胞抗体（Islet Cell Antibody,ICA)检测,发现ICA阳性反应有两种完全不同的形态学表现;弥漫型ICA和边缘型ICA,经免疫组织化学双标技术鉴别。弥漫型ICA可同时有着染α细胞和β细胞,边缘型ICA则仅着染α细胞。这种只着染α细胞的ICA国内外尚未见有报道,为探讨其在糖尿病发病中所起的作用。选择1型糖尿病（1-DM）的弥漫型ICA和边缘型ICA各3例。另选正常3例作对照,用患血清分别以2、4、8小时三个时相与分离并贴壁生长的正常人胰岛细胞孵育后,进行原位细胞凋亡检测。结果发现,弥漫型ICA,边缘型ICA均可导致胰岛细胞产生凋亡,其中弥漫型ICA使β细胞及α细胞出现凋亡;边缘型ICA使α细胞产生凋亡,这一结果提示;糖尿病发病机制除与分泌胰岛素的β细胞有密切关系的经典途径之外,可能还与分泌胰高血糖素的α细胞存在某种关系。     

Primary Succession on a Hawaiian Dryland Chronosequence

We used measurements from airborne imaging spectroscopy and LiDAR to quantify the biophysical structure and composition of vegetation on a dryland substrate age gradient in Hawaii. Both vertical stature and species composition changed during primary succession, and reveal a progressive increase in vertical stature on younger substrates followed by a collapse on Pleistocene-aged flows. Tall-stature Metrosideros polymorpha woodlands dominated on the youngest substrates (hundreds of years), and were replaced by the tall-stature endemic tree species Myoporum sandwicense and Sophora chrysophylla on intermediate-aged flows (thousands of years). The oldest substrates (tens of thousands of years) were dominated by the short-stature native shrub Dodonaea viscosa and endemic grass Eragrostis atropioides. We excavated 18 macroscopic charcoal fragments from Pleistocene-aged substrates. Mean radiocarbon age was 2,002 years and ranged from < 200 to 7,730. Genus identities from four fragments indicate that Osteomeles spp. or M. polymorpha once occupied the Pleistocene-aged substrates, but neither of these species is found there today. These findings indicate the existence of fires before humans are known to have occupied the Hawaiian archipelago, and demonstrate that a collapse in vertical stature is prevalent on the oldest substrates. This work contributes to our understanding of prehistoric fires in shaping the trajectory of primary succession in Hawaiian drylands.     

Function of phenolic substances in the degradation system of indole-3-acetic acid in strawberries

The homogenate of different strawberry organs inhibits the degradation of IAA in the presence of horse radish peroxidase, while intact strawberry tissues are able to degrade IAA. The chemical nature of peroxidase inhibitors present, in strawberry tissues was in vestigated. Using paper chromatography the following polyphenolic substances inhibiting peroxidase activity were identified: chlorogenic, caffeic, ellagic, gentisic, gallic, and vanillic acids, quercetin and pelarginidin. Monophenolic compounds, also present in strawberry, such as p-hydroxy-phenyloacetic acid and p-hydroxybenzoic acid, are strong stimulators of IAA oxidase. Abscisic acid in very high concentration (1×10^?4M) enhances degradation of IAA by peroxidase. When both poly-and monophenolic compounds at equimolar concentrations are present in the system, only the inhibition of IAA degradation occurs. Tissue explants from the strawberry leaves and petiole degrade less IAA if they are previously forced to synthetize more polyphenols under illumination. Although the difference in IAA-decarboxylation activity between the illumination and dark treated explants was relatively small, nevertheless it was consistent and appears to be very important from a physiological point of view suggesting that there exists a regulatory relationin vivo between IAA degradation and the presence of phenolsin plant tissue. Electron microscope data revealed that phenolic substances are specially isolated from cytoplasm of the receptacle cells.     

Different amyloid aggregation of smooth muscles titin in vitro

A comparative study of amyloid properties of the aggregates of smooth muscle titin (SMT) from chicken gizzard was carried out. These aggregates were formed in two solutions: 0.15 M glycine-KOH, pH 7.2–7.4 (SMT(Gly)) and 0.2 M KCl, 10 mM imidazole, pH 7.0 (SMT(KCl)). Electron microscopy data showed that SMT aggregates has an amorphous structure in both cases. The results of atomic-force microscopy demonstrated slight differences in morphology in two types of aggregates. The SMT(Gly) aggregates were represented as branching chains, composed of spherical aggregates approximately 300–500 nm in diameter and up to 35 nm in height. The SMT(KCl) aggregates formed sponge-like structures with strands of 8–10 nm in height. Structural analysis of SMT aggregates by X-ray diffraction revealed the presence of cross-β-sheet structure in the samples under study. In the presence of SMT(Gly) aggregates, thioflavine T fluorescence intensity was higher (~3-fold times) compared with that in the presence of SMT(KCl) aggregates. Congo red-stained SMT(Gly) aggregates had yellow to apple-green birefringence under polarized light, which was not observed for SMT(KCl) aggregates. Dynamic light scattering data showed the similar rate of aggregation for both types of aggregates, though SMT(KCl) aggregates were able to partially disaggregate under increased ionic strength of the solution. The ability of SMT to aggregation followed by disaggregation may be functionally significant in the cell.     

Environmental and Biotic Controls over Aboveground Biomass Throughout a Tropical Rain Forest

The environmental and biotic factors affecting spatial variation in canopy three-dimensional (3-D) structure and aboveground tree biomass (AGB) are poorly understood in tropical rain forests. We combined field measurements and airborne light detection and ranging (lidar) to quantify 3-D structure and AGB across a 5,016 ha rain forest reserve on the northeastern flank of Mauna Kea volcano, Hawaii Island. We compared AGB among native stands dominated by Metrosideros polymorpha found along a 600–1800 m elevation/climate gradient, and on three substrate-age classes of 5, 20, and 65 kyr. We also analyzed how alien tree invasion, canopy species dominance and topographic relief influence AGB levels. Canopy vertical profiles derived from lidar measurements were strong predictors (r ² = 0.78) of AGB across sites and species. Mean AGB ranged from 48 to 363 Mg ha⁻¹ in native forest stands. Increasing elevation corresponded to a 53–84% decrease in AGB levels, depending upon substrate age. Holding climate constant, changes in substrate age from 5 to 65 kyr corresponded to a 23–53% decline in biomass. Invasion by Psidium cattleianum and Ficus rubiginosa trees resulted in a 19–38% decrease in AGB, with these carbon losses mediated by substrate age. In contrast, the spread of former plantation tree species Fraxinus uhdei corresponded to a 7- to 10-fold increase in biomass. The effects of topographic relief at both local and regional scales were evident in the AGB maps, with poorly drained terrain harboring 76% lower biomass than forests on well-drained relief. Our results quantify the absolute and relative importance of environmental factors controlling spatial variation in tree biomass across a rain forest landscape, and highlight the rapid changes in carbon storage incurred following biological invasion. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Author Contributions  GPA and RFH conceived of or designed the study. GPA, RFH, TAV, DEK, and TKB performed research and analyzed data. GPA, RFH, DEK, and TKB contributed new methods or models. GPA wrote the article.     

Localizing triplet periodicity in DNA and cDNA sequences

Background  

The protein-coding regions (coding exons) of a DNA sequence exhibit a triplet periodicity (TP) due to fact that coding exons contain a series of three nucleotide codons that encode specific amino acid residues. Such periodicity is usually not observed in introns and intergenic regions. If a DNA sequence is divided into small segments and a Fourier Transform is applied on each segment, a strong peak at frequency 1/3 is typically observed in the Fourier spectrum of coding segments, but not in non-coding regions. This property has been used in identifying the locations of protein-coding genes in unannotated sequence. The method is fast and requires no training. However, the need to compute the Fourier Transform across a segment (window) of arbitrary size affects the accuracy with which one can localize TP boundaries. Here, we report a technique that provides higher-resolution identification of these boundaries, and use the technique to explore the biological correlates of TP regions in the genome of the model organism C. elegans.