Linking aboveground and belowground food webs through carbon and nitrogen stable isotope analyses

Carbon and nitrogen stable isotope ratios (δ¹³C and δ¹⁵N) have been used for more than two decades in analyses of food web structure. The utility of isotope ratio measurements is based on the observation that consumer δ¹³C values are similar (<1‰ difference) to those of their diet, while consumer δ¹⁵N values are about 3‰ higher than those of their diet. The technique has been applied most often to aquatic and aboveground terrestrial food webs. However, few isotope studies have examined terrestrial food web structure that includes both above- and belowground (detrital) components. Here, we review factors that may influence isotopic signatures of terrestrial consumers in above- and belowground systems. In particular, we emphasize variations in δ¹³C and δ¹⁵N in belowground systems, e.g., enrichment of ¹³C and ¹⁵N in soil organic matter (likely related to soil microbial metabolism). These enrichments should be associated with the high ¹³C (~3‰) enrichment in belowground consumers relative to litter and soil organic matter and with the large variation in δ¹⁵N (~6‰) of the consumers. Because such enrichment and variation are much greater than the trophic enrichment generally used to estimate consumer trophic positions, and because many general predators are considered dependent on energy and material flows from belowground, the isotopic variation in belowground systems should be taken into account in δ¹³C and δ¹⁵N analyses of terrestrial food webs. Meanwhile, by measuring the δ¹³C of key predators, the linkage between above- and belowground systems could be estimated based on observed differences in δ¹³C of primary producers, detritivores and predators. Furthermore, radiocarbon (¹⁴C) measurements will allow the direct estimation of the dependence of predators on the belowground systems.     

XGAP, an ArfGAP, is required for polarized localization of PAR proteins and cell polarity in Xenopus gastrulation

To dissect the molecular mechanisms underlying convergent extension (CE), a prominent set of cell movements during Xenopus gastrulation, we performed a functional expression screen and identified a GTPase-activating protein for ADP ribosylation factors (ArfGAP), which we termed XGAP. We demonstrated that XGAP is required to confine or restrict the cellular protrusive activity to the mediolateral ends of cells, where XGAP is normally localized, and therefore for the proper intercalation of cells participating in CE. We also demonstrated that a C-terminal conserved domain of XGAP, but not its GAP activity, is required and sufficient for this intracellular localization and function. We further showed that XGAP physically interacts with the known polarity proteins 14-3-3epsilon, aPKC, and PAR-6 and directs them to the mediolateral ends of dorsal mesoderm cells during gastrulation. We propose that XGAP controls CE through the restriction and maintenance of partitioning-defective (PAR) proteins in the regions that harbor protrusive activity.     

First application of X-ray refraction-based computed tomography to a biomedical object

We have developed X-ray refraction-based computed tomography (CT) that is able to visualize soft tissue in between hard tissue. The experimental system consists of Si(220) diffraction double-crystals and is called the DEI (diffraction-enhanced imaging) method, in which the object is located between the crystals and a CCD camera to acquire data as 360 X-ray images. The X-ray energy used was 17.5 keV. The algorithm used to reconstruct CT images was developed by A. Maksimenko and colleagues. We successfully visualized articular cartilage and the distribution of bone marrow, which are inner structures. Our method has much higher contrast compared to the conventional absorption-based CT system.     

Mechanism of Cold Injury in Sweet Potatoes

The biochemical mechanism of cold injury occurring in sweet potatoes stored at 0°C was studied. Oxygen uptake and RC ratio of mitochondria from sweet potatoes kept at 0°C for about 15 days declined when succinate or malate was used as substrate. As sweet potatoes suffered slight cold injury, a decrease in the respiratory rate of state 3 of mitochondria was observed. This decrease could be restored approximately to the level of that of healthy sweet potato mitochondria by the addition of cytochrome c when succinate was used as substrate. When sweet potatoes suffered severe damage, only partial recovery was observed with cytochrome c. While it was found that the respiratory rate in state 3 of mitochondria from chilled sweet potatoes was less inhibited by cyanide than that of healthy sweet potato mitochondria, the inhibition could be restored to that of healthy sweet potato mitochondria by the addition of cytochrome c. When malate was used as substrate, no effect of cytochrome c and NADH₂ was observed. There was no difference between chilled and healthy sweet potato mitochondria in enzyme activities of the electron transport system except for malate dehydrogenase.     

The Screening of RNA Aptamers Specific for Carbonic Anhydrase I Using the Systematic Evolution of Ligands by an Exponential Enrichment Method (SELEX)

Carbonic anhydrases (CA) or carbonate dehydratases are a family of enzymes that catalyze the rapid interconversion of carbon dioxide and water to bicarbonate. CA I is the most abundant protein in the cytosol and has been reported to the partially associated with a number of fatal diseases. A newly established Systematic Evolution of Ligands by EXponential enrichment (SELEX) method referred to as Protein-SELEX was used to select RNA aptamers against the human erythrocyte CA I (CA I) protein. After five rounds of selection and counter selection the specific binding of the 6th cycle in vitro transcribed RNA library to CA I was detected by an Electrophoretic Mobility Shift Assay (EMSA). Three Specific sequences were identified as binding candidates after cloning and sequence analysis and one of the selected CA I specific RNA aptamers, CAapt1, was used to confirm specific binding and the Kd values were determined using an EMSA. The CAapt1 RNA aptamer showed no affinity towards any other protein and in comparison to the “0” cycle library, a significant enrichment was obtained. This methodology permitted us to successfully investigate the ssRNA aptamer CAapt1 for CA I protein.     

SHCBP1 is required for midbody organization and cytokinesis completion

The centralspindlin complex, which is composed of MKLP1 and MgcRacGAP, is one of the crucial factors involved in cytokinesis initiation. Centralspindlin is localized at the middle of the central spindle during anaphase and then concentrates at the midbody to control abscission. A number of proteins that associate with centralspindlin have been identified. These associating factors regulate furrowing and abscission in coordination with centralspindlin. A recent study identified a novel centralspindlin partner, called Nessun Dorma, which is essential for germ cell cytokinesis in Drosophila melanogaster. SHCBP1 is a human ortholog of Nessun Dorma that associates with human centralspindlin. In this report, we analyzed the interaction of SHCBP1 with centralspindlin in detail and determined the regions that are required for the interaction. In addition, we demonstrate that the central region is necessary for the SHCBP1 dimerization. Both MgcRacGAP and MKLP1 are degraded once cells exit mitosis. Similarly, endogenous and exogenous SHCBP1 were degraded with mitosis progression. Interestingly, SHCBP1 expression was significantly reduced in the absence of centralspindlin, whereas centralspindlin expression was not affected by SHCBP1 knockdown. Finally, we demonstrate that SHCBP1 depletion promotes midbody structure disruption and inhibits abscission, a final stage of cytokinesis. Our study gives novel insight into the role of SHCBP in cytokinesis completion.     

Changes in stable nitrogen and carbon isotope ratios of plants and soil across a boreal forest fire chronosequence

Background and Aim

Nitrogen (N) and carbon (C) isotopic signatures (δ¹⁵N and δ¹³C) serve as powerful tools for understanding temporal changes in ecosystem processes, but how these signatures change across boreal forest chronosequences is poorly understood.

Methods

The δ¹⁵N, δ¹³C, and C/N ratio of foliage of eight dominant plant species, including trees, understory shrubs, and a moss, as well as humus, were examined across a 361 years fire-driven chronosequence in boreal forest in northern Sweden.

Results

The δ¹³C and C/N ratio of plants and humus increased along the chronosequence, suggesting increasing plant stress through N limitation. Despite increasing biological N fixation by cyanobacteria associated with feather mosses, δ¹⁵N showed an overall decline, and δ¹⁵N of the feather moss and associated vascular plants diverged over time from that of atmospheric N₂.

Conclusions

Across this chronosequence the N fixed by cyanobacteria is unlikely to be used by mosses and vascular plants without first undergoing mineralization and mycorrhizal transport, which would cause a change in δ¹⁵N signature due to isotopic fractionation. The decreasing trend of δ¹⁵N suggests that as the chronosequence proceeds, the plants may become more dependent on N transferred from mycorrhizal fungi or from N deposition.