Experimental allometry: effect of size manipulation on metabolic rate of colonial ascidians

The allometric scaling of metabolic rate of organisms, the three-quarters power rule, has led to a questioning of the basis for the relation. We attacked this problem experimentally for the first time by employing the modular organism, the ascidian that forms a single layered flat colony, as a model system. The metabolic rate and colony size followed the three-quarters power relation, which held even after the colony size was experimentally manipulated. Our results established that the three-quarters power relation is a real continuous function, not an imaginary statistical regression. The fact that all the hypotheses failed to explain why the two-dimensional organism adhered to the three-quarters power relation led us to propose a new hypothesis, in which the allometric relation derives from the self-organized criticality based on local interaction between modulus-comprising organisms.     

Effect of the V3 loop deletion of envelope glycoprotein on cellular responses and protection against challenge with recombinant vaccinia virus expressing gp160 of primary human immunodeficiency virus type 1 isolates

The magnitude and breadth of cytotoxic-T-lymphocyte (CTL) responses induced by human immunodeficiency virus type 1 (HIV-1) envelope protein from which the hypervariable V3 loop had been deleted (DeltaV3) were evaluated in the HLA-A2/K(b) transgenic mice. It was demonstrated that vaccines expressing the DeltaV3 mutant of either HIV-1(IIIB) or HIV-1(89.6) envelope glycoprotein induced broader CD8(+) T-cell activities than those elicited by the wild-type (WT) counterparts. Specifically, the differences were associated with higher responses to conserved HLA-A2-restricted CTL epitopes of the envelope glycoprotein and could be correlated with an increased cell surface occupancy by the epitope-HLA-A2 complexes in target cells expressing the DeltaV3 mutant. Using recombinant vaccinia virus expressing heterologous gp160 of primary HIV-1 isolates in a murine challenge system, we observed that the extent of resistance to viral transmission was higher in animals immunized with the DeltaV3 than the WT envelope vaccine. The protection was linked to the presence of envelope-specific CD8(+) T cells, since depletion of these cells by anti-CD8 antibody treatment at the time of challenge abolished the vaccine-induced protection. The results from our studies provide insights into approaches for boosting the breadth of envelope-specific CTL responses.     

Linking Transcriptional Changes over Time in Stimulated Dendritic Cells to Identify Gene Networks Activated during the Innate Immune Response

The innate immune response is primarily mediated by the Toll-like receptors functioning through the MyD88-dependent and TRIF-dependent pathways. Despite being widely studied, it is not yet completely understood and systems-level analyses have been lacking. In this study, we identified a high-probability network of genes activated during the innate immune response using a novel approach to analyze time-course gene expression profiles of activated immune cells in combination with a large gene regulatory and protein-protein interaction network. We classified the immune response into three consecutive time-dependent stages and identified the most probable paths between genes showing a significant change in expression at each stage. The resultant network contained several novel and known regulators of the innate immune response, many of which did not show any observable change in expression at the sampled time points. The response network shows the dominance of genes from specific functional classes during different stages of the immune response. It also suggests a role for the protein phosphatase 2a catalytic subunit α in the regulation of the immunoproteasome during the late phase of the response. In order to clarify the differences between the MyD88-dependent and TRIF-dependent pathways in the innate immune response, time-course gene expression profiles from MyD88-knockout and TRIF-knockout dendritic cells were analyzed. Their response networks suggest the dominance of the MyD88-dependent pathway in the innate immune response, and an association of the circadian regulators and immunoproteasomal degradation with the TRIF-dependent pathway. The response network presented here provides the most probable associations between genes expressed in the early and the late phases of the innate immune response, while taking into account the intermediate regulators. We propose that the method described here can also be used in the identification of time-dependent gene sub-networks in other biological systems.     

Synergistic Proinflammatory Responses by IL-17A and Toll-Like Receptor 3 in Human Airway Epithelial Cells

Viral respiratory infections activate the innate immune response in the airway epithelium through Toll-like receptors (TLRs) and induce airway inflammation, which causes acute exacerbation of asthma. Although increases in IL-17A expression were observed in the airway of severe asthma patients, the interaction between IL-17A and TLR activation in airway epithelium remains poorly understood. In this study, we demonstrated that IL-17A and polyI:C, the ligand of TLR3, synergistically induced the expression of proinflammatory cytokines and chemokines (G-CSF, IL-8, CXCL1, CXCL5, IL-1F9), but not type I interferon (IFN-α1, -β) in primary culture of normal human bronchial epithelial cells. Synergistic induction after co-stimulation with IL-17A and polyI:C was observed from 2 to 24 hours after stimulation. Treatment with cycloheximide or actinomycin D had no effect, suggesting that the synergistic induction occurred without de novo protein synthesis or mRNA stabilization. Inhibition of the TLR3, TLR/TIR-domain-containing adaptor-inducing interferon β (TRIF), NF-κB, and IRF3 pathways decreased the polyI:C- and IL-17A/polyI:C-induced G-CSF and IL-8 mRNA expression. Comparing the levels of mRNA induction between co-treatment with IL-17A/polyI:C and treatment with polyI:C alone, blocking the of NF-κB pathway significantly attenuated the observed synergism. In western blotting analysis, activation of both NF-κB and IRF3 was observed in treatment with polyI:C and co-treatment with IL-17A/polyI:C; moreover, co-treatment with IL-17A/polyI:C augmented IκB-α phosphorylation as compared to polyI:C treatment alone. Collectively, these findings indicate that IL-17A and TLR3 activation cooperate to induce proinflammatory responses in the airway epithelium via TLR3/TRIF-mediated NF-κB/IRF3 activation, and that enhanced activation of the NF-κB pathway plays an essential role in synergistic induction after co-treatment with IL-17A and polyI:C in vitro.     

Post-Drilling Changes in Seabed Landscape and Megabenthos in a Deep-Sea Hydrothermal System,the Iheya North Field,Okinawa Trough

There has been an increasing interest in seafloor exploitation such as mineral mining in deep-sea hydrothermal fields, but the environmental impact of anthropogenic disturbance to the seafloor is poorly known. In this study, the effect of such anthropogenic disturbance by scientific drilling operations (IODP Expedition 331) on seabed landscape and megafaunal habitation was surveyed for over 3 years using remotely operated vehicle video observation in a deep-sea hydrothermal field, the Iheya North field, in the Okinawa Trough. We focused on observations from a particular drilling site (Site C0014) where the most dynamic change of landscape and megafaunal habitation was observed among the drilling sites of IODP Exp. 331. No visible hydrothermal fluid discharge had been observed at the sedimentary seafloor at Site C0014, where Calyptogena clam colonies were known for more than 10 years, before the drilling event. After drilling commenced, the original Calyptogena colonies were completely buried by the drilling deposits. Several months after the drilling, diffusing high-temperature hydrothermal fluid began to discharge from the sedimentary subseafloor in the area of over 20 m from the drill holes, ‘artificially’ creating a new hydrothermal vent habitat. Widespread microbial mats developed on the seafloor with the diffusing hydrothermal fluids and the galatheid crab Shinkaia crosnieri endemic to vents dominated the new vent community. The previously soft, sedimentary seafloor was hardened probably due to barite/gypsum mineralization or silicification, becoming rough and undulated with many fissures after the drilling operation. Although the effects of the drilling operation on seabed landscape and megafaunal composition are probably confined to an area of maximally 30 m from the drill holes, the newly established hydrothermal vent ecosystem has already lasted 2 years and is like to continue to exist until the fluid discharge ceases and thus the ecosystem in the area has been altered for long-term.     

Usual Interstitial Pneumonia Preceding Collagen Vascular Disease: A Retrospective Case Control Study of Patients Initially Diagnosed with Idiopathic Pulmonary Fibrosis

Background

The aim of this study was to evaluate the cumulative incidence and the predictive factors for collagen vascular disease (CVD) in patients initially diagnosed with idiopathic pulmonary fibrosis (IPF), and to examine the features of patients who then developed CVD.

Methods

This was a retrospective review of 111 consecutive patients with IPF diagnosed at our institution. None of the patients fulfilled any of the CVD criteria from the American College of Rheumatology (ACR) within 6 months or more after the diagnosis of IPF.

Results

Ten patients (9.0%) developed CVD during the follow-up period: four had rheumatoid arthritis (RA); four had microscopic polyangiitis (MPA); one had systemic sclerosis (SSc); and one had SSc and Sjogren’s syndrome (SjS). The mean time until CVD diagnosis was 3.9 years. The cumulative incidences of CVD at 1, 5, and 10 years were 0.91%, 9.85%, and 15.5%, respectively. Patients who developed CVD were significantly younger, more likely to be women and had a better prognosis than those with IPF. Cox proportional hazards regression analysis showed that female sex and the presence of lymphoid aggregates with germinal centers were significantly associated with the occurrence of CVD in patients initially diagnosed with IPF.

Conclusions

CVD is an important underlying condition in IPF, and shows better prognosis. The possibility of the development of CVD should remain a consideration in the follow-up of IPF.     

Environmental influences on fish assemblages in irrigation ponds

Ponds are common features of the landscape and are considered important for freshwater biodiversity conservation. Although fish have a significant impact on the lentic ecosystems, the environmental factors that regulate fish assemblages in human-created water bodies, such as irrigation ponds, remain unclear. We evaluated the relationship between environmental factors and the fish assemblage structure in 31 ponds located in northern Japan. Species richness (range: 1–9) was positively correlated with the size of the inflow channel. Multivariate analyses revealed that the size of the inflow channel was a better predictor for species richness than lake morphology (surface area and maximum depth), vegetation coverage, water quality (turbidity, pH, DO, and EC), distance to the main channel, and distance to an adjacent pond. Species richness was significantly different between ponds with and without an inflow channel. Furthermore, three of the four most commonly observed species are thought to be relatively tolerant to low oxygen. Given that ponds have a relatively high local extinction rate resulting from exposure to stressful conditions, such as low oxygen and/or small population sizes, our results suggest that immigration from surrounding water bodies plays an important role in maintaining species richness of pond-dwelling fish.     

Decrease of WNK4 ubiquitination by disease-causing mutations of KLHL3 through different molecular mechanisms

Recently, we demonstrated that WNK4 is a substrate for KLHL3–Cullin3 (CUL3) E3 ubiquitin ligase complexes and that impaired WNK4 ubiquitination is a common mechanism for pseudohypoaldosteronism type II (PHAII) caused by WNK4, KLHL3, and CUL3 mutations. Among the various KLHL3 mutations that cause PHAII, we demonstrated that the R528H mutation in the Kelch domain decreased the binding to WNK4, thereby causing less ubiquitination and increased intracellular levels of WNK4. However, the pathogenic mechanisms of PHAII caused by other KLHL3 mutants remain to be determined. In this study, we examined the pathogenic effects of three PHAII-causing mutations in different KLHL3 domains; the protein levels of these mutants significantly differed when they were transiently expressed in HEK293T cells. In particular, S410L expression was low even with increased plasmid expression. The cycloheximide chase assay revealed that an S410L mutation in the Kelch domain significantly decreased the intracellular stability. Mutations in E85A in the BTB domain and C164F in the BACK domain decreased the binding to CUL3, and S410L as well as R528H demonstrated less binding to WNK4. In vitro and in vivo assays revealed that these mutants decreased the ubiquitination and increased the intracellular levels of WNK4 compared with wild-type KLHL3. Therefore, the KLHL3 mutants causing PHAII investigated in this study exhibited less ability to ubiquitinate WNK4 because of KLHL3’s low stability and/or decreased binding to CUL3 or WNK4.