A series of novel indazole derivatives of Sirt 1 activator as osteogenic regulators

A series of indazole derivatives were identified as Sirt 1 activators though high-throughput screening. Optimization of each substituent on the indazole ring led to the identification of compound 13. Compound 13 appeared to give the best Sirt 1 activity of the compounds tested and also showed osteogenesis activity in a cell assay. Sirt 1 activators are therefore potential candidates for the treatment of osteoporosis.     

DNA barcoding of freshwater zooplankton in Lake Kasumigaura,Japan

Although DNA barcoding is a promising tool for the identification of organisms, it requires the development of a specific reference sequence library for sample application. In the present study we developed a Lake Kasumigaura, Japan, zooplankton DNA barcode library to increase the sensitivity of future zooplankton monitoring for detecting lake ecosystem condition changes. Specifically, the mitochondrial cytochrome c oxidase subunit I (mtCOI) haplotype, i.e., the primary DNA barcode, was examined for each zooplankton taxon. In crustaceans, 37 mtCOI haplotypes were obtained from 99 individuals, representing four and 15 morpho-species of Copepoda and Cladocera, respectively. Comparing these sequences with those in GenBank shows that the lake harbors putative non-indigenous species, such as Daphnia ambigua. In rotifers, 132 mtCOI haplotypes were obtained from 302 individuals, representing 11 genera and one unclassified taxon. The automatic barcode gap discovery (ABGD) algorithm separated these haplotypes into 43 species. Brachionus cf. calyciflorus was divided into five ABGD species, and different ABGD species tended to occur in different seasons. Seasonal ABGD-species succession was also observed within Polyarthra spp. and Synchaeta spp. These seasonal successions were not detected by inspections of external morphology alone. Accepting up to 7% sequence divergence within the same species, mtCOI reference sequences were available in GenBank for three, 13, and 17 species in Copepoda, Cladocera, and Rotifera, respectively. The present results, therefore, reveal the serious shortage of mtCOI reference sequences for rotifers, and underscore the urgency of developing rotifer mtCOI barcode libraries on a global scale.     

Distinct immunohistochemical localization in Kuru plaques using novel anti-prion protein antibodies

By immunizing Prnp-knockout mice with synthetic polypeptides, a panel of mAbs directed to bovine PrP(C) was obtained. The mAb panel was characterized by the ELISA method, where synthetic polypeptides were used for epitope mapping. Different reactivity patterns were identified. The ability of these mAbs to detect abnormal PrP(Sc) in CJD cases was studied by immunohistochemistry. All mAbs were tested for PrP(Sc) in murine, bovine, monkey and human brain tissues. Three mAbs recognized the fragmented PrP epitope in our ELISA. Antibody 1D12 was strongly reactive to ovine and squirrel monkey tissues infected with a scrapie agent, although non-reactive to scrapie-infected mouse tissues. Antibody 2D8 was clearly reactive to type-2 but not type-1 CJD human tissues. Of particular interest was the reactivity of mAb 6C4 with the inner structure of Kuru plaques (peripheral pattern) in a type-2 CJD case and mAb T2, 1D12, 2B11, 2D8, 4B5 and 6G3-2 with the central area (central pattern). The fact that different anti-PrP mAbs possess distinct staining properties suggests that the PrP(c) to PrP(Sc) conversion might involve a multiple-step process.     

Localization of insulinoma associated protein 2, IA-2 in mouse neuroendocrine tissues using two novel monoclonal antibodies

AimsInsulinoma-associated protein 2 (IA-2) is a member of the protein tyrosine phosphatase family that is localized on the insulin granule membrane. IA-2 is also well known as one of the major autoantigens in Type 1 diabetes mellitus. IA-2 gene deficient mice were recently established and showed abnormalities in insulin secretion. Thus, detailed localization of IA-2 was studied using wild-type and IA-2 gene deficient mice.Main methodsTo localize IA-2 expression in mouse neuroendocrine tissues, monoclonal antibodies were generated against IA-2 and western blot and immunohistochemical analyses were carried out in IA-2^+/+ mice. IA-2^?/? mice served as a negative control.Key findingsWestern blot analysis revealed that the 65 kDa form of IA-2 was observed in the cerebrum, cerebellum, medulla oblongata, pancreas, adrenal gland, pituitary gland, muscular layers of the stomach, small intestine, and colon. By immunohistochemical analysis, IA-2 was produced in endocrine cells in pancreatic islets, adrenal medullary cells, thyroid C-cells, Kulchitsky cells, and anterior, intermediate, and posterior pituitary cells. In addition, IA-2 was found in somatostatin-producing D-cells and other small populations of cells were scattered in the gastric corpus. IA-2 expression in neurites was confirmed by the immunostaining of IA-2 using primary cultured neurons from the small intestine and nerve growth factor (NGF)-differentiated PC12 cells.SignificanceThe IA-2 distribution in peripheral neurons appeared more intensely in neurites rather than in the cell bodies.     

Unbiased Quantitation of Escherichia coli Membrane Proteome Using Phase Transfer Surfactants

We developed a sample preparation protocol for rapid and unbiased analysis of the membrane proteome using an alimentary canal-mimicking system in which proteases are activated in the presence of bile salts. In this rapid and unbiased protocol, immobilized trypsin is used in the presence of deoxycholate and lauroylsarcosine to increase digestion efficiency as well as to increase the solubility of the membrane proteins. Using 22.5 μg of Escherichia coli whole cell lysate, we quantitatively demonstrated that membrane proteins were extracted and digested at the same level as soluble proteins without any solubility-related bias. The recovery of membrane proteins was independent of the number of transmembrane domains per protein. In the analysis of the membrane-enriched fraction from 22.5 μg of E. coli cell lysate, the abundance distribution of the membrane proteins was in agreement with that of the membrane protein-coding genes when this protocol, coupled with strong cation exchange prefractionation prior to nano-LC-MS/MS analysis, was used. Because this protocol allows unbiased sample preparation, protein abundance estimation based on the number of observed peptides per protein was applied to both soluble and membrane proteins simultaneously, and the copy numbers per cell for 1,453 E. coli proteins, including 545 membrane proteins, were successfully obtained. Finally, this protocol was applied to quantitative analysis of guanosine tetra- and pentaphosphate-dependent signaling in E. coli wild-type and relA knock-out strains.Despite the importance of cell surface biology, the conventional shotgun proteomics strategy generally underrepresents the membrane proteome because of inadequate solubilization and protease digestion (1, 2). The ageless gel strategy, consisting of SDS-PAGE followed by in-gel digestion, can partially solve this problem (3–5), but the recovery from in-gel digestion is generally lower than that from in-solution digestion, and this approach is far from suitable for a rapid, simple, and high throughput automated system. Numerous approaches have been reported to overcome the difficulties in membrane proteome analysis, such as the use of surfactants (2, 6–11), organic solvents (6, 7, 12–15), or chaotropic reagents (2, 6, 16). Acid-labile surfactants, such as RapiGest SF, are among the most promising additives to enhance protein solubilization without interfering with LC-MS performance (6, 10, 17–19). However, the cleavage step at acidic pH causes loss of hydrophobic peptides because of coprecipitation with the hydrophobic part of RapiGest SF (20). Recently, we developed a new protocol to dissolve and digest membrane proteins with the aid of a removable phase transfer surfactant (PTS),1 such as sodium deoxycholate (SDC) (20). The solubility of membrane proteins with SDC was comparable to that with sodium dodecyl sulfate. In addition, the activity of trypsin was enhanced ∼5-fold in the presence of 1% SDC because this rapid PTS method mimics conditions in the alimentary canal in which bile salts such as cholate and deoxycholate are secreted together with trypsin. After tryptic digestion, SDC is removed prior to LC-MS/MS analysis by adding an organic solvent followed by pH-induced transfer of the surfactant to the organic phase, whereas tryptic peptides remain in the aqueous phase. This protocol offers a significant improvement in identifying membrane proteins by increasing the recovery of hydrophobic tryptic peptides compared with the protocols using urea and RapiGest SF.The goal of this study is to establish a membrane proteomics method that is unbiased with respect to protein solubility, hydrophobicity, and protein abundance; i.e. membrane proteins can be as efficiently extracted and digested as soluble proteins. So far, to our knowledge, little information about the recovery of the membrane proteome has been reported. Instead, the number of identified membrane proteins or the content of membrane proteins identified in the membrane-enriched fraction has been used as an indicator of the efficiency of procedures for membrane proteome analysis (4, 5, 21–23). However, these parameters usually depend on the experimental conditions, including the sample preparation procedure and LC-MS instrument used. Therefore, it is difficult to compare data obtained with these protocols except in the case of direct comparison. Furthermore, there has been no report quantitatively comparing the recovery of membrane proteome with that of soluble proteins.In this study, we used a modified version of our PTS protocol with immobilized trypsin columns to reduce the digestion time and evaluated its suitability for unbiased quantitation of the membrane proteome. In addition, we applied this protocol to estimate the copy numbers per cell of 1,453 proteins, including 545 membrane proteins, using the exponentially modified protein abundance index (emPAI). Finally, this rapid and unbiased PTS protocol was applied to the quantitative analysis of Escherichia coli BW25113 wild-type and relA knock-out (KO) strains.     

Stomatal Ultrastructure, Molecular Phylogeny, and Description of Parasitodiplogaster laevigata n. sp. (Nematoda: Diplogastridae), a Parasite of Fig Wasps

Parasitodiplogaster comprises a potentially large radiation of nematode species that appear to be parasitically bound to their Agaonid fig wasp hosts, which are mutualistically associated in the syconia (figs) of the diverse plant genus Ficus. Parasitodiplogaster laevigata n. sp. is described and illustrated as an associate of the fig wasp, Pegoscapus sp. from Ficus laevigata from southern Florida. It is the first species of Parasitodiplogaster reported from North America and is closest to P. trigonema from F. trigonata from Panama. Parasitodiplogaster laevigata n. sp. can be differentiated from all described species of Parasitodiplogaster based on stomatal morphology (presence of a large dorsal and a right subventral tooth) in the adults of both sexes, molecular comparisons of two expansion segments (D2,D3) of the large subunit (LSU) rRNAgene, and fig-fig wasp host affinities. The ultrastructure of P. laevigata n. sp. was elucidated using TEM and SEM for comparisons with other species of Parasitodiplogaster. The stoma of P. laevigata n. sp. possesses a nonsegmented cheilostomal ring that connects to the longitudinal body musculature per- and interradially, a claw-like dorsal tooth, a right subventral tooth, and telostegostomatal apodemes arising from the dorsal side of each subventral sector. The unification of the pro-, meso-, and metastegostom with the gymnostom in P. laevigata n. sp. and further simplification in other described species may be due to derived adaptations associated with the internal parasitism of fig wasps.     

E3 ubiquitin ligase synoviolin is involved in liver fibrogenesis

Background and Aim

Chronic hepatic damage leads to liver fibrosis, which is characterized by the accumulation of collagen-rich extracellular matrix. However, the mechanism by which E3 ubiquitin ligase is involved in collagen synthesis in liver fibrosis is incompletely understood. This study aimed to explore the involvement of the E3 ubiquitin ligase synoviolin (Syno) in liver fibrosis.

Methods

The expression and localization of synoviolin in the liver were analyzed in CCl₄-induced hepatic injury models and human cirrhosis tissues. The degree of liver fibrosis and the number of activated hepatic stellate cells (HSCs) was compared between wild type (wt) and Syno^+/− mice in the chronic hepatic injury model. We compared the ratio of apoptosis in activated HSCs between wt and Syno^+/− mice. We also analyzed the effect of synoviolin on collagen synthesis in the cell line from HSCs (LX-2) using siRNA-synoviolin and a mutant synoviolin in which E3 ligase activity was abolished. Furthermore, we compared collagen synthesis between wt and Syno^−/− mice embryonic fibroblasts (MEF) using quantitative RT-PCR, western blotting, and collagen assay; then, we immunohistochemically analyzed the localization of collagen in Syno^−/− MEF cells.

Results

In the hepatic injury model as well as in cirrhosis, synoviolin was upregulated in the activated HSCs, while Syno^+/− mice developed significantly less liver fibrosis than in wt mice. The number of activated HSCs was decreased in Syno^+/− mice, and some of these cells showed apoptosis. Furthermore, collagen expression in LX-2 cells was upregulated by synoviolin overexpression, while synoviolin knockdown led to reduced collagen expression. Moreover, in Syno^−/− MEF cells, the amounts of intracellular and secreted mature collagen were significantly decreased, and procollagen was abnormally accumulated in the endoplasmic reticulum.

Conclusion

Our findings demonstrate the importance of the E3 ubiquitin ligase synoviolin in liver fibrosis.     

Unintentional introductions of microscopic organisms associated with forest insects

International trade and travel are devastating native flora and fauna in many countries through the intentional and/or unintentional introduction of exotic organisms. Pathway control appears to be particularly effective for microscopic organisms such as mites, nematodes, and fungi that are difficult to see with the naked eye. However, taxonomic and ecological information on such organisms is scarce, sometimes causing time lags or failure in eradication programs. Several groups of mites, nematodes, and fungi commonly share a habitat with insects or use them as dispersal agents (phoresy). Some exotic mites and nematodes are introduced simultaneously with exotic insects, sometimes in wood materials. In Japan, mites, nematodes, and fungi have been collected from lucanid beetles introduced as pets from Southeast Asia. While no lethal nematode species have been collected from lucanid beetles, one hemolymph-sucking mite species, inhabiting the sub-elytral space of its native host, is able to easily switch to the Japanese beetle, Dorcus rectus, killing the insect. Yeasts have also been reported on exotic beetles and laboulbeniomycetes have been found on mites associated with the beetles, although their interactions are unknown. Despite the lack of information available about other mites, nematodes, and fungi associated with intentionally and unintentionally introduced forest insects, our analysis of insect species listed by the International Union for Conservation of Nature suggests that unintentional introductions of the microscopic organisms are quite common as a consequence of the existence of symbiotic relationships such as phoresy and parasitism.     

CREB represses p53-dependent transactivation of MDM2 through the complex formation with p53 and contributes to p53-mediated apoptosis in response to glucose deprivation

Recently, we have described that CREB (cAMP-responsive element-binding protein) has the ability to transactivate tumor suppressor p53 gene in response to glucose deprivation. In this study, we have found that CREB forms a complex with p53 and represses p53-mediated transactivation of MDM2 but not of p21^WAF1. Immunoprecipitation analysis revealed that CREB interacts with p53 in response to glucose deprivation. Forced expression of CREB significantly attenuated the up-regulation of the endogenous MDM2 in response to p53. By contrast, the mutant form of CREB lacking DNA-binding domain (CREBΔ) had an undetectable effect on the expression level of the endogenous MDM2. During the glucose deprivation-mediated apoptosis, there existed an inverse relationship between the expression levels of MDM2 and p53/CREB. Additionally, p53/CREB complex was dissociated from MDM2 promoter in response to glucose deprivation. Collectively, our present results suggest that CREB preferentially down-regulates MDM2 and thereby contributing to p53-mediated apoptosis in response to glucose deprivation.