Community structures of actively growing bacteria shift along a north-south transect in the western North Pacific

Bacterial community structures and their activities in the ocean are tightly coupled with organic matter fluxes and thus control ocean biogeochemical cycles. Bromodeoxyuridine (BrdU), halogenated nucleoside and thymidine analogue, has been recently used to monitor actively growing bacteria (AGB) in natural environments. We labelled DNA of proliferating cells in seawater bacterial assemblages with BrdU and determined community structures of the bacteria that were possible key species in mediating biochemical reactions in the ocean. Surface seawater samples were collected along a north-south transect in the North Pacific in October 2003 and subjected to BrdU magnetic beads immunocapture and PCR-DGGE (BUMP-DGGE) analysis. Change of BrdU-incorporated community structures reflected the change of water masses along a north-south transect from subarctic to subtropical gyres in the North Pacific. We identified 25 bands referred to AGB as BrdU-incorporated phylotypes, belonging to Alphaproteobacteria (5 bands), Betaproteobacteria (1 band), Gammaproteobacteria (4 bands), Cytophaga-Flavobacterium-Bacteroides (CFB) group bacteria (5 bands), Gram-positive bacteria (6 bands), and Cyanobacteria (4 bands). BrdU-incorporated phylotypes belonging to Vibrionales , Alteromonadales and Gram-positive bacteria appeared only at sampling stations in a subtropical gyre, while those belonging to Roseobacter -related bacteria and CFB group bacteria appeared at the stations in both subarctic and subtropical gyres. Our result revealed phylogenetic affiliation of AGB and their dynamic change along with north-south environmental gradients in open oceans. Different species of AGB utilize different amount and kinds of substrates, which can affect the change of organic matter fluxes along transect.     

The abortifacient effect of 16,16-dimethyl-trans-δ-PGE1 methyl ester, a new prostaglandin analogue, on mid-trimester pregnancies and long-term follow-up observations

The present clinical trials revealed that 16,16-Dimethyl-trans-δ²-PGE₁ methyl ester in the form of vaginal suppositories is highly effective in inducing mid-trimester termination of pregnancies. It also showed that prior treatment with laminaria and metreurynter may enhance the success rate while reducing the incidence and severity of side effects. It is easy and safe to use clinically, with minimal side effects, and in our series, revealed no deleterious effects on ensuing reproductive physiology. However, the definite mechanism involved in the action of this new analogue to cause myometrial contractions is still not completely understood, and requires further intensive investigation.     

DNA strand breaks based on Monte Carlo simulation in and around the Lipiodol with flattening filter and flattening filter-free photon beams

BackgroundThe current study aims to investigate the DNA strand breaks based on the Monte Carlo simulation within and around the Lipiodol with flattening filter (FF) and flattening filter-free (FFF) photon beams.Materials and methodsThe dose-mean lineal energy (y_D) and DNA single- and double strand breaks (DSB/SSB) based on spatial patterns of inelastic interactions were calculated using the Monte Carlo code: particle and heavy ion transport system (PHITS). The ratios of dose using standard radiation (200 kVX) to the dose of test radiation (FF and FFF of 6 MV X-ray (6MVX) and 10 MVX beams) to produce the same biological effects was defined as RBE_DSB. The RBE_DSB within the Lipiodol and in the build-up and build-down regions was evaluated.ResultsThe RBE_DSB values with the Lipiodol was larger than that without the Lipiodol at the depth of 4.9 cm by 4.2% and 2.5% for 6 MVX FFF and FF beams, and 3.3% and 2.5% for 10 MVX FFF and FF beams. The RBE_DSB values with the Lipiodol was larger than that without the Lipiodol at the depth of 6.5 cm by 2.9% and 2.4% for 6 MVX FFF and FF beams, and 1.9% and 1.4% for 10 MVX FFF and FF beams. In the build-down region at the depth of 8.1 cm, the RBE_DSB values with the Lipiodol was smaller than that without the Lipiodol by 4.2% and 2.9% for 6 MVX FFF and FF beams, and 1.4% and 0.1% for 10 MVX FFF and FF beams.ConclusionsThe current study simulated the DNA strand break except for the physical dose difference. The lower and FFF beam occurred the higher biological effect.     

Interruption of CryAB-amyloid oligomer formation by HSP22

An R120G missense mutation in alpha-B-crystallin (CryAB), a small heat-shock protein (HSP), causes a desmin-related cardiomyopathy (DRM) that is characterized by the formation of aggregates containing CryAB and desmin. The mutant CryAB protein leads to the formation of inclusion bodies, which contain amyloid oligomer intermediates (amyloid oligomer) in the cardiomyocytes. To further address the underlying mechanism(s) of amyloid oligomer formation in DRM linked to the CryAB R120G, a recombinant CryAB R120G protein was generated. The purified CryAB R120G protein can form a toxic amyloid oligomer, whereas little immunoreactivity was observed in the wild-type CryAB protein. A native PAGE showed that the oligomerized form was present in the CryAB R120G protein, whereas only a high molecular mass was detected in the wildtype CryAB. The oligomerized CryAB R120G of around 240-480 kDa showed strong positive immunoreactivity against an anti-oligomer antibody. The CryAB R120G amyloid oligomer was unstable and easily lost its conformation by beta-mercaptoethanol and SDS. Recombinant HSP25 or HSP22 proteins can directly interrupt oligomer formation by the CryAB R120G protein, whereas the amyloid oligomer is still present in the mixture of the wild-type CryAB and CryAB R120G proteins. This interruption by HSP25 and HSP22 was confirmed in a cardiomyocyte-based study using an adenoviral transfection system. Blockade of amyloid oligomer formation by HSP25 and HSP22 recovered the ubiquitin proteosomal activity and cellular viability. Blockade of oligomer formation by small HSP may be a new therapeutic strategy for treating DRM as well as other types of amyloid-based degenerative diseases.     

A low-density cDNA microarray with a unique reference RNA: pattern recognition analysis for IFN efficacy prediction to HCV as a model

We have designed and established a low-density (295 genes) cDNA microarray for the prediction of IFN efficacy in hepatitis C patients. To obtain a precise and consistent microarray data, we collected a data set from three spots for each gene (mRNA) and using three different scanning conditions. We also established an artificial reference RNA representing pseudo-inflammatory conditions from established hepatocyte cell lines supplemented with synthetic RNAs to 48 inflammatory genes. We also developed a novel algorithm that replaces the standard hierarchical-clustering method and allows handling of the large data set with ease. This algorithm utilizes a standard space database (SSDB) as a key scale to calculate the Mahalanobis distance (MD) from the center of gravity in the SSDB. We further utilized sMD (divided by parameter k: MD/k) to reduce MD number as a predictive value. The efficacy prediction of conventional IFN mono-therapy was 100% for non-responder (NR) vs. transient responder (TR)/sustained responder (SR) (P < 0.0005). Finally, we show that this method is acceptable for clinical application.     

The chemical NJ15 affects hypocotyl elongation and shoot gravitropism via cutin polymerization

We previously found a chemical, designated as NJ15, which inhibited both auxin and brassinosteroid responses in dark-grown Arabidopsis. To study its mode of action, we performed a phenotypic screening of NJ15-low-sensitive lines among mutant pools of Arabidopsis. One line (f127) showed clear NJ15-low-sensitivity in terms of hypocotyl elongation and shoot gravitropism. After further testing, it was determined that DCR, an enzyme involved in cutin polymerization, had lost its function in the mutant, which caused its low sensitivity to NJ15. Fatty acids are the base materials for polymers such as cutin and cuticular wax. We confirmed that NJ15 affects fatty acid biosynthesis, and that it does differently from cafenstrole, a known inhibitor of cuticular wax formation. Based on these results, we propose that the target of NJ15 is likely located within the cutin polymer formation pathway.

Abbreviations: Caf: cafenstrole; DEG: differentially expressed gene; FDR: false discovery rate; FOX: full length cDNA-overexpressor; VLCFA: very-long-chain fatty acid     

Selective elution of target protein from affinity resins by a simple reductant with a thiol group

We have made a chance discovery of selective elution of a specific binding protein from affinity resins by mixing them with aqueous solutions of a widely used reductant, 2-mercaptoethanol (2ME), under mild conditions. Our studies suggest this phenomenon would be generic, and could be a powerful method for identification of a specific binding protein. We here exhibit the experimental conditions and successful examples in which target proteins of benzensulfonamide and FK506 were selectively eluted from affinity resins bearing these compounds, while non-specific ones remained.