Halocynthiibacter namhaensis gen. nov., sp. nov., a novel alphaproteobacterium isolated from sea squirt Halocynthia roretzi

A Gram-negative, non-motile and rod-shaped bacterial strain, designated RA2-3^T, was isolated from a sea squirt (Halocynthia roretzi) collected from the South Sea, Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain RA2-3^T was observed to grow optimally at 25 °C, at pH 7.0–7.5 and in the presence of 2 % (w/v) NaCl. Strain RA2-3^T exhibited the highest 16S rRNA gene sequence similarity values to the type strains of Litoreibacter meonggei (95.7 %), Planktotalea frisia (95.6 %), Thalassobius gelatinovorus (95.5 %) and Pelagicola litoralis (95.4 %). A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain RA2-3^T clustered with the type strains of Planktotalea frisia, Pelagicola litoralis, Pacificibacter maritimus and Roseovarius marinus. Strain RA2-3^T was found to contain Q-10 as the predominant ubiquinone and C_18:1 ω7c as the major fatty acid. The major polar lipids detected in strain RA2-3^T were phosphatidylcholine, phosphatidylglycerol, one unidentified aminolipid and one unidentified lipid. The DNA G+C content of strain RA2-3^T was 52.9 mol%. On the basis of the phylogenetic, chemotaxonomic and phenotypic properties, strain RA2-3^T is considered to represent a new genus and species within the family Rhodobacteraceae, for which the name Halocynthiibacter namhaensis gen. nov., sp. nov. is proposed. The type strain of H. namhaensis is RA2-3^T (=KCTC 32362^T=NBRC 109999^T).     

Novel Interaction of the Z-DNA Binding Domain of Human ADAR1 with the Oncogenic c-Myc Promoter G-Quadruplex

Both G-quadruplex and Z-DNA can be formed in G-rich and repetitive sequences on genome, and their formation and biological functions are controlled by specific proteins. Z-DNA binding proteins, such as human ADAR1, have a highly conserved Z-DNA binding domain having selective affinity to Z-DNA. Here, our study identifies the Z-DNA binding domain of human ADAR1 (hZα_ADAR1) as a novel G-quadruplex binding protein that recognizes c-myc promoter G-quadruplex formed in NHEIII₁ region and represses the gene expression. An electrophoretic migration shift assay shows the binding of hZα_ADAR1 to the intramolecular c-myc promoter G-quadruplex-forming DNA oligomer. To corroborate the binding of hZα_ADAR1 to the G-quadruplex, we conducted CD and NMR chemical shift perturbation analyses. CD results indicate that hZα_ADAR1 stabilizes the parallel-stranded conformation of the c-myc G-quadruplex. The NMR chemical shift perturbation data reveal that the G-quadruplex binding region in hZα_ADAR1 was almost identical with the Z-DNA binding region. Finally, promoter assay and Western blot analysis show that hZα_ADAR1 suppresses the c-myc expression promoted by NHEIII₁ region containing the G-quadruplex-forming sequence. This finding suggests a novel function of Z-DNA binding protein as a regulator of G-quadruplex-mediated gene expression.     

LED light for in vitro and ex vitro efficient growth of economically important highbush blueberry (<Emphasis Type="Italic">Vaccinium corymbosum</Emphasis> L.)

Light-emitting diodes (LEDs) are useful for the growth of many plants, but not known for blueberry species. This study examined the effects of fluorescent lamps and 100 % red, 80 % red plus 20 % blue, 50 % red plus 50 % blue, and 100 % blue LEDs on the growth and development of highbush blueberry shoots under aseptic and non-aseptic conditions. Results revealed that monochromatic blue LEDs accumulated the highest contents of leaf chlorophylls. In contrast, monochromatic red LEDs inhibited chlorophyll accumulation, but produced the longest shoots and roots and provided high percentages of side shoot formation from ex vitro plants. Mixed LEDs, particularly 50 % red plus 50 % blue light, improved plant growth with respect to notably increased shoot and root biomass. Direct rooting of in vitro shoots under non-aseptic conditions was readily achieved using a commercial mixture of perlite and peat moss with high humidity controls. These findings obviously suggest the efficient use of LEDs to replace traditional fluorescent lamps in large-scale propagation of the highbush blueberry, and also pave the way for future studies on LEDs for standardizing micropropagation protocols to shrub crops and woody plants.     

Differential Expression of Programmed Cell Death on the Follicular Development in Normal and Miniature Pig Ovary

Follicles are important in oocyte maturation. Successful estrous cycle requires remodeling of follicular cells, and proper execution of programmed cell death is crucial for normal follicular development. The objectives of the present study were to understand programmed cell death during follicle development, to analyze the differential follicle development patterns, and to assess the patterns of apoptosis and autophagy expression during follicle development in normal and miniature pigs. Through the analysis of differential patterns of programmed cell death during follicular development in porcine, MAP1LC3A, B and other autophagy-associated genes (ATG5, mTOR, Beclin-1) were found to increase in normal pigs, while it decreased in miniature pigs. However, for the apoptosis-associated genes, progression of genes during follicular development increased in miniature pigs, while it decreased in normal pigs. Thus, results show that normal and miniature pigs showed distinct patterns of follicular remodeling manifesting that programmed cell death largely depends on the types of pathway during follicular development (Type II or autophagy for normal pigs and Type I or apoptosis for miniature pigs).     

Faunal changes and geographic crypticism indicate the occurrence of a biogeographic transition zone along the southern East Pacific Rise

Aim Deep‐sea hydrothermal vents have now been reported along all active mid‐ocean ridges and back‐arc basins, but the boundaries of biogeographic entities remain questionable owing to methodological issues. Here we examine biogeographic patterns of the vent fauna along the East Pacific Rise (EPR) and determine the relative roles of regional and local factors on the distribution of biodiversity associated with mussel beds along a poorly explored zone, the southern EPR (SEPR). Location East Pacific Rise. Methods A species list of macrobenthic invertebrates along the EPR was compiled from the literature and supplemented with data recovered during the French research cruise BIOSPEEDO carried out in 2004 along the SEPR. Biogeographic patterns were assessed by combining the identification of morphological species with a molecular barcoding approach. A multivariate regression tree (MRT) analysis was performed to identify any geographic breaks, and an empirical distribution of species richness was compared with predictions provided by a mid‐domain effect model. Macrofaunal community structure associated with mussel beds along the SEPR was analysed in relation to environmental factors using cluster and canonical redundancy analyses. Results Sequencing of the cytochrome c oxidase subunit I gene revealed the occurrence of several cryptic species complexes along the EPR, with the equator separating the southern and northern clades. Furthermore, during the BIOSPEEDO cruise at least 10 still unnamed species were collected between 7°25′ S and 21°33′ S. The shift in community structure identified by MRT analysis was located south of 17°34′ S or south of 13°59′ S, depending on the data used, suggesting that the southern part of the SEPR (17°25′–21°33′ S) constitutes a biogeographic transition zone in the vent fauna along the EPR. At a regional scale, latitude combined with the type of venting was significantly correlated with the community structure associated with mussel beds. Main conclusions Together, the molecular data, in situ observations, and the distribution of species suggest that the high diversity of vent fauna species presently observed between 17°25′ S and 21°33′ S is probably a result of the overlap of several distinct biogeographic provinces. We argue that this area thus constitutes a biogeographic vent fauna transition zone along the EPR.     

Spatial morphology of the mitochondria of the proximal and distal tubules of the kidney]

A new histological technique of block staining based on the use of a double lead and copper citrate is described in order to observe thick sections (0.5-1.5 micron) with a transmission electron microscope. With this technique, a network of mitochondrial with many morphological communications was seen in the epithelial cells of the proximal and distal convoluted tubules of the rat nephron. A new schematic view of the proximal and distal tubular cell is presented to illustrate the communications of the chondriome, which could become more or less accentuated following the functional status of the cell.     

Desulfurization of model and diesel oils by resting cells of Gordona sp.

The desulfurization activity of the resting cells of Gordona sp. CYKS1 was strongly depended on harvest time and the highest value when the cells had been harvested in the early growth phase (0.12 mg sulfur g^–1 cell^–1 h^–1). For the model oil, hexadecane containing dibenzothiophene, the specific desulfurization rate decreased as the reaction proceeded. Both the specific and the volumetric desulfurization rates were not significantly affected by the aqueous-to-oil phase ratio. The diesel oils, light gas oil and a middle distillate unit feed were desulfurized at higher rates (ca. 0.34 mg sulfur g^–1 cell^–1 h^–1) than the model oil (0.12 mg sulfur g^–1 cell^–1 h^–1).     

The Empirical Analysis of Cigarette Tax Avoidance and Illicit Trade in Vietnam, 1998-2010

Illicit trade carries the potential to magnify existing tobacco-related health care costs through increased availability of untaxed and inexpensive cigarettes. What is known with respect to the magnitude of illicit trade for Vietnam is produced primarily by the industry, and methodologies are typically opaque. Independent assessment of the illicit cigarette trade in Vietnam is vital to tobacco control policy. This paper measures the magnitude of illicit cigarette trade for Vietnam between 1998 and 2010 using two methods, discrepancies between legitimate domestic cigarette sales and domestic tobacco consumption estimated from surveys, and trade discrepancies as recorded by Vietnam and trade partners. The results indicate that Vietnam likely experienced net smuggling in during the period studied. With the inclusion of adjustments for survey respondent under-reporting, inward illicit trade likely occurred in three of the four years for which surveys were available. Discrepancies in trade records indicate that the value of smuggled cigarettes into Vietnam ranges from $100 million to $300 million between 2000 and 2010 and that these cigarettes primarily originate in Singapore, Hong Kong, Macao, Malaysia, and Australia. Notable differences in trends over time exist between the two methods, but by comparison, the industry estimates consistently place the magnitude of illicit trade at the upper bounds of what this study shows. The unavailability of annual, survey-based estimates of consumption may obscure the true, annual trend over time. Second, as surveys changed over time, estimates relying on them may be inconsistent with one another. Finally, these two methods measure different components of illicit trade, specifically consumption of illicit cigarettes regardless of origin and smuggling of cigarettes into a particular market. However, absent a gold standard, comparisons of different approaches to illicit trade measurement serve efforts to refine and improve measurement approaches and estimates.     

Comparative Functional Analysis of ZFP36 Genes during Xenopus Development

ZFP36 constitutes a small family of RNA binding proteins (formerly known as the TIS11 family) that target mRNA and promote their degradation. In mammals, ZFP36 proteins are encoded by four genes and, although they show similar activities in a cellular RNA destabilization assay, there is still a limited knowledge of their mRNA targets and it is not known whether or not they have redundant functions. In the present work, we have used the Xenopus embryo, a model system allowing gain- and loss-of-function studies, to investigate, whether individual ZFP36 proteins had distinct or redundant functions. We show that overexpression of individual amphibian zfp36 proteins leads to embryos having the same defects, with alteration in somites segmentation and pronephros formation. In these embryos, members of the Notch signalling pathway such as hairy2a or esr5 mRNA are down-regulated, suggesting common targets for the different proteins. We also show that mouse Zfp36 protein overexpression gives the same phenotype, indicating an evolutionary conserved property among ZFP36 vertebrate proteins. Morpholino oligonucleotide-induced loss-of-function leads to defects in pronephros formation, reduction in tubule size and duct coiling alterations for both zfp36 and zfp36l1, indicating no functional redundancy between these two genes. Given the conservation in gene structure and function between the amphibian and mammalian proteins and the conserved mechanisms for pronephros development, our study highlights a potential and hitherto unreported role of ZFP36 gene in kidney morphogenesis.