Hyphomonas atlanticus sp. nov., isolated from the Atlantic Ocean and emended description of the genus Hyphomonas

A taxonomic study was carried out on strains 22II1-22F38^T and 22II-S13e, which were isolated from sea water and sediment from the Atlantic Ocean, respectively. The two strains were Gram-negative, oxidase and catalase positive, oval to pear shaped, and motile by a single polar flagellum. Phylogenetic analysis based on 16S rRNA gene sequences indicated that both strains belonged to the genus Hyphomonas, with highest sequence similarity (98.2%) to the type strains H. jannaschiana DSM 5153^T and H. johnsonii ATCC 43964^T. The genomic ANIm values and DNA-DNA hybridization estimate values between strain 22II1-22F38^T and seven type strains ranged from 82.84% to 84.10% and from 18.0% to 19.1%, respectively. Isolate 22II1-22F38^T had a G + C content of 58.3% and used Q-11 as the predominant respiratory quinone. The combined phenotypic and genotypic data showed that both strains represented a novel species of the genus Hyphomonas, for which the name Hyphomonas atlanticus sp. nov. is proposed, with the type strain being 22II1-22F38^T (=LMG 27916^T = MCCC 1A09418^T). In addition, we conclude that Hyphomonas hirschiana is a later synonym of Hyphomonas neptunium.     

PI3 kinase/Akt signaling mediates epithelial-mesenchymal transition in hypoxic hepatocellular carcinoma cells

Hypoxia activates genetic programs that facilitate cell survival; however, in cancer, it may promote invasion and metastasis. Although the exact mechanisms driving hypoxia-induced invasion and metastasis remain elusive, we hypothesized that epithelial-mesenchymal transition (EMT) may play a major role. We investigated this in vitro by treating hepatocellular carcinoma cells under 1.0% O₂. After the hypoxia treatment, the cells exhibited some morphological changes including cell elongation, cytoskeletal rearrangement, and junctional disruption. Moreover, expression of the epithelia-specific marker E-cadherin was decreased and expression of the myofibroblast-specific marker vimentin was detected in the treated cells. Cell migration and ECM gel invasion were increased. These findings were consistent with events observed during EMT. Hypoxia-induced EMT is accompanied by increased phosphorylation, activation of Akt and the downstream signaling. Hypoxia-induced EMT was blocked by PI3K inhibitor LY294002. The results suggest that the PI3K/Akt-dependent signaling pathways serve to regulate hypoxia-induced EMT of hepatocellular carcinoma cells.     

Structural analysis of the lipid A isolated from Hafnia alvei 32 and PCM 1192 lipopolysaccharides

Hafnia alvei, a Gram-negative bacterium, is an opportunistic pathogen associated with mixed hospital infections, bacteremia, septicemia, and respiratory diseases. The majority of clinical symptoms of diseases caused by this bacterium have a lipopolysaccharide (LPS, endotoxin)-related origin. The lipid A structure affects the biological activity of endotoxins predominantly. Thus, the structure of H. alvei lipid A was analyzed for the first time. The major form, asymmetrically hexa-acylated lipid A built of β-d-GlcpN4P-(1→6)-α-d-GlcpN1P substituted with (R)-14:0(3-OH) at N-2 and O-3, 14:0(3-(R)-O-12:0) at N-2′, and 14:0(3-(R)-O-14:0) at O-3′, was identified by ESI-MSⁿ and MALDI-time-of-flight (TOF) MS. Comparative analysis performed by MS suggested that LPSs of H. alvei 32, PCM 1192, PCM 1206, and PCM 1207 share the identified structure of lipid A. LPSs of H. alvei are yet another example of enterobacterial endotoxins having the Escherichia coli-type structure of lipid A. The presence of hepta-acylated forms of H. alvei lipid A resulted from the addition of palmitate (16:0) substituting 14:0(3-OH) at N-2 of the α-GlcpN residue. All the studied strains of H. alvei have an ability to modify their lipid A structure by palmitoylation.     

广东省蔬菜种质资源收集保存与鉴定利用

2002-2004年,广东省农业科学院蔬菜研究所引进收集蔬菜种质资源501份,对已有的1642份蔬菜种质进行了繁种和农艺性状鉴定,入广东省蔬菜种质资源库（GVG）保存蔬菜种质1400份,同时对182份蔬菜种质资源进行了抗病性鉴定或营养品质分析,从中鉴定出高抗资源8份,抗病资源16份;完成了广东省蔬菜种质资源数据库的构建,其中包含了1019份已入库保存蔬菜种质的植株或果实图片,实现了广东省蔬菜种质资源数据网上共享。2003-2005年,共有12个利用优异蔬菜种质资源育成的蔬菜新品种通过广东省或国家农作物品种审定。     

Getting a grip on proteomics data – Proteomics Data Collection (ProDaC)

In proteomics, rapid developments in instrumentation led to the acquisition of increasingly large data sets. Correspondingly, ProDaC was founded in 2006 as a Coordination Action project within the 6th European Union Framework Programme to support data sharing and community‐wide data collection. The objectives of ProDaC were the development of documentation and storage standards, setup of a standardized data submission pipeline and collection of data. Ending in March 2009, ProDaC has delivered a comprehensive toolbox of standards and computer programs to achieve these goals.     

Tracing Ancestors and Relatives of Escherichia coli B, and the Derivation of B Strains REL606 and BL21(DE3)

Antecedents of Escherichia coli B have been traced through publications, inferences, and personal communication to a strain from the Institut Pasteur in Paris used by d'Herelle in his studies of bacteriophages as early as 1918 (a strain not in the current collection). This strain appears to have passed from d'Herelle to Bordet in 1920, and from Bordet to at least three other laboratories by 1925. The strain that Gratia received from Bordet was apparently passed to Bronfenbrenner by 1924 and from him to Luria around 1941. Delbrück and Luria published the first paper calling this strain B in 1942. Its choice as the common host for phages T1-T7 by the phage group that developed around Delbrück, Luria, and Hershey in the 1940s led to widespread use of B along with E. coli K-12, chosen about the same time for biochemical and genetic studies by Tatum and Lederberg. Not all currently available strains related to B are descended from the B of Delbrück and Luria; at least three strains with somewhat different characteristics were derived independently by Hershey directly from the Bronfenbrenner strain, and a strain that appears to have passed from Bordet to Wollman is in the current Collection of the Institut Pasteur. The succession of manipulations and strains that led from the B of Delbrück and Luria to REL606 and BL21(DE3) is given, established in part through evidence from their recently determined complete genome sequences.     

Luminostat operation: a tool to maximize microalgae photosynthetic efficiency in photobioreactors during the daily light cycle?

The luminostat regime has been proposed as a way to maximize light absorption and thus to increase the microalgae photosynthetic efficiency within photobioreactors. In this study, simulated outdoor light conditions were applied to a lab-scale photobioreactor in order to evaluate the luminostat control under varying light conditions. The photon flux density leaving the reactor (PFD_out) was varied from 4 to 20 μmol photons m⁻² s⁻¹and the productivity and photosynthetic efficiency of Chlorella sorokiniana were assessed.Maximal volumetric productivity (1.22 g kg⁻¹ d⁻¹) and biomass yield on PAR photons (400-700 nm) absorbed (1.27 g mol⁻¹) were found when PFD_out was maintained between 4 and 6 μmol photons m⁻² s⁻¹. The resultant photosynthetic efficiency was comparable to that already reported in a chemostat-controlled reactor. A strict luminostat regime could not be maintained under varying light conditions. Further modifications to the luminostat control are required before application under outdoor conditions.     

Quantitative proteomic analysis of lignocellulolytic enzymes by Phanerochaete chrysosporium on different lignocellulosic biomass

Lignocellulosic biomass from agricultural crop residues and forest waste represents an abundant renewable resource for bioenergy and future biofuel. The current bottleneck of lignocellulosic biofuel production is the hydrolysis of biomass to sugar. To understand the enzymatic hydrolysis of complex biomasses, in this report, lignocellulolytic enzymes secretion by Phanerochaete chrysosporium cultivated in different natural lignocellulosic biomass such as corn stover, hay, sawdust, sugarcane baggase, wheat bran and wood chips were quantitatively analyzed with the iTRAQ technique using LC-MS/MS. A diverse groups of enzymes, including cellulases, glycoside hydrolases, hemicellulases, lignin degrading enzymes, peroxidases, esterases, lipases, chitinases, peptidases, protein translocating transporter and hypothetical proteins were quantified, of which several were novel lignocellulosic biomass hydrolyzing enzymes. The quantitative expression and regulation of lignocellulolytic enzymes by P. chrysosporium were dependent on the nature and complexity of lignocellulosic biomass as well as physical size of the biomass. The iTRAQ data revealed oxidative and hydrolytic lignin degrading mechanism of P. chrysosporium. Numerous proteins presumed to be involved in natural lignocellulosic biomass transformation and degradation were expressed and produced in variable quantities in response to different agricultural and forest wastes.