AMPK mediates autophagy during myocardial ischemia in vivo

We have recently shown that autophagy is induced by ischemia and reperfusion in the mouse heart in vivo. Ischemia stimulates autophagy through an AMP activated protein kinase (AMPK)-dependent mechanism, whereas reperfusion after ischemia stimulates autophagy through a Beclin 1-dependent, but AMPK-independent, mechanism. Autophagy plays distinct roles during ischemia and reperfusion: autophagy may be protective during ischemia, whereas it may be detrimental during reperfusion. We will discuss the role of AMPK in mediating autophagy during myocardial ischemia in vivo.     

Personalized medicine and proteomics: lessons from non-small cell lung cancer

Personalized medicine allows the selection of treatments best suited to an individual patient and disease phenotype. To implement personalized medicine, effective tests predictive of response to treatment or susceptibility to adverse events are needed, and to develop a personalized medicine test, both high quality samples and reliable data are required. We review key features of state-of-the-art proteomic profiling and introduce further analytic developments to build a proteomic toolkit for use in personalized medicine approaches. The combination of novel analytical approaches in proteomic data generation, alignment and comparison permit translation of identified biomarkers into practical assays. We further propose an expanded statistical analysis to understand the sources of variability between individuals in terms of both protein expression and clinical variables and utilize this understanding in a predictive test.     

Double-layered collagen gel hemisphere for cell invasion assay: successful visualization and quantification of cell invasion activity

Although various methods for collagen gel-based cell invasion assays have been described, there continues to be a need for a simpler and more objective assay. Here, we describe an easy-to-prepare double-layered collagen gel hemisphere (DL-CGH) system that satisfies these requirements, and we demonstrate the advantages of this new system for visualizing cell movements during invasion. DL-CGH consists of a central core collagen layer surrounded by an outer cover collagen layer. A droplet of collagen I solution (containing cells to be examined) naturally forms a small hemisphere on the bottom of the culture dish. After this central core layer gels, a second droplet is placed atop the first gel, encapsulating it completely. The hemisphere is submerged in the medium and cultured. The invasive activity of cells that infiltrate from the inner to the outer layer can be evaluated optically. Using this in vitro system, we measured the inhibitory effect of E-cadherin expression on cancer cell invasion. DL-CGH also allowed visualization of interactions between invading cancer cells and the stroma. Cancer cells, which lack the proteases required for direct entrance into the three-dimensional collagen matrix, were seen to slip like amoebas through matrix gaps generated by the pericellular proteolytic activity of fibroblasts. [Supplementary materials are available for this article. Go to the publisher's online edition of Cell Communication and Adhesion for the following free supplemental resources: Movies 1-3; 4a and b].     

Age-Associated Different Transcriptome Profiling in Zebrafish and Rats: an Insight into the Diversity of Vertebrate Aging

Marine Biotechnology - Most mammals, including humans, show obvious aging phenotypes, for example, loss of tissue plasticity and sarcopenia. In this regard, fish can be attractive models to study...     

Lake-wide assessment of microplastics in the surface waters of Lake Baikal,Siberia

Limnology - Small microplastic particles < 330 µm, sometimes called mini-microplastics (MMP), are far more abundant than those larger than 330 µm....     

Identification of assembly precursors to photosystems emitting fluorescence at 683 nm and 687 nm by cryogenic fluorescence microspectroscopy

Photosystem I (PSI) and photosystem II (PSII) play key roles in photoinduced electron-transfer reaction in oxygenic photosynthesis. Assemblies of these PSs can be initiated by illumination of the etiolated seedlings (greening). The study aimed to identify specific fluorescence spectral components relevant to PSI and PSII assembly intermediates emerging in greening seedlings of Zea mays, a typical C4 plant. The different PSII contents between the bundle sheath (BS) and mesophyll (M) cells were utilized to spectrally isolate the precursors to PSI and PSII. The greening Zea mays leaf thin sections were observed with the cryogenic microscope combined with a spectrometer. With the aid of the singular-value decomposition analysis, we could identify four independent fluorescent species, SAS677, SAS685, SAS683, and SAS687, named after their fluorescence peak wavelengths. SAS677 and SAS685 are the dominant components after the 30-minute greening, and the distributions of these components showed no clear differences between M and BS cells, indicating immature cell differentiation in this developing stage. On the other hand, the 1-hour greening resulted in reduced distributions of SAS683 in BS cells leading us to assign this species to PSII precursors. The 2-hour greening induced the enrichment of SAS687 in BS cells suggesting its PSI relevance. Similarity in the peak wavelengths of SAS683 and the reported reaction center of PSII implied their connection. SAS687 showed an intense sub-band at around 740 nm, which can be assigned to the emission from the red chlorophylls specific to the mature PSI.     

Redox-state dependent blinking of single photosystem I trimers at around liquid-nitrogen temperature

Efficient light harvesting in a photosynthetic antenna system is disturbed by a ragged and fluctuating energy landscape of the antenna pigments in response to the conformation dynamics of the protein. This situation is especially pronounced in Photosystem I (PSI) containing red shifted chlorophylls (red Chls) with the excitation energy much lower than the primary donor. The present study was conducted to clarify light-harvesting dynamics of PSI isolated from Synechocystis sp. PCC6803 by using single-molecule spectroscopy at liquid?nitrogen temperatures. Fluorescence emission at around 720?nm from the red Chls in single PSI trimers was monitored at 80–100?K. Intermittent variations in the emission intensities, so-called blinking, were frequently observed. Its time scale lay in several tens of seconds. The blinking amplitude depended on the redox state of the phylloquinone (A₁). Electrochromic shifts of Chls induced by the negative charge on A₁ were calculated based on the X-ray crystallographic structure. A Chl molecule, Chl-A839 (numbering according to PDB 5OY0), bound near A₁ was found to have a large electrochromic shift. This Chl has strong exciton coupling with neighboring Chl (A838) whose site energy was predicted to be determined by interaction with an arginine residue (ArgF84) [Adolphs et al., 2010]. A possible scenario of the blinking was proposed. Conformational fluctuations of ArgF84 seesaw the excitation-energy of Chl-A838, which perturbs the branching ratio of excitation-energy between the red Chl and the cationic form of P700 as a quencher. The electrochromic shift of Chl-A839 enhances the effect of the conformation dynamics of ArgF84.     

Circumnutational movement in rice coleoptiles involves the gravitropic response: analysis of an agravitropic mutant and space‐grown seedlings

Plants exhibit helical growth movements known as circumnutation in growing organs. Some studies indicate that circumnutation involves the gravitropic response, but this notion is a matter of debate. Here, using the agravitropic rice mutant lazy1 and space‐grown rice seedlings, we found that circumnutation was reduced or lost during agravitropic growth in coleoptiles. Coleoptiles of wild‐type rice exhibited circumnutation in the dark, with vigorous oscillatory movements during their growth. The gravitropic responses in lazy1 coleoptiles differed depending on the growth stage, with gravitropic responses detected during early growth and agravitropism during later growth. The nutation‐like movements observed in lazy1 coleoptiles at the early stage of growth were no longer detected with the disappearance of the gravitropic response. To verify the relationship between circumnutation and gravitropic responses in rice coleoptiles, we conducted spaceflight experiments in plants under microgravity conditions on the International Space Station. Wild‐type rice seeds were germinated, and the resulting seedlings were grown under microgravity or a centrifuge‐generated 1 g environment in space. We began filming the seedlings 2 days after seed imbibition and obtained images of seedling growth every 15 min. The seed germination rate in space was 92–100% under both microgravity and 1 g conditions. LED‐synchronized flashlight photography induced an attenuation of coleoptile growth and circumnutational movement due to cumulative light exposure. Nevertheless, wild‐type rice coleoptiles still showed circumnutational oscillations under 1 g but not microgravity conditions. These results support the idea that the gravitropic response is involved in plant circumnutation.     

Regio-selective preparation of vinyl adenosine ester catalyzed by alkaline protease

The transesterification of divinyladipate with adenosine in DMF containing 20% (v/v) DMSO was catalyzed by Streptomyces sp. alkaline protease and esterification occurred exclusively at the 3-position of hydroxyl group of ribofuranose in adenosine to give 3-O-vinyladipoyl adenosine without other products.