Monitoring Autophagy Flux and Activity: Principles and Applications

Macroautophagy is a major degradation mechanism of cell components via the lysosome. Macroautophagy greatly contributes to not only cell homeostasis but also the prevention of various diseases. Because macroautophagy proceeds through multi-step reactions, researchers often face a persistent question of how macroautophagic activity can be measured correctly. To make a straightforward determination of macroautophagic activity, diverse monitoring assays have been developed. Direct measurement of lysosome-dependent degradation of radioisotopically labeled cell proteins has long been applied. Meanwhile, indirect monitoring procedures have been developed. In these assays, autophagosome marker proteins, microtubule-associated proteins 1A/1B light chain 3B-II (LC3B-II) and gamma-aminobutyric acid receptor-associated protein-II (GABARAP-II) have been analyzed and the validity of the assays strongly depends on appropriate assessment of the fluctuation of LC3-II and/or GABARAP-II levels in the presence or absence of lysosomal inhibitors. This article describes these monitoring methods, paying special attention to the principles and characteristics of each procedure.     

Decrease in bacterial production over the past three decades in the north basin of Lake Biwa,Japan

Limnology - In Lake Biwa, the largest lake in Japan, external pollutant loads have decreased since the 1980s, leading to improved water quality, such as reduction in biochemical oxygen demand (BOD)...     

Invasive legume management strategies differentially impact mutualist abundance and benefit to native and invasive hosts

Determining the best management practices for plant invasions is a critical, but often elusive goal. Invasive removals frequently involve complex and poorly understood biotic interactions. For example, invasive species can leave potent legacies that influence the success of native species restoration efforts, and positive plant‐microbial feedbacks may promote continued reinvasion by an exotic species following restoration. Removal methods can vary in their effects on plant–soil feedbacks, with consequences for restoration of native species. We determined the effects of invasion by a leguminous shrub (French broom; Genista monspessulana) on the density and community composition of, and benefit conferred by, its microbial mutualists in its invading range. Densities of soil‐dwelling rhizobia were much higher in areas invaded by G. monspessulana relative to uninvaded areas, and this increased density of rhizobia fed back to increase seedling growth of both the invader and native legumes. We further compared how three techniques for removing G. monspessulana affected the densities of rhizobia relative to areas where G. monspessulana was still present. Removal by hand‐pulling reduced soil rhizobial densities, and reduced growth of one native legume, while having no effect on the growth of the invader. Overall, our results show that the consequences of restoration techniques, both above‐ and belowground, could be critical for the successful removal of an invasive legume and restoration of native species.     

Enhancing coral larval supply and seedling production using a special bundle collection system “coral larval cradle” for large‐scale coral restoration

Larval recruitment is essential for sustaining coral communities and a fundamental tool in some interventions for reef restoration. To improve larval supply and post‐settlement survival in sexually assisted coral restoration efforts, an integrated in situ collector system, the larval cradle, was designed to collect spawned gametes then culture the resulting larvae until settled on artificial substrates. The final design of the larval cradle was cylindrical, a nylon mesh structure with a volume of 9 m³, suspended in the sea and extending vertically toward the seabed. We found three key design features that improved the efficiency of the apparatus: (1) an open area of sea surface and mesh size of less than 100 μm produced high fertilization and optimal survival (>90%), (2) a special skirt‐shaped net (3 m in diameter) with a connection hose for attaching the cradle to collect bundles from many adult colonies over a wide area and at various depths, and (3) adding short square tube pieces, called square hollow sections, as a substrate for enhancing larval settlement and survival, to a larval cradle at 4 days after spawning was optimal for uniform settlement. This system allowed not only the collection of several million eggs, but also subsequent production of several thousand settled juvenile corals, without land facilities. Our design achieved several hundred times higher survival for early life stages of Acropora tenuis compared to nature.     

Proteomic Study to Understand Promotive Effects of Plant-Derived Smoke on Soybean (Glycine max L.) Root Growth Under Flooding Stress

Plant-derived smoke plays a key role in plant growth. Proteomic technique was used for underlying mechanisms of plant-derived smoke on the growth of soybean (Glycine max L.) under flooding stress. The length and weight of soybean root increased with 2000 parts per million plant-derived smoke under flooding stress within 4 days. Altered proteins by plant-derived smoke treatment under flooding stress were mainly related to protein metabolism, stress, and redox. Furthermore, proteins related to mitochondrial electron transport chain decreased by flooding stress; however, they increased by addition of plant-derived smoke under flooding stress. Based on the results of proteomic analysis, confirmation experiments were performed. ATPase abundance and ATP content increased with the treatment of plant-derived smoke under flooding stress. Furthermore, the ascorbate/glutathione cycle was activated with the treatment of plant-derived smoke under flooding stress. These results suggest that plant-derived smoke improves the root growth of soybean with energy production and reactive oxygen scavenging even if it is under flooding stress, which might positively regulate soybean tolerance towards flooding stress.

     

Dehydroepiandrosterone increased oxidative stress in a human cell line during differentiation

Dehydroepiandrosterone (DHEA), a reversible inhibitor of glucose-6-phosphate dehydrogenase (G6PD), is increasingly taken as an antioxidative and anti-ageing supplement. This study investigated the effects of DHEA on the expression of G6PD and on the state of oxidative stress in a human promyelocytic leukaemia cell line, HL60, during the differentiation to neutrophil-like cell. This study differentiated HL60 with dimethyl sulfoxide (DMSO) in the presence (DMSO-HL60/DHEA) or absence (DMSO-HL60) of DHEA. During the differentiation, activity, mRNA and protein levels of G6PD were increased. DHEA increased these levels further. DHEA by itself suppressed the production of superoxide from DMSO-HL60 upon stimulation with phorbol myristate acetate (PMA). However, DMSO-HL60/DHEA stimulated with PMA in the absence of DHEA produced superoxide and 8-oxo-deoxyguanosine more than PMA-stimulated DMSO-HL60. After addition of H₂O₂, the ratio of reduced glutathione to oxidized glutathione was lower in DMSO-HL60/DHEA than in DMSO-HL60. These findings indicate that DHEA acts both as an antioxidant and as a pro-oxidant.     

No ATG is an island—the connection of autophagy with diverse pathways and functions

The sixth International Symposium on Autophagy took place in October 2012 in Okinawa, Japan. It brought together scientists from all over the world to cultivate a better understanding of cutting‐edge autophagy research from molecular mechanisms to disease states.     

DGCR8‐mediated disruption of miRNA biogenesis induces cellular senescence in primary fibroblasts

The regulation of gene expression by microRNAs (miRNAs) is critical for normal development and physiology. Conversely, miRNA function is frequently impaired in cancer, and other pathologies, either by aberrant expression of individual miRNAs or dysregulation of miRNA synthesis. Here, we have investigated the impact of global disruption of miRNA biogenesis in primary fibroblasts of human or murine origin, through the knockdown of DGCR8, an essential mediator of the synthesis of canonical miRNAs. We find that the inactivation of DGCR8 in these cells results in a dramatic antiproliferative response, with the acquisition of a senescent phenotype. Senescence triggered by DGCR8 loss is accompanied by the upregulation of the cell‐cycle inhibitor p21CIP1. We further show that a subset of senescence‐associated miRNAs with the potential to target p21CIP1 is downregulated during DGCR8‐mediated senescence. Interestingly, the antiproliferative response to miRNA biogenesis disruption is retained in human tumor cells, irrespective of p53 status. In summary, our results show that defective synthesis of canonical microRNAs results in cell‐cycle arrest and cellular senescence in primary fibroblasts mediated by specific miRNAs, and thus identify global miRNA disruption as a novel senescence trigger.     

DNA-Binding Properties of the Antibody Specific for the Dewar Photoproduct of Thymidylyl-(3′′-5′′)-Thymidine

A monoclonal antibody (DEM-1) specific for the Dewar photoproduct is used for detection and quantification of photolesions in DNA. To help understand the molecular recognition of damaged DNA by the antibody protein, we have cloned and sequenced the variable region genes of DEM-1. We have also prepared Fab fragments of DEM-1 (DEM1Fab), and synthesized two kinds of 3′-biotinylated oligonucleotides of different lengths containing a central Dewar photoproduct of TpT to analyze the effects of the antigen size on the binding rates by means of surface plasmon resonance (SPR). Results obtained from SPR analyses suggest that DEM1Fab may recognize tetranucleotide unit as the epitope.