The ER-embedded UBE2J1/RNF26 ubiquitylation complex exerts spatiotemporal control over the endolysosomal pathway

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Streamlined particle quantification (SParQ) plug-in is an automated fluorescent vesicle quantification plug-in for particle quantification in Fiji/ImageJ

ABSTRACT

The endolysosomal system is critical for protein homeostasis in cells. A common way of studying protein transport and degradation (e.g. via autophagy) is by labeling vesicular structures such as endosomes, autophagosomes, lysosomes, or model substrates with fluorescent tags or by fluorescent antibody staining. Detailed analyses require quantification of hundreds of structures under various conditions. Typically, the images are analyzed individually with software such as the widely available Fiji/ImageJ (https://imagej.net/Fiji/Downloads), adjusting and thresholding each image and channel independently, which is a very labor intensive and fastidious task. To streamline the process, we developed a plug-in that, integrated into Fiji, enables the automated quantification of vesicular (i.e. punctate) structures. Importantly, the process still allows the operator to evaluate and have control over all the phases of quantification process.     

The negative regulator of β-lactamase induction AmpD is a N-acetyl-anhydromuramyl-L-alanine amidase

Abstract Construction of a malE-ampD gene fusion allowed purification of biologically active fusion protein by affinity chromatography. The cloned malE-ampD gene fusion complemented a chromosomal ampD mutation. Purified MalE-AmpD fusion protein was found to have murein amidase activity with a pronounced specificity for 1,6-anhydromuropeptides, the characteristic murein turnover products in Escherichia coli . Being a N-acetyl-anhydromuramyl-L-alanine amidase AmpD is likely to be involved in recycling of the turnover products. It is suggested that the negative regulatory effect of AmpD is due to the hydrolysis of anhydro-muropeptides which may function as signals for β-lactamase induction.     

Class IA PI3Ks regulate subcellular and functional dynamics of IDO1

Knowledge of a protein’s spatial dynamics at the subcellular level is key to understanding its function(s), interactions, and associated intracellular events. Indoleamine 2,3‐dioxygenase 1 (IDO1) is a cytosolic enzyme that controls immune responses via tryptophan metabolism, mainly through its enzymic activity. When phosphorylated, however, IDO1 acts as a signaling molecule in plasmacytoid dendritic cells (pDCs), thus activating genomic effects, ultimately leading to long‐lasting immunosuppression. Whether the two activities—namely, the catalytic and signaling functions—are spatially segregated has been unclear. We found that, under conditions favoring signaling rather than catabolic events, IDO1 shifts from the cytosol to early endosomes. The event requires interaction with class IA phosphoinositide 3‐kinases (PI3Ks), which become activated, resulting in full expression of the immunoregulatory phenotype in vivo in pDCs as resulting from IDO1‐dependent signaling events. Thus, IDO1’s spatial dynamics meet the needs for short‐acting as well as durable mechanisms of immune suppression, both under acute and chronic inflammatory conditions. These data expand the theoretical basis for an IDO1‐centered therapy in inflammation and autoimmunity.     

Acid sensitive background potassium channels K2P3.1 and K2P9.1 undergo rapid dynamin-dependent endocytosis

Acid-sensitive, two-pore domain potassium channels, K_2P3.1 and K_2P9.1, are implicated in cardiac and nervous tissue responses to hormones, neurotransmitters and drugs. K_2P3.1 and K_2P9.1 leak potassium from the cell at rest and directly impact membrane potential. Hence altering channel number on the cell surface drives changes in cellular electrical properties. The rate of K_2P3.1 and K_2P9.1 delivery to and recovery from the plasma membrane determines both channel number at the cell surface and potassium leak from cells. This study examines the endocytosis of K_2P3.1 and K_2P9.1. Plasma membrane biotinylation was used to follow the fate of internalized GFP-tagged rat K_2P3.1 and K_2P9.1 transiently expressed in HeLa cells. Confocal fluorescence images were analyzed using Imaris software, which revealed that both channels are endocytosed by a dynamin-dependent mechanism and over the course of 60 min, move progressively toward the nucleus. Endogenous endocytosis of human K_2P3.1 and K_2P9.1 was examined in the lung carcinoma cell line, A549. Endogenous channels are endocytosed over a similar time-scale to the channels expressed transiently in HeLa cells. These findings both validate the use of recombinant systems and identify an endogenous model system in which K_2P3.1 and K_2P9.1 trafficking can be further studied.     

Implementing Individual Producer Responsibility for Waste Electrical and Electronic Equipment through Improved Financing

Under the European Union (EU) Waste Electrical and Electronics Equipment (WEEE) Directive, producers are responsible for financing the recycling of their products at end of life. A key intention of such extended producer responsibility (EPR) legislation is to provide economic incentives for producers to develop products that are easier to treat and recycle at end of life. Recent research has shown, however, that the implementation of EPR for WEEE has so far failed in this respect. Current WEEE systems calculate their prices according to simple mass‐based allocation of costs to producers, based on broad collection categories containing a mixture of different product types and brands. This article outlines two alternative approaches, which instead calculate charges for products sold by producers by classifying them according to their eventual end‐of‐life treatment requirements and cost. Worked examples indicate that these methods provide both effective and efficient frameworks for financing WEEE, potentially delivering financial incentives to producers substantial enough to affect their potential profitability and, as a likely consequence, the decisions relating to the design of their products. In particular they fulfill three important criteria required by the WEEE Directive: they can financially reward improved design, allocate costs of historic waste proportionately (on the basis of tonnes of new products sold), and provide sufficient financial guarantees against future waste costs and liabilities. They are also relatively practical for implementation because they are based solely on cost allocation and financing. Further research and investigation would be worthwhile to test and verify this approach using real‐world data and under various scenarios.     

Energy use efficiency of soil microorganisms: Driven by carbon recycling and reduction

Carbon use efficiency (CUE) is being intensively applied to quantify carbon (C) cycling processes from microbial cell to global scales. Energy use efficiency (EUE) is at least as important as the CUE because (i) microorganisms use organic C mainly as an energy source and not as elemental C per se, and (ii) microbial growth and maintenance are limited by energy, but not by C as a structural element. We conceptualize and review the importance of EUE by soil microorganisms and focus on (i) the energy content in organic compounds depending on the nominal oxidation state of carbon (NOSC), (ii) approaches to assess EUE, (iii) similarities and differences between CUE and EUE, and (iv) discuss mechanisms responsible for lower EUE compared to CUE. The energy content per C atom (enthalpy of combustion, the total energy stored in a compound) in organic compounds is very closely (R² = 0.98) positively related to NOSC and increases by 108 kJ mol⁻¹ C per one NOSC unit. For the first time we assessed the NOSC of microbial biomass in soil (−0.52) and calculated the corresponding energy content of −510 kJ mol⁻¹ C. We linked CUE and EUE considering the NOSC of microbial biomass and element compositions of substrates utilized by microorganisms. The mean microbial EUE (0.32–0.35) is 18% lower than CUE (0.41) using glucose as a substrate. This definitely indicates that microbial growth is limited by energy relative to C. Based on the comparison of a broad range of processes of C and energy utilization for cell growth and maintenance, as well as database of experimental CUE from various compounds, we clearly explained five mechanisms and main factors why EUE is lower than CUE. The two main mechanisms behind lower EUE versus CUE are: (i) microbial recycling: C can be microbially recycled, whereas energy is always utilized only once, and (ii) chemical reduction of organic and inorganic compounds: Energy is used for reduction, which is ongoing without C utilization.     

Application of Markov Chain Model to Calculate the Average Number of Times of Use of a Material in Society. An Allocation Methodology for Open-Loop Recycling. Part 2: Case Study for Steel (6 pp)

- Preamble. In this series of two papers, a methodology to calculate the average number of times a material is used in a society from cradle to grave is presented and applied to allocation of environmental impact of virgin material. Part 1 focused on methodology development and showed how the methodology works with hypothetical examples of material flows. Part 2 presents case studies for steel recycling in Japan, in which the methodology is applied and allocation of environmental impact of virgin steel is conducted. - Abstract Goal, Scope and Background. The life cycle of steel begins with the mining of iron ore from the earth. Steel is produced in steel works and used in various products. Some of the steels are recycled at the products' end of life and used as a resource for the production of new steel in electric furnaces, while the remaining steel is used just once in products before being discarded (landfilled). In this paper, case studies were conducted to analyze the average number of times the element of iron is used and its residence time in society, in which the methodology developed in Part 1 of the paper was applied. CO2 emissions caused by steel productions and recycling were allocated by the number of times the element of steel is used in a society. Results and Discussion On the basis of the material flows of steel in Japan in 2000, it was calculated that at least 70% of the BF crude iron produced in Japan in 2000 was ultimately exported. On the assumption that steel is used in other countries in the same way as it is in Japan, the average number of times of use and the residence time of elemental iron in society are 2.67 and 62.9 years, respectively. Both of these values depend significantly on the recycling ratios of steel from construction and automobiles. Our model indicated that if the recycling ratio of steel from civil engineering and construction increased from 50% to 60%, the average number of times used would increase to 3.17 and the residence time of elemental iron in society would increase to 75.8 years. If CO2 emissions caused by steel productions and recycling are allocated by the number of times the element of steel is used in a society, it was calculated that steel use of one time generates in average an environmental burden of 1.03 t-CO2/t. Conclusion A method was developed to calculate the average number of times a material is used in a society from cradle to grave. Our methodology is based on Markov chain model using matrix-based numerical analysis, and has been successfully applied to steel. The results obtained by this methodology, i.e. the average number of times the element of iron is used in society, could be used for allocation of environmental burdens of virgin material as well as an indicator for assessing the state of material use in a certain year, based on material flow of material in that year. Recommendation and Perspective It is recognized that further researches must be conducted to gather data on steel production, use, and recovery in other countries and incorporate them into the transition probability matrix to obtain more precise results. Although this paper deals only with steel, this method can also be applied to other materials.     

Enhanced selective oxidation of trimethylolpropane to 2,2-bis(hydroxymethyl)butyric acid using Corynebacterium sp. ATCC 21245

2,2-Bis(hydroxymethyl)butyric acid (BHMB) is an important multifunctional chemical for the emerging bio-based polymer industry. It can be produced from trimethylolpropane (TMP) by selective oxidation using growing cells of Corynebacterium sp. ATCC 21245. However, this process is limited by the low volumetric productivity and low concentration of the final product. In the present study, we performed sequential batch operation with cell recycling in media containing glycerol, acetic acid, and increasing concentrations of yeast extract. This approach enhanced the conversion of 10 and 15 g/L TMP to 11.0 and 16.3 g/L BHMB at rates of 0.50 and 0.20 g/L^.h, respectively. Applying a cell bleeding strategy resulted in an overall 10-fold improvement in productivity. The consequently prolonged biocatalyst viability resulted in a quantitative conversion of 20 g/L TMP to 22.3 g/L BHMB and a yield of 1.10 g_BHMB/g_TMP (100% molar yield). This work facilitates further studies of the selective oxidation on other industrially important polyols.     

The Economic and Environmental Impact of Wastepaper Trade and Recycling in India

There have been increasing pressures by governments and nongovernmental organizations to restrict international trade in waste in the conviction that each nation has to take care of its own waste. We develop a sectoral flow model to investigate if free trade in nontoxic waste can support economic development and simultaneously reduce environmental degradation. The model is formulated as a nonlinear programming model with an objective function that minimizes environmental and economic costs. The model in principle describes the life cycle of Indian paper: Preliminary results suggest that trade in wastepaper is both economically and environmentally advantageous. The results also show that domestic and imported waste-paper are complementary and that import of wastepaper does not "crowd out" the domestic waste paper sector. This implies that the current trend of increasing trade of wastepaper does contribute to a more sustainable paper cycle in India.