Contribution of unvegetated tidal flats to coastal carbon flux

Unvegetated flats occupy a large area in the intertidal zone. However, compared to vegetated areas, the carbon sequestration of unvegetated tidal flats is rarely quantified, even though these areas are highly threatened by human development and climate change. We determined benthic maximum gross primary production (GPP_m), net primary production (NPP) and total respiration (TR) during emersion on seven tidal flats along a latitudinal gradient (from 22.48°N to 40.60°N) in winter and summer from 2012 to 2016 to assess the spatial and temporal variability of carbon dioxide flux. In winter, these processes decreased by 89%–104% towards higher latitudes. In summer, however, no clear trend was detected across the latitudinal gradient. Quadratic relationships between GPP_m, NPP and TR and sediment temperature can be described along the latitudinal gradient. These curves showed maximum values of GPP_m and NPP when the sediment temperatures reached 28.7 and 26.6°C respectively. TR increased almost linearly from 0 to 45°C. The maximum daily NPP across the latitudinal gradient averaged 0.24 ± 0.28 g C m^?2 day^?1, which was only 10%–20% of the global average of NPP of vegetated coastal habitats. Multiplying with the global area of unvegetated tidal flats, our results suggest that the contribution of NPP on unvegetated tidal flats to the coastal carbon cycle is small (11.04 ± 13.32 Tg C/year). If the land cover of vegetated habitats is continuously degraded to unvegetated tidal flats, the carbon sequestration capacity in the intertidal zone is expected to reduce by at least 13.10 Tg C/year, equivalent to 1% of global carbon emissions from land‐use change.     

The effects of metabolites from the indigenous Acidithiobacillus thiooxidans and temperature on the bioleaching of cadmium from soil

The effect of metabolites from the indigenous Acidithiobacillus thiooxidans and temperature on the bioleaching of cadmium from soil was investigated in the present study. Bioleaching was found to be more effective than chemical leaching of cadmium. The metabolite, mainly sulfuric acid, which was shown to be growth-associated in the exponential phase, plays a major role in bioleaching. The maximum amount of cadmium leached was obtained after 8 days of precultivation when cells were directly involved in the leaching process. It indicates that cells in the exponential growth phase exhibit higher activity toward bioleaching. In contrast, the maximum amount of cadmium leached and the maximum initial rate for bioleaching were reached after 16 days of precultivation when only metabolites were involved in the bioleaching process. It implies that higher sulfuric acid concentration results in higher leaching efficiency. In addition, higher temperature leads to higher leaching efficiency. The optimal operation condition for bioleaching was determined to be a two-stage process: The first stage involves the precultivation of the indigenous A. thiooxidans at 30 degrees C for 8 days followed by 20 minutes of centrifugation to discard cells. The second stage involves the bioleaching with the subsequent supernatant at 50 degrees C.     

Biosynthesis of protein products by animal cells. Are growth and non-growth associated concepts valid or useful?

The application of simple growth and non-growth associated concepts from microbial systems describing substrate uptake and production formation is considered unlikely to assist in the understanding of antibody formation and, hence, in maximising antibody yield. Such concepts have many significant limitations — notably, their strict application only to products of catabolic pathways and their inability to include metabolisms which either have multiple catabolic pathways (eg, fermentation and respiration in yeast and animal cells) or in which the major product of interest is predominantly anabolic in nature (eg. amino acid production in bacteria and antibody formation in animal cells). In addition, products which undergo an assembly and secretion process or a secretion process which allows intracellular pools of product to exist are also not well described by such simple relationships. In this work, inadequacies in the current approach to the study of the kinetics of growth of hybridoma cells and antibody production are described and the examples of growth ofSaccharomyces cerevisiae andCandida utilis, amino acid production by bacteria and antibody production by animal cells are used to illustrate these limitations. Having identified these limitations, suggestions are made as to how studies might be undertaken to assist our future understanding of the process of antibody manufacture and, subsequently, maximizing antibody yield. The process of characterising the metabolism of anabolic products is subject to detailed computer simulation of the pathways involved. It is argued that such approaches will assist us in understanding more fully the nature of biosynthetic products and how they integrate with the major energy producing pathways of the cell and the cell cycle. This will assist in maximising the yield of such products.     

PAPP‐A: a new anti‐aging target?

This article focuses on the role of PAPP‐A in mammalian aging. It introduces PAPP‐A and a little of its history, briefly discusses the function of PAPP‐A in the insulin‐like growth factor (IGF) system and the regulators of PAPP‐A expression, and then reviews data concerning PAPP‐A in aging and age‐related diseases especially in regard to the PAPP‐A knockout (KO) mouse. The PAPP‐A KO mouse is a valuable new model to test hypotheses concerning the control of the tissue availability of IGF, independent from systemic levels, on healthspan as well as lifespan.     

Development and characterization of a cell line for large-scale, serum-free production of recombinant adeno-associated viral vectors

BACKGROUND: One of the major limitations to the use of adeno-associated virus (AAV) vectors for gene therapy has been the difficulty in producing enough vector to supply a clinical trial. More than 20 000 roller bottles may be required to generate AAV by the traditional transient transfection process to treat 50 patients. A scalable AAV producer cell line grown in serum-free media will meet the needs for the manufacture of AAV gene therapeutics. METHODS: A packaging cell line was generated by introducing the AAV rep and cap genes into A549 cells. From this packaging cell line, a number of producer cell lines were generated by infecting the packaging cell with the appropriate AAV vector. Producer cell lines were then adapted to serum-free suspension conditions for growth in bioreactors. RESULTS: We report here the development of six AAV producer cell lines that generate > 10(4) particles/cell. The rAAV vector preparations from these cell lines have physical and functional characteristics similar to rAAV vectors prepared by transient transfection. To enable large-scale production, producer cell lines were adapted to serum-free suspension and we demonstrate production of AAV at the 15 L scale. In addition, vector preparations from these cell lines were shown to be free of wild-type AAV. CONCLUSIONS: AAV producer cell lines can be readily scaled to meet the needs of clinical trials. One 500 L bioreactor of these producer cells can produce the equivalent of 2500 high capacity roller bottles or 25 000 T-175 tissue culture flasks.     

Development of thermodynamic optimum searching (TOS) to improve the prediction accuracy of flux balance analysis

Flux balance analysis (FBA) has been widely used in calculating steady‐state flux distributions that provide important information for metabolic engineering. Several thermodynamics‐based methods, for example, quantitative assignment of reaction directionality and energy balance analysis have been developed to improve the prediction accuracy of FBA. However, these methods can only generate a thermodynamically feasible range, rather than the most thermodynamically favorable solution. We therefore developed a novel optimization method termed as thermodynamic optimum searching (TOS) to calculate the thermodynamically optimal solution, based on the second law of thermodynamics, the minimum magnitude of the Gibbs free energy change and the maximum entropy production principle (MEPP). Then, TOS was applied to five physiological conditions of Escherichia coli to evaluate its effectiveness. The resulting prediction accuracy was found significantly improved (10.7–48.5%) by comparing with the ¹³C‐fluxome data, indicating that TOS can be considered an advanced calculation and prediction tool in metabolic engineering. Biotechnol. Bioeng. 2013; 110: 914–923. © 2012 Wiley Periodicals, Inc.     

Scalable production of adeno-associated virus type 2 vectors via suspension transfection

Vectors derived from adeno-associated virus type 2 (AAV2) are promising gene delivery vehicles, but it is still challenging to get the large number of recombinant adeno-associated virus (rAAV) particles required for large animal and clinical studies. Current transfection technology requires adherent cultures of HEK 293 cells that can only be expanded by preparing multiple culture plates. A single large-scale suspension culture could replace these multiple culture preparations, but there is currently no effective co-transfection scheme for generating rAAV from cells in suspension culture. Here, we weaned HEK 293 cells to suspension culture using hydrogel-coated six-well culture plates and established an efficient transfection strategy suitable for these cells. Then the cultures were gradually scaled up. We used linear polyethylenimine (PEI) to mediate transfection and obtained high transfection efficiencies ranging from 54% to 99%, thereby allowing efficient generation of rAAV vectors. Up to 10(13) rAAV particles and, more importantly, up to 10(11) infectious particles were generated from a 2-L bioreactor culture. The suspension-transfection strategy of this study facilitates the homogeneous preparation of rAAV at a large scale, and holds further potential as the basis for establishing a manufacturing process in a larger bioreactor.     

SARI suppresses colitis‐associated cancer development by maintaining MCP‐1‐mediated tumour‐associated macrophage recruitment

SARI (suppressor of AP‐1, regulated by IFN) impaired tumour growth by promoting apoptosis and inhibiting cell proliferation and tumour angiogenesis in various cancers. However, the role of SARI in regulating tumour‐associated inflammation microenvironment is still elusive. In our study, the colitis‐dependent and ‐independent primary model were established in SARI deficiency mice and immuno‐reconstructive mice to investigate the functional role of SARI in regulating tumour‐associated inflammation microenvironment and primary colon cancer formation. The results have shown that SARI deficiency promotes colitis‐associated cancer (CAC) development only in the presence of colon inflammation. SARI inhibited tumour‐associated macrophages (TAM) infiltration in colon tissues, and SARI deficiency in bone marrow cells has no observed role in the promotion of intestinal tumorigenesis. Mechanism investigations indicated that SARI down‐regulates p‐STAT1 and STAT1 expression in colon cancer cells, following inhibition of MCP‐1/CCR2 axis activation during CAC development. Inverse correlations between SARI expression and macrophage infiltration, MCP‐1 expression and p‐STAT1 expression were also demonstrated in colon malignant tissues. Collectively, our results prove the inhibition role of SARI in colon cancer formation through regulating TAM infiltration.     

Benthic oxygen flux in the highly productive subarctic Lake Myvatn, Iceland: In situ benthic flux chamber study

In situ paired light and dark-stirred benthic flux chambers were used to estimate dissolved oxygen flux across the sediment–water interface in Lake Mývatn, Iceland. Three sampling stations were selected, each station reflecting a specific sedimentary environment, benthic communities, and water depth. During this study the phytoplankton density was low. Spatial and seasonal variations of bottom DO concentration and DO flux have been observed during this study. The oxygen consumption rate at all study sites had a mean of –89 (±44) mmol m^–2 d^–1 while the oxygen production rate due to benthic algae had a mean of 131 (±103) mmol m^–2 d^–1. There was a strong correlation (r=0.91) between oxygen consumption rate and temperature. This was presumably because of the temperature influence on rates of microbial and macrobenthic processes. The mean benthic primary production rate at all study sites was 1216 (±957) mg C m^–2 d^–1 between June 2000 and February 2001. Annual gross benthic primary production was estimated from the gross mean daily benthic DO production (P) and Redfield's C:O₂ ratio of 106:138 to be 420 g C m^–2 y^–1 at station HO, 250 g C m^–2 y^–1 at B2 and 340 g C m^–2 y^–1 at station 95. Thus, the mean gross benthic primary production was estimated as 1151 mg C m^–2 d^–1 at station HO, 685 mg C m^–2 d^–1 at station B2, and 932 mg C m^–2 d^–1 at station 95.     

Aurantiamide acetate suppresses the growth of malignant gliomas in vitro and in vivo by inhibiting autophagic flux

We aim to investigate the effect of aurantiamide acetate isolated from the aerial parts of Clematis terniflora DC against gliomas. Human malignant glioma U87 and U251 cells were incubated with different concentrations (0–100 μM) of aurantiamide acetate. Aurantiamide acetate greatly decreased the cell viability in a dose‐ and time‐dependent manner. It induced moderate mitochondrial fragmentation and the loss of mitochondrial membrane potential. No significant difference was found in the alternation of other intracellular organelles, although F‐actin structure was slightly disturbed. Apparent ultrastructure alternation with increased autophagosome and autolysosome accumulation was observed in aurantiamide acetate‐treated cells. The expression of LC3‐II was greatly up‐regulated in cells exposed to aurantiamide acetate (P < 0.05 compared with control). The cytoplasmic accumulation of autophagosomes and autolysosomes induced by aurantiamide acetate treatment was confirmed by fluorescent reporter protein labelling. Administration of chloroquine (CQ), which inhibits the fusion step of autophagosomes, further increased the accumulation of autophagosomes in the cytoplasm of U87 cells. Autophagy inhibition by 3‐methyladenine, Bafilomycin A1 or CQ had no influence on aurantiamide acetate‐induced cytotoxicity, whereas autophagy stimulator rapamycin significantly suppressed aurantiamide acetate‐induced cell death. The anti‐tumour effects of aurantiamide acetate were further evaluated in tumour‐bearing nude mice. Intratumoural injection of aurantiamide acetate obviously suppressed tumour growth, and increased number of autophagic vacuoles was observed in tumour tissues of animals receiving aurantiamide acetate. Our findings suggest that aurantiamide acetate may suppress the growth of malignant gliomas by blocking autophagic flux.     

Elucidating the role of copper in CHO cell energy metabolism using 13C metabolic flux analysis

¹³C‐metabolic flux analysis was used to understand copper deficiency‐related restructuring of energy metabolism, which leads to excessive lactate production in recombinant protein‐producing CHO cells. Stationary‐phase labeling experiments with U‐¹³C glucose were conducted on CHO cells grown under high and limiting copper in 3 L fed‐batch bioreactors. The resultant labeling patterns of soluble metabolites were measured by GC‐MS and used to estimate metabolic fluxes in the central carbon metabolism pathways using OpenFlux. Fluxes were evaluated 300 times from stoichiometrically feasible random guess values and their confidence intervals calculated by Monte Carlo simulations. Results from metabolic flux analysis exhibited significant carbon redistribution throughout the metabolic network in cells under Cu deficiency. Specifically, glycolytic fluxes increased (25%–79% relative to glucose uptake) whereas fluxes through the TCA and pentose phosphate pathway (PPP) were lower (15%–23% and 74%, respectively) compared with the Cu‐containing condition. Furthermore, under Cu deficiency, 33% of the flux entering TCA via the pyruvate node was redirected to lactate and malate production. Based on these results, we hypothesize that Cu deficiency disrupts the electron transport chain causing ATP deficiency, redox imbalance, and oxidative stress, which in turn drive copper‐deficient CHO cells to produce energy via aerobic glycolysis, which is associated with excessive lactate production, rather than the more efficient route of oxidative phosphorylation. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:1179–1186, 2015     

Longevity is not influenced by prenatal programming of body size

Insulin‐like growth factor (IGF) signaling is essential for achieving optimal body size during fetal development, whereas, in the adult, IGFs are associated with aging and age‐related diseases. However, it is unclear as to what extent lifespan is influenced by events that occur during development. Here, we provide direct evidence that the exceptional longevity of mice with altered IGF signaling is not linked to prenatal programming of body size. Mice null for pregnancy‐associated plasma protein‐A (PAPP‐A), an IGF‐binding protein proteinase that increases local IGF bioavailability, are 60–70% the size of their wild‐type littermates at birth and have extended median and maximum lifespan of 30–40%. In this study, PAPP‐A^?/? mice whose body size was normalized during fetal development through disruption of IgfII imprinting did not lose their longevity advantage. Adult‐specific moderation of IGF signaling through PAPP‐A inhibition may present a unique opportunity to improve lifespan without affecting important aspects of early life physiology.     

The effects of cell density and metabolite flux on cellular dynamics

Summary Density-dependent regulation of cell growth in tissue culture is a well-known phenomenon but the mechanism of regulation remains obscure. Here we explore the effects of cell density and metabolite flux on the collective dynamics of a cell population. The intracellular dynamics are modelled by positive feedback kinetic mechanisms of the kind known to apply to yeast cells. Several experimental observations related to glycolytic oscillations are predicted and it is suggested that the general conclusions may be applicable in a broader context.