A new cultivation method for microbial oil production: cell pelletization and lipid accumulation by Mucor circinelloides

The recent energy crisis has triggered significant attention on the microbial synthesis of lipids, which comprise the raw material for biodiesel production. Microbial oil accumulation with filamentous fungi has great potential because filamentous fungi can form pellets during cell growth, and these pellets are much easier to harvest from cell broth. This paper focuses on the cell pelletization process of the oleaginous Mucor circinelloides. We have studied the effect of various cultural conditions on pelletized cell growth and lipid accumulation. This study is the first to report that pH adjustment during cell growth plays a key role in pellet formation of M. circinelloides and describes a handy method by which to induce cell pelletization in submerged fungal cultivation. Our study reveals that cell growth and lipid production are not significantly affected by pelletization and that lipid accumulation is triggered at stressed conditions, such as a high carbon-to-nitrogen ratio and high temperature

First Arrival Time Auto-Picking Method Based on Multi-Time Windows Energy Ratio

First arrival time auto-picking technique plays an important role in seismic exploration. It is widely used in shallow layer tomography and static correction. Conventional method that based on sliding time windows energy ratio is not stable. Here a new method based on multi-time windows energy ratio is proposed. Combining with automatic quality control and phase-domain first arrival estimation technique, our method performs perfectly on seismic records of normal S/N ratio. In the computational process of conventional sliding time windows energy ratio method, first arrivals are often determined by the maximum energy ratio of two adjacent sliding time windows. It is well known that for low S/N ratio data the conventional picking is not effective, and for high S/N ratio data weak reflections are hardly detected. The reason is that first arrival time does not correspond to the maximum energy ratio. Meanwhile conventional method sometime picks local secondary extreme of energy ratio. The new method of multi-time windows energy ratio method takes both maximum and local secondary extreme in consideration. Hence new method promotes the stability and accuracy of first arrival picking. Combined with automatic quality control and phase-domain first arrival estimation, the new method performs well in its application in the middle part of Dzungarian Basin(Northwest China)

MetaboAnalystR 3.0: Toward an Optimized Workflow for Global Metabolomics.

Liquid chromatography coupled to high-resolution mass spectrometry platforms are increasingly employed to comprehensively measure metabolome changes in systems biology and complex diseases. Over the past decade, several powerful computational pipelines have been developed for spectral processing, annotation, and analysis. However, significant obstacles remain with regard to parameter settings, computational efficiencies, batch effects, and functional interpretations. Here, we introduce MetaboAnalystR 3.0, a significantly improved pipeline with three key new features: (1) efficient parameter optimization for peak picking; (2) automated batch effect correction; and 3) more accurate pathway activity prediction. Our benchmark studies showed that this workflow was 20~100X faster compared to other well-established workflows and produced more biologically meaningful results. In summary, MetaboAnalystR 3.0 offers an efficient pipeline to support high-throughput global metabolomics in the open-source R environment

A thermodynamics coupled modeling approach for analysis and improvement of high-speed motorized spindle system

The performance of high-speed motorized spindle system is greatly affected by spindle’s thermal and dynamic behavior. So, it is very important to predict these properties in design stage of spindle system. However, the thermal and dynamic behaviour reacts upon each other for the high rotational speed and complex structure of the spindle system. To control and optimize the dynamic behaviour and the temperature rise of spindle, this paper developed a dynamic and thermal coupled model of the spindle system by using the finite element method (FEM). The shaft and rotor were modeled as Timoshenko’s beam, the rational interference fit between shaft and rotor was treated as mass-spring combinations, the bearings were modeled as nonlinear spring element. The thermal analysis procedure contained the calculation of heat generation and confirmation of boundary condition. The accuracy of this coupled model was validated by corresponding experiments. With this coupled model, the thermal and dynamic performance of the spindle system was studied. The effects of rotational speed, axial preload and material of bearing and the diameter of shaft on thermal and dynamic behavior were analyzed. The spindle system was optimized with the result of analyses above. After optimization, the temperature rise of spindle system falls significantly to 24.5°C, which was 30.2°C before, while the dynamic stiffness at working speed increases from 156 to 197 N/μm

MetaboMiner – semi-automated identification of metabolites from 2D NMR spectra of complex biofluids

<p>Abstract</p> <p>Background</p> <p>One-dimensional (1D) ¹H nuclear magnetic resonance (NMR) spectroscopy is widely used in metabolomic studies involving biofluids and tissue extracts. There are several software packages that support compound identification and quantification via 1D ¹H NMR by spectral fitting techniques. Because 1D ¹H NMR spectra are characterized by extensive peak overlap or spectral congestion, two-dimensional (2D) NMR, with its increased spectral resolution, could potentially improve and even automate compound identification or quantification. However, the lack of dedicated software for this purpose significantly restricts the application of 2D NMR methods to most metabolomic studies.</p> <p>Results</p> <p>We describe a standalone graphics software tool, called MetaboMiner, which can be used to automatically or semi-automatically identify metabolites in complex biofluids from 2D NMR spectra. MetaboMiner is able to handle both ¹H-¹H total correlation spectroscopy (TOCSY) and ¹H-¹³C heteronuclear single quantum correlation (HSQC) data. It identifies compounds by comparing 2D spectral patterns in the NMR spectrum of the biofluid mixture with specially constructed libraries containing reference spectra of ~500 pure compounds. Tests using a variety of synthetic and real spectra of compound mixtures showed that MetaboMiner is able to identify >80% of detectable metabolites from good quality NMR spectra.</p> <p>Conclusion</p> <p>MetaboMiner is a freely available, easy-to-use, NMR-based metabolomics tool that facilitates automatic peak processing, rapid compound identification, and facile spectrum annotation from either 2D TOCSY or HSQC spectra. Using comprehensive reference libraries coupled with robust algorithms for peak matching and compound identification, the program greatly simplifies the process of metabolite identification in complex 2D NMR spectra.</p

Metabolomic analysis of cold acclimation of arctic mesorhizobium sp. strain N33

Arctic Mesorhizobium sp. N33 isolated from nodules of Oxytropis arctobia in Canada’s eastern Arctic has a growth temperature range from 0°C to 30°C and is a well-known cold-adapted rhizobia. The key molecular mechanisms underlying cold adaptation in Arctic rhizobia remains totally unknown. Since the concentration and contents of metabolites are closely related to stress adaptation, we applied GC-MS and NMR to identify and quantify fatty acids and water soluble compounds possibly related to low temperature acclimation in strain N33. Bacterial cells were grown at three different growing temperatures (4°C, 10°C and 21°C). Cells from 21°C were also cold-exposed to 4°C for different times (2, 4, 8, 60 and 240 minutes). We identified that poly-unsaturated linoleic acids 18∶2 (9, 12) & 18∶2 (6, 9) were more abundant in cells growing at 4 or 10°C, than in cells cultivated at 21°C. The mono-unsaturated phospho/neutral fatty acids myristoleic acid 14∶1(11) were the most significantly overexpressed (45-fold) after 1hour of exposure to 4°C. As reported in the literature, these fatty acids play important roles in cold adaptability by supplying cell membrane fluidity, and by providing energy to cells. Analysis of water-soluble compounds revealed that isobutyrate, sarcosine, threonine and valine were more accumulated during exposure to 4°C. These metabolites might play a role in conferring cold acclimation to strain N33 at 4°C, probably by acting as cryoprotectants. Isobutyrate was highly upregulated (19.4-fold) during growth at 4°C, thus suggesting that this compound is a precursor for the cold-regulated fatty acids modification to low temperature adaptation

c-Jun NH2-terminal kinase activation is essential for up-regulation of LC3 during ceramide-induced autophagy in human nasopharyngeal carcinoma cells

<p>Abstract</p> <p>Background</p> <p>Autophagy is a dynamic catabolic process characterized by the formation of double membrane vacuoles termed autophagosomes. LC3, a homologue of yeast Atg8, takes part in autophagosome formation, but the exact regulation mechanism of LC3 still needs to be elucidated.</p> <p>Methods</p> <p>Ceramide-induced autophagy was determined by detecting LC3 expression with Western blotting and confocal microscopy in human nasopharyngeal carcinoma cell lines CNE2 and SUNE1. The activation of JNK pathway was assessed by Western blotting for phospho-specific forms of JNK and c-Jun. The JNK activity specific inhibitor, SP600125, and siRNA directed against JNK were used to block JNK/c-Jun pathway. ChIP and luciferase reporter analysis were applied to determine whether c-Jun was involved in the regulation of LC3 transcription.</p> <p>Results</p> <p>Ceramide-treated cells exhibited the characteristics of autophagy and JNK pathway activation. Inhibition of JNK pathway could block the ceramide-induced autophagy and the up-regulation of LC3 expression. Transcription factor c-Jun was involved in LC3 transcription regulation in response to ceramide treatment.</p> <p>Conclusions</p> <p>Ceramide could induce autophagy in human nasopharyngeal carcinoma cells, and activation of JNK pathway was involved in ceramide-induced autophagy and LC3 expression.</p