Distinct pools of non-glycolytic substrates differentiate brain regions and prime region-specific responses of mitochondria

Many hereditary diseases are characterized by region-specific toxicity, despite the fact that disease-linked proteins are generally ubiquitously expressed. The underlying basis of the region-specific vulnerability remains enigmatic. Here, we evaluate the fundamental features of mitochondrial and glucose metabolism in synaptosomes from four brain regions in basal and stressed states. Although the brain has an absolute need for glucose in vivo, we find that synaptosomes prefer to respire on non-glycolytic substrates, even when glucose is present. Moreover, glucose is metabolized differently in each brain region, resulting in region-specific “signature” pools of non-glycolytic substrates. The use of non-glycolytic resources increases and dominates during energy crisis, and triggers a marked region-specific metabolic response. We envision that disease-linked proteins confer stress on all relevant brain cells, but region-specific susceptibility stems from metabolism of non-glycolytic substrates, which limits how and to what extent neurons respond to the stress.

LipidBlast in silico tandem mass spectrometry database for lipid identification

Current tandem mass spectral libraries for lipid annotations in metabolomics are limited in size and diversity. We provide a freely available computer generated in-silico tandem mass spectral library of 212,516 MS/MS spectra covering 119,200 compounds from 26 lipid compound classes, including phospholipids, glycerolipids, bacterial lipoglycans and plant glycolipids. Platform independence is shown by using tandem mass spectra from 40 different mass spectrometer types including low-resolution and high-resolution instruments.

Optimal formation of genetically modified and functional pancreatic islet spheroids by using hanging-drop strategy

BACKGROUND

Rejection and hypoxia are important factors causing islet loss at an early stage after pancreatic islet transplantation. Recently, islets have been dissociated into single cells for reaggregation into so-called islet spheroids. Herein, we used a hanging-drop strategy to form islet spheroids to achieve functional equivalence to intact islets.

METHODS

To obtain single islet cells, we dissociated islets with trypsin-EDTA digestion for 10 minutes. To obtain spheroids, we dropped various numbers of single cells (125, 250, or 500 cells/30 μL drop) onto a Petri dish, that was inverted for incubation in humidified air containing 5% CO(2) at 37 °C for 7 days. The aggregated spheroids in the droplets were harvested for further culture.

RESULTS

The size of the aggregated islet spheroids depended on the number of single cells (125-500 cells/30 μL droplet). Their morphology was similar to that of intact islets without any cellular damage. When treated with various concentrations of glucose to evaluate responsiveness, their glucose-mediated stimulation index value was similar to that of intact islets, an observation that was attributed to strong cell-to-cell interactions in islet spheroids. However, islet spheroids aggregated in general culture dishes showed abnormal glucose responsiveness owing to weak cell-to-cell interactions. Cell-to-cell interactions in islet spheroids were confirmed with an anti-connexin-36 monoclonal antibody. Finally, nonviral poly(ethylene imine)-mediated interleukin-10 cytokine gene delivered beforehand into dissociated single cells before formation of islet spheroids increased the gene transfection efficacy and interleukin-10 secretion from islet spheroids >4-fold compared with intact islets.

CONCLUSION

These results demonstrated the potential application of genetically modified, functional islet spheroids with of controlled size and morphology using an hanging-drop technique.

Towards understanding region-specificity of triplet repeat diseases: coupled immunohistology and mass spectrometry imaging

Many trinucleotide repeat disorders exhibit region-specific toxicity within tissues, the basis of which cannot be explained by traditional methods. For example, in Huntington's Disease (HD), the toxic disease-causing protein is ubiquitously expressed. However, only the medium spiny neurons in the striatum are initially targeted for death. Many changes are likely to initiate in these cells at an intracellular and microstructural level long before there is a measureable phenotype, but why some regions of the brain are more susceptible to death is unknown. This chapter describes a method to detect functional changes among brain regions and cell types, and link them directly with region-specific physiology. Due to the neurodegeneration that accompanies many triplet repeat disorders, we focus on the brain, although the methods described in this chapter can be translated to other tissue types. We integrate immunohistology and traditional mass spectrometry with a novel mass spectrometry imaging technique, called nanostructure initiated mass spectrometry (NIMS). When used together, these tools offer unique insights into region-specific physiology of the brain, and a basis for understanding the region-specific toxicity associated with triplet repeat disorders.

Low-dose ionizing radiation-induced blood plasma metabolic response in a diverse genetic mouse population

Understanding the biological effects and biochemical mechanisms of low-dose ionizing radiation (LDIR) is important for setting exposure limits for the safe use of nuclear power and medical diagnostic procedures. Although several studies have highlighted the effects of ionizing radiation on metabolism, most studies have focused on uniform genetic mouse populations. Here, we report the metabolic response to LDIR (10 cGy X ray) on a genetically diverse mouse population (142 mice) generated from a cross of radiation-sensitive (BALB/c) and radiation-resistant (SPRET/EiJ) parental strains. GC-TOF profiling of plasma metabolites was used to compare exposed vs. sham animals. From this, 16 metabolites were significantly altered in the LDIR treated vs. sham group. Use of two significantly altered metabolites, thymine and 2-monostearin, was found to effectively segregate the two treatments. Multivariate statistical analysis was used to identify genetic polymorphisms correlated with metabolite abundance (e.g., amino acids, fatty acids, nucleotides and TCA cycle intermediates). Genetic analysis of metabolic phenotypes showed suggestive linkages for fatty acid and amino acid metabolism. However, metabolite abundance was found to be a function of low-dose ionizing radiation exposure, and not of the underlying genetic variation.

The contributions of MRI-based measures of gray matter, white matter hyperintensity, and white matter integrity to late-life cognition

BACKGROUND AND PURPOSE

GM volume, WMH volume, and FA are each associated with cognition; however, few studies have detected whether these 3 different types of MR imaging measurements exert independent or additive effects on cognitive performance. To detect their extent of contribution to cognitive performance, we explored the independent and additive contributions of GM atrophy, white matter injury, and white matter integrity to cognition in elderly patients.

MATERIALS AND METHODS

Two hundred and 9 elderly patients participated in the study: 97 were CN adults, 65 had MCI, and 47 had dementia. We measured GM on T1-weighted MR imaging, WMH on FLAIR, and FA on DTI, along with psychometrically matched measures of 4 domains of cognitive performance, including semantic memory, episodic memory, executive function, and spatial abilities.

RESULTS

As expected, patients with dementia performed significantly more poorly in all 4 cognitive domains, whereas patients with MCI performed generally less poorly than dementia patients, though considerable overlap in performance was present across groups. GM, FA, and WMH each differed significantly between diagnostic groups and were associated with cognitive measures. In multivariate models that included all 3 MR imaging measures (GM, WMH, and FA), GM volume was the strongest determinant of cognitive performance.

CONCLUSIONS

These results strongly suggest that MR imaging measures of GM are more closely associated with cognitive function than WM measures across a broad range of cognitive and functional impairment.

White matter tract abnormalities in first-episode psychosis

Fibers connecting fronto-temporal and fronto-medial structures that pass through the anterior limb of the internal capsule (ALIC) subserve executive and psychomotor functioning. Both of these functions are adversely affected in schizophrenia, and may be abnormal at illness onset. In a study of first-episode psychosis, we used diffusion tensor imaging (DTI) and cognitive testing to examine ALIC integrity. Fourteen early psychosis patients and 29 healthy volunteers were included. Symptoms were assessed with the Positive and Negative Syndromes Scale (PANSS). All structural and diffusion scans were acquired on a GE Signa 1.5T scanner. A T1-weighted 3D FSPGR Inversion Recovery imaging series was acquired for manual seeding in structural space. Diffusion tensor imaging (DTI) was performed, and all DTI images were co-registered to structural space. Seeds were manually drawn bilaterally on the coronal plane at a specified location. Diffusion images were post-processed for subsequent Tract-based Spatial Statistics (TBSS) analysis. First-episode psychosis patients had significantly smaller fronto-medial and fronto-temporal AIC tract volumes compared to healthy volunteers on the left and the right (p-values<0.04). No differences in mean fractional anisotropy (FA) were seen within either left or right tracts (p-values>0.05), nor did TBSS reveal any other differences in FA values between groups in other regions. Relationships between tract volumes and symptom severity were not observed in this study.

17α-hydroxlyase/17, 20-lyase deficiency in three siblings with primary amenorrhea and absence of secondary sexual development

BACKGROUND

17α-hydroxlyase/17, 20-lyase deficiency (17OHD) is a rare phenotype of congenital adrenal hyperplasia that can cause primary amenorrhea.

CASE

Three phenotypically female siblings visited the adolescent gynecologic clinic complaining of primary amenorrhea and absence of secondary sexual developments. All had constant high blood pressure and showed a hypergonadotropic hypogonadal state with high progesterone and low testosterone levels. Two were genotypically females and one was genotypically a male; all were confirmed to have 17OHD, and estrogen replacement, glucocorticoids, and antihypertensive drugs were Prescribed to the patients.

SUMMARY AND CONCLUSION

Identifying a 17OHD patient complaining of primary amenorrhea in a gynecologic clinic is important for proper management.

Hormonal differences between female kidney transplant recipients and healthy women with the same gynecologic conditions

BACKGROUND

End-stage renal disease is associated with severe abnormalities in reproductive function. However, the abnormalities are reversed by successful kidney transplantation. The aim of the present study was to compare hormonal levels between recipients with successful kidney transplantations and healthy women with the same gynecologic conditions.

METHODS

The study group consisted of 31 women of reproductive age with end-stage renal disease who underwent successful kidney transplantation. The ratio of the control group, composed of healthy woman, to the study group was 3:1 matched for age and symptoms.

RESULTS

Abnormal bleeding (n = 14) and infertility were the most common gynecologic conditions in kidney transplant recipients. The levels of estrogen (E2) and follicle-stimulating hormone (FSH) in the study group were higher than in the control group, but the levels of progesterone (P4) and luteinizing hormone (LH) were lower in the study group than in the control group. There were no significant differences in prolactin and thyroid-stimulating hormone between the two groups. The incidence of infertility in patients who receive steroid was higher than those with no steroid use (P = .007).

CONCLUSIONS

Compared with healthy age- and symptom-matched women, female kidney transplant recipients have increased levels of E2 and FSH and decreased levels of P4 and LH. These differences in hormone profiles may predispose kidney transplant recipients to increased risk of gynecologic pathologies.

System response of metabolic networks in Chlamydomonas reinhardtii to total available ammonium

Drastic alterations in macronutrients are known to cause large changes in biochemistry and gene expression in the photosynthetic alga Chlamydomonas reinhardtii. However, metabolomic and proteomic responses to subtle reductions in macronutrients have not yet been studied. When ammonium levels were reduced by 25-100% compared with control cultures, ammonium uptake and growth rates were not affected at 25% or 50% nitrogen-reduction for 28 h. However, primary metabolism and enzyme expression showed remarkable changes at acute conditions (4 h and 10 h after ammonium reduction) compared with chronic conditions (18 h and 28 h time points). Responses of 145 identified metabolites were quantified using gas chromatography-time of flight mass spectrometry; 495 proteins (including 187 enzymes) were monitored using liquid chromatography-ion trap mass spectrometry with label-free spectral counting. Stress response and carbon assimilation processes (Calvin cycle, acetate uptake and chlorophyll biosynthesis) were altered first, in addition to increase in enzyme contents for lipid biosynthesis and accumulation of short chain free fatty acids. Nitrogen/carbon balance metabolism was found changed only under chronic conditions, for example in the citric acid cycle and amino acid metabolism. Metabolism in Chlamydomonas readily responds to total available media nitrogen with temporal increases in short-chain free fatty acids and turnover of internal proteins, long before nitrogen resources are depleted.

Radiological response predicts survival following transarterial chemoembolisation in patients with unresectable hepatocellular carcinoma

BACKGROUND

It remains unclear whether initial compact lipiodol uptake after transarterial chemoembolisation (TACE) is associated with improved survival in patients with hepatocellular carcinoma (HCC).

AIM

To reveal the clinical relevance of compact lipiodolisation after TACE.

METHODS

We studied 490 patients with unresectable HCC who had first been treated with TACE. Compact lipiodolisation was defined as the absence of an arterial enhancing lesion, reflecting complete lipiodol uptake, as assessed by dynamic computed tomography (CT) 1 month after treatment. The rate of initial compact lipiodolisation was analysed according to multiplicity and size of tumour, and survival of patients who achieved compact lipiodolisation was compared to that of patients who did not.

RESULTS

Of the 490 patients, 409 (83.5%) were in Child-Pugh class A and 81 (16.5%) in class B. The rate of initial compact lipiodolisation in single HCCs was higher than that in multinodular HCCs (33.7% vs. 14.6%, P < 0.001). Among single HCCs, the rate of compact lipiodolisation in tumours ≤5, 5-10 and >10 cm was 46.6%, 13.6%, and 0% respectively. The 1-, 3- and 5-year survival rates of patients with compact uptake were 92.7%, 70.7% and 52.4% compared to 60.8%, 28.0% and 16.9% in patients with noncompact lipiodolisation. Multivariate analysis revealed that Child-Pugh class, alpha-fetoprotein level, tumour node metastasis stage, portal vein thrombosis and initial compact lipiodolisation were independent predictors of survival.

CONCLUSIONS

Initial compact lipiodol uptake after transarterial chemoembolisation is associated with improved survival in patients with unresectable hepatocellular carcinoma. Accordingly, initial complete lipiodolisation should be considered a relevant therapeutic target.

Pharmacogenetics meets metabolomics: discovery of tryptophan as a new endogenous OCT2 substrate related to metformin disposition

Genetic polymorphisms of the organic cation transporter 2 (OCT2), encoded by SLC22A2, have been investigated in association with metformin disposition. A functional decrease in transport function has been shown to be associated with the OCT2 variants. Using metabolomics, our study aims at a comprehensive monitoring of primary metabolite changes in order to understand biochemical alteration associated with OCT2 polymorphisms and discovery of potential endogenous metabolites related to the genetic variation of OCT2. Using GC-TOF MS based metabolite profiling, clear clustering of samples was observed in Partial Least Square Discriminant Analysis, showing that metabolic profiles were linked to the genetic variants of OCT2. Tryptophan and uridine presented the most significant alteration in SLC22A2-808TT homozygous and the SLC22A2-808G>T heterozygous variants relative to the reference. Particularly tryptophan showed gene-dose effects of transporter activity according to OCT2 genotypes and the greatest linear association with the pharmacokinetic parameters (Cl_renal, Cl_sec, Cl/F/kg, and Vd/F/kg) of metformin. An inhibition assay demonstrated the inhibitory effect of tryptophan on the uptake of 1-methyl-4-phenyl pyrinidium in a concentration dependent manner and subsequent uptake experiment revealed differential tryptophan-uptake rate in the oocytes expressing OCT2 reference and variant (808G>T). Our results collectively indicate tryptophan can serve as one of the endogenous substrate for the OCT2 as well as a biomarker candidate indicating the variability of the transport activity of OCT2.

Resolving brain regions using nanostructure initiator mass spectrometry imaging of phospholipids

In a variety of neurological diseases, pathological progression is cell type and region specific. Previous reports suggest that mass spectrometry imaging has the potential to differentiate between brain regions enriched in specific cell types. Here, we utilized a matrix-free surface mass spectrometry approach, nanostructure initiator mass spectrometry (NIMS), to show that spatial distributions of multiple lipids can be used as a 'fingerprint' to discriminate between neuronal- and glial- enriched brain regions. In addition, glial cells from different brain regions can be distinguished based on unique lipid profiles. NIMS images were generated from sagittal brain sections and were matched with immunostained serial sections to define glial cell enriched areas. Tandem mass spectrometry (LC-MS/MS QTOF) on whole brain extracts was used to identify 18 phospholipids. Multivariate statistical analysis (Nonnegative Matrix Factorization) enhanced differentiation of brain regions and cell populations compared to single ion imaging methods. This analysis resolved brain regions that are difficult to distinguish using conventional stains but are known to have distinct physiological functions. This method accurately distinguished the frontal (or somatomotor) and dorsal (or retrosplenial) regions of the cortex from each other and from the pons region.

Conserved features of cancer cells define their sensitivity to HAMLET-induced death; c-Myc and glycolysis

HAMLET is the first member of a new family of tumoricidal protein-lipid complexes that kill cancer cells broadly, while sparing healthy, differentiated cells. Many and diverse tumor cell types are sensitive to the lethal effect, suggesting that HAMLET identifies and activates conserved death pathways in cancer cells. Here, we investigated the molecular basis for the difference in sensitivity between cancer cells and healthy cells. Using a combination of small-hairpin RNA (shRNA) inhibition, proteomic and metabolomic technology, we identified the c-Myc oncogene as one essential determinant of HAMLET sensitivity. Increased c-Myc expression levels promoted sensitivity to HAMLET and shRNA knockdown of c-Myc suppressed the lethal response, suggesting that oncogenic transformation with c-Myc creates a HAMLET-sensitive phenotype. Furthermore, HAMLET sensitivity was modified by the glycolytic state of tumor cells. Glucose deprivation sensitized tumor cells to HAMLET-induced cell death and in the shRNA screen, hexokinase 1 (HK1), 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1 and hypoxia-inducible factor 1α modified HAMLET sensitivity. HK1 was shown to bind HAMLET in a protein array containing ∼8000 targets, and HK activity decreased within 15 min of HAMLET treatment, before morphological signs of tumor cell death. In parallel, HAMLET triggered rapid metabolic paralysis in carcinoma cells. Tumor cells were also shown to contain large amounts of oleic acid and its derivatives already after 15 min. The results identify HAMLET as a novel anti-cancer agent that kills tumor cells by exploiting unifying features of cancer cells such as oncogene addiction or the Warburg effect.

Percutaneous cryoablation of small hepatocellular carcinomas using a 17-gauge ultrathin probe

AIM

To evaluate the feasibility and safety of percutaneous cryoablation (PCA) of small hepatocellular carcinomas (HCCs) using a 17 G ultrathin cryoprobe.

MATERIALS AND METHODS

Twenty patients (male:female ratio14:6) with 20 HCCs, who were not surgical candidates, underwent ultrasound (US)-guided PCA for treatment of HCCs. Single HCCs less than 3cm in diameter were included in this study. Ablation was performed using a 17 G cryoprobe. The effectiveness was determined by the changes in alpha-foetoprotein level and degree of tumour necrosis on follow-up computed tomography (CT); complete response (100% necrosis), partial response (100%>necrosis≥30%), stable disease (any cases not qualifying for either partial response or progressive disease) and progressive disease (increase of at least 20% in diameter of viable tumour). Haemoglobin, white blood cell count (WBC), serum glutamic oxaloacetic transaminase (SGOT), serum glutamic pyruvic transaminase (SGPT), and total bilirubin were compared before and after the procedure, and the technical feasibility, complications, clinical outcomes and survival of each patient were also evaluated.

RESULTS

All procedures were technically successful. Each patient complained of negligible pain and there was no other procedure-related complication or mortality. The mean level of alpha-foetoprotein declined significantly from 53.2 to 20.4ng/ml 1 month after the procedure (p<0.05). At 1-month follow-up CT, there were 13 complete responses, four partial responses, three patients with stable disease, and no patients had progressive disease. Six of seven lesions that did not present with a complete response underwent further treatment. On long-term follow up (6-30 months; mean 20.7), a local recurrence was seen in one of 13 lesions (8%) with complete response revealed. Laboratory findings showed no significant changes except for the transient increase of SGOT and SGPT.

CONCLUSION

US-guided PCA using a 17 G cryoprobe was feasible and safe for the treatment of HCC smaller than 3cm.

Mass spectrometry-based metabolomics, analysis of metabolite-protein interactions, and imaging

Our understanding of biology has been greatly improved through recent developments in mass spectrometry, which is providing detailed information on protein and metabolite composition as well as protein-metabolite interactions. The high sensitivity and resolution of mass spectrometry achieved with liquid or gas chromatography allows for detection and quantification of hundreds to thousands of molecules in a single measurement. Where homogenization-based sample preparation and extraction methods result in a loss of spatial information, mass spectrometry imaging technologies provide the in situ distribution profiles of metabolites and proteins within tissues. Mass spectrometry-based analysis of metabolite abundance, protein-metabolite interactions, and spatial distribution of compounds facilitates the high-throughput screening of biochemical reactions, the reconstruction of metabolic networks, biomarker discovery, determination of tissue compositions, and functional annotation of both proteins and metabolites.

Evaluation of sampling and extraction methodologies for the global metabolic profiling of Saccharophagus degradans

Metabolomics is based on the unbiased and global analysis of metabolites of organisms at specific time points. Therefore, the nonselective and reproducible recovery of all existing metabolites while preventing their transformation is the ideal criterion for metabolome sample preparation. We evaluated currently used sampling methods and extraction solvents for global metabolic profiling of a gram-negative bacterium, Saccharophagus degradans, using gas chromatography-time-of-flight mass spectrometry (GC-TOF MS) with an emphasis on three steps: the sampling method, which consisted of cold methanol quenching or fast filtration; the subsequent washing step; and the extraction solvents. After cold methanol quenching with 70% (v/v) methanol at -70 degrees C, washing with 2.3% NaCl produced a serious loss of intracellular metabolites. In addition, when cold methanol quenching and fast filtration were compared, severe cell leakage caused by cold methanol quenching resulted in a significant loss of intracellular metabolites, which was confirmed by spectrometric analysis at 260 and 280 nm. Upon evaluation of extraction solvents such as pure methanol (MeOH), acetonitrile/water (50ACN; 1:1, v/v), acetonitrile/methanol/water mixture (AMW; 2:2:1), and water/isopropanol/methanol (WiPM; 2:2:5). AMW and WiPM were found to be superior extraction solvents for S. degradans based on the total peak intensities of the metabolites, the total number of metabolite peaks, and the reproducibility of recovered metabolite quantities; however, the metabolite profiles differed significantly between AMW and WiPM. This is the first evaluation of each step of sample preparation involved in global scale metabolic analysis by GC-TOF MS, which can be used as a model in the preparation of organism-specific samples for metabolome analysis.

Decompression and interspinous dynamic stabilization using the locker for lumbar canal stenosis associated with low-grade degenerative spondylolisthesis

BACKGROUND

Decompression and spinal fusion have been generally recommended for spinal stenosis associated with low-grade degenerative spondylolisthesis (DS), although this is still controversial. The purpose of the present study is to analyze the clinical and radiological outcomes of interspinous dynamic stabilization using the Locker (WINNOVA co, Seoul, Korea) for lumbar canal stenosis with grade I DS.

METHODS

The authors performed a retrospective review of 23 consecutive patients who underwent single level decompression and the Locker application for lumbar canal stenosis with grade I DS and were followed up for at least 2 years. Excluded were those with DS grade II or higher and DS combined with foraminal disc herniation/stenosis. The mean age of patients at the time of surgery was 62.1 years (range: 45-81 years).

RESULTS

There were no complications in the perioperative period. At a mean follow-up duration of 28.3 months (range: 24-32 months), visual analogue scale scores for back pain, leg pain, and Oswestry disability index had decreased significantly; from 4.6, 7.2, and 38.5% to 2.4, 2.6, and 15.3%, respectively. Clinical success was achieved in 87% of the patients. The mean percentage of slippage did not change significantly. The mean sagittal rotation angle significantly decreased from 9.7 to 6.5 degrees (p=0.01). One patient (4.3%) underwent secondary fusion surgery due to persistent pain.

CONCLUSIONS

Decompression and interspinous dynamic stabilization using the Locker yielded favorable clinical and radiological outcomes for lumbar canal stenosis with grade I DS and could be an alternative for spinal fusion. However, further long-term follow-up studies are necessary.

Hydrocarbon phenotyping of algal species using pyrolysis-gas chromatography mass spectrometry

BACKGROUND

Biofuels derived from algae biomass and algae lipids might reduce dependence on fossil fuels. Existing analytical techniques need to facilitate rapid characterization of algal species by phenotyping hydrocarbon-related constituents.

RESULTS

In this study, we compared the hydrocarbon rich algae Botryococcus braunii against the photoautotrophic model algae Chlamydomonas reinhardtii using pyrolysis-gas chromatography quadrupole mass spectrometry (pyGC-MS). Sequences of up to 48 dried samples can be analyzed using pyGC-MS in an automated manner without any sample preparation. Chromatograms of 30-min run times are sufficient to profile pyrolysis products from C8 to C40 carbon chain length. The freely available software tools AMDIS and SpectConnect enables straightforward data processing. In Botryococcus samples, we identified fatty acids, vitamins, sterols and fatty acid esters and several long chain hydrocarbons. The algae species C. reinhardtii, B. braunii race A and B. braunii race B were readily discriminated using their hydrocarbon phenotypes. Substructure annotation and spectral clustering yielded network graphs of similar components for visual overviews of abundant and minor constituents.

CONCLUSION

Pyrolysis-GC-MS facilitates large scale screening of hydrocarbon phenotypes for comparisons of strain differences in algae or impact of altered growth and nutrient conditions.

Global metabolic profiling of plant cell wall polysaccharide degradation by Saccharophagus degradans

Plant cell wall polysaccharides can be used as the main feedstock for the production of biofuels. Saccharophagus degradans 2-40 is considered to be a potent system for the production of sugars from plant biomass due to its high capability to degrade many complex polysaccharides. To understand the degradation metabolism of plant cell wall polysaccharides by S. degradans, the cell growth, enzyme activity profiles, and the metabolite profiles were analyzed by gas chromatography-time of flight mass spectrometry using different carbon sources including cellulose, xylan, glucose, and xylose. The specific activity of cellulase was only found to be significantly higher when cellulose was used as the sole carbon source, but the xylanase activity increased when xylan, xylose, or cellulose was used as the carbon source. In addition, principal component analysis of 98 identified metabolites in S. degradans revealed four distinct groups that differed based on the carbon source used. Furthermore, metabolite profiling showed that the use of cellulose or xylan as polysaccharides led to increased abundances of fatty acids, nucleotides and glucuronic acid compared to the use of glucose or xylose. Finally, intermediates in the pentose phosphate pathway seemed to be up-regulated on xylose or xylan when compared to those on glucose or cellulose. Such metabolic responses of S. degradans under plant cell wall polysaccharides imply that its metabolic system is transformed to more efficiently degrade polysaccharides and conserve energy. This study demonstrates that the gas chromatography-time of flight mass spectrometry-based global metabolomics are useful for understanding microbial metabolism and evaluating its fermentation characteristics.

FiehnLib: mass spectral and retention index libraries for metabolomics based on quadrupole and time-of-flight gas chromatography/mass spectrometry

At least two independent parameters are necessary for compound identification in metabolomics. We have compiled 2 212 electron impact mass spectra and retention indices for quadrupole and time-of-flight gas chromatography/mass spectrometry (GC/MS) for over 1000 primary metabolites below 550 Da, covering lipids, amino acids, fatty acids, amines, alcohols, sugars, amino-sugars, sugar alcohols, sugar acids, organic phosphates, hydroxyl acids, aromatics, purines, and sterols as methoximated and trimethylsilylated mass spectra under electron impact ionization. Compounds were selected from different metabolic pathway databases. The structural diversity of the libraries was found to be highly overlapping with metabolites represented in the BioMeta/KEGG pathway database using chemical fingerprints and calculations using Instant-JChem. In total, the FiehnLib libraries comprised 68% more compounds and twice as many spectra with higher spectral diversity than the public Golm Metabolite Database. A range of unique compounds are present in the FiehnLib libraries that are not comprised in the 4345 trimethylsilylated spectra of the commercial NIST05 mass spectral database. The libraries can be used in conjunction with GC/MS software but also support compound identification in the public BinBase metabolomic database that currently comprises 5598 unique mass spectra generated from 19,032 samples covering 279 studies of 47 species (plants, animals, and microorganisms).

FiehnLib: mass spectral and retention index libraries for metabolomics based on quadrupole and time-of-flight gas chromatography/mass spectrometry

At least two independent parameters are necessary for compound identification in metabolomics. We have compiled 2 212 electron impact mass spectra and retention indices for quadrupole and time-of-flight gas chromatography/mass spectrometry (GC/MS) for over 1000 primary metabolites below 550 Da, covering lipids, amino acids, fatty acids, amines, alcohols, sugars, amino-sugars, sugar alcohols, sugar acids, organic phosphates, hydroxyl acids, aromatics, purines, and sterols as methoximated and trimethylsilylated mass spectra under electron impact ionization. Compounds were selected from different metabolic pathway databases. The structural diversity of the libraries was found to be highly overlapping with metabolites represented in the BioMeta/KEGG pathway database using chemical fingerprints and calculations using Instant-JChem. In total, the FiehnLib libraries comprised 68% more compounds and twice as many spectra with higher spectral diversity than the public Golm Metabolite Database. A range of unique compounds are present in the FiehnLib libraries that are not comprised in the 4345 trimethylsilylated spectra of the commercial NIST05 mass spectral database. The libraries can be used in conjunction with GC/MS software but also support compound identification in the public BinBase metabolomic database that currently comprises 5598 unique mass spectra generated from 19,032 samples covering 279 studies of 47 species (plants, animals, and microorganisms).