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1.
Background
Proteins play fundamental and crucial roles in nearly all biological processes, such as, enzymatic catalysis, signaling transduction, DNA and RNA synthesis, and embryonic development. It has been a long-standing goal in molecular biology to predict the tertiary structure of a protein from its primary amino acid sequence. From visual comparison, it was found that a 2D triangular lattice model can give a better structure modeling and prediction for proteins with short primary amino acid sequences.Methods
This paper proposes a hybrid of hill-climbing and genetic algorithm (HHGA) based on elite-based reproduction strategy for protein structure prediction on the 2D triangular lattice.Results
The simulation results show that the proposed HHGA can successfully deal with the protein structure prediction problems. Specifically, HHGA significantly outperforms conventional genetic algorithms and is comparable to the state-of-the-art method in terms of free energy.Conclusions
Thanks to the enhancement of local search on the global search, the proposed HHGA achieves promising results on the 2D triangular protein structure prediction problem. The satisfactory simulation results demonstrate the effectiveness of the proposed HHGA and the utility of the 2D triangular lattice model for protein structure prediction.2.
Li Li Chang-Sheng Wu Guan-Mei Hou Ming-Zhe Dong Zhen-Bo Wang Yi Hou Heide Schatten Gui-Rong Zhang Qing-Yuan Sun 《Reproductive biology and endocrinology : RB&E》2018,16(1):110
Background
Diabetes induces many complications including reduced fertility and low oocyte quality, but whether it causes increased mtDNA mutations is unknown.Methods
We generated a T2D mouse model by using high-fat-diet (HFD) and Streptozotocin (STZ) injection. We examined mtDNA mutations in oocytes of diabetic mice by high-throughput sequencing techniques.Results
T2D mice showed glucose intolerance, insulin resistance, low fecundity compared to the control group. T2D oocytes showed increased mtDNA mutation sites and mutation numbers compared to the control counterparts. mtDNA mutation examination in F1 mice showed that the mitochondrial bottleneck could eliminate mtDNA mutations.Conclusions
T2D mice have increased mtDNA mutation sites and mtDNA mutation numbers in oocytes compared to the counterparts, while these adverse effects can be eliminated by the bottleneck effect in their offspring. This is the first study using a small number of oocytes to examine mtDNA mutations in diabetic mothers and offspring.3.
Lia Bally Cédric Bovet Christos T. Nakas Thomas Zueger Jean-Christophe Prost Jean-Marc Nuoffer Alexander B. Leichtle Georg Martin Fiedler Christoph Stettler 《Metabolomics : Official journal of the Metabolomic Society》2017,13(7):78
Introduction
Exercise-associated metabolism in type 1 diabetes (T1D) remains under-studied due to the complex interplay between exogenous insulin, counter-regulatory hormones and insulin-sensitivity.Objective
To identify the metabolic differences induced by two exercise modalities in T1D using ultra high-performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC–HRMS) based metabolomics.Methods
Twelve T1D adults performed intermittent high-intensity (IHE) and continuous-moderate-intensity (CONT) exercise. Serum samples were analysed by UHPLC–HRMS.Results
Metabolic profiling of IHE and CONT highlighted exercise-induced changes in purine and acylcarnitine metabolism.Conclusion
IHE may increase beta-oxidation through higher ATP-turnover. UHPLC–HRMS based metabolomics as a data-driven approach without an a priori hypothesis may help uncover distinctive metabolic effects during exercise in T1D.Clinical trial registration number is www.clinicaltrials.gov: NCT02068638.4.
Philipp Werner Ernst Meiss Ludger Scheja Joerg Heeren Markus Fischer 《Metabolomics : Official journal of the Metabolomic Society》2017,13(4):44
Introduction
The metabolic alterations accompanying the development of insulin resistance and type 2 diabetes mellitus (T2DM) are complex, not coherently understood and only partially represented by conventional clinical tests like the oral glucose tolerance test. Changes in plasma metabolite concentrations preceding insulin resistance or overt T2DM may help understand the etiology of metabolic disorders and they are potential predictive risk markers.Objectives
Here, we describe a non-targeted metabolomics platform based on UPLC-UHR-QToF-MS(/MS) for the assessment of plasma non-polar metabolites.Methods
This method was applied to a longitudinal mouse obesity study comparing mice on control and high fat diet (HFD), respectively. Plasma metabolites were assessed 2, 4, 8 and 16 weeks after initiation of feeding. Multivariate analysis of the metabolite dataset showed clear differentiation of the feeding groups after 8 weeks when the HFD-fed mice exhibited clear signs of insulin resistance.Results
The discrimination of the groups was due to changes in various metabolic pathways including, among others, glycerophospholipid, sphingolipid and cholesterol metabolism.Conclusion
From 81 compounds with a p-value lower than 0.05, a total of 19 metabolites could be putatively identified due to their accurate mass, isotope and fragmentation pattern. Thirteen of these observed metabolites are known key metabolites to diabetes or its secondary diseases like diabetic nephropathy and neuropathy (Meiss, Werner, John, Scheja, Herbach, Heeren, Fischer 2015). The compounds putatively identified here may provide valuable starting points for further investigations and developments of clinical diagnostics and prediagnostics for T2DM and related diseases.5.
Amro Ilaiwy Miao Liu Traci L. Parry James R. Bain Christopher B. Newgard Jonathan C. Schisler Michael J. Muehlbauer Florin Despa Monte S. Willis 《Metabolomics : Official journal of the Metabolomic Society》2016,12(5):95
Introduction
Chronic hypersecretion of the 37 amino acid amylin is common in type 2 diabetics (T2D). Recent studies implicate human amylin aggregates cause proteotoxicity (cell death induced by misfolded proteins) in both the brain and the heart.Objectives
Identify systemic mechanisms/markers by which human amylin associated with cardiac and brain defects might be identified.Methods
We investigated the metabolic consequences of amyloidogenic and cytotoxic amylin oligomers in heart, brain, liver, and plasma using non-targeted metabolomics analysis in a rat model expressing pancreatic human amylin (HIP model).Results
Four metabolites were significantly different in three or more of the four compartments (heart, brain, liver, and plasma) in HIP rats. When compared to a T2D rat model, HIP hearts uniquely had significant DECREASES in five amino acids (lysine, alanine, tyrosine, phenylalanine, serine), with phenylalanine decreased across all four tissues investigated, including plasma. In contrast, significantly INCREASED circulating phenylalanine is reported in diabetics in multiple recent studies.Conclusion
DECREASED phenylalanine may serve as a unique marker of cardiac and brain dysfunction due to hyperamylinemia that can be differentiated from alterations in T2D in the plasma. While the deficiency in phenylalanine was seen across tissues including plasma and could be monitored, reduced tyrosine was seen only in the brain. The 50 % reduction in phenylalanine and tyrosine in HIP brains is significant given their role in supporting brain chemistry as a precursor for catecholamines (dopamine, norepinephrine, epinephrine), which may contribute to the increased morbidity and mortality in diabetics at a multi-system level beyond the effects on glucose metabolism.6.
Heun-Sik Lee Tao Xu Young Lee Nam-Hee Kim Yeon-Jung Kim Jeong-Min Kim Sang Yun Cho Kwang-Youl Kim Moonsuk Nam Jerzy Adamski Karsten Suhre Wolfgang Rathmann Annette Peters Rui Wang-Sattler Bok-Ghee Han Bong-Jo Kim 《Metabolomics : Official journal of the Metabolomic Society》2016,12(12):178
Introduction
Type 2 diabetes (T2D) is a multifactorial disease resulting from a complex interaction between environmental and genetic risk factors. Metabolomics provide a logical framework that reflects the functional endpoints of biological processes being triggered by genetic information and various external influences.Objectives
Identification of metabolite biomarkers can shed insight into etiological pathways and improve the prediction of disease risk. Here, we aimed to identify serum metabolites as putative biomarkers for T2D and their association with genetic variants in the Korean population.Methods
A targeted metabolomics approach was employed to quantify serum metabolites for 2240 participants in the Korea Association REsource (KARE) cohort. T2D-related metabolites were identified by statistical methods including multivariable linear and logistic regression, and were independently replicated in the Cooperative Health Research in the Region of Augsburg (KORA) cohort. Additionally, by combining a genome wide association study (GWAS) with metabolomics, genetic variants associated with the identified T2D-related metabolites were uncovered.Results
123 metabolites were quantified from fasting serum samples and four metabolites, hexadecanoylcarnitine (C16), glycine, lysophosphatidylcholine acyl C18:2 (lysoPC a C18:2), and phosphatidylcholine acyl-alkyl C36:0 (PC ae C36:0), were significantly altered in T2D compared to non-T2D subjects (after the Bonferroni correction for multiple testing with P < 4.07E ? 04, α = 0.05). Among them, C16, glycine, and lysoPC a C18:2 were independently replicated in the KORA cohort. Alterations of these metabolites were associated with ten genetic loci including six that were previously implicated in T2D or obesity.Conclusion
Using a targeted-metabolomics and in combination with GWAS approach, we identified three serum metabolites associated with risk of T2D in both the KARE and KORA cohort and discovered ten genetic variants in relation to the identified metabolites. These findings provide a better understanding to develop novel preventive strategies for T2D in the Korean population.7.
Sang Youl Rhee Eun Sung Jung Hye Min Park Su Jin Jeong Kiyoung Kim Suk Chon Seung-Young Yu Jeong-Taek Woo Choong Hwan Lee 《Metabolomics : Official journal of the Metabolomic Society》2018,14(7):89
Introduction
Diabetic patients with a long disease duration usually accompanied complication such as diabetic retinopathy, but in some patients had no complication.Objectives
We analyzed differences in plasma metabolites according to the presence or absence of diabetic retinopathy (DR) in type 2 diabetic (T2D) patients with disease duration?≥?15 years.Methods
A cohort of 183 T2D patients was established. Their biospecimens and clinical information were collected in accordance with the guidelines of the National Biobank of Korea, and the Korean Diabetes Association. DR phenotypes of the subjects were verified by ophthalmologic specialists. Plasma metabolites were analyzed using gas chromatography time-of-flight mass spectrometry and ultra-performance liquid chromatography–quadrupole time-of-flight mass spectrometry. And these results were analyzed using multivariate statistics.Results
For metabolomic study, propensity score matched case and control subjects were chosen. Mean age of the subjects was 66.4 years and mean T2D duration was 22.2 years. Metabolomic identification revealed various carbohydrates, amino acids, and organic compounds that distinguished between age- and sex-matched non-diabetic controls and T2D subjects. Among these, glutamine and glutamic acid were suggested as the most distinctive metabolites for the presence of DR. Receiver operating characteristics curves showed an excellent diagnostic value of combined (AUC?=?0.739) and the ratio (AUC?=?0.742) of glutamine and glutamic acid for DR. And these results were consistent in validation analyses.Conclusion
Our results imply that plasma glutamine, glutamic acid, and their ratio may be valuable as novel biomarkers for anticipating DR in T2D subjects.8.
Wen-Han Chuang Arivajiagane Arundhathi Ching Lu Chang-Chiang Chen Wan-Chen Wu Hendra Susanto Jerry D. T. Purnomo Chih-Hong Wang 《Metabolomics : Official journal of the Metabolomic Society》2016,12(6):108
Introduction
Dysregulation of acylcarnitines (AcylCNs) and amino acids metabolism have implicated in abnormality of fatty acid oxidation in type 2 diabetes (T2D). However, it is not well known whether altered plasma AcylCN, and amino acid profiles are associated with albuminuria or diabetic nephropathy (DN) in T2D.Objective
The aim of this study was to elucidate alterations in plasma levels of AcylCNs and amino acids with respect to the T2D patients with various stages of albuminuria.Methods
We recruited 52 healthy subjects as control, and 156 T2D patients which were divided into 52 normoalbuminuria, 52 microalbuminuria, and 52 macroalbuminuria. Plasma 37 AcylCNs and 12 amino acids were analyzed by tandem mass spectrometry.Results
We found that T2D with normoalbuminuria and microalbuminuria had lower shot-, medium-, and long-chain AcylCNs, whereas T2D with macroalbuminuria had higher short-and medium-chain AcylCNs and lower long-chain AcylCNs than healthy subjects. Moreover, estimated glomerular filtration rate (eGFR) was a negative, independent and significant predictor of albumin to creatinine ratio (ACR) levels (β = ?0.376, P < 0.001), whereas plasma Low-density lipoprotein cholesterol (LDL-C) was significantly and positively associated with ACR levels (β = 0.169, P = 0.049). Furthermore, multivariate ordinal logistic regression analysis revealed that isobutyrylcarnitine (C4) was a positive, independent, and significant predictor of ACR levels with higher odds of having T2D patients with progression normoalbuminuria to microalbuminuria [OR = 9.93, 95 % CI (3.51–28.05), P < 0.001].Conclusions
The findings suggest that plasma C4 may serve as a potential biomarker for the early stages of DN.9.
Substantial fibrin amyloidogenesis in type 2 diabetes assessed using amyloid-selective fluorescent stains 总被引:1,自引:0,他引:1
Etheresia Pretorius Martin J. Page Lize Engelbrecht Graham C. Ellis Douglas B. Kell 《Cardiovascular diabetology》2017,16(1):141
Background
We have previously shown that many chronic, inflammatory diseases are accompanied, and possibly partly caused or exacerbated, by various coagulopathies, manifested as anomalous clots in the form of ‘dense matted deposits’. More recently, we have shown that these clots can be amyloid in nature, and that the plasma of healthy controls can be induced to form such clots by the addition of tiny amounts of bacterial lipopolysaccharide or lipoteichoic acid. Type 2 diabetes (T2D) is also accompanied by raised levels of LPS.Methods
We use superresolution and confocal microscopies to investigate the amyloid nature of clots from healthy and T2D individuals.Results
We show here, with the established stain thioflavin T and the novel stains Amytracker? 480 and 680, that the clotting of plasma from type 2 diabetics is also amyloid in nature, and that this may be prevented by the addition of suitable concentrations of LPS-binding protein.Conclusion
This implies strongly that there is indeed a microbial component to the development of type 2 diabetes, and suggests that LBP might be used as treatment for it and its sequelae.10.
D. Jacob C. Deborde M. Lefebvre M. Maucourt A. Moing 《Metabolomics : Official journal of the Metabolomic Society》2017,13(4):36
Introduction
Concerning NMR-based metabolomics, 1D spectra processing often requires an expert eye for disentangling the intertwined peaks.Objectives
The objective of NMRProcFlow is to assist the expert in this task in the best way without requirement of programming skills.Methods
NMRProcFlow was developed to be a graphical and interactive 1D NMR (1H & 13C) spectra processing tool.Results
NMRProcFlow (http://nmrprocflow.org), dedicated to metabolic fingerprinting and targeted metabolomics, covers all spectra processing steps including baseline correction, chemical shift calibration and alignment.Conclusion
Biologists and NMR spectroscopists can easily interact and develop synergies by visualizing the NMR spectra along with their corresponding experimental-factor levels, thus setting a bridge between experimental design and subsequent statistical analyses.11.
Ruifang Li-Gao Renée de Mutsert Patrick C. N. Rensen Jan Bert van Klinken Cornelia Prehn Jerzy Adamski Astrid van Hylckama Vlieg Martin den Heijer Saskia le Cessie Frits R. Rosendaal Ko Willems van Dijk Dennis O. Mook-Kanamori 《Metabolomics : Official journal of the Metabolomic Society》2018,14(1):13
Introduction
Fasting metabolite profiles have been shown to distinguish type 2 diabetes (T2D) patients from normal glucose tolerance (NGT) individuals.Objectives
We investigated whether, besides fasting metabolite profiles, postprandial metabolite profiles associated with T2D can stratify individuals with impaired fasting glucose (IFG) by their similarities to T2D.Methods
Three groups of individuals (age 45–65 years) without any history of IFG or T2D were selected from the Netherlands Epidemiology of Obesity study and stratified by baseline fasting glucose concentrations (NGT (n?=?176), IFG (n?=?186), T2D (n?=?171)). 163 metabolites were measured under fasting and postprandial states (150 min after a meal challenge). Metabolite profiles specific for a high risk of T2D were identified by LASSO regression for fasting and postprandial states. The selected profiles were utilised to stratify IFG group into high (T2D probability?≥?0.7) and low (T2D probability?≤?0.5) risk subgroups. The stratification performances were compared with clinically relevant metabolic traits.Results
Two metabolite profiles specific for T2D (nfasting = 12 metabolites, npostprandial = 4 metabolites) were identified, with all four postprandial metabolites also being identified in the fasting state. Stratified by the postprandial profile, the high-risk subgroup of IFG individuals (n?=?72) showed similar glucose concentrations to the low-risk subgroup (n?=?57), yet a higher BMI (difference: 3.3 kg/m2 (95% CI 1.7–5.0)) and postprandial insulin concentrations (21.5 mU/L (95% CI 1.8–41.2)).Conclusion
Postprandial metabolites identified T2D patients as good as fasting metabolites and exhibited enhanced signals for IFG stratification, which offers a proof of concept that metabolomics research should not focus on the fasting state alone.12.
13.
N. Cesbron A.-L. Royer Y. Guitton A. Sydor B. Le Bizec G. Dervilly-Pinel 《Metabolomics : Official journal of the Metabolomic Society》2017,13(8):99
Introduction
Collecting feces is easy. It offers direct outcome to endogenous and microbial metabolites.Objectives
In a context of lack of consensus about fecal sample preparation, especially in animal species, we developed a robust protocol allowing untargeted LC-HRMS fingerprinting.Methods
The conditions of extraction (quantity, preparation, solvents, dilutions) were investigated in bovine feces.Results
A rapid and simple protocol involving feces extraction with methanol (1/3, M/V) followed by centrifugation and a step filtration (10 kDa) was developed.Conclusion
The workflow generated repeatable and informative fingerprints for robust metabolome characterization.14.
Nazila Ariaee Shima Zarei Mojgan Mohamadi Farahzad Jabbari 《Clinical and molecular allergy : CMA》2017,15(1):22
Background
Spontaneous urticaria is a common allergic skin condition affecting 0.5–1% of individuals and may burden on health care expenditure or may be associated with remarkable morbidity.Aim
In this study, we measured the effect of vitamin D supplementation in patients with a diagnosis of CSU. Furthermore, quality of life and cytokine changes were evaluated.Methods
The clinical trial was conducted on 20 patients with idiopathic chronic urticaria. Vitamin D was administered orally for 8 weeks and disease activity was measured pre- and post-treatment using USS and DLQI. On the other hand expressions of IL-17, IL-10, Foxp3, and TGF-β by Real-time RT-PCR were assessed.Results
USS questionnaire showed that severity of idiopathic urticaria after the intervention, which compared with the first day reached a significant 55% reduction. The DLQI quality of life questionnaire 2 months after treatment showed 55% improvement. Along with the significant improvement of clinical symptoms, use of vitamin D increase FOXP3 gene expression and downregulation of IL-10, TGF-B, and FOXP3, IL-17, but these changes were not statistically significant.Limitation
These might happen due to lack of enrolled population in the investigation.Conclusion
Vitamin D can be used along with standard medical care and it’s a safe and cost-effective method for the treatment of chronic urticaria with deficiency of vitamin D.15.
Nwora Lance Okeke Damian M. Craig Michael J. Muehlbauer Olga Ilkayeva Meredith E. Clement Susanna Naggie Svati H. Shah 《Metabolomics : Official journal of the Metabolomic Society》2018,14(3):23
Introduction
Persons living with HIV (PLWH) are at higher risk for cardiovascular disease (CVD) events than uninfected persons. Current risk-stratification methods to define PLWH at highest risk for CVD events are lacking.Methods
Using tandem flow injection mass spectrometry, we quantified plasma levels of 60 metabolites in 24 matched pairs of PLWH [1:1 with and without known coronary artery disease (CAD)]. Metabolite levels were reduced to interpretable factors using principal components analysis.Results
Factors derived from short-chain dicarboxylacylcarnitines (SCDA) (p?=?0.08) and glutamine/valine (p?=?0.003) were elevated in CAD cases compared to controls.Conclusion
SCDAs and glutamine/valine may be valuable markers of cardiovascular risk among persons living with HIV in the future, pending validation in larger cohorts.16.
Rahil Eftekhari Rezvan Esmaeili Reza Mirzaei Katayoon Bidad Stacy de Lima Maryam Ajami Hedayatollah Shirzad Jamshid Hadjati Keivan Majidzadeh-A 《Cancer cell international》2017,17(1):123
Background
Different cells and mediators in the tumor microenvironment play important roles in the progression of breast cancer. The aim of this study was to determine the composition of the microenvironment during tumor progression in order to discover new related biomarkers and potentials for targeted therapy.Methods
In this study, breast cancer biopsies from four different stages, and control breast biopsies were collected. Then, the mRNA expression of several markers related to different CD4+ T cell subsets including regulatory T cells (Treg), T helper (Th) type 1, 2 and 17 were determined. In addition, we investigated the expression of two inflammatory cytokines (TNF-α and IL-6) and inflammatory mediators including FASL, IDO, SOCS1, VEGF, and CCR7.Results
The results showed that the expression of Th1 and Th17 genes was decreased in tumor tissues compared to control tissues. In addition, we found that the gene expression related to these two cell subsets decreased during cancer progression. Moreover, the expression level of TNF-α increased with tumor progression.Conclusion
We conclude that the expression of genes related to immune response and inflammation is different between tumor tissues and control tissues. In addition, this difference was perpetuated through the different stages of cancer.17.
Rachel A. Spicer Christoph Steinbeck 《Metabolomics : Official journal of the Metabolomic Society》2018,14(1):16
Introduction
Data sharing is being increasingly required by journals and has been heralded as a solution to the ‘replication crisis’.Objectives
(i) Review data sharing policies of journals publishing the most metabolomics papers associated with open data and (ii) compare these journals’ policies to those that publish the most metabolomics papers.Methods
A PubMed search was used to identify metabolomics papers. Metabolomics data repositories were manually searched for linked publications.Results
Journals that support data sharing are not necessarily those with the most papers associated to open metabolomics data.Conclusion
Further efforts are required to improve data sharing in metabolomics.18.
Wojciech Bobela Sameer Nazeeruddin Graham Knott Patrick Aebischer Bernard L. Schneider 《Molecular neurodegeneration》2017,12(1):80
Background
Metabolic perturbations and slower renewal of cellular components associated with aging increase the risk of Parkinson’s disease (PD). Declining activity of AMPK, a critical cellular energy sensor, may therefore contribute to neurodegeneration.Methods
Here, we overexpress various genetic variants of the catalytic AMPKα subunit to determine how AMPK activity affects the survival and function of neurons overexpressing human α-synuclein in vivo.Results
Both AMPKα1 and α2 subunits have neuroprotective effects against human α-synuclein toxicity in nigral dopaminergic neurons. Remarkably, a modified variant of AMPKα1 (T172Dα1) with constitutive low activity most effectively prevents the loss of dopamine neurons, as well as the motor impairments caused by α-synuclein accumulation. In the striatum, T172Dα1 decreases the formation of dystrophic axons, which contain aggregated α-synuclein. In primary cortical neurons, overexpression of human α-synuclein perturbs mitochondrial and lysosomal activities. Co-expressing AMPKα with α-synuclein induces compensatory changes, which limit the accumulation of lysosomal material and increase the mitochondrial mass.Conclusions
Together, these results indicate that modulating AMPK activity can mitigate α-synuclein toxicity in nigral dopamine neurons, which may have implications for the development of neuroprotective treatments against PD.19.
Background
In recent years the visualization of biomagnetic measurement data by so-called pseudo current density maps or Hosaka-Cohen (HC) transformations became popular.Methods
The physical basis of these intuitive maps is clarified by means of analytically solvable problems.Results
Examples in magnetocardiography, magnetoencephalography and magnetoneurography demonstrate the usefulness of this method.Conclusion
Hardware realizations of the HC-transformation and some similar transformations are discussed which could advantageously support cross-platform comparability of biomagnetic measurements.20.
Lavanya Reddivari Bishwa R. Sapkota Apoorva Rudraraju Yundi Liang Christopher Aston Evgeny Sidorov Jairam K. P. Vanamala Dharambir K. Sanghera 《Metabolomics : Official journal of the Metabolomic Society》2017,13(12):154