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1.
Kai Zhang Huijuan Su Muhan Yang Jing Ge Guiyao Li Jun Yi Yang Wang 《Biotechnology letters》2017,39(6):905-909
Objectives
To establish a positive cloning system with a zero background for high-throughput DNA cloning purpose.Results
The cloning vector, pRI857, and the genomic-library construction vector, pRI857-BAC, were constructed based on the mechanism of expression of the thermo-sensitive cI857 repressor gene that can stringently repress the PR promoter and kanamycin resistance gene (PR-kan R ) at 30 °C, but have no effect on PR-kan R gene at 37 °C or at higher temperatures. When the pRI857 vectors were transformed into E. coli with or without a target foreign DNA fragment inserted at the BfrBI site of the cI857 gene, only colonies with the foreign DNA fragment survive. We extended this method to construct a pRI857-BAC vector for genomic library cloning which displays an efficiency of ~107 cfu per µg of genomic DNA, with no empty vectors detected.Conclusions
Cloning by indirect activation of resistance marker gene represents a novel DNA-capturing system, which can be widely applied for high-throughput DNA cloning.2.
Background
Dengue is a common mosquito-borne viral disease epidemic especially in tropical and sub-tropical regions where water sanitation is not substantially controlled. However, dengue epidemics sometimes occur in non-tropical urban cities with substantial water sanitary control. Using a mathematical model, we investigate what conditions can be important for a dengue epidemic to occur in an urban city such as Tokyo, where vectors are active only in summer and there are little number of vectors around hosts.Methods
The model, which is a modified Ross-Macdonald model, consists of two sets of host-vector compartments. The two sets correspond to high-risk and low-risk areas, and only hosts can move between them. Assuming that mosquitoes have constant activity for only 90 days, we assess five potential countermeasures: (1) restricted movement between the two areas, (2) insecticide application, (3) use of repellents, (4) vector control, and (5) isolation of the infected.Results
The basic reproduction number R 0 and the cumulative number of infected hosts for 90 days are evaluated for each of the five countermeasures. In the cases of Measures 2–5, the cumulative number of the infected for 90 days can be reduced substantially for small R 0 even if R 0>1. Although R 0 for Measure 1 monotonically decreases with the mobility rates, the cumulative number of the infected for 90 days has a maximum at a moderate mobility rate. If the mobility rate is sufficiently small, the restricted movement effectively increases the number density of vectors in the high-risk area, and the epidemic starts earlier in the high-risk area than in the low-risk one, while the growth of infections is slow.Conclusions
Measures 2–5 are more or less effective. However, Measure 1 can have the opposite effect, depending on the mobility rates. The restricted movement results in the formation of a kind of core population, which can promote the epidemic in the entire population.3.
Antonella Del-Corso Mario Cappiello Roberta Moschini Francesco Balestri Umberto Mura 《Metabolomics : Official journal of the Metabolomic Society》2018,14(1):2
Introduction
While the evolutionary adaptation of enzymes to their own substrates is a well assessed and rationalized field, how molecules have been originally selected in order to initiate and assemble convenient metabolic pathways is a fascinating, but still debated argument.Objectives
Aim of the present study is to give a rationale for the preferential selection of specific molecules to generate metabolic pathways.Methods
The comparison of structural features of molecules, through an inductive methodological approach, offer a reading key to cautiously propose a determining factor for their metabolic recruitment.Results
Starting with some commonplaces occurring in the structural representation of relevant carbohydrates, such as glucose, fructose and ribose, arguments are presented in associating stable structural determinants of these molecules and their peculiar occurrence in metabolic pathways.Conclusions
Among other possible factors, the reliability of the structural asset of a molecule may be relevant or its selection among structurally and, a priori, functionally similar molecules.4.
Xiaowei Wang Mingjie Wang Shuangshuang Shao Yang Zhang Siyu Liu Yue Gao Yuhang Shen Pinghui Sun 《BMC endocrine disorders》2018,18(1):89
Background
To explore the risk factors of coexisting prediabetes and prehypertension, to provide theoretical basis for early intervention.Methods
A multi-stage stratified random cluster sampling method was used to randomly select adult residents from Jilin Province in 2013 for questionnaire surveys, physical examinations, and laboratory tests.Results
The prevalence of coexisting prediabetes and prehypertension in Jilin Province was 11.3%. The binary Logistic regression results showed that age, sex, education, triglyceride (TG), BMI, waist circumference and alcohol consumption were the effects of factor coexisting prediabetes and prehypertension.Conclusion
It is important to pay attention to the early stage of hypertension and diabetes, control the transition from prehypertension and prediabetes to hypertension and diabetes, and improve the health of residents.5.
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.6.
Yan Ru Wu Yun Gyeong Kang Ji Won Shin Mi Jin Kim Jung-Woog Shin 《Biotechnology letters》2017,39(8):1121-1127
Objective
To control the oscillatory behavior of the intracellular calcium ([Ca2+]i) concentration in endothelial cells via mechanical factors (i.e., various hydrostatic pressures) because [Ca2+]i in these cells is affected by blood pressure.Results
Quantitative analyses based on real-time imaging showed that [Ca2+]i oscillation frequency and relative concentration increased significantly when 200 mm Hg pressure, mimicking hypertension, was applied for >10 min. Peak height and peak width decreased significantly at 200 mm Hg. These trends were more marked as the duration of the 200 mm Hg pressure was increased. However, no change was observed under normal blood pressure conditions 100 mm Hg.Conclusion
We generated a simple in vitro model to study [Ca2+]i behavior in relation to various pathologies and diseases by eliminating possible complicating effects induced by chemical cues.7.
Paulin N. Wahjudi Qing-Yi Lu Mary E. Patterson Xuemei Zhang Vay Liang Go Jian Chen Wei-Lin Li W. N. Paul Lee 《Metabolomics : Official journal of the Metabolomic Society》2017,13(8):91
Introduction
Loquat leaf extract (LLE) is commonly used in China for a variety of ailments including diabetes. Several recent reports implicate LLE and a sesquiterpene glycoside, one of its components, as being an anti-hyperglycemic agent. However, the underlying mechanism of action of this anti-hyperglycemic agent has not been reported.Objective
We have conducted a tracer-based metabolomics study to investigate the effects of sesquiterpene and loquat extract on the balance of flux of central glucose metabolism in HepG2 cells and to compare with those of “insulin sensitizers”, metformin and rosiglitazone.Methods
Human hepatoma HepG2 cells in confluence culture were incubated in Dulbecco’s modified Eagle’s medium containing 50% [1, 2 13C2]-glucose in the presence of rosiglitazone, metformin, LLE or pure sesquiterpene. Cells were harvested in 48 h. Mass isotopomers of metabolites (glycogen, ribose, deoxyribose, glutamate and palmitate) were determined.Results
13C labeling in metabolic intermediates were summarized in a mass isotopomer matrix. Treatment with loquat extract/sesquiterpene, metformin and rosiglitazone each produced distinctive mass isotopomer patterns reflecting disparate effects on the contribution of glucose to various metabolites production, and on several metabolic flux ratios. The overall effect of LLE and sesquiterpene on glucose metabolism is clearly different from those of the known “insulin sensitizers”.Conclusion
Our study demonstrates the utility of isotopomer matrix in summarizing metabolic actions of LLE on the balance of fluxes occurring within the central glucose metabolism in HepG2 cells. 13C carbon tracing (tracer-based metabolomics) is a useful systems biology tool to elucidate glucose metabolic pathways affected by diabetes and its treatment.8.
Andres Gil David Siegel Silke Bonsing-Vedelaar Hjalmar Permentier Dirk-Jan Reijngoud Frank Dekker Rainer Bischoff 《Metabolomics : Official journal of the Metabolomic Society》2017,13(1):1
Introduction
Boiling ethanol extraction is a frequently used method for metabolomics studies of biological samples. However, the stability of several central carbon metabolites, including nucleotide triphosphates, and the influence of the cellular matrix on their degradation have not been addressed.Objectives
To study how a complex cellular matrix extracted from yeast (Saccharomyces cerevisiae) may affect the degradation profiles of nucleotide triphosphates extracted under boiling ethanol conditions.Methods
We present a double-labelling LC–MS approach with a 13C-labeled yeast cellular extract as complex surrogate matrix, and 13C15N-labeled nucleotides as internal standards, to study the effect of the yeast matrix on the degradation of nucleotide triphosphates.Results
While nucleotide triphosphates were degraded to the corresponding diphosphates in pure solutions, degradation was prevented in the presence of the yeast matrix under typical boiling ethanol extraction conditions.Conclusions
Extraction of biological samples under boiling ethanol extraction conditions that rapidly inactivate enzyme activity are suitable for labile central energy metabolites such as nucleotide triphosphates due to the stabilizing effect of the yeast matrix. The basis of this phenomenon requires further study.Graphical abstract
9.
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.10.
Novak V Yang AC Lepicovsky L Goldberger AL Lipsitz LA Peng CK 《Biomedical engineering online》2004,3(1):39
Background
This study evaluated the effects of stroke on regulation of cerebral blood flow in response to fluctuations in systemic blood pressure (BP). The autoregulatory dynamics are difficult to assess because of the nonstationarity and nonlinearity of the component signals.Methods
We studied 15 normotensive, 20 hypertensive and 15 minor stroke subjects (48.0 ± 1.3 years). BP and blood flow velocities (BFV) from middle cerebral arteries (MCA) were measured during the Valsalva maneuver (VM) using transcranial Doppler ultrasound.Results
A new technique, multimodal pressure-flow analysis (MMPF), was implemented to analyze these short, nonstationary signals. MMPF analysis decomposes complex BP and BFV signals into multiple empirical modes, representing their instantaneous frequency-amplitude modulation. The empirical mode corresponding to the VM BP profile was used to construct the continuous phase diagram and to identify the minimum and maximum values from the residual BP (BPR) and BFV (BFVR) signals. The BP-BFV phase shift was calculated as the difference between the phase corresponding to the BPR and BFVR minimum (maximum) values. BP-BFV phase shifts were significantly different between groups. In the normotensive group, the BFVR minimum and maximum preceded the BPR minimum and maximum, respectively, leading to large positive values of BP-BFV shifts.Conclusion
In the stroke and hypertensive groups, the resulting BP-BFV phase shift was significantly smaller compared to the normotensive group. A standard autoregulation index did not differentiate the groups. The MMPF method enables evaluation of autoregulatory dynamics based on instantaneous BP-BFV phase analysis. Regulation of BP-BFV dynamics is altered with hypertension and after stroke, rendering blood flow dependent on blood pressure.11.
Xin-Jian Wang Jiang Wang Yue-Ying Wang Yu-Jie Guo Bei-Bei Chu Guo-Yu Yang 《Biotechnology letters》2016,38(6):949-958
Objectives
To determine the effects of the Sus scrofa matrix attachment region (SusMAR) on transgene expression in HEK293T cells.Results
Three expression vectors with the MAR at different sites in the PiggyBac (PB) transposon vector backbone were compared: two MARs flanking the β-galactosidase (β-gal) expression cassette, and one at the upstream or downstream site. Bos taurus MAR (BosMAR) and a β-gal expression cassette without MARs were the positive and negative controls, respectively. Compared to the control, β-gal activity of all SusMAR and BosMAR vectors was significantly improved in the presence of PB transposase (PBase). However, only the downstream SusMAR and upstream BosMAR vectors showed increased expression in the absence of PBase. Expression was significantly increased in all vectors with the PBase group compared to those without the PBase group. Gene copy numbers were not increased compared to the negative control.Conclusions
SusMAR enhanced recombinant gene expression levels and stability in HEK293T cells, was not increase transgene copy number. These results could facilitate the development of vectors for stable production of therapeutic proteins.12.
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.13.
Xue-Gang Xu Lin Gong Tian-Ling Jiang Yuan-Hong Li Xing-Hua Gao Haishan Tian Hong-Duo Chen 《Biotechnology letters》2018,40(6):1009-1014
Objectives
To explore potential effects of recombinant human fibroblast growth factor 20 (rhFGF20) in the growth of cultured mouse vibrissal follicles.Results
The growth of cultured mouse vibrissal follicles was significantly induced by rhFGF20 in a dose dependent pattern in the in vitro vibrissal follicle organ culture model. However, too high concentration of rhFGF20 could inhibit the growth of vibrissal follicles. We further demonstrated that rhFGF20 stimulated the proliferation of hair matrix cells and activated Wnt/β-catenin signaling pathway.Conclusions
The rhFGF20 might be a potential therapeutic agent to treat hair loss disorders.14.
Jamie V. de Seymour Stephanie Tu Xiaoling He Hua Zhang Ting-Li Han Philip N. Baker Karolina Sulek 《Metabolomics : Official journal of the Metabolomic Society》2018,14(6):79
Introduction
Intrahepatic cholestasis of pregnancy (ICP) is a common maternal liver disease; development can result in devastating consequences, including sudden fetal death and stillbirth. Currently, recognition of ICP only occurs following onset of clinical symptoms.Objective
Investigate the maternal hair metabolome for predictive biomarkers of ICP.Methods
The maternal hair metabolome (gestational age of sampling between 17 and 41 weeks) of 38 Chinese women with ICP and 46 pregnant controls was analysed using gas chromatography–mass spectrometry.Results
Of 105 metabolites detected in hair, none were significantly associated with ICP.Conclusion
Hair samples represent accumulative environmental exposure over time. Samples collected at the onset of ICP did not reveal any metabolic shifts, suggesting rapid development of the disease.15.
Yunbo Wang Bo Meng Shangzhi Zhong Deli Wang Jianying Ma Wei Sun 《Plant and Soil》2018,432(1-2):259-272
Background and aims
Nitrogen deposition and altered precipitation regime are likely to change plant growth, biomass allocation and community structure, which may influence susceptibility of ecosystem functions (i.e. ecosystem carbon exchange) to extreme climatic events, such as drought.Methods
In a meadow steppe, we deployed a drought treatment on a long-term water and nitrogen addition experiment to investigate resource abundance changes induced variation in the sensitivity of ecosystem carbon exchange to extreme drought.Results
Compared to the control plots, long-term water and nitrogen addition caused a strong increase in biomass, and a reduction in diversity and root/shoot ratio. Net ecosystem CO2 exchange (NEE) in water and nitrogen addition plots were more sensitive to drought stress than the control plots. The enhanced NEE drought sensitivity (SNEE) in nitrogen fertilization habitat is associated with changes in aboveground biomass and root/shoot ratio, rather than variation in species diversity, while SNEE in the unfertilized plots was controlled by root/shoot ratio. Compared to the water and nitrogen addition plots, the control plots had the highest percentage recovery of ecosystem carbon exchange (RNEE) during the rehydration period. RNEE is likely determined by aboveground biomass and level of damage in the photosynthetic organ.Conclusion
These findings suggest that long-term changes in precipitation regimes and nitrogen deposition may significant alter the susceptibility of key ecosystem processes to drought stress.16.
17.
Renato de Souza Pinto Lemgruber Kaspar Valgepea Mark P. Hodson Ryan Tappel Sean D. Simpson Michael Köpke Lars K. Nielsen Esteban Marcellin 《Metabolomics : Official journal of the Metabolomic Society》2018,14(3):35
Introduction
Quantification of tetrahydrofolates (THFs), important metabolites in the Wood–Ljungdahl pathway (WLP) of acetogens, is challenging given their sensitivity to oxygen.Objective
To develop a simple anaerobic protocol to enable reliable THFs quantification from bioreactors.Methods
Anaerobic cultures were mixed with anaerobic acetonitrile for extraction. Targeted LC–MS/MS was used for quantification.Results
Tetrahydrofolates can only be quantified if sampled anaerobically. THF levels showed a strong correlation to acetyl-CoA, the end product of the WLP.Conclusion
Our method is useful for relative quantification of THFs across different growth conditions. Absolute quantification of THFs requires the use of labelled standards.18.
Introduction
Untargeted metabolomics is a powerful tool for biological discoveries. To analyze the complex raw data, significant advances in computational approaches have been made, yet it is not clear how exhaustive and reliable the data analysis results are.Objectives
Assessment of the quality of raw data processing in untargeted metabolomics.Methods
Five published untargeted metabolomics studies, were reanalyzed.Results
Omissions of at least 50 relevant compounds from the original results as well as examples of representative mistakes were reported for each study.Conclusion
Incomplete raw data processing shows unexplored potential of current and legacy data.19.
Background
Co-administration of anti-tuberculosis and antiretroviral therapy is often inevitable in high-burden countries where tuberculosis is the most common opportunistic infection associated with HIV/AIDS. Concurrent use of rifampicin and several antiretroviral drugs is complicated by pharmacokinetic drug-drug interaction.Method
Pubmed and Google search following the key words tuberculosis, HIV, emtricitabine, tenofovir efavirenz, interaction were used to find relevant information on each drug of the fixed dose combination AtriplaRResults
Information on generic name, trade name, pharmacokinetic parameter, metabolism and the pharmacokinetic interaction with Anti-TB drugs of emtricitabine, tenofovir, and efavirenz was obtained.Conclusion
Fixed dose combination of emtricitabine/tenofovir/efavirenz (ATRIPLAR) which has been approved by Food and Drug Administration shows promising results as far as safety and efficacy is concerned in TB/HIV co-infection patients, hence can be considered effective and safe antiretroviral drug in TB/HIV management for adult and children above 3 years of age.20.
Seyed Ziyae Aldin Samsam Shariat Fatemeh Borzouee Mohammad Reza Mofid Jaleh Varshosaz 《Biotechnology letters》2018,40(9-10):1343-1353