Background
The rapid development of next-generation sequencing technologies allow people to analyze human complex diseases at the molecular level. It has been shown that rare variants play important ...roles for human diseases besides common variants. Thus, effective statistical methods need to be proposed to test for the associations between traits (
e.g.
, diseases) and rare variants. Currently, more and more rare genetic variants are being detected throughout the human genome, which demonstrates the possibility to study rare variants. Yet complex diseases are usually measured as a variety of forms, such as binary, ordinal, quantitative, or some mixture of them. Therefore, the genetic mapping problem can be attributable to the association detection between multiple traits and multiple loci, with sufficiently considering the correlated structure among multiple traits.
Methods
In this article, we construct a new non-parametric statistic by the generalized Kendall’s
τ
theory based on family data. The new test statistic has an asymptotic distribution, it can be used to study the associations between multiple traits and rare variants, which broadens the way to identify genetic factors of human complex diseases.
Results
We apply our method (called Nonp-FAM) to analyze simulated data and GAW17 data, and conduct comprehensive comparison with some existing methods. Experimental results show that the proposed family-based method is powerful and robust for testing associations between multiple traits and rare variants, even if the data has some population stratification effect.
During the production of L-arginine through high dissolved oxygen and nitrogen supply fermentation, the industrial workhorse Corynebacterium glutamicum is exposed to oxidative stress. This generates ...reactive oxygen species (ROS) and reactive nitrogen species (RNS), which are harmful to the bacteria. To address the issue and to maintain redox homeostasis during fermentation, the flavohaemoprotein (Hmp) was employed. The results showed that the overexpression of Hmp led to a decrease in ROS and RNS content by 9.4% and 22.7%, respectively, and improved the survivability of strains. When the strains were treated with H.sub.2O.sub.2 and NaNO.sub.2, the RT-qPCR analysis indicated an up-regulation of ammonium absorption and transporter genes amtB and glnD. Conversely, the deletion of hmp gives rise to the up-regulation of eight oxidative stress-related genes. These findings suggested that hmp is associated with oxidative stress and intracellular nitrogen metabolism genes. Finally, we released the inhibitory effect of ArnR on hmp. The Cc-DELAarnR-hmp strain produced 48.4 g/L L-arginine during batch-feeding fermentation, 34.3% higher than the original strain. This report revealed the influence of dissolved oxygen and nitrogen concentration on reactive species of Corynebacterium glutamicum and the role of the Hmp in coping with oxidative stress. The Hmp first demonstrates related to redox homeostasis and nitrite metabolism, providing a feasible strategy for improving the robustness of strains.
Summary
This study proposed an expert system approach on the basis of artificial intelligence (AI) in the modeling of cyclic voltammogram (CV) profiles of green tea extracts. AI approach of ...artificial neural networks is applied to generate the model phase‐plane portraits of current output versus applied voltage through CV scan cycles. The predicted current values were validated using experiments, and generic ability of approach was examined by testing on the CV scan cycles generated from Syzygium aromaticum and Citrus reticulate. It was concluded that AI approach can be employed to reveal stable point (cycle and voltage) in CV profiles for bioenergy applications.
Problem in the modeling of cyclic voltammogram (CV) process of Camellia green tea extract to provide a plausible prediction of responding current at different given conditions is undertaken. A comprehensive methodology combining experimental and artificial intelligence for determination of a stable criteria in cyclic voltammogram process of medicinal herbs for biofuel cells is proposed to solve this problem. Results were validated by testing on cyclic voltammogram scan cycles generated for Syzygium aromaticum and Citrus reticulate. The combination of electrochemical cyclic voltammogram tests and artificial intelligence is proved to be a practical and efficient approach for both fundamental understanding and quantification of green tea extract characteristics.
L-valine is an essential amino acid that has wide and expanding applications with a suspected growing market demand. Its applicability ranges from animal feed additive, ingredient in cosmetic and ...special nutrients in pharmaceutical and agriculture fields. Currently, fermentation with the aid of model organisms, is a major method for the production of L-valine. However, achieving the optimal production has often been limited because of the metabolic imbalance in recombinant strains. In this review, the constrains in L-valine biosynthesis are discussed first. Then, we summarize the current advances in engineering of microbial cell factories that have been developed to address and overcome major challenges in the L-valine production process. Future prospects for enhancing the current L-valine production strategies are also discussed.
Abstract
Cytochrome P450 2J2 (CYP2J2) is an enzyme mainly found in human extrahepatic tissues, with predominant expression in the cardiovascular systems and lower levels in the intestine, kidney, ...lung, pancreas, brain, liver, etc. During the past 15 years, CYP2J2 has attracted much attention for its epoxygenase activity in arachidonic acid (AA) metabolism. It converts AA to four epoxyeicosatrienoic acids (EETs) that have various biological effects, especially in the cardiovascular systems. In recent publications, CYP2J2 is shown highly expressed in various human tumor cells, and its EET metabolites are demonstrated to implicate in the pathologic development of human cancers. CYP2J2 is also a human CYP that involved in phase I xenobiotics metabolism. Antihistamine drugs and many other compounds were identified as the substrates of CYP2J2, and studies have demonstrated that these substrates have a broad structural diversity. CYP2J2 is found not readily induced by known P450 inducers; however, its expression could be regulated in some pathological conditions, might through the activator protein-1(AP-1), the AP-1-like element and microRNA let-7b. Several genetic mutations in the CYP2J2 gene have been identified in humans, and some of them have been shown to have potential associations with some diseases. With the increasing awareness of its roles in cancer disease and drug metabolism, studies about CYP2J2 are still going on, and various inhibitors of CYP2J2 have been determined. Further studies are needed to delineate the roles of CYP2J2 in disease pathology, drug development and clinical practice.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
Agmatine is a member of biogenic amines and is an important medicine which is widely used to regulate body balance and neuroprotective effects. At present, the industrial production of agmatine ...mainly depends on the chemical method, but it is often accompanied by problems including cumbersome processes, harsh reaction conditions, toxic substances production and heavy environmental pollution. Therefore, to tackle the above issues, arginine decarboxylase was overexpressed heterologously and rationally designed in Corynebacterium crenatum to produce agmatine from glucose by one-step fermentation.
In this study, we report the development in the Generally Regarded as Safe (GRAS) L-arginine-overproducing C. crenatum for high-titer agmatine biosynthesis through overexpressing arginine decarboxylase based on metabolic engineering. Then, arginine decarboxylase was mutated to release feedback inhibition and improve catalytic activity. Subsequently, the specific enzyme activity and half-inhibitory concentration of I534D mutant were increased 35.7% and 48.1%, respectively. The agmatine production of the whole-cell bioconversion with AGM3 was increased by 19.3% than the AGM2. Finally, 45.26 g/L agmatine with the yield of 0.31 g/g glucose was achieved by one-step fermentation of the engineered C. crenatum with overexpression of speA
.
The engineered C. crenatum strain AGM3 in this work was proved as an efficient microbial cell factory for the industrial fermentative production of agmatine. Based on the insights from this work, further producing other valuable biochemicals derived from L-arginine by Corynebacterium crenatum is feasible.
Prodigiosin (PG), a red linear tripyrrole pigment produced by
Serratia marcescens
, has attracted attention due to its immunosuppressive, antimicrobial, and anticancer properties. Although many ...studies have been used to dissect the biosynthetic pathways and regulatory network of prodigiosin production in
S. marcescens
, few studies have been focused on improving prodigiosin production through metabolic engineering in this strain. In this study, transcription factor engineering and promoter engineering was used to promote the production of prodigiosin in
S. marcescens
JNB5-1. Firstly, through construing of a Tn5G transposon insertion library of strain JNB5-1, it was found that the DNA-binding response regulator BVG89_19895 (OmpR) can promote prodigiosin synthesis in this strain. Then, using RNA-Seq analysis, reporter green fluorescent protein analysis and RT-qPCR analysis, the promoter P17 (P
RplJ
) was found to be a strong constitutive promoter in strain JNB5-1. Finally, the promoter P17 was used for overexpressing of prodigiosin synthesis activator OmpR and PsrA in strain JNB5-1 and a recombinant strain PG-6 was obtained. Shake flask analysis showed that the prodigiosin titer of this strain was increased to 10.25 g/L, which was 1.62-times that of the original strain JNB5-1 (6.33 g/L). Taken together, this is the first well-characterized constitutive promoter library from
S. marcescens
, and the transcription factor engineering and promoter engineering can be also useful strategies to improve the production of other high value-added products in
S. marcescens
.
To improve the androst-1,4-diene-3,17-dione (ADD) production from phytosterol by Mycobacterium neoaurum JC-12, fructose was firstly found favorable as the initial carbon source to increase the ...biomass and eliminate the lag phase of M. neoaurum JC-12 in the phytosterol transformation process. Based on this phenomenon, two-stage fermentation by using fructose as the initial carbon source and feeding glucose to maintain strain metabolism was designed. By applying this strategy, the fermentation duration was decreased from 168 h to 120 h with the ADD productivity increased from 0.071 g/(L·h) to 0.108 g/(L·h). Further, three-stage fermentation by adding phytosterol to improve ADD production at the end of the two-stage fermentation was carried out and the final ADD production reached 18.6 g/L, which is the highest reported ADD production using phytosterol as substrate. Thus, this strategy provides a possible way in enhancing the ADD production in pharmaceutical industry.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Previously, a safe strain, Bacillus amyloliquefaciens B10-127 was identified as an excellent candidate for industrial-scale microbial fermentation of 2,3-butanediol (2,3-BD). However, B. ...amyloliquefaciens fermentation yields large quantities of acetoin, lactate and succinate as by-products, and the 2,3-BD yield remains prohibitively low for commercial production.
In the 2,3-butanediol metabolic pathway, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) catalyzes the conversion of 3-phosphate glyceraldehyde to 1,3-bisphosphoglycerate, with concomitant reduction of NAD(+) to NADH. In the same pathway, 2,3-BD dehydrogenase (BDH) catalyzes the conversion of acetoin to 2,3-BD with concomitant oxidation of NADH to NAD(+). In this study, to improve 2,3-BD production, we first over-produced NAD(+)-dependent GAPDH and NADH-dependent BDH in B. amyloliquefaciens. Excess GAPDH reduced the fermentation time, increased the 2,3-BD yield by 12.7%, and decreased the acetoin titer by 44.3%. However, the process also enhanced lactate and succinate production. Excess BDH increased the 2,3-BD yield by 16.6% while decreasing acetoin, lactate and succinate production, but prolonged the fermentation time. When BDH and GAPDH were co-overproduced in B. amyloliquefaciens, the fermentation time was reduced. Furthermore, in the NADH-dependent pathways, the molar yield of 2,3-BD was increased by 22.7%, while those of acetoin, lactate and succinate were reduced by 80.8%, 33.3% and 39.5%, relative to the parent strain. In fed-batch fermentations, the 2,3-BD concentration was maximized at 132.9 g/l after 45 h, with a productivity of 2.95 g/l·h.
Co-overexpression of bdh and gapA genes proved an effective method for enhancing 2,3-BD production and inhibiting the accumulation of unwanted by-products (acetoin, lactate and succinate). To our knowledge, we have attained the highest 2,3-BD fermentation yield thus far reported for safe microorganisms.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
L-asparaginase, which catalyses the hydrolysis of L-asparagine to L-aspartate, has attracted the attention of researchers due to its expanded applications in medicine and the food industry. In this ...study, a novel thermostable L-asparaginase from Pyrococcus yayanosii CH1 was cloned and over-expressed in Bacillus subtilis 168. To obtain thermostable L-asparaginase mutants with higher activity, a robust high-throughput screening process was developed specifically for thermophilic enzymes. In this process, cell disruption and enzyme activity assays are simultaneously performed in 96-deep well plates. By combining error-prone PCR and screening, six brilliant positive variants and four key amino acid residue mutations were identified. Combined mutation of the four residues showed relatively high specific activity (3108 U/mg) that was 2.1 times greater than that of the wild-type enzyme. Fermentation with the mutant strain in a 5-L fermenter yielded L-asparaginase activity of 2168 U/mL.
PDF
