Characterizing Escherichia coli DH5alpha growth and metabolism in a complex medium using genome-scale flux analysis

Genome-scale flux analysis of Escherichia coli DH5alpha growth in a complex medium was performed to investigate the relationship between the uptake of various nutrients and their metabolic outcomes. During the exponential growth phase, we observed a sequential consumption order of serine, aspartate and glutamate in the complex medium as well as the complete consumption of key carbohydrate nutrients, glucose and trehalose. Based on the consumption and production rates of the measured metabolites, constraints-based flux analysis of a genome-scale E. coli model was then conducted to elucidate their utilization in the metabolism. The in silico analysis revealed that the cell exploited biosynthetic precursors taken up directly from the complex medium, through growth-related anabolic pathways. This suggests that the cell could be functioning in an energetically more efficient manner by reducing the energy needed to produce amino acids. The in silico simulation also allowed us to explain the observed rapid consumption of serine: excessively consumed external serine from the complex medium was mainly converted into pyruvate and glycine, which in turn, led to the acetate accumulation. The present work demonstrates the application of an in silico modeling approach to characterizing microbial metabolism under complex medium condition. This work further illustrates the use of in silico genome-scale analysis for developing better strategies related to improving microbial growth and enhancing the productivity of desirable metabolites.     

Effects of lysine intake during late gestation and lactation on blood metabolites, hormones, milk composition and reproductive performance in primiparous and multiparous sows

Modern genotype primiparous and multiparous sows (Yorkshire x Landrace, n=48) were used to evaluate effects of dietary lysine intake during late gestation and lactation, and their interaction on reproductive performance. Sows were randomly allotted to two gestation lysine (G, 0.6% or 0.8% lysine) treatments based on parity in a 2 x 2 factorial arrangement, and each treatment had 12 replicates comprising 1 sow. Then all the sows were assigned to two lactation lysine (L, 1.0% or 1.3% lysine) treatments within parity and gestation treatments in a 2 x 2 x 2 factorial design, and each treatment comprised six replicates with 1 sow/replicate during lactation. Feeding higher lysine level during gestation increased sow body weight and backfat thickness (P=0.001) and body condition was better (P=0.001) in multiparous than that of primiparous sows. Both of the lysine levels during lactation and parity influenced sow body condition and reproductive performance (P<0.05). Higher lysine intake during lactation increased the concentrations of total solids (P=0.024), protein (P=0.001) and solids not-fat (P=0.042) in colostrum and total solids (P=0.001), protein (P=0.001), fat (P=0.001) and solids not-fat (P=0.005) in milk. Protein concentration of milk was greater (P=0.001) in multiparous sows than that of primiparous sows. Feeding of high lysine diets resulted in an increment of plasma urea N (P=0.010; P=0.047) and a decrease of creatinine (P=0.045; P=0.002) on the day of postfarrowing and weaning, respectively. Furthermore, as lysine intake increased, the secretions of insulin, FSH, and LH were increased (P<0.05) and multiparous sows showed higher (P<0.05) concentrations of FSH and LH pulses on the day of postfarrowing and weaning, respectively. These results indicated that higher lysine intake than that recommended by NRC [NRC, 1998. Nutrient Requirements of Swine, 10th ed. National Academy Press, 458 Washington, DC] could improve sow performance during late gestation and lactation. Furthermore primiparous sows need higher lysine intake than multiparous sows. Moreover, nutritional impacts on reproduction may be mediated in part through associated effects on circulating LH concentration.     

Overexpression of the downward leaf curling (DLC) gene from melon changes leaf morphology by controlling cell size and shape in Arabidopsis leaves

A plant-specific gene was cloned from melon fruit. This gene was named downward leaf curling (CmDLC) based on the phenotype of transgenic Arabidopsis plants overexpressing the gene. This expression level of this gene was especially upregulated during melon fruit enlargement. Overexpression of CmDLC in Arabidopsis resulted in dwarfism and narrow, epinastically curled leaves. These phenotypes were found to be caused by a reduction in cell number and cell size on the adaxial and abaxial sides of the epidermis, with a greater reduction on the abaxial side of the leaves. These phenotypic characteristics, combined with the more wavy morphology of epidermal cells in overexpression lines, indicate that CmDLC overexpression affects cell elongation and cell morphology. To investigate intracellular protein localization, a CmDLC-GFP fusion protein was made and expressed in onion epidermal cells. This protein was observed to be preferentially localized close to the cell membrane. Thus, we report here a new plant-specific gene that is localized to the cell membrane and that controls leaf cell number, size and morphology.     

Functionality improvement of fungal lignin peroxidase by DNA shuffling for 2,4-dichlorophenol degradability and H2O2 stability

One of the major problems of wild-type lignin peroxidase (LiP) is its inactivity at the presence of excess H(2)O(2) and high concentration of aromatic compounds. Little is known about the substrate-binding site of LiP, and functionality improvement of LiP was not actively tried by genetic engineering and directed evolution. In order to improve LiPs functionality, we performed directed evolution with a colorimetric screening method. Finally, three types of LiP mutants were screened. The catalytic efficiency of the variants toward 2,4-dichlorophenol (DCP) degradation activity and the stability against H(2)O(2) was increased over the wild type. The K(m) value of the variants toward H(2)O(2) was increased, but K(m) value toward 2,4-DCP degradation was reduced. Overall, The K(cat)/K(m) values of the mutants toward 2,4-DCP was increased ca. 4-fold, and that toward H(2)O(2) was increased ca. 89-fold. Amino acid sequence analysis indicated that the most of the mutations were located on the enzyme surface. We expect that these results coupled with recombining mutation can be successfully applied to the molecular evolution cycles for screening of LiPs and other oxidative enzymes with improved functionality and stability.     

Development and validation of a high performance liquid chromatography-tandem mass spectrometry for the determination of etodolac in human plasma

A simple and specific method using a one-step liquid-liquid extraction (LLE) with butyl acetate followed by high performance liquid chromatography (HPLC) coupled with positive ion electrospray ionization tandem mass spectrometry (ESI-MS/MS) detection was developed for the determination of etodolac in human plasma, using indomethacin as an internal standard (IS). Chromatographic separation was performed isocratically using a Capcellpak MGII C(18) column with 65% acetonitrile and 35% water containing 10mM ammonium formate (adjusted to pH 3.5 with formic acid). Acquisition was performed in multiple reaction monitoring (MRM) mode by monitoring the transitions: m/z 287.99>172.23 for etodolac and m/z 357.92>139.01 for IS. The method was validated to determine its selectivity, linearity, sensitivity, precision, accuracy, recovery and stability. The limit of quantitation (LLOQ) was 0.1microg/mL with a relative standard deviation of less than 15%. The devised method provides an accurate, precise and sensitive tool for determining etodolac levels in plasma.     

Effect of maternal restraint stress on fetal development of ICR mice.

The present study was conducted to elucidate the susceptibility of embryos and fetuses at different gestational stages to the maternal stress in mice. Groups of pregnant ICR mice were subjected to daily 12-h restraint stress, taped in the supine position on a plastic board, on gestational days (GD) 1-4, 5-8, 9-12 and 13-16, respectively. Caesarean sections were performed on gestational day 18, and the fetuses were weighed and examined for morphological defects. During the daily restraint for 4 days, the maternal body weights markedly decreased. Although the body weights recovered gradually after termination of the stress, the recovery was not full until the final stage of pregnancy. Interestingly, restraint stress caused growth retardation of the fetuses, leading to a significant decrease in their body weights, and increased early and late resorptions of embryos and fetuses according to the stress periods. Although the preceding (GD1-4) and concurrent (GD5-8) stresses did not affect embryonic implantation, restraint stress on GD9-12 caused cleft palate. Whereas vertebral abnormalities, mainly bipartite ossification, were observed only in animals stressed on GD5-8, abnormalities of sternebrae, exhibiting asymmetric or bipartite ossification, were enhanced by the stress at all of the gestational stages. On the other hand, the incidence of other malformations including renal malposition and costal abnormalities was not increased by stress at any of the 4 stages. Taken together, the results suggest that intensive restraint stress influences the maternal body weight resulting in growth retardation and increased mortality of embryos and fetuses, in addition to gestational stage-specific ventricular dilatation, cleft palate and sternal abnormalities.     

Chenodeoxycholic Acid Reduces Hypoxia Inducible Factor-1α Protein and Its Target Genes

This study evaluated HIF-1α inhibitors under different hypoxic conditions, physiological hypoxia (5% O₂) and severe hypoxia (0.1% O₂). We found that chenodeoxy cholic acid (CDCA) reduced the amount of HIF-1α protein only under physiological hypoxia but not under severe hypoxia without decreasing its mRNA level. By using a proteasome inhibitor MG132 and a translation inhibitor cyclohexamide, we showed that CDCA reduced HIF-1α protein by decreasing its translation but not by enhancing its degradation. The following findings indicated that farnesoid X receptor (FXR), a CDCA receptor and its target gene, Small heterodimer partner (SHP) are not involved in this effect of CDCA. Distinctly from CDCA, MG132 prevented SHP and an exogenous FXR agonist, GW4064 from reducing HIF-1α protein. Furthermore a FXR antagonist, guggulsterone failed to prevent CDCA from decreasing HIF-1α protein. Furthermore, guggulsterone by itself reduced HIF-1α protein even in the presence of MG132. These findings suggested that CDCA and guggulsterone reduced the translation of HIF-1α in a mechanism which FXR and SHP are not involved. This study reveals novel therapeutic functions of traditional nontoxic drugs, CDCA and guggulsterone, as inhibitors of HIF-1α protein.     

NDRG3-mediated lactate signaling in hypoxia

Hypoxia is associated with many pathological conditions as well as the normal physiology of metazoans. We identified a lactate-dependent signaling pathway in hypoxia, mediated by the oxygen- and lactate-regulated protein NDRG family member 3 (NDRG3). Oxygen negatively regulates NDRG3 expression at the protein level via the PHD2/VHL system, whereas lactate, produced in excess under prolonged hypoxia, blocks its proteasomal degradation by binding to NDRG3. We also found that the stabilized NDRG3 protein promotes angiogenesis and cell growth under hypoxia by activating the Raf-ERK pathway. Inhibiting cellular lactate production abolishes NDRG3-mediated hypoxia responses. The NDRG3-Raf-ERK axis therefore provides the genetic basis for lactate-induced hypoxia signaling, which can be exploited for the development of therapies targeting hypoxia-induced diseases in addition to advancing our understanding of the normal physiology of hypoxia responses. [BMB Reports 2015; 48(6): 301-302]     

Autophagic response to a single bout of moderate exercise in murine skeletal muscle

The effect of a single bout of exercise on autopahgy in murine gastrocnemius muscle was investigated. Autophagy is a process for the degradation system of cytoplasmic components, which may help maintain intracellular quality control of cell survival and turnover under normal conditions. The present study investigated the changes of autophagy-related proteins including microtubule-associated protein 1b light chain 3 (LC3), Beclin-1, Atg7 (autophagy-related gene 7), conjugation form of Atg12 to Atg5, lysosome-associated membrane protein (LAMP2a), and muscle-specific RING finger protein-1 (MURF-1) protein level in gastrocnemius muscle after a single bout of treadmill exercise. Mice exercised on a treadmill for 50 min at a speed of 12.3 m/min with a slope of 5°. The animals were sacrificed by cervical dislocation 0, 3, 6, or 12 h after exercise, and muscle samples were collected immediately. Western blot analysis demonstrated that the autophagy marker LC3-II was significantly decreased during the recovery period (3, 6, and 12 h) whereas there was no decrease immediately after exercise (0 h). To identify factors related to this decrease, autophagosome component proteins were examined in murine gastrocnemius muscle. A decrease in Beclin-1, Atg7, and LAMP2a during recovery period was concomitant with the decreased level of LC3-II. Additionally, MuRF-1 expression was significantly increased after a single bout of exercise. This study is the first to demonstrate autophasic related protein expression after a single bout of treadmill exercise and our results suggest that a single bout of treadmill exercise attenuates the autophagic response in murine skeletal muscle.