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11.
Eleftheria Polychronidou Ilias Kalamaras Andreas Agathangelidis Lesley-Ann Sutton Xiao-Jie Yan Vasilis Bikos Anna Vardi Konstantinos Mochament Nicholas Chiorazzi Chrysoula Belessi Richard Rosenquist Paolo Ghia Kostas Stamatopoulos Panayiotis Vlamos Anna Chailyan Nanna Overby Paolo Marcatili Anastasia Hatzidimitriou Dimitrios Tzovaras 《BMC bioinformatics》2018,19(14):414
12.
13.
Dylan Alexander Carlin Ryan W. Caster Xiaokang Wang Stephanie A. Betzenderfer Claire X. Chen Veasna M. Duong Carolina V. Ryklansky Alp Alpekin Nathan Beaumont Harshul Kapoor Nicole Kim Hosna Mohabbot Boyu Pang Rachel Teel Lillian Whithaus Ilias Tagkopoulos Justin B. Siegel 《PloS one》2016,11(1)
The use of computational modeling algorithms to guide the design of novel enzyme catalysts is a rapidly growing field. Force-field based methods have now been used to engineer both enzyme specificity and activity. However, the proportion of designed mutants with the intended function is often less than ten percent. One potential reason for this is that current force-field based approaches are trained on indirect measures of function rather than direct correlation to experimentally-determined functional effects of mutations. We hypothesize that this is partially due to the lack of data sets for which a large panel of enzyme variants has been produced, purified, and kinetically characterized. Here we report the kcat and KM values of 100 purified mutants of a glycoside hydrolase enzyme. We demonstrate the utility of this data set by using machine learning to train a new algorithm that enables prediction of each kinetic parameter based on readily-modeled structural features. The generated dataset and analyses carried out in this study not only provide insight into how this enzyme functions, they also provide a clear path forward for the improvement of computational enzyme redesign algorithms. 相似文献
14.
Pulmonary and systemic endotoxin tolerance in preterm fetal sheep exposed to chorioamnionitis 总被引:1,自引:0,他引:1
Kallapur SG Jobe AH Ball MK Nitsos I Moss TJ Hillman NH Newnham JP Kramer BW 《Journal of immunology (Baltimore, Md. : 1950)》2007,179(12):8491-8499
In a model of human chorioamnionitis, fetal sheep exposed to a single injection, but not repeated injections, of intra-amniotic endotoxin develop lung injury responses. We hypothesized that repeated exposure to intra-amniotic endotoxin induces endotoxin tolerance. Fetal sheep were given intra-amniotic injections of saline (control) or Escherichia coli LPS O55:B5 (10 mg) either 2 days (2-day group, single exposure), 7 days (7-day group, single exposure), or 2 plus 7 days (2- and 7-day repeat exposure) before preterm delivery at 124 days gestation (term=150 days). Endotoxin responses were assessed in vivo in the lung and liver, and in vitro in monocytes from the blood and the lung. Compared with the single 2-day LPS exposure group, the (2 plus 7 days) repeat LPS-exposed lambs had: 1) decreased lung neutrophil and monocyte inducible NO synthase (NOSII) expression, and 2) decreased lung cytokine and liver serum amyloid A3 mRNA expression. In the lung, serum amyloid A3 mRNA expression decreased in the airway epithelial cells but not in the lung inflammatory cells. Unlike the single 7-day LPS exposure group, peripheral blood and lung monocytes from the repeat-LPS group did not increase IL-6 secretion or hydrogen peroxide production in response to in vitro LPS. Compared with controls, TLR4 expression did not change but IL-1R-associated kinase M expression increased in the monocytes from repeat LPS-exposed lambs. These results are consistent with the novel finding of endotoxin tolerance in preterm fetal lungs exposed to intra-amniotic LPS. The findings have implications for preterm infants exposed to chorioamnionitis for both responses to lung injury and postnatal nosocomial infections. 相似文献
15.
Sloboda DM Moss TJ Li S Doherty D Nitsos I Challis JR Newnham JP 《American journal of physiology. Endocrinology and metabolism》2007,292(1):E61-E70
Fetal exposure to synthetic glucocorticoids in sheep results in increased fetal hypothalamic-pituitary-adrenal (HPA) activity persisting to one year of age. We aimed to determine the effects of single or repeated maternal or fetal betamethasone injections on offspring HPA activity at 2 and 3 yr of age and whether changes in adrenal mediators of steroidogenesis contribute to changes in pituitary-adrenal function. Pregnant ewes or their fetuses received either repeated intramuscular saline or betamethasone injections (0.5 mg/kg) at 104, 111, 118, and 124 days of gestation (dG) or a single betamethasone injection at 104 dG followed by saline at 111, 118, and 124 dG. Offspring were catheterized at 2 and 3 yr of age and given corticotrophin-releasing hormone + arginine vasopressin challenges. Adrenal tissue was collected for quantitative RT-PCR mRNA determination at 3.5 yr of age. In 2-yr-old offspring, maternal betamethasone injections did not alter basal ACTH or cortisol levels, but repeated injections elevated ACTH responses. At 3 yr of age, basal ACTH was elevated, and both basal and stimulated cortisol levels were suppressed by repeated maternal injections. Basal and stimulated cortisol-to-ACTH ratios and basal cortisol-to-cytochrome P-450 17alpha-hydroxylase (P450c17) mRNA ratios were suppressed by repeated injections. Repeated fetal betamethasone injections attenuated basal ACTH and cortisol levels in offspring at 2 but not 3 yr of age. Plasma changes were not associated with altered adrenal P450c17, ACTH receptor, beta-hydroxysteroid dehydrogenase, or glucocorticoid receptor mRNA levels. These data suggest that maternal, but not fetal, betamethasone administration results in adrenal suppression in adulthood. 相似文献
16.
Misexpression screen in Drosophila melanogaster aiming to reveal novel factors involved in formation of body parts 下载免费PDF全文
To identify novel factors that lead a fly imaginal disc to adopt its developmental fate, we carried out a modular dominant misexpression screen in imaginal discs. We have identified two factors that appear to change the fate of the respective body structure and appear to lead to the transformation of a body part. In one mutant line, notum tissue, normally derived from wing imaginal tissue, formed close to the site of the sternopleural bristles, which are leg disc derivatives. In the other line, the arista is transformed into a tubular structure, resembling an abnormal leg. We found that ectopic expression of abrupt was responsible for this potential transformation of the arista. 相似文献
17.
Piouka A Farmakiotis D Katsikis I Macut D Gerou S Panidis D 《American journal of physiology. Endocrinology and metabolism》2009,296(2):E238-E243
The objective of the study was the comparison of anti-Müllerian hormone (AMH) levels among obese or overweight and normal-weight women with the four different polycystic ovary syndrome (PCOS) phenotypes and healthy control subjects. AMH levels were evaluated in four age- and body mass index (BMI)-matched groups of 25 normal-weight and 25 obese or overweight women each, belonging to the four main subsets of the syndrome resulting from combinations of the three diagnostic criteria [group 1: oligo- and/or anovulation (ANOV), hyperandrogenemia (HA), and polycystic ovaries (PCO) on ultrasonographic evaluation; group 2: ANOV and HA; group 3: HA and PCO, group 4: ANOV and PCO], and in 50 (25 obese or overweight and 25 normal weight) age- and BMI-matched healthy control subjects. Age, BMI, waist circumference, FSH, LH, prolactin, testosterone, Delta(4)-androstenedione, dehydroepiandrosterone-sulfate, 17alpha-OH-progesterone, fasting insulin, glucose, AMH, free androgen index, and homeostasis model assessment for insulin resistance index were analyzed. AMH levels were significantly higher in PCOS groups 1 and 2 compared with groups 3 and 4 and the control group and higher in PCOS groups 3 and 4 compared with the control group. AMH levels were significantly increased in normal-weight compared with obese and overweight women. AMH concentrations were independently predicted, in order of significance, by LH and testosterone levels, BMI (negatively), and the total number of follicles 2-9 mm in diameter. The differences in circulating AMH levels between the main phenotypic groups of PCOS women appear to reflect the severity of the syndrome, but are negatively affected by obesity. Increased LH levels might be the most significant independent link between PCOS-associated disorders of ovulation and the observed increase in circulating AMH concentration. 相似文献
18.
Isolation and Characterization of Chromium(VI)-Reducing Bacteria from Tannery Effluents 总被引:3,自引:0,他引:3
Ilias M Rafiqullah IM Debnath BC Mannan KS Mozammel Hoq M 《Indian journal of microbiology》2011,51(1):76-81
Two chromium-resistant bacteria (IFR-2 and IFR-3) capable of reducing/transforming Cr(VI) to Cr(III) were isolated from tannery
effluents. Isolates IFR-2 and IFR-3 were identified as Staphylococcus aureus and Pediococcus pentosaceus respectively by 16S rRNA gene sequence analyses. Both isolates can grow well on 2,000 mg/l Cr(VI) (as K2Cr2O7) in Luria-Bertani (LB) medium. Reduction of Cr(VI) was found to be growth-associated in both isolates and IFR-2 and IFR-3
reduced 20 mg/l Cr(VI) completely in 6 and 24 h respectively. The Cr(VI) reduction due to chromate reductase activity was
detected in the culture supernatant and cell lysate but not at all in the cell extract supernatant of both isolates. Whole
cells of IFR-2 and IFR-3 converted 24 and 30% of the initial Cr(VI) concentration (1 mg/l) in 45 min respectively at 37°C.
NiCl2 stimulated the growth of IFR-2 whereas HgCl2 and CdCl2 significantly inhibited the growth of both isolates. Optimum temperature and pH for growth of and Cr(VI) reduction by both
isolates were found to be between 35 and 40°C and pH 7.0 to 8.0. The two bacterial isolates can be good candidates for detoxification
of Cr(VI) in industrial effluents. 相似文献
19.
Ilias Kounatidis Nikolaos Papadopoulos Kostas Bourtzis Penelope Mavragani-Tsipidou 《Génome》2008,51(7):479-491
The European cherry fruit fly, Rhagoletis cerasi, is a major agricultural pest for which biological, genetic, and cytogenetic information is limited. We report here a cytogenetic analysis of 4 natural Greek populations of R. cerasi, all of them infected with the endosymbiotic bacterium Wolbachia pipientis. The mitotic karyotype and detailed photographic maps of the salivary gland polytene chromosomes of this pest species are presented here. The mitotic metaphase complement consists of 6 pairs of chromosomes, including one pair of heteromorphic sex chromosomes, with the male being the heterogametic sex. The analysis of the salivary gland polytene complement has shown a total of 5 long chromosomes (10 polytene arms) that correspond to the 5 autosomes of the mitotic nuclei and a heterochromatic mass corresponding to the sex chromosomes. The most prominent landmarks of each polytene chromosome, the "weak points", and the unusual asynapsis of homologous pairs of polytene chromosomes at certain regions of the polytene elements are also presented and discussed. 相似文献
20.
Konstantinos Z. Vardakas Ilias I. Siempos Alexandros Grammatikos Zoe Athanassa Ioanna P. Korbila Matthew E. Falagas 《CMAJ》2008,179(12):1269-1277