GC/MS Profiling,In Vitro and In Silico Pharmacological Screening and Principal Component Analysis of Essential Oils from Three Exotic and Two Endemic Plants from Mauritius

The chemical and pharmacological profiles of essential oils (EOs) hydrodistilled in yields of 0.03–0.77 % (w/w) from three exotic (Cinnamomum camphora, Petroselinum crispum, and Syzygium samarangense) and two endemic (Pittosporum senacia subsp. senacia and Syzygium coriaceum) medicinal plants were studied. GC-MS/GC-FID analysis of the EOs identified the most dominant components to be myristicin (40.3 %), myrcene (62.2 %), 1,8-cineole (54.0 %), β-pinene (21.3 %) and (E)-β-ocimene (24.4 %) in P. crispum, P. senacia and C. camphora, S. samarangense and S. coriaceum EOs, respectively. All EOs were found to possess anti-amylase (0.70–1.50 mM ACAE/g EO) and anti-tyrosinase (109.35–158.23 mg KAE/g) properties, whereas no glucosidase inhibition was displayed. Only Syzygium EOs acted as dual inhibitors of both acetyl- and butyryl-cholinesterases, while P. senacia and C. camphora EOs inhibited acetylcholinesterase selectively and P. crispum EO was inactive (AChE: 4.64–4.96 mg GALAE/g; BChE: 5.96 and 7.10 mg GALAE/g). Molecular docking revealed 1,8-cineole to present the best binding affinities with butyrylcholinesterase, amylase and tyrosinase, while both myristicin and β-pinene with acetylcholinesterase and finally β-pinene with glucosidase. In vitro antioxidant potency was also demonstrated in different assays (DPPH: 13.52–53.91 mg TE/g, ABTS: 5.49–75.62 mg TE/g; CUPRAC: 45.38–243.21 mg TE/g, FRAP: 42.49–110.64 mg TE/g; and phosphomolybdenum assay: 82.61–160.93 mM TE/g). Principal component analysis revealed the EOs to differ greatly in their bioactivities due to their chemodiversity. This study has unveiled some interesting preliminary pharmacological profiles of the EOs that could be explored for their potential applications as phytotherapeutics.     

Trophoblast-specific DNA methylation occurs after the segregation of the trophectoderm and inner cell mass in the mouse periimplantation embryo

The first cell differentiation in the mammalian development separates the trophoblast and embryonic cell lineages, resulting in the formation of the trophectoderm (TE) and inner cell mass (ICM) in blastocysts. Although a lower level of global DNA methylation in the genome of the TE compared with ICM has been suggested, the dynamics of the DNA methylation profile during TE/ICM differentiation has not been elucidated. To address this issue, first we identified tissue-dependent and differentially methylated regions (T-DMRs) between trophoblast stem (TS) and embryonic stem (ES) cells. Most of these TS–ES T-DMRs were also methylated differentially between trophoblast and embryonic tissues of embryonic day (E) 6.5 mouse embryos. Furthermore, we found that the human genomic regions homologous to mouse TS–ES T-DMRs were methylated differentially between human placental tissues and ES cells. Collectively, we defined them as cell-lineage-based T-DMRs between trophoblast and embryonic cell lineages (T–E T-DMRs). Then, we examined TE and ICM cells isolated from mouse E3.5 blastocysts. Interestingly, all T-DMRs examined, including the Elf5, Pou5f1 and Nanog loci, were in the nearly unmethylated status in both TE and ICM and exhibited no differences. The present results suggest that the establishment of DNA methylation profiles specific to each cell lineage follows the first morphological specification. Together with previous reports on asymmetry of histone modifications between TE and ICM, the results of the current study imply that histone modifications function as landmarks for setting up cell-lineage-specific differential DNA methylation profiles.     

Different regulatory mechanisms underlie similar transposable element profiles in pufferfish and fruitflies

Comparative analysis of recently sequenced eukaryotic genomes has uncovered extensive variation in transposable element (TE) abundance, diversity, and distribution. The TE profile in the sequenced pufferfish genomes is more similar to that of Drosophila melanogaster than to human or mouse, in that pufferfish TEs exhibit low overall abundance, high family diversity, and localization in the heterochromatin. It has been suggested that selection against the deleterious effects of ectopic recombination between TEs has structured the TE profile in Drosophila and pufferfish but not in humans. We test this hypothesis by measuring the sample frequency of 48 euchromatic TE insertions in the genome of the green spotted pufferfish (Tetraodon nigroviridis). We estimate the strength of selection acting on recent insertions by analyzing the site frequency spectrum using a maximum-likelihood approach. We show that in contrast to Drosophila, euchromatic TE insertions in Tetraodon are selectively neutral and that the low copy number and compartmentalized distribution of TEs in the Tetraodon genome must be caused by regulation by means other than purifying selection acting on recent insertions. Inference of regulatory processes governing TE profiles should take into account factors such as effective population size, incidence of inbreeding/outcrossing, and other species-specific traits.     

PASTEC: An Automatic Transposable Element Classification Tool

Summary

The classification of transposable elements (TEs) is key step towards deciphering their potential impact on the genome. However, this process is often based on manual sequence inspection by TE experts. With the wealth of genomic sequences now available, this task requires automation, making it accessible to most scientists. We propose a new tool, PASTEC, which classifies TEs by searching for structural features and similarities. This tool outperforms currently available software for TE classification. The main innovation of PASTEC is the search for HMM profiles, which is useful for inferring the classification of unknown TE on the basis of conserved functional domains of the proteins. In addition, PASTEC is the only tool providing an exhaustive spectrum of possible classifications to the order level of the Wicker hierarchical TE classification system. It can also automatically classify other repeated elements, such as SSR (Simple Sequence Repeats), rDNA or potential repeated host genes. Finally, the output of this new tool is designed to facilitate manual curation by providing to biologists with all the evidence accumulated for each TE consensus.

Availability

PASTEC is available as a REPET module or standalone software (http://urgi.versailles.inra.fr/download/repet/REPET_linux-x64-2.2.tar.gz). It requires a Unix-like system. There are two standalone versions: one of which is parallelized (requiring Sun grid Engine or Torque), and the other of which is not.     

Quantitatively Increased Somatic Transposition of Transposable Elements in Drosophila Strains Compromised for RNAi

In Drosophila melanogaster, small RNAs homologous to transposable elements (TEs) are of two types: piRNA (piwi-interacting RNA) with size 23-29nt and siRNA (small interfering RNA) with size 19-22nt. The siRNA pathway is suggested to silence TE activities in somatic tissues based on TE expression profiles, but direct evidence of transposition is lacking. Here we developed an efficient FISH (fluorescence in Situ hybridization) based method for polytene chromosomes from larval salivary glands to reveal new TE insertions. Analysis of the LTR-retrotransposon 297 and the non-LTR retroposon DOC shows that in the argonaut 2 (Ago2) and Dicer 2 (Dcr2) mutant strains, new transposition events are much more frequent than in heterozygous strains or wild type strains. The data demonstrate that the siRNA pathway represses TE transposition in somatic cells. Nevertheless, we found that loss of one functional copy of Ago2 or Dcr2 increases somatic transpositions of the elements at a lower level depending on the genetic background, suggesting a quantitative role for RNAi core components on mutation frequency.     

Correlation of dose-antimicrobial effect in modeling in vitro pharmacokinetic profiles of normal and impaired elimination of antibiotics

Relationships between concentration and antimicrobial effect (AME) of sisomicin (SMN) and cefotaxime (CTX) were established by simulating their pharmacokinetic profiles in an in vitro dynamic model. The AME duration (TE, time shift between the curves of bacteria heat output in the presence and absence of the antibiotics) or intensity (IE, area between the above curves) for both the antibiotics depended in the same way on the area under the concentration/time curve (AUC, mimicing of intravenous administration of the antibiotics in various doses). At low and moderate values of the AUC the dependences of IE or TE vs the AUC (the bacteriostatic phase of the AME development) were of the sigmoid shape while at high values of the AUC there was a marked increase in IE or TE (the bactericidal phase). The patterns of the IE or TE vs AUC curves in impaired antibiotic elimination were analogous. At the same time the IE or TE vs AUC curves for both the antibiotics under simulation of normal elimination (T 1/2, SMN-2.1 h, T 1/2, CTX-1.2 h) and impaired one (T 1/2, SMN-8.3 h, T 1/2, CTX-4.6 h) did not match. In the first case the AMESMN was on the whole higher and the AMECTX was lower than in the second case. Therefore, in patients with renal failure the efficient concentration of the aminoglycoside in blood can be higher and that of the cephalosporin on the contrary can be lower than the normal.     

Transposable element profiles reveal cell line identity and loss of heterozygosity in Drosophila cell culture

Cell culture systems allow key insights into biological mechanisms yet suffer from irreproducible outcomes in part because of cross-contamination or mislabeling of cell lines. Cell line misidentification can be mitigated by the use of genotyping protocols, which have been developed for human cell lines but are lacking for many important model species. Here, we leverage the classical observation that transposable elements (TEs) proliferate in cultured Drosophila cells to demonstrate that genome-wide TE insertion profiles can reveal the identity and provenance of Drosophila cell lines. We identify multiple cases where TE profiles clarify the origin of Drosophila cell lines (Sg4, mbn2, and OSS_E) relative to published reports, and also provide evidence that insertions from only a subset of long-terminal repeat retrotransposon families are necessary to mark Drosophila cell line identity. We also develop a new bioinformatics approach to detect TE insertions and estimate intra-sample allele frequencies in legacy whole-genome sequencing data (called ngs_te_mapper2), which revealed loss of heterozygosity as a mechanism shaping the unique TE profiles that identify Drosophila cell lines. Our work contributes to the general understanding of the forces impacting metazoan genomes as they evolve in cell culture and paves the way for high-throughput protocols that use TE insertions to authenticate cell lines in Drosophila and other organisms.     

Locus-specific chromatin profiling of evolutionarily young transposable elements

Despite a vast expansion in the availability of epigenomic data, our knowledge of the chromatin landscape at interspersed repeats remains highly limited by difficulties in mapping short-read sequencing data to these regions. In particular, little is known about the locus-specific regulation of evolutionarily young transposable elements (TEs), which have been implicated in genome stability, gene regulation and innate immunity in a variety of developmental and disease contexts. Here we propose an approach for generating locus-specific protein–DNA binding profiles at interspersed repeats, which leverages information on the spatial proximity between repetitive and non-repetitive genomic regions. We demonstrate that the combination of HiChIP and a newly developed mapping tool (PAtChER) yields accurate protein enrichment profiles at individual repetitive loci. Using this approach, we reveal previously unappreciated variation in the epigenetic profiles of young TE loci in mouse and human cells. Insights gained using our method will be invaluable for dissecting the molecular determinants of TE regulation and their impact on the genome.     

The characterization of bovine embryos obtained from prepubertal calf oocytes and their viability after non surgical embryo transfer

We have previously shown that the addition of epidermal growth factor (EGF) during in vitro maturation was capable of stimulating the cytoplasmic maturation of cow and calf oocytes. The aim of the present study was to compare calf and cow blastocysts produced in the presence of EGF in terms of total cell number and cell distribution between trophectoderm (TE) and inner cell mass (ICM), pattern of protein synthesis, and ability to establish pregnancy after embryo transfer to recipients. For all experiment, embryos at Day 7 were obtained from IVM/IVF/IVC oocytes. No significant differences were noted in total cell number (cow= 138±46 vs CALF= 142±59; mean±SD) or ICM and TE cell number between calf (ICM= 35 ± 19, TE= 107± 52) and cow (ICM= 38± 21, TE= 99 ± 32) blastocysts, nor in the ICM/total cell number ratio (cow= 0.27± 11, CALF= 0.25 ± 12). No differences were noted in the constitutive and the neosynthetic protein profiles between cow and calf embryos obtained in vitro. The results of embryo transfer, showed that there was higher pregnancy loss following transfer of calf compared with cow embryos. After Day 35, the rate of pregnancy decreases, with only 22% of calf embryos maintaining pregnancy until calving compared with 39% for cow embryos. In conclusion, it would seem that embryos originating from calf oocytes are less capable of establishing pregnancies than embryos obtained from adult oocytes, althrough this difference was not significant. This low viability cannot be explained by differences in cell number or by the protein profiles identifed between these 2 groups of embryos.     

Serotonin involvement in analgesia induced by transcranial electrostimulation

The experiments described here were intended to investigate whether serotonin (5HT) may be involved in analgesia induced by low current transcranial electrostimulation (TE). The TE stimulus is a 10 mu-ampere, 10 Hz, pulsed current transmitted via electrodes in the pinnae. Combinations of the following were given as intraperitoneal injections: 300 mg/kg p-chlorophenylalanine (pCPA) 48 hours before testing, 100 mg/kg 5-hydroxytryptophan (5HTP) 30 min before testing and the saline vehicle for these drugs. Rats were tested prior to and 30 minutes after TE or sham TE. Testing for analgesia consisted of putting progressively increasing pressure on the rat tail 1/4 inch from the tip with a pneumatically driven, right angle wedge. The amount of pressure at which the rat moved its tail was measured both before and after TE, or sham TE, and recorded as the difference in tolerated peak pressure (DTPP). TE produced analgesia as manifested by a 613 percent increase in DTPP compared with sham TE treatment values. Among TE treated rats, pretreatment with pCPA decreased DTPP 91.5 percent compared with saline control values, indicating 5HT involvement. 5HTP restored TE induced analgesia in pCPA treated rats to the level of saline treated control animals, confirming 5HT involvement.     

Expansion of human embryonic stem cells: a comparative study

Objectives: Human embryonic stem cells (hESC) are promising for tissue engineering (TE) purposes due to their unique properties. However, current standard mechanical passaging techniques limit rates of possible TE experiments, as it is difficult to obtain high enough numbers of the cells for experimentation. In this study, several dissociative solutions and application methods are tested for their applicability to, and influence on, hESC culture and expansion. Materials and methods: Expansion of two hESC lines, H1 and VUB01, subjected to different passaging techniques, was evaluated. Four dissociative solutions – TrypLE? Express, Trypsin‐EDTA, Cell Dissociation Solution and Accutase?– were combined with two application protocols. As reference conditions, manual and bead‐based passaging techniques were used. Results: Results showed that use of Cell Dissociation Solution in combination with a slow adaptation protocol, generated the best expansion profile for both cell lines. The hESC single cell lines remained pluripotent, had good expansion profiles and were capable of differentiation into representatives of all three germ layers. Reproducibility of the results was confirmed by adaptation for three other hESC lines. Conclusion: Use of Cell Dissociation Solution, combined with slow adaptation protocol, allows a fast switch from the mechanical passaging technique to a single‐cell split technique, generating stable and robust hESC cell lines, which allow for large scale expansion of hESC for TE purposes.     

A direct solid‐phase assay specific for heavy‐metal toxicity. II. Assessment of heavy‐metal immobilization in soils and bioavailability to plants

We have used the solid‐phase MetPLA TE, an enzyme assay that is specific for heavy‐metal toxicity, to investigate metal toxicity of soils that have been amended with urban wastewater sludges or contaminated with dry deposition from metal‐plating industries. We have shown that soil toxicity, using MetPLA TE, ranged from 21 to 72.5% inhibition of enzyme activity. Evin soil, which displayed the highest toxicity, also had the highest concentrations of Pb and Zn. Metal uptake studies with ryegrass grown on Evin soil, showed Zn, Cd, and Pb accumulation in the plant that exceeds the standard levels reported for grasses

Solid‐phase MetPLA TE was also used as a tool to study the reduction of heavy‐metal toxicity following soil amendments to immobilize metals in soil and thus reduce their toxicity. It was found that the addition of 1% hydrated manganese oxide significantly reduced dissolved metals in soil, their accumulation by ryegrass, and soil toxicity as shown by MetPLA TE.     

Insertion polymorphism of transposable elements and population structure of Anopheles gambiae M and S molecular forms in Cameroon

The insertion polymorphism of five transposable element (TE) families was studied by Southern blots in several populations of the M and S molecular forms of the mosquito Anopheles gambiae sensu stricto from southern Cameroon. We showed that the mean TE insertion site number and the within-population insertion site polymorphism globally differed between the M and S molecular forms. The comparison of the TE insertion profiles of the populations revealed a significant differentiation between these two molecular forms (0.163 < Phi(ST) < 0.371). We cloned several insertions of a non-LTR retrotransposon (Aara8) that were fixed in one form and absent in the other one. The only insertion that could be clearly located on a chromosome arm mapped to cytological division 6 of chromosome X, confirming the importance of this region in the ongoing speciation between the M and S molecular forms.     

Offspring of male and female parents with thalidomide embryopathy: birth defects and functional anomalies

BACKGROUND: The aim of the study was to evaluate congenital malformations and functional anomalies in the offspring of Swedish parents with thalidomide embryopathy (TE). METHODS: Sixty-four children (29 girls, 35 boys) with ages ranging from 0-18 years, born to 34 Swedish parents (14 women, 20 men) with TE, were studied. Data on malformations and dysfunction were collected from medical records at maternity and child healthcare units, delivery units, hospitals, outpatient clinics and schools. RESULTS: Five children had both a mother and father with TE, 23 had a mother suffering from TE, and in 36 children the father had TE. One girl had a major malformation consisting of pulmonary stenosis, and single cases of minor physical features and positional deformities were observed. One boy had autism. Four children were born preterm, all to a TE mother. One child died within 24 hr after birth. Seven spontaneous abortions were registered, five of them in TE mothers. The cesarian section rate was 39% among the TE mothers, compared to 14% among the non-TE mothers. CONCLUSIONS: Malformations or functional anomalies similar to those typical for TE were not found in this group of children born to Swedish parents with TE. Cesarian sections were more frequently performed in TE mothers, partly because of pelvic and uterine malformations.     

Oxygen gradients in tissue-engineered PEGT/PBT cartilaginous constructs: measurement and modeling

The supply of oxygen within three-dimensional tissue-engineered (TE) cartilage polymer constructs is mainly by diffusion. Oxygen consumption by cells results in gradients in the oxygen concentration. The aims of this study were, firstly, to identify the gradients within TE cartilage polymer constructs and, secondly, to predict the profiles during in vitro culture. A glass microelectrode system was adapted and used to penetrate cartilage and TE cartilaginous constructs, yielding reproducible measurements with high spatial resolution. Cartilage polymer constructs were cultured for up to 41 days in vitro. Oxygen concentrations, as low as 2-5%, were measured within the center of these constructs. At the beginning of in vitro culture, the oxygen gradients were steeper in TE constructs in comparison to native tissue. Nevertheless, during the course of culture, oxygen concentrations approached the values measured in native tissue. A mathematical model was developed which yields oxygen profiles within cartilage explants and TE constructs. Model input parameters were assessed, including the diffusion coefficient of cartilage (2.2 x 10(-9)) + (0.4 x 10(-9) m(2) s(-1)), 70% of the diffusion coefficient of water and the diffusion coefficient of constructs (3.8 x 10(-10) m(2) s(-1)). The model confirmed that chondrocytes in polymer constructs cultured for 27 days have low oxygen requirements (0.8 x 10(-19) mol m(-3) s(-1)), even lower than chondrocytes in native cartilage. The ability to measure and predict local oxygen tensions offers new opportunities to obtain more insight in the relation between oxygen tension and chondrogenesis.     

重组人内皮抑素对食管癌细胞生长抑制作用的体外研究

目的:探讨重组人内皮抑素(rhES)对食管鳞癌系KYSE-150及TE1细胞生长的影响。方法:应用四甲基偶氮唑盐(MTT)法,以大鼠成纤维细胞L929为对照细胞,检测rhES不同浓度(0、12.5、25、50、100、200、400、600μg/ml)和作用时间(24h、48h)对食管鳞癌系KYSE-150、TE1和L929细胞的生长抑制作用。结果:大鼠L929细胞经rhES处理后,吸光度A值轻微降低,差异不具有统计学意义(P>0.05),食管鳞癌系KYSE-150、TE1经rhES处理后,吸光度A值明星降低,差异具有统计学意义(P<0.05)。结论:rhES明显抑制食管鳞癌系KYSE-150及TE1细胞增殖,且呈时间-剂量依赖性。     

Uncertainty in techno-economic estimates of cellulosic ethanol production due to experimental measurement uncertainty

ABSTRACT: BACKGROUND: Cost-effective production of lignocellulosic biofuels remains a major financial and technical challenge at the industrial scale. A critical tool in biofuels process development is the techno-economic (TE) model, which calculates biofuel production costs using a process model and an economic model. The process model solves mass and energy balances for each unit, and the economic model estimates capital and operating costs from the process model based on economic assumptions. The process model inputs include experimental data on the feedstock composition and intermediate product yields for each unit. These experimental yield data are calculated from primary measurements. Uncertainty in these primary measurements is propagated to the calculated yields, to the process model, and ultimately to the economic model. Thus, outputs of the TE model have a minimum uncertainty associated with the uncertainty in the primary measurements. RESULTS: We calculate the uncertainty in the Minimum Ethanol Selling Price (MESP) estimate for lignocellulosic ethanol production via a biochemical conversion process: dilute sulfuric acid pretreatment of corn stover followed by enzymatic hydrolysis and co-fermentation of the resulting sugars to ethanol. We perform a sensitivity analysis on the TE model and identify the feedstock composition and conversion yields from three unit operations (xylose from pretreatment, glucose from enzymatic hydrolysis, and ethanol from fermentation) as the most important variables. The uncertainty in the pretreatment xylose yield arises from multiple measurements, whereas the glucose and ethanol yields from enzymatic hydrolysis and fermentation, respectively, are dominated by a single measurement: the fraction of insoluble solids (fIS) in the biomass slurries. CONCLUSIONS: We calculate a $0.15/gal uncertainty in MESP from the TE model due to uncertainties in primary measurements. This result sets a lower bound on the error bars of the TE model predictions. This analysis highlights the primary measurements that merit further development to reduce the uncertainty associated with their use in TE models. While we develop and apply this mathematical framework to a specific biorefinery scenario here, this analysis can be readily adapted to other types of biorefining processes and provides a general framework for propagating uncertainty due to analytical measurements through a TE model.