Origin of eukaryotic cells: 40 years on

The year 1970 saw the publication of Origin of Eukaryotic Cells by Lynn Margulis. This influential book brought the exciting and weighty problems of cellular evolution to the scientific mainstream, simultaneously breaking new ground and ‘re-discovering’ the decades-old ideas of German and Russian biologists. In this commemorative review, I discuss the 40 years that have elapsed since this landmark publication, with a focus on the ‘molecular era’: how DNA sequencing and comparative genomics have proven beyond all doubt the central tenets of the endosymbiont hypothesis for the origin of mitochondria and plastids, and, at the same time, revealed a genetic and genomic complexity in modern-day eukaryotes that could not have been imagined in decades past.     

Culture of human mesenchymal stem cells on microcarriers in a 5 l stirred-tank bioreactor

For the first time, fully functional human mesenchymal stem cells (hMSCs) have been cultured at the litre-scale on microcarriers in a stirred-tank 5 l bioreactor, (2.5 l working volume) and were harvested via a potentially scalable detachment protocol that allowed for the successful detachment of hMSCs from the cell-microcarrier suspension. Over 12 days, the dissolved O₂ concentration was >45 % of saturation and the pH between 7.2 and 6.7 giving a maximum cell density in the 5 l bioreactor of 1.7 × 10⁵ cells/ml; this represents >sixfold expansion of the hMSCs, equivalent to that achievable from 65 fully-confluent T-175 flasks. During this time, the average specific O₂ uptake of the cells in the 5 l bioreactor was 8.1 fmol/cell h and, in all cases, the 5 l bioreactors outperformed the equivalent 100 ml spinner-flasks run in parallel with respect to cell yields and growth rates. In addition, yield coefficients, specific growth rates and doubling times were calculated for all systems. Neither the upstream nor downstream bioprocessing unit operations had a discernible effect on cell quality with the harvested cells retaining their immunophenotypic markers, key morphological features and differentiation capacity.     

Workload characterization in a high-energy data grid and impact on resource management

The analysis of data usage in a large set of real traces from a high-energy physics collaboration revealed the existence of an emergent grouping of files that we coined “filecules”. This paper presents the benefits of using this file grouping for prestaging data and compares it with previously proposed file grouping techniques along a range of performance metrics. Our experiments with real workloads demonstrate that filecule grouping is a reliable and useful abstraction for data management in science Grids; that preserving time locality for data prestaging is highly recommended; that job reordering with respect to data availability has significant impact on throughput; and finally, that a relatively short history of traces is a good predictor for filecule grouping. Our experimental results provide lessons for workload modeling and suggest design guidelines for data management in data-intensive resource-sharing environments.

In vitro and in vivo efficacy of rosmarinic acid on quorum sensing mediated biofilm formation and virulence factor production in Aeromonas hydrophila

Rosmarinic acid (RA) was assessed for its quorum sensing inhibitory (QSI) potential against Aeromonas hydrophila strains AH 1, AH 12 and MTCC 1739. The pathogenic strains of A. hydrophila were isolated from infected zebrafish and identified through biochemical analysis and amplification of a species-specific gene (rpsL). The biofilm inhibitory concentration (BIC) of RA against A. hydrophila strains was found to be 750 μg ml^?1. At this concentration, RA reduced the QS mediated hemolysin, lipase and elastase production in A. hydrophila. In FT-IR analysis, RA treated A. hydrophila cells showed a reduction in cellular components. Gene expression analysis confirmed the down-regulation of virulence genes such as ahh1, aerA, lip and ahyB. A. hydrophila infected zebrafish upon treatment with RA showed increased survival rates. Thus, the present study demonstrates the use of RA as a plausible phytotherapeutic compound to control QS mediated biofilm formation and virulence factor production in A. hydrophila.     

Antagonic effects of oestradiol in interaction with IGF-1 on proliferation of lactotroph cells in vitro

The effects of IGF-1, 17 β oestradiol and its functional interaction on lactotrophs cell proliferation were evaluated. In addition we investigated the involvement of PKC α, ɛ and phosphorilated ERK, in the mitogenic process. Primary cell cultures of adenohypophysis from female Wistar rats were studied in serum free conditions. The proliferation of lactotrophs was determined by double immunostaining for BrdU and PRL. The incubation with IGF-1 5, 30 or 100 ng/ml during 48 or 72 h increased lactotrophs proliferation two–threefold depending on IGF-1 concentration. Co-incubation of IGF-1 (30 ng/ml) with genistein (25 μM) or BIM (0.5 or 2 μM), lowered of tyrosine kinase receptor or of PKC respectively, inhibited the induced IGF-1 lactotrophs proliferation. 17 β oestradiol (1, 10 or 100 nM) had not mitogenic effect, whereas in the presence of serum PRL cells proliferation was stimulated. Co-incubation with 1 nM oestradiol and IGF-1 significantly decreased the lactotroph BrdU-labelling achieved with IGF-1. PKC α, ɛ and ERK1/2 levels measured by western blot augmented in the presence of IGF-1 and were inhibited with the addition of genistein, supporting a participation of these enzymes in the proliferate process. Co-incubation of IGF-1 with 1 nM oestradiol decreased both PKC isoforms and activated ERK1/2 levels, suggesting that oestradiol would exert its antiproliferative effect by acting on the signalling pathway of IGF-1. The results revealed antagonic effects of oestradiol on lactotroph proliferation depending on its concentration and the presence of IGF-1.     

Effects of a lipid environment on the fibrillogenic pathway of the N-terminal polypeptide of human apolipoprotein A-I, responsible for in vivo amyloid fibril formation

In amyloidosis associated with apolipoprotein A-I (ApoA-I), heart amyloid deposits are mainly constituted by the 93-residue ApoA-I N-terminal region. A recombinant form of the amyloidogenic polypeptide, named [1-93]ApoA-I, shares conformational properties and aggregation propensity with its natural counterpart. The polypeptide, predominantly in a random coil state at pH 8.0, following acidification to pH 4.0 adopts a helical/molten globule transient state, which leads to formation of aggregates. Here we provide evidence that fibrillogenesis occurs also in physiologic-like conditions. At pH 6.4, [1-93]ApoA-I was found to assume predominantly an α-helical state, which undergoes aggregation at 37°C over time at a lower rate than at pH 4.0. After 7 days at pH 6.4, protofibrils were observed by atomic force microscopy (AFM). Using a multidisciplinary approach, including circular dichroism (CD), fluorescence, electrophoretic, and AFM analyses, we investigated the effects of a lipid environment on the conformational state and aggregation propensity of [1-93]ApoA-I. Following addition of the lipid-mimicking detergent Triton X-100, the polypeptide was found to be in a helical state at both pH 8.0 and 6.4, with no conformational transition occurring upon acidification. These helical conformers are stable and do not generate aggregated species, as observed by AFM after 21 days. Similarly, analyses of the effects of cholesterol demonstrated that this natural ApoA-I ligand induces formation of α-helix at physiological concentrations at both pH 8.0 and 6.4. Zwitterionic, positively charged, and negatively charged liposomes were found to affect [1-93]ApoA-I conformation, inducing helical species. Our data support the idea that lipids play a key role in [1-93]ApoA-I aggregation in vivo.     

Stress-induced formation of echinatin and a metabolite, 5′-prenyl-licodione,in cultured Glycyrrhiza echinata cells

The production of a retrochalcone, echinatin, by isoflavone-rich Glycyrrhiza echinata (M-2) cultured cells was stimulated by the addition of yeast extract or calcium alginate beads to the culture medium. Combined addition of yeast extract and cycloheximide suppressed the formation of retrochalcone, suggesting de novo synthesis. A new metabolite was isolated from the induced cells and its structure was determined to be 1-[2,4-dihydroxy-5-(3-methyl-2-butenyl)phenyl]-3-(4-hydroxyphenyl)-1,3-propanedione (5′-prenyl-licodione).     

Frequency of Antibiotic Resistance in a Swine Facility 2.5 Years After a Ban on Antibiotics

The addition of antibiotics to livestock feed has contributed to the selection of antibiotic-resistant bacteria in concentrated animal feeding operations and agricultural ecosystems. The objective of this study was to assess the occurrence of resistance to chlortetracycline and tylosin among bacterial populations at the Swine Complex of McGill University (Province of Quebec, Canada) in the absence of antibiotic administration to pigs for 2.5 years prior to the beginning of this study. Feces from ten pigs born from the same sow and provided feed without antibiotic were sampled during suckling (n = 6 for enumerations, n = 10 for PCR), weanling (n = 10 both for PCR and enumerations), growing (n = 10 both for PCR and enumerations), and finishing (n = 10 both for PCR and enumerations). The percentage of chlortetracycline-resistant anaerobic bacterial populations (Tet^R) was higher than that of tylosin-resistant anaerobic bacterial populations (Tyl^R) at weanling, growing, and finishing. Prior to the transportation of animals to the slaughterhouse, resistant populations varied between 6.5 and 9.4 Log colony-forming units g humid feces⁻¹. In all pigs, tet(L), tet(O), and erm(B) were detected at suckling and weanling, whereas only tet(O) was detected at growing and finishing. The abundance of tet(O) was similar between males and females at weanling and growing and reached 5.1 × 10⁵ and 5.6 × 10⁵ copies of tet(O)/ng of total DNA in males and females, respectively, at finishing. Results showed high abundances and proportions of Tet^R and Tyl^R anaerobic bacterial populations, as well as the occurrence of tet and erm resistance genes within these populations despite the absence of antibiotic administration to pigs at this swine production facility since January 2007, i.e., 2.5 years prior to the beginning of this study. This work showed that the occurrence of bacterial resistance to chlortetracycline and tylosin is high at the Swine Complex of McGill University.     

Trail formation in ants. A generalized Polya urn process

Faced with a choice of paths, an ant chooses a path with a higher concentration of pheromone. Subsequently, it drops pheromone on the path chosen. The reinforcement of the pheromone-following behavior favors the selection of an initially discovered path as the preferred path. This may cause a long path to emerge as the preferred path, were it discovered earlier than a shorter path. However, the shortness of the shorter path offsets some of the pheromone accumulated on the initially discovered longer path. In this paper, we model the trail formation behavior as a generalized Polya urn process. For k equal length paths, we give the distribution of pheromone at any time and highlight its sole dependence on the initial pheromone concentrations on paths. Additionally, we propose a method to incorporate the lengths of paths in the urn process and derive how the pheromone distribution alters on its inclusion. Analytically, we show that it is possible, under certain conditions, to reverse the initial bias that may be present in favor of paths that were discovered prior to the discovery of more efficient (shorter) paths. This addresses the Plasticity–Stability dilemma for ants, by laying out the conditions under which the system will remain stable or become plastic and change the path. Finally, we validate our analysis and results using simulations.     

Tubuloglomerular Feedback Signal Transduction in a Short Loop of Henle

In previous studies, we used a mathematical model of the thick ascending limb (TAL) to investigate nonlinearities in the tubuloglomerular feedback (TGF) loop. That model does not represent other segments of the nephron, the water, and NaCl transport along which may impact fluid flow rate and NaCl transport along the TAL. To investigate the extent to which those transport processes affect TGF mediation, we have developed a mathematical model for TGF signal transduction in a short loop nephron. The model combines a simple representation of the renal cortex with a highly-detailed representation of the outer medulla (OM). The OM portion of the model is based on an OM urine concentrating mechanism model previously developed by Layton and Layton (Am. J. Renal 289:F1346–F1366, 2005a). When perturbations are applied to intratubular fluid flow at the proximal straight tubule entrance, the present model predicts oscillations in fluid flow and solute concentrations in the cortical TAL and interstitium, and in all tubules, vessels, and interstitium in the OM. Model results suggest that TGF signal transduction by the TAL is a generator of nonlinearities: if a sinusoidal oscillation is added to constant intratubular fluid flow, the time required for an element of tubular fluid to traverse the TAL is oscillatory, but nonsinusoidal; those results are consistent with our previous studies. As a consequence, oscillations in NaCl concentration in tubular fluid alongside the macula densa (MD) will be nonsinusoidal and contain harmonics of the original sinusoidal frequency. Also, the model predicts that the oscillations in NaCl concentration at the loop-bend fluid are smaller in amplitude than those at the MD, a result that further highlights the crucial role of TAL in the nonlinear transduction of TGF signal from SNGFR to MD NaCl concentration.     

Enzymatic alterations in developing rat brain cells exposed to a low-intensity 16.5 GHz microwave radiation

The present study deals with the effects of chronic exposure of low-level microwave radiation on developing rat brain. Starting at 35 days of age, male rats were exposed to 2?h/day for another 35 days to a 16.5-GHz microwave radiation field. After the exposure period, the rats were sacrificed, and brain tissues dissected out and used for biochemical assay. Results showed that exposure to a 16.5-GHz radiation caused significant changes in the activity of protein kinase C as compared to the control group. Furthermore, electron microscopic study revealed an increase in glial cell population. These results confirm that brain cell membrane is an interactive site for electromagnetic field causing an inflammation and possibly tumor promotion.     

Production of interferon-β in a culture of fibroblast cells on some polymeric films

Normal human skin (NB1-RGB) cells were cultured in the presenceof polyinosinic and polycytidylic acids, diethylaminoethyldextran, cycloheximide and actinomycin D, which induced humaninterferon-. The simplest induction method, that requiredonly polyinosinic and polycytidylic acids and diethylaminoethyldextran was found to give the highest production ofinterferon- by the cells. The cell growth and productionof interferon- were investigated for NB1-RGB cellscultured on silk fibroin, poly(-methyl-L-glutamate),poly(-benzyl-L-glutamate) and collagen films prepared bythe Langmuir-Blodgett (LB) and casting methods. The cell densityof NB1-RGB cells cultured on the LB films was found to be higherthan that on the cast films made of the same polymer. Thisindicates that not only the chemical structure of the polymersused for the preparation of the films but the preparationmethods of the films, i.e., casting and LB methods, are also astrong factor affecting the cell growth. The production ofinterferon- per unit number of cells was found to behigher on the cast films than that on the LB films made of thesame polymer. This is explained by the fact that the optimalsuppressed growth of NB1-RGB cells on the cast films leads tothe enhanced production of interferon- on the cast filmscompared to those on the LB films prepared by the same polymer.     

Accumulation of lead in root cells of Pisum sativum

The ever-increasing environmental pollution necessitates organisms to develop specific defense systems in order to survive and function effectively. Lead is taken up by plants mainly through roots and over 96% are accumulated there.Pea plants were cultivated hydroponically for 4 days with 0.1, 0.5 and 1 mM Pb(NO₃)₂. Uptake of lead ions from nutrient solution and accumulation in root stems and leaves during 96-h cultivation was estimated. The root tip cells were observed with transmission electron microscope to analyse their ultrastructure and lead localization. Pb was accumulated in the cell wall, cell membrane, vacuoles, mitochondria and peroxisomes. The fractions of mitochondria and peroxisomes were isolated from pea roots purified by means Percoll gradient, and were observed by means of electron microscope with the attachment for X-ray microanalysis. Visible deposits containing Pb were observed in both cell organelles.