Clustered diffusion of integrins

We discuss the diffusion of clusters of integrins (and other similar membrane proteins) on a cell membrane with a cortical cytoskeleton. We argue that protein clusters—in contrast with normal oligomers, which are forced to pass through cytoskeletal barriers all at once—should be treated essentially as many-legged random walkers that can pass through a cytoskeletal barrier by putting one leg at a time through the fence. We present the mathematics that should describe the phenomenon, which result in a two-parameter model of diffusion that should apply to any cluster size. We also perform and discuss numerical simulations of the effect in the erythrocyte model system.     

Genes co-expressed with CPSAR1 identified using ATTED-II

Identification of interacting proteins will help to investigate further the relationship between CPSAR1 and the vesicle transport system or the ribosomes. Thus, we adopted a bioinformatic approach, using the publicly available Arabidopsis thaliana trans-factor and cis-element prediction database, ATTED-II (http://atted.jp/), to identify putative protein interactors. The proteins directly linked to CPSAR1 were almost exclusively nucleus encoded and several were involved in protein synthesis of which three were thylakoid localized. The list of putative interacting proteins does not exclude any of the previous proposed actions of CPSAR1 but encourage more detailed examination of the role of CPSAR1.Key words: Arabidopsis, chloroplast, co-expression, protein cargo, vesicle transportChloroplast protein targeting has been intensively studied.^1–4 Transport of non-proteinaceous material, such as lipids, to the thylakoid has not been studied to the same extent, although several reports do exist.^5–8 Since thylakoids do not produce lipids themselves any lipids present must have been transported from the production site, i.e., the envelope.^9,10 Experimental data support the theory of a vesicular transport system and it has been predicted that several proteins resembling those important in the cytosolic vesicle transport system are chloroplast localized.¹¹ Recently we confirmed that one of these proteins, CPSAR1, is located in the chloroplast and has features similar to the cytosolic COPII-related Sar1 protein, i.e., it is found at the donor membrane and in the vesicle, but not at the acceptor membrane. In addition, other research groups^12,13 have also found that CPSAR1 is chloroplast localized but refer to it as atOBGL or atObgM, respectively, since CPSAR1 shares high sequence similarity with proteins belonging to the Obg-family. The roles of Obg proteins are very diverse, but a role closely connected to ribosomes has been suggested for CPSAR1.¹² CPSAR1 being part of a vesicle system does not exclude it from having a role in relation to ribosomes. The existence of a coiled-coil motif and a GTP binding domain, in combination with the suggested role as part of a vesicle transport system, makes it a highly attractive idea that CPSAR1 interacts with other proteins.     

An ultra performance liquid chromatography-tandem MS assay for tamoxifen metabolites profiling in plasma: first evidence of 4'-hydroxylated metabolites in breast cancer patients

There is increasing evidence that the clinical efficacy of tamoxifen, the first and most widely used targeted therapy for estrogen-sensitive breast cancer, depends on the formation of the active metabolites 4-hydroxy-tamoxifen and 4-hydroxy-N-desmethyl-tamoxifen (endoxifen). Large inter-individual variability in endoxifen plasma concentrations has been observed and related both to genetic and environmental (i.e. drug-induced) factors altering CYP450s metabolizing enzymes activity. In this context, we have developed an ultra performance liquid chromatography-tandem mass spectrometry method (UPLC-MS/MS) requiring 100 μL of plasma for the quantification of tamoxifen and three of its major metabolites in breast cancer patients. Plasma is purified by a combination of protein precipitation, evaporation at room temperature under nitrogen, and reconstitution in methanol/20 mM ammonium formate 1:1 (v/v), adjusted to pH 2.9 with formic acid. Reverse-phase chromatographic separation of tamoxifen, N-desmethyl-tamoxifen, 4-hydroxy-tamoxifen and 4-hydroxy-N-desmethyl-tamoxifen is performed within 13 min using elution with a gradient of 10 mM ammonium formate and acetonitrile, both containing 0.1% formic acid. Analytes quantification, using matrix-matched calibration samples spiked with their respective deuterated internal standards, is performed by electrospray ionization-triple quadrupole mass spectrometry using selected reaction monitoring detection in the positive mode. The method was validated according to FDA recommendations, including assessment of relative matrix effects variability, as well as tamoxifen and metabolites short-term stability in plasma and whole blood. The method is precise (inter-day CV%: 2.5-7.8%), accurate (-1.4 to +5.8%) and sensitive (lower limits of quantification comprised between 0.4 and 2.0 ng/mL). Application of this method to patients' samples has made possible the identification of two further metabolites, 4'-hydroxy-tamoxifen and 4'-hydroxy-N-desmethyl-tamoxifen, described for the first time in breast cancer patients. This UPLC-MS/MS assay is currently applied for monitoring plasma levels of tamoxifen and its metabolites in breast cancer patients within the frame of a clinical trial aiming to assess the impact of dose increase on tamoxifen and endoxifen exposure.     

Primary Human Bronchial Epithelial Cells Grown from Explants

Human bronchial epithelial cells are needed for cell models of disease and to investigate the effect of excipients and pharmacologic agents on the function and structure of human epithelial cells. Here we describe in detail the method of growing bronchial epithelial cells from bronchial airway tissue that is harvested by the surgeon at the times of lung surgery (e.g. lung cancer or lung volume reduction surgery). With ethics approval and informed consent, the surgeon takes what is needed for pathology and provides us with a bronchial portion that is remote from the diseased areas. The tissue is then used as a source of explants that can be used for growing primary bronchial epithelial cells in culture. Bronchial segments about 0.5-1cm long and ≤1cm in diameter are rinsed with cold EBSS and excess parenchymal tissue is removed. Segments are cut open and minced into 2-3mm³ pieces of tissue. The pieces are used as a source of primary cells. After coating 100mm culture plates for 1-2 hr with a combination of collagen (30 μg/ml), fibronectin (10 μg/ml), and BSA (10 μg/ml), the plates are scratched in 4-5 areas and tissue pieces are placed in the scratched areas, then culture medium (DMEM/Ham F-12 with additives) suitable for epithelial cell growth is added and plates are placed in an incubator at 37°C in 5% CO₂ humidified air. The culture medium is changed every 3-4 days. The epithelial cells grow from the pieces forming about 1.5 cm diameter rings in 3-4 weeks. Explants can be re-used up to 6 times by moving them into new pre-coated plates. Cells are lifted using trypsin/EDTA, pooled, counted, and re-plated in T75 Cell Bind flasks to increase their numbers. T75 flasks seeded with 2-3 million cells grow to 80% confluence in 4 weeks. Expanded primary human epithelial cells can be cultured and allowed to differentiate on air-liquid interface. Methods described here provide an abundant source of human bronchial epithelial cells from freshly isolated tissues and allow for studying these cells as models of disease and for pharmacology and toxicology screening.Download video file.^{(144M, mp4)}     

Pharmacognostic evaluation of Artemisia maritima L. a highly medicinal specie of genus Artemisia

The light and scanning electron microscopic observations were carried out for anatomical features of leaf, pollens and powder.Microscopic studies provide useful information for identification and authentication of adulteration in A. maritima. Nutritional analysis of A. maritima revealed that life fundamental macromolecules such as carbohydrates (49.63 %) crude proteins (13.17 %) and crude fibers (21.06 %) were present in sufficient quantity while crude fats (4.11 %) reported in low quantity. The life essential elements such as Mg (9.472 ± 0.011), Ca (4.152 ± 0.135) and Fe (4.112 ± 0.002) were found in high concentration while heavy metals reported under the safety threshold of WHO. These observations favored A. maritima an alternative of food.Appreciable quantity of phenolics (17.64 ± 0.574) and flavonoids (7.67 ± 0.069) were found while qualitatively active phytochemicals were reported.The FTIR characterization of A. maritima crude powder revealed chromatogram in 3328.61 to 408.68 frequency range and 24 characteristic peaks on the basis of which different compounds of biological importance were classified. HPLC-UV technique quantifiedand identified six phenolic compounds morin,epigallocatechin gallate, catechin hydrate,ellagic acid, pyrogallol andrutin. Identification of compounds through GC–MS chromatogram revealed the presence of 46 compounds in methanolic fraction however 17 compounds of biological importance were selected.In-vitro biological evaluation of A. maritima for antioxidant, antimicrobial, antidiabetic (12.61 ± 0.113 %) and cytotoxic activities (LC₅₀ = 20 μg/ml) suggested that methanolic fractions exhibited the highest activity as compared to chloroform and ethyl acetate fractions. The MIC values of 10 or 15 mg/ml were recorded for most of the fungal pathogens. Antibacterial activity revealed 3.75 mg/ml of MIC values against B. subtilis and 1.87 mg/ml against S. aureus, E. coli and P. aeruginosa. In-vivo biological evaluation revealed thatmaximum inhibition was observed for crude extract at 250 mg/kg body weight. The mechanism underlined in-vivo analgesic responses was carried out which revealed that naloxone (morphine and tramadol antagonist) showed no prominent effect while Glibenclamide pretreatment minutely modified the analgesic action. These observations clearly indicted the absence of opiod receptors and involvement of ATP sensitive potassium channels.     

Carbofuran accelerates the cellular senescence and declines the life span of spns1 mutant zebrafish

Carbofuran is a carbamate pesticide, widely used in agricultural practices to increase crop productivity. In mammals, carbofuran is known to cause several untoward effects, such as apoptosis in the hippocampal neuron, oxidative stress, loss of memory and chromosomal anomalies. Most of these effects are implicated with cellular senescence. Therefore, the present study aimed to determine the effect of carbofuran on cellular senescence and biological ageing. Spinster homolog 1 (Spns1) is a transmembrane transporter, regulates autolysosomal biogenesis and plays a role in cellular senescence and survival. Using senescence-associated β-galactosidase staining, we found that carbofuran accelerates the cellular senescence in spns1 mutant zebrafish. The yolk opaqueness, a premature ageing phenotype in zebrafish embryos, was accelerated by carbofuran treatment. In the survival study, carbofuran shortened the life span of spns1 mutant zebrafish. Autophagy is the cellular lysosomal degradation, usually up-regulated in the senescent cells. To know the impact of carbofuran exposure on autophagy progress, we established a double-transgenic zebrafish line, harbouring EGFP-tagged LC3-II and mCherry-tagged Lamp1 on spns1 mutant background, whereas we found, carbofuran exposure synergistically accelerates autolysosome formation with insufficient lysosome-mediated degradation. Our data collectively suggest that carbofuran exposure synergistically accelerates the cellular senescence and affects biological ageing in spns1 defective animals.     

Jangomolide,a novel limonoid from flacourtia jangomas

Jangomolide, a novel limonoid has been isolated, together with limonin, from Flacourtia jangomas.     

eTumorMetastasis: A Network-based Algorithm Predicts Clinical Outcomes Using Whole-exome Sequencing Data of Cancer Patients

Continual reduction in sequencing cost is expanding the accessibility of genome sequencing data for routine clinical applications. However, the lack of methods to construct machine learning-based predictive models using these datasets has become a crucial bottleneck for the application of sequencing technology in clinics. Here, we develop a new algorithm, eTumorMetastasis, which transforms tumor functional mutations into network-based profiles and identifies network operational gene (NOG) signatures. NOG signatures model the tipping point at which a tumor cell shifts from a state that doesn’t favor recurrence to one that does. We show that NOG signatures derived from genomic mutations of tumor founding clones (i.e., the ‘most recent common ancestor’ of the cells within a tumor) significantly distinguish the recurred and non-recurred breast tumors as well as outperform the most popular genomic test (i.e., Oncotype DX). These results imply that mutations of the tumor founding clones are associated with tumor recurrence and can be used to predict clinical outcomes. As such, predictive tools could be used in clinics to guide treatment routes. Finally, the concepts underlying the eTumorMetastasis pave the way for the application of genome sequencing in predictions for other complex genetic diseases. eTumorMetastasis pseudocode and related data used in this study are available at https://github.com/WangEdwinLab/eTumorMetastasis.     

Optimal treatment of an SIR epidemic model with time delay

In this paper the optimal control strategies of an SIR (susceptible–infected–recovered) epidemic model with time delay are introduced. In order to do this, we consider an optimally controlled SIR epidemic model with time delay where a control means treatment for infectious hosts. We use optimal control approach to minimize the probability that the infected individuals spread and to maximize the total number of susceptible and recovered individuals. We first derive the basic reproduction number and investigate the dynamical behavior of the controlled SIR epidemic model. We also show the existence of an optimal control for the control system and present numerical simulations on real data regarding the course of Ebola virus in Congo. Our results indicate that a small contact rate(probability of infection) is suitable for eradication of the disease (Ebola virus) and this is one way of optimal treatment strategies for infectious hosts.