Integrated network reconstruction,visualization and analysis using YANAsquare

Background  

Modeling of metabolic networks includes tasks such as network assembly, network overview, calculation of metabolic fluxes and testing the robustness of the network.     

Insight into the role of HSPG in the cellular uptake of apolipoprotein E-derived peptide micelles and liposomes

Liposomes and micellar carriers equipped with targeting and cellular uptake mediating peptides have attracted attention for numerous applications. The optimization of the carrier requires an understanding of how their properties influence target cell recognition and uptake. We developed a dipalmitoylated apolipoprotein E-derived peptide, named P2A2 as promising vector to mediate cellular uptake of potential micellar and liposomal carriers. Confocal laser scanning microscopy (CLSM) and fluorescence-activated cell sorting (FACS) were used to get insight into the internalization mediated by carboxyfluoresceine-labeled P2fA2 and the all-D amino acid analogue P2fa2 into brain capillary endothelial cells. Both peptide micelles and liposomes entered cells via endocytosis. Cell surface heparan sulfate proteoglycans (HSPGs) were involved in the internalization process of peptide-bearing liposomes characterized by a diameter of 100 nm, a low surface density of 100 peptide molecules per vesicle and a helical conformation of the vector. In contrast, peptide micelles characterized by a diameter of about 10 nm, a high peptide density caused by 19 associated molecules and a high conformational flexibility of the vector sequence did not address HSPG. Unspecific interactions between the carriers and membrane constituents predominate the two uptake processes but stereospecific components seem to be involved. Both routes differ with respect to transport efficiency. The results provide a prospective basis to optimize liposomes and micelles as drug delivery systems.     

ArfGAP1 restricts Mycobacterium tuberculosis entry by controlling the actin cytoskeleton

The interaction of Mycobacterium tuberculosis (Mtb) with pulmonary epithelial cells is critical for early stages of bacillus colonization and during the progression of tuberculosis. Entry of Mtb into epithelial cells has been shown to depend on F‐actin polymerization, though the molecular mechanisms are still unclear. Here, we demonstrate that mycobacterial uptake into epithelial cells requires rearrangements of the actin cytoskeleton, which are regulated by ADP‐ribosylation factor 1 (Arf1) and phospholipase D1 (PLD1), and is dependent on the M3 muscarinic receptor (M₃R). We show that this pathway is controlled by Arf GTPase‐activating protein 1 (ArfGAP1), as its silencing has an impact on actin cytoskeleton reorganization leading to uncontrolled uptake and replication of Mtb. Furthermore, we provide evidence that this pathway is critical for mycobacterial entry, while the cellular infection with other pathogens, such as Shigella flexneri and Yersinia pseudotuberculosis, is not affected. Altogether, these results reveal how cortical actin plays the role of a barrier to prevent mycobacterial entry into epithelial cells and indicate a novel role for ArfGAP1 as a restriction factor of host–pathogen interactions.     

Synthesis of the compatible solutes glucosylglycerol and trehalose by salt-stressed cells of Stenotrophomonas strains

In this study, physiological processes were analysed, which are involved in salt acclimation of two Stenotrophomonas species, Stenotrophomonas maltophilia strain DSM 50170 and Stenotrophomonas rhizophila strain DSM 14405. S. maltophilia accumulated trehalose as the only osmolyte, whereas S. rhizophila produced additionally to trehalose glucosylglycerol (GG). The different spectrum and amounts of compatible solutes in these two strains led to differences in terms of their salt tolerance. The human-associated S. maltophilia was able to grow in media containing up to 3% NaCl (w/v). In contrast, S. rhizophila propagated in salinities up to 5% NaCl (w/v). The strain was isolated from the rhizosphere, a microenvironment which is characterised by high and changing salinities. Light microscopic analysis of S. rhizophila cells showed a significant increase in cell length of salt-treated cells in comparison to control cells. Cells of S. rhizophila exposed to more than 2% NaCl excreted GG into the medium during the transition from exponential to stationary growth phase, while the internal trehalose pool remained constant. This feature offers a high potential for the biotechnological production of GG.     

Mixed-ligand rhenium-188 complexes with tetradentate/monodentate NS3/P ('4 + 1') coordination: relation of structure with antioxidation stability

Development of new radiopharmaceuticals based on rhenium-188 depends on finding appropriate ligands able to give complexes with high in vivo stability. Rhenium(III) mixed-ligand complexes with tetradentate/monodentate ('4 + 1') coordination of the general formula [Re(NS(3))(PRR'R' ')] (NS(3) = tris(2-mercaptoethyl)amine and derivatives thereof, PRR'R' ' = phosphorus(III) ligands) appear to be among the promising tools to achieve this goal. According to this approach, we synthesized and characterized a series of rhenium model complexes. In vitro stabilities of the corresponding rhenium-188 complexes were determined by incubating 2-3 MBq or alternatively 37 MBq of the complexes in phosphate buffer, human plasma, and rat plasma, respectively, at 22 degrees C or 37 degrees C, followed by checking the amount of (188)ReO(4)(-) formed after 1 h, 24, and 48 h by thin-layer chromatography. The rate of perrhenate formation varied over a wide range, depending primarily on the nature of the phosphorus(III) ligand. Physicochemical parameters of the corresponding nonradioactive rhenium complexes were analyzed in detail to find out the factors influencing their different stability and furthermore to design new substitution-inert '4 + 1' complexes. Tolman's cone angle of phosphorus(III) ligands and the lipophilic character of the inner coordination sphere were found to be crucial factors to build up stable rhenium '4 + 1' complexes. Additional information useful to describe electronic and steric properties of these compounds were selected from electronic spectra (wavelength of the Re-->S charge-transfer band), cyclovoltammetric measurements (E degrees of the Re(III)/Re(IV) couple), and NMR investigations ((31)P chemical shift of coordinated P(III) ligands).     

Seasonal variations in the chemical composition and dry matter degradability of exclosure forages in the semi-arid region of northern Ethiopia

The present study was conduced at two sites (Tembien and Wukro) in the semi-arid region of Tigray in northern Ethiopia to investigate the seasonal dynamics in the chemical composition and dry matter digestibility of grass and browse species of exclosures. The browse species studied in Tembien and Wukro had a mean crude protein (CP) value of 166 and 117 g/kg dry matter (DM), respectively. The mean in vitro dry matter digestibility (IVDMD) coefficient and predicted metabolizable energy (ME) density of the browse species were 0.72 and 9.83 MJ/kg DM, respectively at Tembien, 0.62 and 8.38 MJ/kg DM, respectively, at Wukro. Neutral detergent fibre (NDF) and acid detergent fibre (ADF) values of the browse species varied from 192 to 437 and 127 to 391 g/kg DM, respectively. Acid detergent lignin (ADL) values ranged from 36 to 190 g/kg DM. The mean CP of the grass species in Tembien and Wukro during the long rainy season was 76 and 73 g/kg DM, respectively and values declined below a critical maintenance level during the dry and short rain seasons. Mean IVDMD and ME values for the two sites were 0.41 and 0.47, and 5.38 and 6.11 MJ/kg DM, respectively. The NDF, ADF, and lignin values of the grass species were generally above 700, 400, and 70 g/kg DM, respectively. The CP, IVDMD and ME values of the mixed grass samples differed (P<0.05) among harvesting months and values ranged from 20 to 103 g/kg DM, 0.47 to 0.72 MJ/kg DM, and 6.16 to 9.91 MJ/kg DM, respectively. The browse species could be used as useful dry season protein supplements to the N deficient native grass species. Especial emphasis should be given to propagate Maerua angolensis and Cadaba farinosa at community nursery sites. Harvesting in September, rather than the current extended harvest period that took place in October and November, can considerably improve the feeding value of native grass hay for smallholder ruminant production systems.     

Ocular Ultrasound as an Easy Applicable Tool for Detection of Terson's Syndrome after Aneurysmal Subarachnoid Hemorrhage

Introduction

Intraocular hemorrhage in patients suffering from aneurysmal subarachnoid hemorrhage is known as Terson''s syndrome and is an underestimated but common pathology. We therefore designed a prospective single-blinded study to evaluate the validity of ocular ultrasound compared to the gold standard indirect funduscopy in the diagnosis of Terson''s syndrome.

Material and Methods

Fifty-two patients (104 eyes in total) suffering from aneurysmal subarachnoid hemorrhage were enrolled in this study. Two investigators independently performed a single-blinded ocular ultrasound using a standard intensive care ultrasound system to detect an intraocular hemorrhage. Indirect funduscopy following iatrogenic mydriasis served as the gold standard for confirmation or exclusion of an intraocular hemorrhage. Statistical analyses were performed to evaluate the sensitivity and specificity, positive and negative predictive values of the method as well as the learning curve of ocular ultrasound.

Results

Indirect funduscopy detected Terson''s syndrome in 11 of 52 (21.2%) respectively in 21 of 104 (20.2%) eyes in patients suffering from subarachnoid hemorrhage. Sensitivity and specificity increased with the number of ocular ultrasound examinations for both investigators, reaching 81.8% and 100% respectively. Positive and negative predictive values were different for both investigators (63.6% vs. 100% positive and 100% vs. 95.7% negative) but were both correlated to the amount of intraocular hemorrhage. A low Glasgow Coma scale (p = 0.015) and high Hunt & Hess grade (p = 0.003) was associated with a higher rate of Terson''s syndrome.

Conclusions

Ocular ultrasound using standard ultrasound equipment has been confirmed as a reliable, easy-to-handle bedside screening tool for detecting Terson''s syndrome. Nevertheless funduscopy remains the gold standard to detect Terson''s syndrome.