Dissociation between mature phenotype and impaired transmigration in dendritic cells from heparanase-deficient mice

To reach the lymphatics, migrating dendritic cells (DCs) need to interact with the extracellular matrix (ECM). Heparanase, a mammalian endo-β-D-glucuronidase, specifically degrades heparan sulfate proteoglycans ubiquitously associated with the cell surface and ECM. The role of heparanase in the physiology of bone marrow-derived DCs was studied in mutant heparanase knock-out (Hpse-KO) mice. Immature DCs from Hpse-KO mice exhibited a more mature phenotype; however their transmigration was significantly delayed, but not completely abolished, most probably due to the observed upregulation of MMP-14 and CCR7. Despite their mature phenotype, uptake of beads was comparable and uptake of apoptotic cells was more efficient in DCs from Hpse-KO mice. Heparanase is an important enzyme for DC transmigration. Together with CCR7 and its ligands, and probably MMP-14, heparanase controls DC trafficking.     

Isolation and bioaugmentation of an estradiol-degrading bacterium and its integration into a mature biofilm

Bioaugmentation can alter the potential activity as well as the composition of the naturally occurring microbial biota during bioremediation of a contaminated site. The focus of the current study is the pollutant 17β-estradiol (E2), which can cause endocrine effects and is potentially harmful to aquatic biota and to public health. The community composition and function of biofilms, originating from a wetland system, as affected by augmentation of an estradiol-degrading bacterium (EDB-LI1) under different conditions, were investigated. EDB-LI1 inoculation into biofilm from two wetland ponds representing early and advanced water treatment stages, respectively, yielded three significant observations, as follows: (i) EDB-LI1, enriched from a biofilm of a constructed wetland wastewater treatment system, was detected (by quantitative PCR [qPCR] analysis) in this environment in the augmented biofilm only; (ii) the augmented biofilm acquired the ability to remove estradiol; and (iii) the bacterial community composition (analyzed by PCR-denaturing gradient gel electrophoresis [DGGE]) of the augmented biofilm differed from that of the control biofilm. Furthermore, EDB-LI1 bioaugmentation showed a higher level of removal of estradiol with biofilms that originated from the advanced-treatment-stage wetland pond than those from the early-treatment-stage pond. Hence, the bioaugmentation efficiency of EDB-LI1 depends on both the quality of the feed water and the microbial community composition in the pond.     

Composition and dynamics of the gill microbiota of an invasive Indo-Pacific oyster in the eastern Mediterranean Sea

Gill bacterial communities of Chama pacifica, an Indo-Pacific invasive oyster to the eastern Mediterranean Sea, were compared with those of Chama savignyi, its northern Red Sea congeneric species. Summer and winter bacterial populations were characterized and compared using 16S rDNA clone libraries, and seasonal population dynamics were monitored by automated ribosomal intergenic spacer analysis (ARISA). Clone libraries revealed a specific clade of bacteria, closely related to marine endosymbionts from the Indo-Pacific, found in both ecosystems, of which one taxon was conserved in oysters from both sites. This taxon was dominant in summer libraries and was weakly present in winter ones, where other members of this group were dominant. ARISA results revealed significant seasonal variation in bacterial populations of Mediterranean Sea oysters, as opposed to Red Sea ones that were stable throughout the year. We suggest that this conserved association between bacteria and oyster reflects either a symbiosis between the oyster host and some of its bacteria, a co-invasion of both parties, or both.     

Congestive heart failure complicating non-ST segment elevation acute coronary syndrome: incidence, predictors, and clinical outcomes

There are limited data regarding the incidence and clinical significance of congestive heart failure (CHF) in patients with non-ST segment elevation acute coronary syndromes (ACS). The objectives of this study were to examine the incidence, predictors, and clinical outcomes in patients with ACS without ST elevation who develop CHF. We studied patients with unstable angina or non-ST segment elevation myocardial infarction (NSTEMI) randomized to hirudin or unfractionated heparin in the Organisation to Assess Strategies for Ischemic Syndromes (OASIS-2) trial. The diagnosis of CHF was based on a combination of clinical and radiographic features. Patients were followed for 6 months. Of 10 141 randomized patients, 501 (4.9%) developed CHF within the first week and 643 (6.3%) during 6 months of followup. Independent predictors for the development of CHF were older age, female sex, diabetes, prior MI, prior CHF, and NSTEMI at presentation. Compared with patients who did not develop CHF, patients who developed CHF were at increased risk of death (odds ratio (OR) 3.4, 95% CI 2.7-4.3), new MI (OR 2.8, 95% CI 2.2-3.6), and the need for intra-aortic balloon pump insertion (OR 5.4, 95% CI 3.5-8.4) at 7 days and 6 months. There was no increase in use of cardiac catheterization (OR 0.8, 95% CI 0.7-1.0) or revascularization (OR 0.9, 95% CI 0.7-1.1) in patients who developed CHF. CHF is a common complication in patients presenting with non-ST segment elevation ACS and is strongly associated with adverse clinical outcomes including new MI and death. Despite this worse prognosis, patients with ACS developing CHF are less likely to be referred for invasive management.     

Neuronal growth via hybrid system of self-growing and diffusion based grammar rules: I

The formation of neuronal networks requires axonal growth towards target neutons. A simple set of grammar rules is introduced to describe axonal growth towards target cells situated both at short and long distances from the growing neuron. Growth for short distances is descrbed by growth following the highest gradient of a chemical compound (which is spread by diffusion from the targets). This approach fails to describe long-distance growth, which is addressed by adopting a graph grammar theory for growing trees. With these rules a flexible tool to draw network of neurons by computer can be developed.     

The MORPH Algorithm: Ranking Candidate Genes for Membership in Arabidopsis and Tomato Pathways

Closing gaps in our current knowledge about biological pathways is a fundamental challenge. The development of novel computational methods along with high-throughput experimental data carries the promise to help in the challenge. We present an algorithm called MORPH (for module-guided ranking of candidate pathway genes) for revealing unknown genes in biological pathways. The method receives as input a set of known genes from the target pathway, a collection of expression profiles, and interaction and metabolic networks. Using machine learning techniques, MORPH selects the best combination of data and analysis method and outputs a ranking of candidate genes predicted to belong to the target pathway. We tested MORPH on 230 known pathways in Arabidopsis thaliana and 93 known pathways in tomato (Solanum lycopersicum) and obtained high-quality cross-validation results. In the photosynthesis light reactions, homogalacturonan biosynthesis, and chlorophyll biosynthetic pathways of Arabidopsis, genes ranked highly by MORPH were recently verified to be associated with these pathways. MORPH candidates ranked for the carotenoid pathway from Arabidopsis and tomato are derived from pathways that compete for common precursors or from pathways that are coregulated with or regulate the carotenoid biosynthetic pathway.     

Regulation of output from the plant circadian clock

Plants, like many other organisms, have endogenous biological clocks that enable them to organize their physiological, metabolic and developmental processes so that they occur at optimal times. The best studied of these biological clocks are the circadian systems that regulate daily (approximately 24 h) rhythms. At the core of the circadian system in every organism are oscillators responsible for generating circadian rhythms. These oscillators can be entrained (set) by cues from the environment, such as daily changes in light and temperature. Completing the circadian clock model are the output pathways that provide a link between the oscillator and the various biological processes whose rhythms it controls. Over the past few years there has been a tremendous increase in our understanding of the mechanisms of the oscillator and entrainment pathways in plants and many useful reviews on the subject. In this review we focus on the output pathways by which the oscillator regulates rhythmic plant processes. In the first part of the review we describe the role of the circadian system in regulation at all stages of a plant's development, from germination and growth to reproductive development as well as in multiple cellular processes. Indeed, the importance of a circadian clock for plants can be gauged by the fact that so many facets of plant development are under its control. In the second part of the review we describe what is known about the mechanisms by which the circadian system regulates these output processes.     

Recruitment of rare <Emphasis Type="Italic">3</Emphasis>-grams at functional sites: Is this a mechanism for increasing enzyme specificity?

Background  

A wealth of unannotated and functionally unknown protein sequences has accumulated in recent years with rapid progresses in sequence genomics, giving rise to ever increasing demands for developing methods to efficiently assess functional sites. Sequence and structure conservations have traditionally been the major criteria adopted in various algorithms to identify functional sites. Here, we focus on the distributions of the 20³ different types of 3-grams (or triplets of sequentially contiguous amino acid) in the entire space of sequences accumulated to date in the UniProt database, and focus in particular on the rare 3-grams distinguished by their high entropy-based information content.     

Correlation of magnetic AC field on cardiac myocyte Ca2+ transients at different magnetic DC levels

The purpose of this study was to determine the effect of extremely low frequency and weak magnetic fields (WMF) on cardiac myocyte Ca²⁺ transients, and to explore the involvement of potassium channels under the WMF effect. In addition, we aimed to find a physical explanation for the effect of WMF on cardiac myocyte Ca²⁺ transients. Indo‐1 loaded cells, which were exposed to a WMF at 16 Hz and 40 nT, demonstrated a 75 ± 4% reduction in cytosolic Ca²⁺ transients versus control. Treatment with the K_ATP channel blocker, glibenclamide, followed by WMF at 16 Hz exposure, blocked the reduction in cytosolic calcium transients while treatment with pinacidil, a K_ATP channel opener, or chromanol 293B, a selective potassium channel blocker of the delayed rectifier K⁺ channels, did not inhibit the effect. Based on these finding and the ion cyclotron resonance frequency theory, we further investigated the effect of WMF by changing the direct current (DC) magnetic field (B₀). When operating different DC magnetic fields we showed that the WMF value changed correspondingly: for B₀ = 44.5 µT, the effect was observed at 17.05 Hz; for B₀ = 46.5 µT, the effect was observed at 18.15 Hz; and for B₀ = 49 µT the effect was observed at 19.1 Hz. We can conclude that the effect of WMF on Ca²⁺ transients depends on the DC magnetic field level. Bioelectromagnetics 33:634–640, 2012. © 2012 Wiley Periodicals, Inc.