Genetic characterization of pAsa6, a new plasmid from Aeromonas salmonicida subsp. salmonicida that encodes a type III effector protein AopH homolog

A new plasmid designated pAsa6 from an Aeromonas salmonicida subsp. salmonicida strain isolated from diseased turbot has been characterized. pAsa6 consists of 18536 bp, has a G+C content of 53.8% and encodes 20 predicted open-reading frames (ORFs). Eight ORFs showed homology to transposases, of which six are complete and two are partial IS sequences. Two ORFs showed homology to replication proteins, and six ORFs showed homology to hypothetical proteins. Two ORFs are truncated homologs of putative A. salmonicida sulfatases. Two genes, aopH and sycH encode homologs of an effector protein for which a role in fish colonization by A. salmonicida has been previously reported, and its chaperone, respectively. The results of filter conjugation experiments suggested that pAsa6 is not mobilizable, as it failed to be conjugally-transferred to several species of marine bacteria tested. All the ORFs of pAsa6 with the exception of four copies of a IS1 transposase gene, have a counterpart in the recently sequenced 155-kb A. salmonicida plasmid pAsa5, suggesting either that pAsa6 is a derivative of pAsa5, or that pAsa5 is the result of the fusion of a pAsa6-like plasmid and a larger plasmid of ca. 135-kb. The pAsa6-encoded repA and aopH genes could be PCR-amplified from strains lacking pAsa6, suggesting presence of a large, possibly pAsa5-like plasmid that was not detected on agarose gels, or the existence of chromosome-integrated plasmid sequences. This study demonstrates that genomic locations for the aopH gene different to pAsa5 or pAsa5-like plasmids exist in A. salmonicida.     

Collective migration and cell jamming

Our traditional physical picture holds with the intuitive notion that each individual cell comprising the cellular collective senses signals or gradients and then mobilizes physical forces in response. Those forces, in turn, drive local cellular motions from which collective cellular migrations emerge. Although it does not account for spontaneous noisy fluctuations that can be quite large, the tacit assumption has been one of linear causality in which systematic local motions, on average, are the shadow of local forces, and these local forces are the shadow of the local signals. New lines of evidence now suggest a rather different physical picture in which dominant mechanical events may not be local, the cascade of mechanical causality may be not so linear, and, surprisingly, the fluctuations may not be noise as much as they are an essential feature of mechanism. Here we argue for a novel synthesis in which fluctuations and non-local cooperative events that typify the cellular collective might be illuminated by the unifying concept of cell jamming. Jamming has the potential to pull together diverse factors that are already known to contribute but previously had been considered for the most part as acting separately and independently. These include cellular crowding, intercellular force transmission, cadherin-dependent cell–cell adhesion, integrin-dependent cell–substrate adhesion, myosin-dependent motile force and contractility, actin-dependent deformability, proliferation, compression and stretch.     

Synergistic Effects of Selenium Nanoparticles and Vitamin E on Growth,Immune-Related Gene Expression,and Regulation of Antioxidant Status of Nile Tilapia (Oreochromis niloticus)

Biological Trace Element Research - The present study was conducted to investigate the effects of nano-selenium (Nano Se) or/and vitamin E (VE) on growth performance, blood health, intestinal...     

Aquaporin 4 in Traumatic Brain Injury: From Molecular Pathways to Therapeutic Target

Traumatic brain injury (TBI) is known as an acute degenerative pathology of the central nervous system, and has been shown to increase brain aquaporin 4 (AQP4) expression. Various molecular mechanisms affect AQP4 expression, including neuronal high mobility group box 1, forkhead box O3a, vascular endothelial growth factor, hypoxia-inducible factor-1 α (HIF-1 α) sirtuin 2, NF-κB, Malat1, nerve growth factor and Angiotensin II receptor type 1. In addition, inhibition of AQP4 with FK-506, MK-801 (indirectly by targeting N-methyl-d-aspartate receptor), inactivation of adenosine A2A receptor, levetiracetam, adjudin, progesterone, estrogen, V1aR inhibitor, hypertonic saline, erythropoietin, poloxamer 188, brilliant blue G, HIF-1alpha inhibitor, normobaric oxygen therapy, astaxanthin, epigallocatechin-3-gallate, sesamin, thaliporphine, magnesium, prebiotic fiber, resveratrol and omega-3, as well as AQP4 gene silencing lead to reduced edema upon TBI. This review summarizes current knowledge and evidence on the relationship between AQP4 and TBI, and the potential mechanisms involved.

     

Assessment of population structure,genetic diversity and relationship of Mediterranean olive accessions using SSR markers and computational tools

Biotechnology Letters - Olive tree is an emblematic crop of the Mediterranean region, mainly renowned for its fruit oil, although the species provides several industrial purposes. The Mediterranean...     

The effects of grain geometry on waterflooding and viscous fingering in micro-fractures and porous media from a lattice Boltzmann method study

The study of fluid fronts formed in porous media is important for enhanced oil recovery. The purposes of this study are to simulate waterflooding and to investigate influential factors on the fluid front movement through a micro-fracture and through simple porous media with different grain geometries. This study used the Shan–Chen form of the Lattice Boltzmann Method (LBM). An increase in the velocity is found to result in viscous fingering, whereas an increase in the wettability of the displacing fluid and the dynamic viscosity ratio creates a piston form of the fluid front. In porous media with the same porosities, various geometries act differently as obstacles against fluid flow from the inlet to the outlet. By enlarging the cross-sectional area of grains in the fluid paths and making them more tortuous, narrower and more twisted films of viscous fingering are formed. The sweep efficiency was also determined under various conditions: with a fixed capillary number, neutral wettability and different viscosity ratios; and with a fixed capillary number, viscosity ratio of (1/3) and wet or non-wet conditions. In all cases, the best sweep efficiency was obtained with grains of diamond geometry. Generally, the least sweep efficiency occurs with grains of star geometry. Simulation results verified the strength and accuracy of LBM predictions.     

Discerning intersecting fusion‐activation pathways in the Nipah virus using machine learning

The fusion of Nipah with host cells is facilitated by two of their glycoproteins, the G and the F proteins. The binding of cellular ephrins to the G head domain causes the G stalk domain to interact differently with F, which activates F to mediate virus–host fusion. To gain insight into how the ephrin‐binding signal transduces from the head to the stalk domain of G, we examine quantitatively the differences between the conformational ensembles of the G head domain in its ephrin‐bound and unbound states. We consider the human ephrins B2 and B3, and a double mutant of B2, all of which trigger fusion. The ensembles are generated using molecular dynamics, and the differences between them are quantified using a new machine learning method. We find that the portion of the G head domain whose conformational density is altered equivalently by the three ephrins is large, and comprises ～25% of the residues in the G head domain. This subspace also includes the residues that are known to be important to F activation, which suggests that it contains at least one common signaling pathway. The spatial distribution of the residues constituting this subspace supports the model of signal transduction in which the signal transduces via the G head dimer interface. This study also adds to the growing list of examples where signaling does not depend solely on backbone deviations. In general, this study provides an approach to filter out conserved patterns in protein dynamics. Proteins 2014; 82:3241–3254. © 2014 Wiley Periodicals, Inc.     

Fasting induces prominent proteomic changes in liver in very long chain Acyl-CoA dehydrogenase deficient mice

Very long chain acyl-CoA dehydrogenase (VLCAD) deficiency (VLCADD) is a clinically heterogeneous disorder of mitochondrial fatty acid β-oxidation usually identified through newborn screening. Genotype-phenotype correlations have been defined, but considerable clinical heterogeneity still exists. Symptoms are often induced by physiological stress such as fasting or intercurrent illness, setting it as an important example of environmental effects altering clinical course in an individual with a genetic disease. However, neither the cellular changes that predispose to this phenomenon nor the alterations it induces are well characterized. We examined the effects of fasting in a knockout mouse model to explore changes in global mitochondria protein profiles in liver and to investigate the physiologically relevant changes that lead to the clinical presentations. An isobaric tags for relative and absolute quantification (iTRAQ) labeling approach was employed to examine mitochondrial proteome changes in VLCAD deficient compared to wild type mice in the fed and fasted states. We identified numerous proteomic changes associated with the gene defect and fasting within relevant metabolic pathways. Few changes induced by fasting were shared between the VLCAD deficient and wild type mice, with more alterations found in the deficient mice on fasting. Particularly, fasting in the deficient mice could reverse the protective response in oxidative phosphorylation pathway seen in wild type animals. In addition, we found that changes in chaperone proteins including heat shock protein 60 (HSP60) and 10 (HSP10) during fasting differed between the two genotypes, highlighting the importance of these proteins in VLCAD deficiency. Finally, the effects on the liver proteome imposed by changes in fasted VLCAD deficient mice indicates that this environmental factor may be an inducer of both cellular and physiological changes.