Candidate molecular mechanisms for establishing cell identity in the developing retina

In the developing nervous system, individual neurons must occupy appropriate positions within circuits. This requires that these neurons recognize and form connections with specific pre- and postsynaptic partners. Cellular recognition is also required for the spacing of cell bodies and the arborization of dendrites, factors that determine the inputs onto a given neuron. These issues are particularly evident in the retina, where different types of neurons are evenly spaced relative to other cells of the same type. This establishes a reiterated columnar circuitry resembling the insect retina. Establishing these mosaic patterns requires that cells of a given type (homotypic cells) be able to sense their neighbors. Therefore, both synaptic specificity and mosaic spacing require cellular identifiers. In synaptic specificity, recognition often occurs between different types of cells in a pre- and postsynaptic pairing. In mosaic spacing, recognition is often occurring between different cells of the same type, orhomotypic self-recognition. Dendritic arborization can require recognition of different neurites of the same cell, or isoneuronal self-recognition. The retina is an extremely amenable system for studying the molecular identifiers that drive these various forms of recognition. The different neuronal types in the retina are well defined, and the genetic tools for marking cell types are increasingly available. In this review we will summarize retinal anatomy and describe cell types in the retina and how they are defined. We will then describe the requirements of a recognition code and discuss newly emerging candidate molecular mechanisms for recognition that may meet these requirements.     

Entry of Yersinia pestis into the viable but nonculturable state in a low-temperature tap water microcosm

Yersinia pestis, the causative agent of plague, has caused several pandemics throughout history and remains endemic in the rodent populations of the western United States. More recently, Y. pestis is one of several bacterial pathogens considered to be a potential agent of bioterrorism. Thus, elucidating potential mechanisms of survival and persistence in the environment would be important in the event of an intentional release of the organism. One such mechanism is entry into the viable but non-culturable (VBNC) state, as has been demonstrated for several other bacterial pathogens. In this study, we showed that Y. pestis became nonculturable by normal laboratory methods after 21 days in a low-temperature tap water microcosm. We further show evidence that, after the loss of culturability, the cells remained viable by using a variety of criteria, including cellular membrane integrity, uptake and incorporation of radiolabeled amino acids, and protection of genomic DNA from DNase I digestion. Additionally, we identified morphological and ultrastructural characteristics of Y. pestis VBNC cells, such as cell rounding and large periplasmic spaces, by electron microscopy, which are consistent with entry into the VBNC state in other bacteria. Finally, we demonstrated resuscitation of a small number of the non-culturable cells. This study provides compelling evidence that Y. pestis persists in a low-temperature tap water microcosm in a viable state yet is unable to be cultured under normal laboratory conditions, which may prove useful in risk assessment and remediation efforts, particularly in the event of an intentional release of this organism.     

Acute and chronic administration of disodium disuccinate astaxanthin (CardaxTM) produces marked cardioprotection in dog hearts

Previous results from our laboratory have shown that a novel carotenoid derivative (disodium disuccinate astaxanthin; Cardax^TM) produced dose-related reductions in myocardial infarct size (IS) in Sprague–Dawley rats when it was administered at any of three doses (25, 50 and 75 mg/kg, iv) on four consecutive days, followed by the acute infarct size study on day 5. Maximum salvage occurred at the highest dose (75 mg/kg) tested, and was shown as a 56% reduction in IS. In the present follow-up study, we used a more relevant large animal model, the dog, and looked at the effect of administering Cardax^TM iv either acutely 2 h prior to occlusion (N = 8) or for 4 days at 50 mg/kg iv as previously done in the rat model (N = 6). The results were compared to a saline vehicle-treated group (N = 10). In all groups, dogs were subjected to 60 min of left anterior descending (LAD) coronary artery occlusion and 3 h of reperfusion. IS was determined using a triphenyltetrazolium chloride (TTZ) histochemical stain and was expressed as a percent of the area at risk (IS/AAR). IS/AAR was 20.9 ± 1.6 % (mean ± S.E.M.) in controls and was reduced to 11.0± 1.7% (47.3% salvage; p < 0.01) in dogs treated only once iv at 2 h prior to occlusion, and 6.6± 2.8% (68.4% salvage; p < 0.001) in dogs treated for 4 days. In the chronic treatment group, two of the three dogs with plasma concentrations of non-esterified astaxanthin above 1 M had 0% IS/AAR (100% cardioprotection). These results suggest that Cardax^TM has marked cardioprotective properties in both rodents and canines. Thus, Cardax^TM may be a novel and powerful new means to prevent myocardial injury and/or necrosis associated with elective and/or urgent cardiac surgical interventions such as coronary angioplasty and stenting, as well as coronary artery bypass surgery (CABG).     

Extending the cardioprotective window using a novel delta-opioid agonist fentanyl isothiocyanate via the PI3-kinase pathway

Selective delta-opioid agonists produce delayed cardioprotection that lasts for 24-48 h in rats; however, the maximum length of the cardioprotective window is unclear. In this study, we attempted to prolong the cardioprotective window using a unique delta-opioid agonist, fentanyl isothiocyanate (FIT), which binds irreversibly to the delta-receptor, and determined the role of the phosphatidylinositol 3-kinase (PI3K) pathway as a trigger or end effector of FIT-induced cardioprotection. Initially, male rats were administered FIT (10 microg/kg) 10 min before hearts were subjected to 30 min of ischemia and 2 h of reperfusion followed by infarct size (IS) assessment. Acute FIT administration reduced IS when given before ischemia, 5 min before reperfusion, or 10 s after reperfusion compared with control. IS reduction also occurred following a single dose of FIT at 48, 72, 96, and 120 h after administration vs. control, with the maximum effect observed at 96 h. FIT-induced IS reduction at 96 h was completely abolished when the irreversible PI3K inhibitor wortmannin (15 microg/kg) was given before FIT during the trigger phase; however, the effect was only partially abrogated when wortmannin was given 96 h later. These data suggest that FIT has a prolonged cardioprotective window greater than that of any previously described cardioprotective agent that requires PI3K primarily in the trigger phase but also partially, as a mediator or end effector.     

Viral diversity in hot springs of Pozzuoli, Italy, and characterization of a unique archaeal virus, Acidianus bottle-shaped virus, from a new family, the Ampullaviridae

Virus-like particles with five different morphotypes were observed in an enriched environmental sample from a hot, acidic spring (87 to 93 degrees C, pH 1.5) in Pozzuoli, Italy. The morphotypes included rigid rods, flexible filaments, and novel, exceptional forms. Particles of each type were isolated, and they were shown to represent viable virions of five novel viruses which infect members of the hyperthermophilic archaeal genus Acidianus. One of these, named the Acidianus bottle-shaped virus, ABV, exhibits a previously unreported morphotype. The bottle-shaped virion carries an envelope which encases a funnel-shaped core. The pointed end of the virion is likely to be involved in adsorption and channeling of viral DNA into host cells. The broad end exhibits 20 (+/- 2) thin filaments which appear to be inserted into a disk, or ring, and are interconnected at their bases. These filaments are apparently not involved in adsorption. ABV virions contain six proteins in the size range 15 to 80 kDa and a 23.9-kb linear, double-stranded DNA genome. Virus replication does not cause lysis of host cells. On the basis of its unique morphotype and structure, we propose to assign ABV to a new viral family, the Ampullaviridae.     

On the use of qualitative reasoning to simulate and identify metabolic pathways

MOTIVATION: Perhaps the greatest challenge of modern biology is to develop accurate in silico models of cells. To do this we require computational formalisms for both simulation (how according to the model the state of the cell evolves over time) and identification (learning a model cell from observation of states). We propose the use of qualitative reasoning (QR) as a unified formalism for both tasks. The two most commonly used alternative methods of modelling biochemical pathways are ordinary differential equations (ODEs), and logical/graph-based (LG) models. RESULTS: The QR formalism we use is an abstraction of ODEs. It enables the behaviour of many ODEs, with different functional forms and parameters, to be captured in a single QR model. QR has the advantage over LG models of explicitly including dynamics. To simulate biochemical pathways we have developed 'enzyme' and 'metabolite' QR building blocks that fit together to form models. These models are finite, directly executable, easy to interpret and robust. To identify QR models we have developed heuristic chemoinformatics graph analysis and machine learning procedures. The graph analysis procedure is a series of constraints and heuristics that limit the number of ways metabolites can combine to form pathways. The machine learning procedure is generate-and-test inductive logic programming. We illustrate the use of QR for modelling and simulation using the example of glycolysis. AVAILABILITY: All data and programs used are available on request.     

Volatile organic compound fate in phytoremediation applications: natural and engineered systems

Unique sampling techniques have generated a new understanding regarding the fate of volatile organic compounds (VOCs) in phytoremediation systems. Tissue sampling and diffusion traps were used to determine how VOCs are transported in and diffuse from vegetation, particularly woody species. These techniques were then utilized to observe how plants interact with different contaminated media, showing transport of contaminants occurs from the vadose zone (vapor phase) as well as the saturated zone (aqueous phase). Data was gathered in laboratory studies, in native vegetation, and in engineered phytoremediation systems. The findings reveal that diffusion from the xylem tissues to the atmosphere is a major fate for VOCs in phytoremediation applications. Linking VOCs' fate with groundwater hydraulics, mass removal rates from contaminant plumes can be estimated. These techniques were also utilized to observe the impact of engineered plant/microbe systems, which utilize recombinant, root-colonizing organisms to selectively degrade compounds and subsequently alter the fate of VOCs and other organic compounds. The genetically enhanced rhizoremediation methods pose a novel approach that may allow for biodegradation of compounds that formerly were considered recalcitrant.