Nitric oxide: a cytotoxic activated macrophage effector molecule

The experiments reported here identify nitric oxide as a molecular effector of activated macrophage induced cytotoxicity. Cytotoxic activated macrophages synthesize nitric oxide from a terminal guanidino nitrogen atom of L-arginine which is converted to L-citrulline without loss of the guanidino carbon atom. In addition, authentic nitric oxide gas causes the same pattern of cytotoxicity in L10 hepatoma cells as is induced by cytotoxic activated macrophages (iron loss as well as inhibition of DNA synthesis, mitochondrial respiration, and aconitase activity). The results suggest that nitric oxide is the precursor of nitrite/nitrate synthesized by cytotoxic activated macrophages and, via formation of iron-nitric oxide complexes and subsequent degradation of iron-sulfur prosthetic groups, an effector molecule.     

Multi-node graphs: a framework for multiplexed biological assays.

Multiplex polymerase chain reaction (PCR) is an extension of the standard PCR protocol in which primers for multiple DNA loci are pooled together within a single reaction tube, enabling simultaneous sequence amplification, thus reducing costs and saving time. Potential cost saving and throughput improvements directly depend on the level of multiplexing achieved. Designing reliable and highly multiplexed assays is challenging because primers that are pooled together in a single reaction tube may cross-hybridize, though this can be addressed either by modifying the choice of primers for one or more amplicons, or by altering the way in which DNA loci are partitioned into separate reaction tubes. In this paper, we introduce a new graph formalism called a multi-node graph, and describe its application to the analysis of multiplex PCR scalability. We show, using random multi-node graphs that the scalability of multiplex PCR is constrained by a phase transition, suggesting fundamental limits on efforts to improve the cost-effectiveness and throughput of standard multiplex PCR assays. In particular, we show that when the multiplexing level of the reaction tubes is roughly theta(log (sn)) (where s is the number of primer pair candidates per locus and n is the number of loci to be amplified), then with very high probability we can 'cover' all loci with a valid assignment to one of the tubes in the assay. However, when the multiplexing level of the tube exceeds these bounds, there is no possible cover and moreover the size of the cover drops dramatically. Simulations using a simple greedy algorithm on real DNA data also confirm the presence of this phase transition. Our theoretical results suggest, however, that the resulting phase transition is a fundamental characteristic of the problem, implying intrinsic limits on the development of future assay design algorithms.     

Human adipose-derived adult stem cells upregulate palladin during osteogenesis and in response to cyclic tensile strain

Cell morphology may be an important stimulus during differentiation of human adipose-derived adult stem (hADAS) cells, but there are limited studies that have investigated the role of the cytoskeleton or associated proteins in hADAS cells undergoing differentiation. Palladin is an actin-associated protein that plays an integral role in focal adhesion and cytoskeleton organization. In this study we show that palladin was expressed by hADAS cells and was modulated during osteogenic differentiation and in response to cyclic tensile strain. Human ADAS cells expressed the 90- and 140-kDa palladin isoforms and upregulated expression of both isoforms after culture in conditions that promoted osteogenesis. Palladin mRNA expression levels were also increased in hADAS cells subjected to cyclic tensile strain. Knockdown of the palladin gene during osteogenesis resulted in decreased actin stress fibers and decreased protein levels of Eps8, an epidermal growth factor receptor tyrosine kinase that colocalizes with actin. Silencing the palladin gene, however, did not affect hADAS cells' commitment down the osteogenic lineage.     

A simple method for the preparation of fish chromosomes applicable to field work, teaching and banding

A method is described which has broad application for field acquisition of fish karyotypes for research and teaching. The benefits of the method include: low initial skill level, relatively inexpensive equipment and supplies, simplicity and speed, and the high quality of preparations. The technique was applied to a field study of Apogon maculatus which was shown to contain 34 chromosomes, 2 nucleolar organizing regions (NOR's), and resolvable G-bands.     

A behavioral analysis of altruism

Altruistic acts have been defined, in economic terms, as “…costly acts that confer economic benefits on other individuals” (Fehr and Fischbacher, 2003). In multi-player, one-shot prisoner's dilemma games, a significant number of players behave altruistically; their behavior benefits each of the other players but is costly to them. We consider three potential explanations for such altruism. The first explanation, following a suggestion by the philosopher Derek Parfit, assumes that players devise a strategy to avoid being free-loaders—and that in the present case this strategy dictates cooperation. The second explanation says that cooperators reject the one-shot aspect of the game and behave so as to maximize reward over a series of choices extending beyond the present situation (even though reward is not maximized in the present case). This explanation assumes that people may learn to extend the boundaries of their selves socially (beyond their own skin) as well as temporally (beyond the present moment). We propose a learning mechanism for such behavior analogous to the biological, evolutionary mechanism of group selection. The third explanation assumes that people's altruism is based on a straightforward balancing of undiscounted costs to themselves against discounted benefits to others (social discounting). The three proposed explanations of altruism complement each other.     

Teaching and learning in a probabilistic prisoner's dilemma

The prisoner's dilemma is much studied in social psychology and decision-making because it models many real-world conflicts. In everyday terms, the choice to 'cooperate' (maximize reward for the group) or 'defect' (maximize reward for the individual) is often attributed to altruistic or selfish motives. Alternatively, behavior during a dilemma may be understood as a function of reinforcement and punishment. Human participants played a prisoner's-dilemma-type game (for points exchangeable for money) with a computer that employed either a teaching strategy (a probabilistic version of tit-for-tat), in which the computer reinforced or punished participants' cooperation or defection, or a learning strategy (a probabilistic version of Pavlov), in which the computer's responses were reinforced and punished by participants' cooperation and defection. Participants learned to cooperate against both computer strategies. However, in a second experiment which varied the context of the game, they learned to cooperate only against one or other strategy; participants did not learn to cooperate against tit-for-tat when they believed that they were playing against another person; participants did not learn to cooperate against Pavlov when the computer's cooperation probability was signaled by a spinner. The results are consistent with the notion that people are biased not only to cooperate or defect on individual social choices, but also to employ one or other strategy of interaction in a pattern across social choices.     

The proline-rich protein palladin is a binding partner for profilin

Palladin is an actin-associated protein that has been suggested to play critical roles in establishing cell morphology and maintaining cytoskeletal organization in a wide variety of cell types. Palladin has been shown previously to bind directly to three different actin-binding proteins vasodilator-stimulated phosphoprotein (VASP), alpha-actinin and ezrin, suggesting that it functions as an organizing unit that recruits actin-regulatory proteins to specific subcellular sites. Palladin contains sequences resembling a motif known to bind profilin. Here, we demonstrate that palladin is a binding partner for profilin, interacting with profilin via a poly proline-containing sequence in the amino-terminal half of palladin. Double-label immunofluorescence staining shows that palladin and profilin partially colocalize in actin-rich structures in cultured astrocytes. Our results suggest that palladin may play an important role in recruiting profilin to sites of actin dynamics.     

Palladin is an actin cross-linking protein that uses immunoglobulin-like domains to bind filamentous actin

Palladin is a recently described phosphoprotein that plays an important role in cell adhesion and motility. Previous studies have shown that palladin overexpression results in profound changes in actin organization in cultured cells. Palladin binds to the actin-associated proteins alpha-actinin, vasodilator-stimulated phosphoprotein, profilin, Eps8, and ezrin, suggesting that it may affect actin organization indirectly. To determine its molecular function in generating actin arrays, we purified palladin and asked if it is also capable of binding to F-actin directly. In co-sedimentation and differential sedimentation assays, palladin was found to both bind and cross-link actin filaments. This bundling activity was confirmed by fluorescence and electron microscopy. Palladin fragments were then purified and used to determine the sequences necessary to bind and bundle F-actin. The Ig3 domain of palladin bound to F-actin, and a palladin fragment containing Ig3, Ig4, and the region linking these domains was identified as a fragment that was able to bundle F-actin. Because palladin has multiple Ig domains, and only one of them binds to F-actin, this suggests that different Ig domains may be specialized for distinct biological functions. In addition, our results suggest a potential role for palladin in generating specialized, actin-based cell morphologies via both direct actin cross-linking activity and indirect scaffolding activity.