Jamaica Bay: An Urban Marshland in Transition

This article will briefly examine the environmental problems that affect the lives of the hundreds of thousands of people who live adjacent to Jamaica Bay, and the extraordinary opportunities for recreation and enjoyment for which the Bay, freed of sewage, air pollution and aircraft noise, could be employed

Role of Internal Calcium Stores in Exocytosis and Neurotransmission: A Dissertation

A central concept in the physiology of neurosecretion is that a rise in cytosolic [Ca2+] in the vicinity of plasmalemmal Ca2+ channels due to Ca2+ influx, elicits exocytosis. This dissertation examines the effect on both spontaneous and elicited exocytosis of a rise in focal cytosolic [Ca2+] in the vicinity of ryanodine receptors (RYRs) due to release from internal stores in the form of Ca2+ syntillas. Ca2+ syntillas are focal cytosolic transients mediated by RYRs, which we first found in hypothalamic magnocellular neuronal terminals. (Scintilla, Latin for spark, found in nerve terminals, normally synaptic structures.) We have also observed Ca2+ syntillas in mouse adrenal chromaffin cells (ACCs). Here the effect of Ca2+syntillas on exocytosis is examined in ACCs, which are widely used as model cells for the study of neurosecretion. Elicited exocytosis employs two sources of Ca2+, one due to influx from the cell exterior through voltage-gated Ca2+ channels (VGCCs) and another due to release from intracellular stores. To eliminate complications arising from Ca2+ influx, the first part of this dissertation examines spontaneous exocytosis where influx is not activated. We report that decreasing syntillas leads to an increase in spontaneous exocytosis measured amperometrically. Two independent lines of experimentation each lead to this conclusion. In one case release from stores was blocked by ryanodine; in another, stores were partially emptied using thapsigargin plus caffeine after which syntillas were decreased. We conclude that Ca2+syntillas act to inhibit spontaneous exocytosis, and we propose a simple model to account quantitatively for this action of syntillas. The second part of this dissertation examines the role of syntillas in elicited exocytosis whereby Ca2+ influx is activated by physiologically relevant levels of stimulation. Catecholamine and neuropeptide release from ACCs into the circulation is controlled by the sympathetic division of the Autonomic Nervous System. To ensure proper homeostasis tightly controlled exocytic mechanisms must exist both in resting conditions, where minimal output is desirable and under stress, where maximal, but not total release is necessary. It is thought that sympathetic discharge accomplishes this task by regulating the frequency of Ca2+ influx through VGCCs, which serves as a direct trigger for exocytosis. But our studies on spontaneous release in ACCs revealed the presence of Ca2+ syntillas, which had the opposite effect of inhibiting release. Therefore, assuming Ca2+-induced Ca2+ release (CICR) via RYRs due to Ca2+ influx through VGCCs, we are confronted with a contradiction. Sympathetic discharge should increase syntilla frequency and that in turn should decreaseexocytosis, a paradox. A simple “explanation” might be that the increase in syntillas would act as a brake to prevent an overly great exocytic release. But upon investigation of this question a different finding emerged. We examined the role of syntillas under varying levels of physiologic stimulation in ACCs using simulated action potentials (sAPs) designed to mimic native input at frequencies associated with stress, 15 Hz, and the basal sympathetic tone, 0.5 Hz. Surprisingly, we found that sAPs delivered at 15 Hz or 0.5 Hz were able to completely abolish Ca2+ syntillas within a time frame of two minutes. This was not expected. Further, a single sAP is all that was necessary to initiate suppression of syntillas. Syntillas remained inhibited after 0.5 Hz stimulation but were only temporarily suppressed (for 2 minutes) by 15 Hz stimulation, where global [Ca2+]i was raised to 1 – 2 μM. Thus we propose that CICR, if present in these cells, is overridden by other processes. Hence it appears that inhibition of syntillas by action potentials in ACCs is due to a new process which is the opposite of CICR. This process needs to be investigated, and that will be one of the very next steps in the future. Finally we conclude that syntilla suppression by action potentials is part of the mechanism for elicited exocytosis, resolving the paradox. In the last chapter speculation is discussed into the mechanisms by which physiologic input in the form of an action potential can inhibit Ca2+ syntillas and furthermore, how the Ca2+ syntilla can inhibit exocytic output

SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters

BACKGROUND: Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a useful source of functional and structural information about these sequences. Using software such as the basic local alignment search tool (BLAST) or HMMPFAM to identify statistically significant matches between newly sequenced segments of genetic material and those in databases is an important task for most molecular biologists. Searching algorithms are intrinsically slow and data-intensive, especially in light of the rapid growth of biological sequence databases due to the emergence of high throughput DNA sequencing techniques. Thus, traditional bioinformatics tools are impractical on PCs and even on dedicated UNIX servers. To take advantage of larger databases and more reliable methods, high performance computation becomes necessary. RESULTS: We describe the implementation of SS-Wrapper (Similarity Search Wrapper), a package of wrapper applications that can parallelize similarity search applications on a Linux cluster. Our wrapper utilizes a query segmentation-search (QS-search) approach to parallelize sequence database search applications. It takes into consideration load balancing between each node on the cluster to maximize resource usage. QS-search is designed to wrap many different search tools, such as BLAST and HMMPFAM using the same interface. This implementation does not alter the original program, so newly obtained programs and program updates should be accommodated easily. Benchmark experiments using QS-search to optimize BLAST and HMMPFAM showed that QS-search accelerated the performance of these programs almost linearly in proportion to the number of CPUs used. We have also implemented a wrapper that utilizes a database segmentation approach (DS-BLAST) that provides a complementary solution for BLAST searches when the database is too large to fit into the memory of a single node. CONCLUSIONS: Used together, QS-search and DS-BLAST provide a flexible solution to adapt sequential similarity searching applications in high performance computing environments. Their ease of use and their ability to wrap a variety of database search programs provide an analytical architecture to assist both the seasoned bioinformaticist and the wet-bench biologist

Robust computer-aided synthesis and optimization of linear multivariable control systems with varying plant dynamics via AUTOCON

AUTOCON is an automated computer-aided design tool for the synthesis and optimization of linear multivariable control systems based upon user-defined control parameter optimization. Violations in stability and performance requirements are computed from constraints on Single Input/Single Output (SISO) open- and closed-loop transfer function frequency responses, and from constraints on the singular-value frequency responses of Multiple Input/Multiple Output (MIMO) transfer functions, for all critical plant variations. Optimum nonlinear programming algorithms are used in the search for local constrained solutions in which violations in stability and performance are caused either to vanish or be minimized for a proper selection of the control parameters. Classical control system stability and performance design can, in this way, be combined with modern multivariable robustness methods to offer general frequency response loop-shaping via a computer-aided design tool. Complete Nichols, Nyquist, Bode, singular-value Bode magnitude and transient response plots are produced, including user-defined boundary responses. AUTOCON is used to synthesize and optimize the lateral/directional flight control system for a typical high-performance aircraft

Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV)

The International Committee on Taxonomy of Viruses (ICTV) is charged with the task of developing, refining, and maintaining a universal virus taxonomy. This task encompasses the classification of virus species and higher-level taxa according to the genetic and biological properties of their members; naming virus taxa; maintaining a database detailing the currently approved taxonomy; and providing the database, supporting proposals, and other virus-related information from an open-access, public web site. The ICTV web site (http://ictv.global) provides access to the current taxonomy database in online and downloadable formats, and maintains a complete history of virus taxa back to the first release in 1971. The ICTV has also published the ICTV Report on Virus Taxonomy starting in 1971. This Report provides a comprehensive description of all virus taxa covering virus structure, genome structure, biology and phylogenetics. The ninth ICTV report, published in 2012, is available as an open-access online publication from the ICTV web site. The current, 10th report (http://ictv.global/report/), is being published online, and is replacing the previous hard-copy edition with a completely open access, continuously updated publication. No other database or resource exists that provides such a comprehensive, fully annotated compendium of information on virus taxa and taxonomy

Genomic multiple sequence alignments: refinement using a genetic algorithm

BACKGROUND: Genomic sequence data cannot be fully appreciated in isolation. Comparative genomics – the practice of comparing genomic sequences from different species – plays an increasingly important role in understanding the genotypic differences between species that result in phenotypic differences as well as in revealing patterns of evolutionary relationships. One of the major challenges in comparative genomics is producing a high-quality alignment between two or more related genomic sequences. In recent years, a number of tools have been developed for aligning large genomic sequences. Most utilize heuristic strategies to identify a series of strong sequence similarities, which are then used as anchors to align the regions between the anchor points. The resulting alignment is globally correct, but in many cases is suboptimal locally. We describe a new program, GenAlignRefine, which improves the overall quality of global multiple alignments by using a genetic algorithm to improve local regions of alignment. Regions of low quality are identified, realigned using the program T-Coffee, and then refined using a genetic algorithm. Because a better COFFEE (Consistency based Objective Function For alignmEnt Evaluation) score generally reflects greater alignment quality, the algorithm searches for an alignment that yields a better COFFEE score. To improve the intrinsic slowness of the genetic algorithm, GenAlignRefine was implemented as a parallel, cluster-based program. RESULTS: We tested the GenAlignRefine algorithm by running it on a Linux cluster to refine sequences from a simulation, as well as refine a multiple alignment of 15 Orthopoxvirus genomic sequences approximately 260,000 nucleotides in length that initially had been aligned by Multi-LAGAN. It took approximately 150 minutes for a 40-processor Linux cluster to optimize some 200 fuzzy (poorly aligned) regions of the orthopoxvirus alignment. Overall sequence identity increased only slightly; but significantly, this occurred at the same time that the overall alignment length decreased – through the removal of gaps – by approximately 200 gapped regions representing roughly 1,300 gaps. CONCLUSION: We have implemented a genetic algorithm in parallel mode to optimize multiple genomic sequence alignments initially generated by various alignment tools. Benchmarking experiments showed that the refinement algorithm improved genomic sequence alignments within a reasonable period of time

Regulation of Membrane Targeting of the G Protein-coupled Receptor Kinase 2 by Protein Kinase A and Its Anchoring Protein AKAP79

The beta 2 adrenergic receptor (beta 2AR) undergoes desensitization by a process involving its phosphorylation by both protein kinase A (PKA) and G protein-coupled receptor kinases (GRKs). The protein kinase A-anchoring protein AKAP79 influences beta 2AR phosphorylation by complexing PKA with the receptor at the membrane. Here we show that AKAP79 also regulates the ability of GRK2 to phosphorylate agonist-occupied receptors. In human embryonic kidney 293 cells, overexpression of AKAP79 enhances agonist-induced phosphorylation of both the beta 2AR and a mutant of the receptor that cannot be phosphorylated by PKA (beta 2AR/PKA-). Mutants of AKAP79 that do not bind PKA or target to the beta 2AR markedly inhibit phosphorylation of beta 2AR/PKA-. We show that PKA directly phosphorylates GRK2 on serine 685. This modification increases Gbeta gamma subunit binding to GRK2 and thus enhances the ability of the kinase to translocate to the membrane and phosphorylate the receptor. Abrogation of the phosphorylation of serine 685 on GRK2 by mutagenesis (S685A) or by expression of a dominant negative AKAP79 mutant reduces GRK2-mediated translocation to beta 2AR and phosphorylation of agonist-occupied beta 2AR, thus reducing subsequent receptor internalization. Agonist-stimulated PKA-mediated phosphorylation of GRK2 may represent a mechanism for enhancing receptor phosphorylation and desensitization

67/10/25 Brief of Attorney General of the State of New York as Amicus Curiae in Support of Appellees

New York Attorney General Amicus Curiae brief argues that police should be able to stop and question suspects whom they reasonably believe have or are planning to commit a felony

Orthopoxvirus Genome Evolution: The Role of Gene Loss

Poxviruses are highly successful pathogens, known to infect a variety of hosts. The family Poxviridae includes Variola virus, the causative agent of smallpox, which has been eradicated as a public health threat but could potentially reemerge as a bioterrorist threat. The risk scenario includes other animal poxviruses and genetically engineered manipulations of poxviruses. Studies of orthologous gene sets have established the evolutionary relationships of members within the Poxviridae family. It is not clear, however, how variations between family members arose in the past, an important issue in understanding how these viruses may vary and possibly produce future threats. Using a newly developed poxvirus-specific tool, we predicted accurate gene sets for viruses with completely sequenced genomes in the genus Orthopoxvirus. Employing sensitive sequence comparison techniques together with comparison of syntenic gene maps, we established the relationships between all viral gene sets. These techniques allowed us to unambiguously identify the gene loss/gain events that have occurred over the course of orthopoxvirus evolution. It is clear that for all existing Orthopoxvirus species, no individual species has acquired protein-coding genes unique to that species. All existing species contain genes that are all present in members of the species Cowpox virus and that cowpox virus strains contain every gene present in any other orthopoxvirus strain. These results support a theory of reductive evolution in which the reduction in size of the core gene set of a putative ancestral virus played a critical role in speciation and confining any newly emerging virus species to a particular environmental (host or tissue) niche