A scientist's guide for submitting data to ZFIN.

The Zebrafish Model Organism Database (ZFIN; zfin.org) serves as the central repository for genetic and genomic data produced using zebrafish (Danio rerio). Data in ZFIN are either manually curated from peer-reviewed publications or submitted directly to ZFIN from various data repositories. Data types currently supported include mutants, transgenic lines, DNA constructs, gene expression, phenotypes, antibodies, morpholinos, TALENs, CRISPRs, disease models, movies, and images. The rapidly changing methods of genomic science have increased the production of data that cannot readily be represented in standard journal publications. These large data sets require web-based presentation. As the central repository for zebrafish research data, it has become increasingly important for ZFIN to provide the zebrafish research community with support for their data sets and guidance on what is required to submit these data to ZFIN. Regardless of their volume, all data that are submitted for inclusion in ZFIN must include a minimum set of information that describes the data. The aim of this chapter is to identify data types that fit into the current ZFIN database and explain how to provide those data in the optimal format for integration. We identify the required and optional data elements, define jargon, and present tools and templates that can help with the acquisition and organization of data as they are being prepared for submission to ZFIN. This information will also appear in the ZFIN wiki, where it will be updated as our services evolve over time.

Retroviral inhibition of cAMP-dependent protein kinase inhibits myelination but not Schwann cell mitosis stimulated by interaction with neurons.

Schwann cells are the myelinating glia of the peripheral nervous system. Neuron-Schwann cell contact profoundly affects several aspects of Schwann cell phenotype, including stimulation of mitosis and myelin formation. Many reports suggest that neuronal contact exerts this influence on Schwann cells by elevating Schwann cell cAMP and activating cAMP-dependent protein kinase A (PKA). To elucidate the importance of Schwann cell PKA in neuronal stimulation of Schwann cell mitosis and myelination, the gene encoding the PKA inhibitory protein RIalphaAB or PKIEGFP was delivered to Schwann cells using retroviral vectors. PKA inhibitory retroviral vectors effectively blocked forskolin-stimulated Schwann cell mitosis and morphological change, demonstrating the ability of the vectors to inhibit PKA in infected Schwann cells. Treatment of dorsal root ganglia neuron-Schwann cell cocultures with H-89 (10 microm) or KT5720 (1-10 microm), chemical inhibitors selective for PKA, significantly inhibited neuronal stimulation of Schwann cell mitosis. In contrast, retrovirus-mediated inhibition of Schwann cell PKA had no effect on the ability of neurons to stimulate Schwann cell mitosis. However, markedly fewer myelin segments were formed by Schwann cells expressing PKA inhibitory proteins compared with controls. These results suggest that activation of Schwann cell PKA is required for myelin formation but not for Schwann cell mitosis stimulated by interaction with neurons.

A dicistronic retroviral vector and culture model for analysis of neuron-Schwann cell interactions.

A dicistronic retroviral gene delivery system and tissue culture model has been developed for studies of neuron-Schwann cell interactions at the single cell level. The dicistronic retroviral vector contains a multiple cloning site followed by the encephalomyocarditis virus internal ribosomal entry site (EMCV-IRES) and a green fluorescent protein gene. This design allows for 5'-cap dependent translation of any gene of interest and 5'-cap independent translation of green fluorescent protein (GFP) from a single dicistronic RNA. The culture model consists of dorsal root ganglia (DRG) explants grown in defined medium. Under these conditions the Schwann cell population is selectively expanded and infected by the retroviral vector, allowing for rapid transfer of genes of interest selectively to a large percentage of Schwann cells in coculture with neurons. Infected cells are subsequently identified in living cultures by their expression of GFP. Infected (GFP expressing) Schwann cells in contact with neurites continued to exhibit: (1) increased mitotic activity, (2) increased sensitivity to elevate intracellular calcium in response to extracellular application of ATP, and (3) myelination. This viral construct has the added advantage that it allows identification of cells expressing transgenes among a heterogeneous population by fluorescence microscopy, FACS, or flow cytometry.

Reliability estimates for data recovered from compact discs.

Data reliability at the output of the error-correction code decoderin a compact-disc system is influenced by the decoding strategyemployed by the decoder, as well as by the statistical distribution oferrors that contaminate the recorded data. Recovered-datareliability estimates have been computed by use of error statisticsobtained from the measurement of errors that contaminate the actualdata stored on clean write-once and read-only-memory compactdiscs. These estimates consist of probabilities that specify theoccurrence of residual errors in the data that appear at the output ofa compact-disc player's cross-interleaved Reed-Solomon code(CIRC) decoder. Data reliability estimates that apply to fivespecific CIRC decoding strategies are reported.

Oligodendroglial signal transduction systems are regulated by neuronal contact.

Previous reports indicate that oligodendrocytes express signaling systems activated by classical neurotransmitters. Several signaling systems linked to mobilization of intracellular calcium have been demonstrated, and some of these are developmentally lost in vitro and in vivo. The experiments described here use oligodendrocyte-neuron cocultures to examine the effects of neuronal contact on the expression of these signaling pathways. Neonatal rat cerebral oligodendrocytes in contact with dorsal root ganglia (DRG) neurites responded to bath application of histamine, ATP, carbachol, glutamate, or bradykinin with increases in intracellular Ca2+ concentration. Similar results were obtained in coculture with superior cervical ganglia neurons. Preventing neuronal contact by transection of DRG neurites significantly reduced the percentage of oligodendrocytes responsive to each ligand, with the exception of bradykinin responsiveness, which was unaffected. Oligodendroglia isolated from adult rat spinal cord were also examined for responsiveness to these neuroligands. Few isolated adult oligodendroglia were responsive to these ligands, and coculture with DRG neurons failed to restore responsiveness. Neuroligand responsiveness was not induced in oligodendrocytes maintained 8 days in purified culture before establishment of cocultures. A significant reduction in the number of neuroligand-responsive oligodendroglia was noted for histamine, carbachol, glutamate, and ATP after including tetrodotoxin for the final 6 days of coculture. These results suggest that both neuronal contact and neuronal activity contribute to the maintenance of functional neurotransmitter-activated signaling pathways coupled to mobilization of intracellular calcium in oligodendrocytes.

Error characteristics of read-only-memory versus write-once-read-many compact discs: CD-ROM versus CD-WORM.

The data recorded on several write-once (WO) and read-only-memory (ROM) compact discs has been examined byte by byte to determine the locations of all erroneous bytes along the spiral data tracks. This information has been used to determine error-burst and good-data-gap distributions, which specify the occurrence probability versus the length of an error event (burst) and the intervening segments of good data (gaps). The means for determining whether a given error event is a hard or a soft error event have also been developed. The burst and gap distributions exhibit generally similar characteristics for WO and ROM compact discs that are clean, although clustering of errors on the WO media is evident.

Partial-response equalization in magneto-optical disk readout: a theoretical investigation.

We analyze the application of partial-response equalization and maximum-likelihood sequence estimation in magneto-optical readout. Two filters are proposed, and several aspects of their performance are examined. Filter I has 8 states in its state-transition diagram and is therefore easier to implement than filter II, which has 32 states. We discuss the required signal-to-noise ratio as function of the recorded bit density for these filters. The effects of jitter and bloom on the eye patterns of the output signals are also examined by computer simulation. This analysis indicates that filter II is somewhat superior to filter I, presumably because the output of filter II is more similar to the actual readout signal. We determine the distribution of Euclidean distance between pairs of output sequences and compute upper bounds on the probability of sequence error for both filters. Using two different methods of precoding (i.e., mapping of the user data to the magnetic pattern on the disk), we also compute the probability of bit error for the user data and show that one precoding scheme is slightly better than the other.