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Upon binding to thalidomide and other immunomodulatory drugs, the E3 ligase substrate receptor cereblon (CRBN) promotes proteosomal destruction by engaging the DDB1–CUL4A–Roc1–RBX1 E3 ubiquitin ligase in human cells but not in mouse cells, suggesting that sequence variations in CRBN may cause its inactivation. Therapeutically, CRBN engagers have the potential for broad applications in cancer and immune therapy by specifically reducing protein expression through targeted ubiquitin-mediated degradation. To examine the effects of defined sequence changes on CRBN's activity, we performed a comprehensive study using complementary theoretical, biophysical, and biological assays aimed at understanding CRBN's nonprimate sequence variations. With a series of recombinant thalidomide-binding domain (TBD) proteins, we show that CRBN sequence variants retain their drug-binding properties to both classical immunomodulatory drugs and dBET1, a chemical compound and targeting ligand designed to degrade bromodomain-containing 4 (BRD4) via a CRBN-dependent mechanism. We further show that dBET1 stimulates CRBN's E3 ubiquitin–conjugating function and degrades BRD4 in both mouse and human cells. This insight paves the way for studies of CRBN-dependent proteasome-targeting molecules in nonprimate models and provides a new understanding of CRBN's substrate-recruiting function.

Devices containing III–V semiconductors such as InAs are increasingly being used in the electronic industry for a variety of optoelectronic applications. Furthermore, the attractive chemical, material, electronic properties make such materials appealing for use in devices designed for biological applications, such as biosensors. However, in biological applications the leaching of toxic materials from these devices could cause harm to cells or tissue. Additionally, after disposal, toxic inorganic materials can leach from devices and buildup in the environment, causing long-term ecological harm. Therefore, the toxicity of these materials along with their stability in physiological conditions are important factors to consider. Surface modifications are one common method of stabilizing semiconductor materials in order to chemically and electronically passivate them. Such surface modifications could also prevent the leaching of toxic materials by preventing the regrowth of the unstable surface oxide layer and by creating an effective barrier between the semiconductor surface and the surrounding environment. In this study, various surface modifications on InAs are developed with the goal of decreasing the leaching of indium and arsenic. The leaching of indium and arsenic from modified substrates was assessed in physiological conditions using inductively coupled plasma mass spectrometry (ICP-MS). Substrates modified with 11-mercapto-1-undecanol (MU) and graft polymerized with poly(ethylene) glycol (PEG) were most effective at preventing indium and arsenic leaching. These surfaces were characterized using contact angle analysis, ellipsometry, atomic force microscopy (AFM), and X-ray photoelectron spectroscopy (XPS). Substrates modified with collagen and synthetic polyelectrolytes were least effective, due to the destructive nature of acidic environments on InAs. The toxicity of modified and unmodified InAs, along with raw indium, arsenic, and PEG components was assessed using zebrafish embryos.

The Sp family of transcription factors is required for the expression of cell cycle- and developmentally regulated genes, and the deregulated expression of a handful of family members is associated with human tumorigenesis. Sp2 is a relatively poorly characterized member of the Sp family that, although widely expressed, exhibits little or no DNA binding or transcriptional activity in human and mouse cell lines. To begin to address the role(s) played by Sp2 in early metazoan development we have cloned and characterized Sp2 from zebrafish (Danio rerio). We report that 1) the intron/exon organization and amino acid sequence of zebrafish Sp2 is closely conserved with its mammalian orthologues, 2) zebrafish Sp2 weakly stimulates an Sp-dependent promoter in vitro and associates with the nuclear matrix in a DNA-independent fashion, 3) zebrafish Sp2 is inherited as a maternal transcript, is transcribed in zebrafish embryos and adult tissues, and is required for completion of gastrulation, and 4) zebrafish lines carrying transgenes regulated by the Sp2 promoter recapitulate patterns of endogenous Sp2 expression.

Transmembrane bound receptors comprised of extracellular immunoglobulin (Ig) or lectin domains play integral roles in a large number of immune functions including inhibitory and activating responses. The function of many of the activating receptors requires a physical interaction with an adaptor protein possessing a cytoplasmic regulatory motif. The partnering of an activating receptor with an adaptor protein relies on complementary charged residues in the two transmembrane domains. The mammalian natural killer (NK) and Fc receptors (FcR) represent two of many receptor families, which possess activating receptors that partner with adaptor proteins for signaling. Zebrafish represent a powerful experimental model for understanding developmental regulation at early stages of embryogenesis and for efficiently generating transgenic animals. In an effort to understand developmental aspects of immune receptor function, we have accessed the partially annotated zebrafish genome to identify six different adaptor molecules: Dap10, Dap12, Cd3zeta, Cd3zeta-like, FcRgamma and FcRgamma-like that are homologous to those effecting immune function in mammals. Their genomic organizations have been characterized, cDNA transcripts have been recovered, phylogenetic relationships have been defined and their cell lineage-specific expression patterns have been established.

Two decades of research have established the zebrafish (Danio rerio) as a significant model system for studying vertebrate development and gene structure-function relationships. Recent advances in mutation screening, the creation of genomic resources, including the Zebrafish Genome Project and the development of efficient transgenesis procedures, make this model increasingly attractive for immunological study.

A novel gene, BIVM (for basic, immunoglobulin-like variable motif-containing), has been identified using an electronic search based on the conservation of short sequence motifs within the variable region of immunoglobulin (Ig) genes. BIVM maps to human chromosome 13q32-q33 and is predicted to encode a 503-amino-acid protein with a pI of 9.1. The 5' untranslated region of BIVM is encoded in two exons; the coding portion is encoded in nine exons. BIVM is tightly linked (41 bp) and in the opposite transcriptional orientation to MGC5302 (also known as KDEL1 and EP58) in human. The ubiquitous expression of BIVM in normal tissues and the presence of a 5' CpG island suggest that BIVM is a housekeeping gene. Characterization of BIVM in representative species demonstrates significant conservation throughout deuterostomes; no sequence with significant identity to BIVM has been detected in proteostomes. However, an unusual gene has been identified in the protozoan pathogen Giardia lamblia that is similar to the core sequence of BIVM, suggesting the possibility of a horizontal gene transfer.

In addition to being an excellent model system for studying vertebrate development, the zebrafish has become a great tool for gene discovery by mutational analysis. The recent availability of the zebrafish EST database and radiation hybrid mapping panels has dramatically expanded the framework for genomic research in this species. Developing comparative maps of the zebrafish and human genomes is of particular importance for zebrafish mutagenesis studies in which human orthologs are sought for zebrafish genes. However, only partial cDNA sequences are determined routinely for mapped ESTs, leaving the identity of the EST in question. It previously had been reported that zebrafish linkage group 7 shares conserved synteny with human chromosome 11q13. In an effort to further define this relationship, five full-length zebrafish cDNAs, fth1, slc3a2, prkri, cd81, and pc, as well as one putative human gene, DBX were identified and their map positions ascertained. These six genes, along with men1, fgf3 and cycd1 define two regions of conserved synteny between linkage group 7 and 11q13.

The addition of Na(2,6-diphenylphenoxide) to a diethyl ether solution of the monomeric Zn(2,6-diphenylphenoxide)2(THF)2 derivative affords the trisphenoxide complex, Na[Zn(2,6-diphenylphenoxide)3(H2O)] (1). An X-ray crystal structure analysis of 1 reveals the zinc to possess a distorted tetrahedral geometry and that the sodium counterion is essentially six-coordinate, being bound to the three oxygen atoms of the aryloxide ligands and the aromatic carbon atoms of one of the phenyl substituent on each of these ligands. An additional zinc phenoxide complex, Na[Zn2(2,6-diisopropylphenoxide)4Cl]·3THF (2), was obtained during the synthesis of Zn(2,6-diisopropylphenoxide)2(THF)2 in the presence of NaCl. The X-ray structure of 2 again shows the sodium ion to be six-coordinate, involved in an η6-interaction with the phenoxide π-system and bound to two THF ligands and a chloride ion.

Most of the 5-methylcytosine in mammalian DNA resides in transposons, which are specialized intragenomic parasites that represent at least 35% of the genome. Transposon promoters are inactive when methylated and, over time, C → T transition mutations at methylated sites destroy many transposons. Apart from that subset of genes subject to X inactivation and genomic imprinting, no cellular gene in a non-expressing tissue has been proven to be methylated in a pattern that prevents transcription. It has become increasingly difficult to hold that reversible promoter methylation is commonly involved in developmental gene control; instead, suppression of parasitic sequence elements appears to be the primary function of cytosine and methylation, with crucial secondary roles in allele-specific gene expression as seen in X inactivation and genomic imprinting.