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PubMed1999

Cloning and characterization of the murine genes for bHLH-ZIP transcription factors TFEC and TFEB reveal a common gene organization for all MiT subfamily members.

The microphthalmia-TFE (MiT) subfamily of basic helix-loop-helix leucine zipper (bHLH-ZIP) transcription factors, including TFE3, TFEB, TFEC, and Mitf, has been implicated in the regulation of tissue-specific gene expression in several cell lineages. In this report, we investigate the genomic organization and structural relatedness of MiT transcription factors. We characterized the gene for mTFEC, which covers a region of more than 50 kb and is composed of seven exons. Further, we cloned a cDNA for the murine TFEB homologue and characterized its genomic structure. The eight coding exons of mTFEB are distributed over a 6-kb region. A multiple alignment of amino acid sequences of known MiT subfamily members indicates undescribed, conserved N-terminal regions and common putative phosphorylation sites for TFE3, TFEB, and Mitf. Also, intron-exon borders for characterized MiT genes appear completely conserved. A new family member and closely related putative transcription factor in Caenorhabditis elegans was identified by database searches that show a similar genomic organization within the bHLH-ZIP region and the acidic domain. Evolutionary aspects and implications for structure-function relationships are discussed.

Amino Acid Sequence↗

PubMed2000

Characterization, chromosomal localization, and expression during hematopoietic differentiation of the gene encoding Arl6ip, ADP-ribosylation-like factor-6 interacting protein (ARL6).

Proliferation and differentiation of hematopoietic stem cells and progenitors are regulated by signals from the microenvironment, involving both secreted cytokines and adhesion molecules. The exact mechanisms by which cytokines act on hematopoietic development are still not well understood. To extend the molecular characterization of gene regulation during cytokine-induced hematopoiesis, we applied mRNA differential display to identify genes regulated when multipotent progenitor cells are allowed to differentiate into monocytes and neutrophils. Here we report the isolation and characterization of a gene that is downregulated during myeloid differentiation and encodes a 23-kDa protein with four putative transmembrane segments. The gene, which we named Arl6ip, is identical to a mouse gene recently identified by its physical interaction with ADP-ribosylation-like factor-6 (ARL6), belonging to the Ras superfamily. We add information on its full-length characterization as well as its regulation during hematopoiesis. It is expressed in all hematopoietic cell lineages, but the highest level of expression is found in early myeloid progenitor cells. Preliminary studies by immunofluorescence microscopy revealed that the ARL6IP protein is predominantly localized to intracytoplasmic membranes. This suggests an involvement of the Arl6ip gene in protein transport, membrane trafficking, or cell signaling during hematopoietic maturation.

Adaptor Proteins, Signal Transducing↗

PubMed2000

Mapping of five new putative anion transporter genes in human and characterization of SLC26A6, a candidate gene for pancreatic anion exchanger.

A second distinct family of anion transporters, in addition to the classical SLC4 (or AE) family, has recently been delineated. Members of the SLC26 family are structurally well conserved and can mediate the electroneutral exchange of Cl(-) for HCO(-)(3) across the plasma membrane of mammalian cells like members of the SLC4 family. Three human transporter proteins have been functionally characterized: SLC26A2 (DTDST), SLC26A3 (CLD or DRA), and SLC26A4 (PDS) can transport with different specificities the chloride, iodine, bicarbonate, oxalate, and hydroxyl anions, whereas SLC26A5 (prestin) was suggested to act as the motor protein of the cochlear outer hair cell. We report the expansion of the SLC26 family with five new members in chromosomes 3, 6, 8, 12, and 17 and mapping of SLC26A1 to 4p16.3. We have characterized one of them, SLC26A6, in more detail. It maps to chromosome 3p21.3, encodes a predicted 738-amino-acid transmembrane protein, and is most abundantly expressed in the kidney and pancreas. Pancreatic ductal cell lines Capan-1 and Capan-2 express SLC26A6, and immunohistochemistry localizes SLC26A6 protein to the apical surface of pancreatic ductal cells, suggesting it as a candidate for a luminal anion exchanger. The functional characterization of the novel members of this tissue-specific gene family may provide new insights into anion transport physiology in different parts of the body.

Alternative Splicing↗

PubMed1997

Characterization of the Interface between a Rough Metal and Smooth Mica in Contact

We introduce a technique to characterize, in situ, the solid-solid interface formed when a rough metal surface is placed in contact with a smooth mica surface. The technique is based on the use of extended spectral analysis of multiple beam interferometry in conjunction with the surface forces apparatus (SFA). The intensity versus wavelength spectra of light transmitted through the rough metal/mica interface is measured and compared to that transmitted through a smooth metal/mica interface. Interference theory is used to characterize the rough interface based on differences in the measured spectra. Roughness on the order of nanometers can be resolved. The key to our technique is the creation of a perfectly smooth metal/mica interface that is in all respects, except for roughness, identical to the metal/mica interface created in the SFA. We accomplish this by thermal evaporation of a metal film directly onto mica. We demonstrate the effectiveness of the technique by characterizing the structure of silver/mica and gold/mica interfaces. We also show how the technique can be used to investigate the exchange of fluids within the contact region.

Journal Article↗

PubMed1995

Partially folded states of proteins: characterization by X-ray scattering.

Partially folded states of proteins are found to occur with a wide variety of degrees of unfolding, ranging from the compact molten globule to the fully unfolded forms, depending on solvent conditions and the specific protein involved. Small to intermediate angle X-ray scattering from partially folded states of proteins yields low resolution scattering profiles that may be used to explore the degree of folding of a protein under given solution conditions. By Monte Carlo simulation of a highly simplified homopolymer model, we show that such partially folded states will yield a characteristic scattering profile that may be written as a linear superposition of scattering from a compact core and of scattering from random coil loops that emerge from this core. We also find a term resulting from interference of X-rays scattering from the core with those scattering from the loops. This interference term oscillates in sign and tends to enhance the core portion of the scattering profile. We compare the model calculations of the scattering profile with measurements of the scattering profile as a function of salt concentration for cytochrome c at pH 2. Because of our characterization of the scattering profiles, we suggest that these results may be re-interpreted in terms of the presence of a range of partially folded states as a function of pH and salt concentration, and that the observed scattering profiles are consistent with the characterization of the partially folded states in terms of random coil loops emerging from a compact core with the loop fraction increasing as the salt concentration is decreased. This characterization is consistent with data on amide protection against H-2H exchange of compact regions within partially folded states observed for a number of proteins, including cytochrome c.

Computer Simulation↗

PubMed2000

Characterization of novel proteins based on known protein structures.

The genome sciences face the challenge to characterize structure and function of a vast number of novel genes. Sequence search techniques are used to infer functional and structural information from similarities to experimentally characterized genes or proteins. The persistent goal is to refine these techniques and to develop alternative and complementary methods to increase the range of reliable inference.Here, we focus on the structural and functional assignments that can be inferred from the known three-dimensional structures of proteins. The study uses all structures in the Protein Data Bank that were known by the end of 1997. The protein structures released in 1998 were then characterized in terms of functional and structural similarity to the previously known structures, yielding an estimate of the maximum amount of information on novel protein sequences that can be obtained from inference techniques. The 147 globular proteins corresponding to 196 domains released in 1998 have no clear sequence similarity to previously known structures. However, 75 % of the domains have extensive structure similarity to previously known folds, and most importantly, in two out of three cases similarity in structure coincides with related function. In view of this analysis, full utilization of existing structure data bases would provide information for many new targets even if the relationship is not accessible from sequence information alone. Currently, the most sophisticated techniques detect of the order of one-third of these relationships.

Amino Acid Sequence↗

PubMed2002

Wavelet transforms for the characterization and detection of repeating motifs.

The role of repeating motifs in protein structures is thought to be as modular building blocks which allow an economic way of constructing complex proteins. In this work novel wavelet transform analysis techniques are used to detect and characterize repeating motifs in protein sequence and structure data, where the Kyte-Doolittle hydrophobicity scale (Eta Phi) and relative accessible surface area (rASA) data provide residue information about the protein sequence and structure, respectively. We analyze a variety of repeating protein motifs, TIM barrels, propellor blades, coiled coils and leucine-rich repeat structures. Detection and characterization of these motifs is performed using techniques based on the continuous wavelet transform (CWT). Results indicate that the wavelet transform techniques developed herein are a promising approach for the detection and characterization of repeating motifs for both structural and in some instances sequence data.

Algorithms↗

PubMed1996

Function and Regulation of Natural Killer (NK) Cells during Viral Infections: Characterization of Responses in Vivo

Although in vitro systems have provided important information about the composition and nature of various immune responses, understanding physiologically relevant function and regulation requires evaluating in vivo conditions. Two different models of acute viral infections have made possible the characterization of a variety of responses to these agents, including natural killer (NK) cell activation and regulation during infection; these are mouse infections with lymphocytic choriomeningitis virus (LCMV) and murine cytomegalovirus (MCMV). The results of our characterization of the NK cell responses elicited in these models and the methods used to dissect the regulation of these responses are reviewed here. Cytotoxicity, proliferation, and cytokine expression assays as well as flow cytometric analyses are used to characterize the in vivo responses. Both of the infections induce early NK cell cytotoxicity and blastogenesis. Infection with MCMV but not LCMV also induces NK cell production of the antiviral cytokine, interferon-gamma (IFN-gamma). Antibodies, to mediate in vivo cell subset depletion or cytokine neutralization, and mice, genetically altered to have cell subset or cytokine deficiencies, are utilized to identify the regulatory pathways and mechanisms controlling endogenous NK cell responses to the infections. The major mediators of the regulation of NK cell function during viral infection of normal mice are IFN-alpha/beta and interleukin-12 but not interleukin-2. Furthermore, the induction of later T-cell responses contributes to the negative regulation of NK cells by promoting the production of inhibitory factors including biologically active transforming growth factors-beta. Thus, the study of immune responses to viral infections has provided and will continue to provide important insights into the characteristics of endogenous NK cell responses and the cells and factors that regulate these responses in vivo.

Journal Article↗

PubMed1999

Characterization of mRNA endonucleases.

Endonucleases are key effectors of mRNA degradation, particularly for mRNAs whose turnover rates are regulated by extracellular stimuli. The rapid clearance of mRNA degradation products in vivo and the need to selectively identify mRNA endonucleases in the presence of many other cellular ribonucleases make the study of these enzymes particularly challenging. We have successfully purified and cloned one such enzyme, termed polysomal RNase 1, or PMR-1. Presented here are protocols either developed in our laboratory or adapted from the work of others that we have used successfully in characterizing PMR-1. We first describe methods to determine whether a particular mRNA is degraded in vivo through an endonuclease-initiated mechanism, and then present approaches for developing an in vitro mRNA degradation system. Next we describe experiments one should perform to optimize reaction conditions, determine cofactor requirements for an endonuclease, map in vitro cleavage sites, and characterize endonucleolytic cleavage products. Finally we describe kinetic parameters one should evaluate in characterizing the enzymology of mRNA endonucleases, with particular concern focused on the relative selectivity of these enzymes for cleavage at preferred sites within target mRNAs.

Base Sequence↗

PubMed1999

Cytokine fingerprinting: characterization of chemical allergens.

Chemical allergy is a common and important occupational health issue. Allergic sensitization induced by chemicals may take a variety of forms, including allergic contact dermatitis (skin sensitization) and allergic asthma and rhinitis (sensitization of the respiratory tract). There is a need to identify and characterize chemicals that have the potential to cause such sensitization reactions. Although a number of methods are available for the prospective analysis of skin sensitizing activity, there are currently no widely accepted tests for the identification of chemical respiratory allergens. We here describe a novel approach, cytokine fingerprinting, that has the potential to distinguish between chemical contact and respiratory allergens. The pattern of cytokine production by draining lymph node cells (LNCs) is evaluated following repeated topical exposure of mice to test chemicals. Experience to date reveals that contact allergens stimulate the selective development of type 1 immune responses associated with the secretion by draining LNCs of interferon gamma (IFN-gamma), but little interleukin-4 (IL-4) or interleukin-10 (IL-10). In contrast, chemical respiratory allergens are found to induce the appearance of preferential type 2 immune responses characterized by IL-4 and IL-10 production, but comparatively low levels of IFN-gamma. It is proposed that cytokine fingerprinting may permit the simultaneous identification and characterization of those chemicals that have the potential to cause allergic sensitization.

Allergens↗

PubMed1998

Cloning and characterization of the mouse and rat type II arginase genes.

Two forms of arginase, both catalyzing the hydrolysis of arginine to ornithine and urea, are found in animals ranging from amphibians to mammals. In humans, inherited deficiency of hepatic or type I arginase results in hyperargininemia, a syndrome characterized by periodic episodes of hyperammonemia, spasticity, and neurological deterioration. In these patients, a second extrahepatic or type II arginase activity is significantly increased, an induction that may partially compensate for the lack of AI activity and apparently mitigates some of the clinical effects of the condition. Cloning and characterization of the human AII cDNA was recently accomplished. The cloning, sequencing, and partial characterization of the mouse and rat AII cDNAs are reported herein. The DNA sequences predicted polypeptides of 354 amino acids, including a N-terminal mitochondrial import signal. Sequence homology to the human type II arginase, arginase activity data, and immunoprecipitation with an anti-AII antibody confirm the identity of these cloned genes as rodent extrahepatic type II arginases.

Amino Acid Sequence↗

PubMed1998

Identification, isolation, and characterization of a 32-kDa fatty acid-binding protein missing from lymphocytes in humans with Bietti crystalline dystrophy (BCD).

Bietti crystalline dystrophy (BCD) is an autosomal recessive retinal degeneration characterized by intraretinal lipid inclusions with degeneration of the retina and sclerosis of the choroidal vessels, resulting clinically in progressive night blindness and constriction of the visual fields. Characterization of fatty acid metabolism in Bietti crystalline dystrophy suggested that BCD might result from abnormalities in lipid-binding proteins or one or more enzymes active in fatty acid elongation and desaturation. To further investigate the first possibility, the docosahexaenoic acid-binding proteins (DHABPs) of human lymphocytes from patients with Bietti crystalline dystrophy were studied and compared with those of normal controls. For fatty acid-binding protein (FABP) identification, lymphocyte cytosol was first subjected to Lipidex 1000 chromatography. FABPs were then cross-linked with [14C]22:6n-3 and identified by HPLC and SDS-PAGE. Ten major peaks corresponding to calculated molecular weights of 13, 14, 32, 43, 45, 50, 64, 96, 105, and 186 kDa exhibit high-affinity binding of fatty acids. Significantly, peaks corresponding to two fatty acid-binding proteins of 32 and 45 kDa present in age-matched controls are absent from lymphocytes of patients with BCD. The 32-kDa fatty acid-binding protein present in normal individuals but absent from patients with BCD was isolated from cultured control human lymphocytes, its fatty acid-binding properties were characterized, and its amino acid composition was analyzed. It shows specific binding of 3n-3 fatty acids, consistent with the pattern of abnormalities of lipid metabolism demonstrated in patients with BCD. These results suggest that the 32- and 43-kDa FABPs are reasonable candidates for causing BCD.

Amino Acids↗

PubMed1998

Isolation and characterization of Schwann cells from neurofibromatosis type 2 patients.

Neurofibromatosis type 2 (NF2) is an autosomal dominant disease of the nervous system characterized by multiple schwannomas. The NF2 gene product, termed schwannomin or merlin, was hypothesized to function as a cytoskeleton-membrane linking protein due to homology to members of the protein 4.1 superfamily and to function as a tumor suppressor. We isolated and characterized pure Schwann cell cultures from schwannomas derived from neurofibromatosis 2 patients with identified germline mutations and loss of heterozygosity. We describe striking differences between NF2 and control Schwann cells in morphology, cell-cell contacts, and growth. NF2 Schwann cells form multiple long processes with filopodial and lamellopodial extensions. NF2 Schwann cells lack contact inhibition, grow in multiple layers, and show a higher proliferation rate than control cells. For the first time Schwann cells derived from patients with the NF2 genotype were cultured and characterized in vitro. These cultures are highly valuable for investigating the effects of NF2 mutations and the development of therapies.

Cell Division↗

PubMed2001

Molecular characterization of a cryptic plasmid from Campylobacter jejuni.

Campylobacter jejuni is a leading bacterial cause of human enterocolitis. Molecular genetic characterization of this pathogen has been hampered by the lack of genetic tools that are functional in this organism. Cloning vectors commonly used in other organisms usually do not replicate within C. jejuni. To develop a system for functional analysis of C. jejuni genes, a small plasmid (pCJ01) identified in a poultry isolate of C. jejuni was sequenced and characterized in this study. By using inverse PCR, the full sequence of pCJ01 was amplified and subsequently determined. Results indicate that pCJ01 is a circular molecule of 3212 bp, with a G + C content of 33.5%. A typical plasmid replication origin with iteron sequences is identified upstream of the DNA sequences encoding replication initiation proteins. Four open reading frames (ORFs) are present in pCJ01. ORF1 and ORF2 share high homology with the putative RepA and RepB proteins, respectively, of known C. coli plasmids. ORF3 and ORF4, of unknown function, do not exhibit homology with any sequences deposited in the GenBank database. Hydropathy analysis predicts that ORF3 and ORF4 contain multiple stretches of hydrophobic amino acids, suggesting that they may encode transmembrane proteins. Since pCJ01 is a small plasmid and can be readily prepared from C. jejuni, it may be modified for use in molecular characterization of C. jejuni virulence genes.

Base Sequence↗

PubMed1997

Beyond screening: problems and prospects for risk characterization of endocrine disruptors.

Over time, the NAS's original concept of "risk characterization" has broadened to include not just explication of the risk inferences themselves, but a forthright discussion of their dependence on the many less-than-certain elements of the inferential process. Ideally, such characterization communicates the span of possible conclusions that emerge from alternative reasonable interpretations of the information at hand, together with considered judgment regarding the likelihood that each interpretation provides a good representation of the actual situation. Uncertainties regarding the magnitudes of parameters in the various equations used in quantitative risk assessment are increasingly characterized using statistical tools for analysis and propagation of variance through the calculations. Of potentially greater concern, however, is "model uncertainty"-the more fundamental uncertainty regarding the soundness of our conception of what biological phenomena are operating, how they interact, and how they can be represented in quantitative models. This is particularly true for assessment of potential endocrine disruptors, since much fundamental information is lacking and unanswered questions exist about the consequences and interpretation of empirically observable effects. An approach is to define a series of alternative models, each embodying a different conception, and using expert scientific judgment to weight the individual results.

Animals↗

PubMed2001

PCBs and neurodevelopmental effects in Michigan children: an evaluation of exposure and dose characterization.

Despite the fact that PCB levels in the general environment have continued to decline over the past decade, concern for potential neurodevelopmental deficits from in utero exposure to these compounds remains unabated. In fact, some regulatory and scientific bodies have concluded that the evidence suggesting that prenatal exposure to PCBs may lead to neurodevelopmental deficits is one of the greatest public health concerns surrounding PCBs. The primary basis for the concern that low-level in utero exposure to PCBs causes neurodevelopmental deficits in children is a series of reports on a cohort of Michigan children presumably exposed to PCBs as a result of their mother's consumption of Great Lakes fish. These children, known collectively as the Jacobson cohort, have been followed from birth to 11 years of age. The investigators following these children concluded that they have demonstrated persistent neurodevelopmental effects in this cohort attributable solely to PCBs. However, a detailed analysis of the cohort's exposure characterization, particularly in the initial reports, reveals considerable uncertainty as to the actual exposure status of mothers characterized as "fish eaters" and their offspring. Failure to adequately characterize the PCB exposure of these mothers, or their children, precludes any causal association between in utero exposure to PCBs and neurodevelopmental deficits.

Adult↗

PubMed1998

Low inducibility of CYP1A activity by polychlorinated biphenyls (PCBs) in flounder (Platichthys flesus): characterization of the Ah receptor and the role of CYP1A inhibition.

Several studies have reported a low inducibility of hepatic cytochrome P4501A (CYP1A) activity in European flounder (Platichthys flesus) following exposure to mixtures of polychlorinated biphenyls (PCBs). Here we report on mechanistic studies toward understanding this low CYP1A inducibility of flounder, involving molecular characterization of the Ah receptor (AhR) pathway as well as inhibition of the CYP1A catalytic activity by PCB congeners. Hepatic cytosolic AhR levels in flounder were determined using hydroxylapatite, protamine sulfate adsorption analysis, or velocity sedimentation on sucrose gradients. AhR levels in flounder (approximately 2-7 fmol/mg protein) were much lower than observed generally in rodents (approximately 50-300 fmol/mg protein). Molecular characterization of the flounder AhR was provided by first-strand cDNA synthesis and amplification of flounder hepatic poly(A)+ RNA using RT-PCR. A 690-bp product was found, similar in size to a Fundulus AhR cDNA. The specificity of the 690-bp band was established by Southern blotting and hybridization with a degenerate AhR oligonucleotide. The deduced amino acid sequence of the flounder AhR fragment was 59-60% identical to mammalian AhR sequences. Although the AhR is present in flounder cytosol, we were unable to demonstrate detectable amounts of inducible TCDD-AhR-DRE complex in gel-retardation assays. High induction levels of CYP1A protein and associated EROD activity have been previously found in flounder following exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). In contrast, the induction of CYP1A catalytic activity by PCB mixtures remains unexpectedly low. Therefore, we further characterized the inhibitory potential of PCB congeners on CYP1A activity in flounder and compared this with inhibitory effects of PCB congeners on rat CYP1A activity. Analysis in vitro demonstrated that 3,3',4,4'-tetraCB, 3,3',4,4',5-pentaCB, 2,2',4,4',5,5'-hexaCB, 3,3',4,4',5,5'-hexaCB, and the commercial PCB mixture Clophen A50 are potent competitive inhibitors of hepatic microsomal CYP1A catalytic activity in flounder and rat. The K(m) for ethoxyresorufin (0.095 microM) in flounder is strikingly close to Ki's found for the tested PCBs. This emphasizes the possible involvement of PCB congeners in inhibition of EROD activity in PHAH exposed fish. Finally, our data indicate that flounder CYP1A is more efficient in metabolizing ethoxyresorufin than that of rat CYP1A.

Amino Acid Sequence↗

PubMed2001

Rotavirus cross-species pathogenicity: molecular characterization of a bovine rotavirus pathogenic for pigs.

Rotaviruses which cause disease in heterologous animal species have been reported but the molecular basis of cross-species infectivity and disease is not established. We report the molecular characterization of a cloned rotavirus, PP-1, which was originally obtained from cattle and which had been biologically characterized in vivo in two target animal species, gnotobiotic pigs and calves. In pigs, PP-1 caused severe clinical disease but in experimental calves it replicated subclinically. PP-1 was characterized as a G3 reassortant with a porcine VP4 and NSP4 but a bovine NSP1. The PP-1 VP4 had 96 to 97% deduced amino acid identity to P[7] porcine rotaviruses and P[7] specificity was confirmed with VP4-specific monoclonal antibodies. Sequence analysis of the PP-1 NSP1 showed 94 to 99.6% deduced amino acid identity to bovine rotaviruses but the NSP4 protein had 94 to 98% identity to the NSP4 genotype B porcine rotaviruses. G-typing PCR initially classified PP-1 as a G10 rotavirus but sequence analysis revealed 92 to 96% identity of the PP-1 VP7 with porcine, simian, and human G3 rotaviruses. These results, combined with the in vivo properties of PP-1 in the two target species, supported the concept that species-specific VP4 and NSP4, but not NSP1, are required to induce rotavirus disease, at least in calves and pigs. The results illustrate experimentally that rotaviruses circulating in one animal species can pose a risk to another by the emergence of a pathogenic reassortant rotavirus under appropriate conditions.

Amino Acid Sequence↗