Genome-wide location and function of DNA binding proteins

Understanding how DNA binding proteins control global gene expression and chromosomal maintenance requires knowledge of the chromosomal locations at which these proteins function in vivo. We developed a microarray method that reveals the genome-wide location of DNA-bound proteins and used this method to monitor binding of gene-specific transcription activators in yeast. A combination of location and expression profiles was used to identify genes whose expression is directly controlled by Gal4 and Ste12 as cells respond to changes in carbon source and mating pheromone, respectively. The results identify pathways that are coordinately regulated by each of the two activators and reveal previously unknown functions for Gal4 and Ste12. Genome-wide location analysis will facilitate investigation of gene regulatory networks, gene function, and genome maintenance.

Remodeling of yeast genome expression in response to environmental changes

We used genome-wide expression analysis to explore how gene expression in Saccharomyces cerevisiae is remodeled in response to various changes in extracellular environment, including changes in temperature, oxidation, nutrients, pH, and osmolarity. The results demonstrate that more than half of the genome is involved in various responses to environmental change and identify the global set of genes induced and repressed by each condition. These data implicate a substantial number of previously uncharacterized genes in these responses and reveal a signature common to environmental responses that involves approximately 10% of yeast genes. The results of expression analysis with MSN2/MSN4 mutants support the model that the Msn2/Msn4 activators induce the common response to environmental change. These results provide a global description of the transcriptional response to environmental change and extend our understanding of the role of activators in effecting this response.

PRDI-BF1/Blimp-1 repression is mediated by corepressors of the Groucho family of proteins

The PRDI-BF1/Blimp-1 protein is a transcriptional repressor required for normal B-cell differentiation, and it has been implicated in the repression of beta-interferon (IFN-beta) and c-myc gene expression. Here, we show that PRDI-BF1 represses transcription of the IFN-beta promoter and of an artificial promoter through an active repression mechanism. We also identified a minimal repression domain in PRDI-BF1 that is sufficient for transcriptional repression when tethered to DNA as a Gal4 fusion protein. Remarkably, this repression domain interacts specifically with hGrg, TLE1, and TLE2 proteins, all of which are members of the Groucho family of transcriptional corepressors. In addition, the hGrg protein itself can function as a potent repressor when tethered to DNA through the Gal4 DNA-binding domain. We also find that the amino-terminal glutamine-rich domains of hGrg and TLE1 are sufficient to mediate dimerization of the two Groucho family proteins. Proteins containing only this domain can function as a dominant-negative inhibitor of PRDI-BF1 repression, and can significantly increase the IFN-beta promoter activity after virus induction. We conclude that PRDI-BF1/Blimp-1 represses transcription by recruiting a complex of Groucho family proteins to DNA, and suggest that such corepressor complexes are required for the postinduction repression of the IFN-beta promoter.

Polyunsaturated fatty acid suppression of hepatic fatty acid synthase and S14 gene expression does not require peroxisome proliferator-activated receptor alpha

Dietary polyunsaturated fatty acids (PUFA) induce hepatic peroxisomal and microsomal fatty acid oxidation and suppress lipogenic gene expression. The peroxisome proliferator-activated receptor alpha (PPARalpha) has been implicated as a mediator of fatty acid effects on gene transcription. This report uses the PPARalpha-deficient mouse to examine the role of PPARalpha in the PUFA regulation of mRNAs encoding hepatic lipogenic (fatty acid synthase (FAS) and the S14 protein (S14)), microsomal (cytochrome P450 4A2 (CYP4A2)), and peroxisomal (acyl-CoA oxidase (AOX)) enzymes. PUFA ingestion induced mRNAAOX (2.3-fold) and mRNACYP4A2 (8-fold) and suppressed mRNAFAS and mRNAS14 by >/=80% in wild type mice. In PPARalpha-deficient mice, PUFA did not induce mRNAAOX or mRNACYP4A2, indicating a requirement for PPARalpha in the PUFA-mediated induction of these enzymes. However, PUFA still suppressed mRNAFAS and mRNAS14 in the PPARalpha-deficient mice. Studies in rats provided additional support for the differential regulation of lipogenic and peroxisomal enzymes by PUFA. These studies provide evidence for two distinct pathways for PUFA control of hepatic lipid metabolism. One requires PPARalpha and is involved in regulating peroxisomal and microsomal enzymes. The other pathway does not require PPARalpha and is involved in the PUFA-mediated suppression of lipogenic gene expression.

Computed tomography of x-ray index of refraction using the diffraction enhanced imaging method

Diffraction enhanced imaging (DEI) is a new, synchrotron-based, x-ray radiography method that uses monochromatic, fan-shaped beams, with an analyser crystal positioned between the subject and the detector. The analyser allows the detection of only those x-rays transmitted by the subject that fall into the acceptance angle (central part of the rocking curve) of the monochromator/analyser system. As shown by Chapman et al, in addition to the x-ray attenuation, the method provides information on the out-of-plane angular deviation of x-rays. New images result in which the image contrast depends on the x-ray index of refraction and on the yield of small-angle scattering, respectively. We implemented DEI in the tomography mode at the National Synchrotron Light Source using 22 keV x-rays, and imaged a cylindrical acrylic phantom that included oil-filled, slanted channels. The resulting 'refraction CT image' shows the pure image of the out-of-plane gradient of the x-ray index of refraction. No image artefacts were present, indicating that the CT projection data were a consistent set. The 'refraction CT image' signal is linear with the gradient of the refractive index, and its value is equal to that expected. The method, at the energy used or higher, has the potential for use in clinical radiography and in industry.

MCM7 amplification and overexpression are associated with prostate cancer progression

The genomic DNA profiles of prostate cancers with aggressive features were compared to the profiles of matched normal DNA to identify genes that are selectively amplified in the cancer cells. One of the identified genes, MCM7, which is a component of the DNA replication licensing complex, has been studied extensively both at the DNA and protein levels in human prostate tissues. Approximately half of the prostate cancer specimens studied showed MCM7 gene amplification, and 60% of the aggressive prostate cancer specimens had increased MCM7 protein expression. Amplification or overexpression of MCM7 was significantly associated with relapse, local invasion and a worse tumor grade. Constitutive expression of MCM7 in a human prostate cancer cell line, DU145, resulted in markedly increased DNA synthesis and cell proliferation compared to vector-only controls, and an increased cell invasion in vitro. Indeed, MCM7 overexpression produced primary tumors 12 times larger than vector-only controls and resulted in a rapid demise of mice bearing those tumors. These studies implicate MCM7, and the DNA replication licensing gene family, in prostate cancer progression, growth and invasion.

The crystal structure of seleno-glutathione peroxidase from human plasma at 2.9 A resolution

Glutathione peroxidase belongs to the family of selenoproteins and plays an important role in the defense mechanisms of mammals, birds and fish against oxidative damage by catalyzing the reduction of a variety of hydroperoxides, using glutathione as the reducing substrate. However, the physiological role of human plasma glutathione peroxidase remains unclear due to the low levels of reduced glutathione in human plasma and the low reactivity of this enzyme. The crystal structure of human plasma glutathione peroxidase was determined by Patterson search methods using a polyalanine model modified from the known structure of bovine erythrocyte glutathione peroxidase. The structure was refined to a crystallographic R-factor of 0.228 (R(free) = 0.335) with I > 2sigma(I) reflections in the resolution range of 8 to 2.9 A. The asymmetric unit contains a dimer. Tetramers are built up from dimers by crystallographic symmetry. The subunit structure of the plasma enzyme shows the typical structure motif of the thioredoxin fold consisting of a central beta-sheet and several flanking alpha-helices. The active site selenocysteine residue is situated in the loop between beta1 and alpha1 and is located in a pocket on the protein surface. The overall structure of the human plasma enzyme is similar to that of the bovine erythrocyte enzyme. The main differences in their subunit structures are an extended N terminus and the possible existence of a disulfide bridge in the plasma enzyme. Compared to the bovine erythrocyte enzyme, a number of residues in the active site are mutated or deleted in the plasma enzyme, including all the residues that were previously suggested to be involved in glutathione binding. The observed structural differences between the two enzymes suggest differences in substrate binding and specificity.

Spinal cord stimulation in animal models of mononeuropathy: effects on the withdrawal response and the flexor reflex

Spinal cord stimulation (SCS) is efficacious for pain due to injury of peripheral nerves, and therefore models of mononeuropathy appear to be particularly suitable for an experimental approach to the study of mechanisms underlying the clinical effect of this mode of treatment in chronic neuropathic pain. Virtually all previous experimental studies on SCS have utilized acute and nociceptive types of peripheral pain stimuli to explore the attenuating effects of SCS. In the present study we made use of the two models of supposedly painful neuropathy developed by Bennett and Xie (1988) and Seltzer et al. (1990) to explore the effect of SCS applied with stimulus parameters similar to those used in clinical practice. In rats subjected to ligatures of the sciatic nerve according to these two methods, SCS was applied via chronically implanted electrodes, or acutely via a laminectomy in the lower thoracic region. In awake, freely moving animals SCS produced a marked increase of the withdrawal thresholds to innocuous mechanical stimuli in the form of von Frey filaments. This threshold elevation lasted for up to 40 min after 10 min of SCS. In about one-half of the animals there was also a moderate, but short-lasting increase in the intact leg. The degree and duration of the withdrawal threshold elevation was clearly related to the intensity of SCS which was kept below the level of which a response in the thoracic or leg musculature was produced. In a second series of experiments the effect of SCS, applied acutely via a laminectomy, on the early component (latency: 8-12 msec) of the flexor reflex was studied. As a result of nerve ligation with either of the methods used, the thresholds for evoking the early as well as the late component in the nerve-ligated leg were significantly lower than in the intact one. SCS resulted in a marked and long-lasting increase of the threshold of the early component in the nerve-ligated leg. On the intact side only a slight and short-lasting increase was observed. The late, C fibre-mediated component was not influenced by SCS. The first component of the flexor reflex is conceivably mediated by A beta-fibre activation and it presumably corresponds to the withdrawal response induced by innocuous mechanical stimuli. The lack of effect of SCS on the late reflex component indicates that it selectively influences transmission of A-fibre activity. (ABSTRACT TRUNCATED AT 400 WORDS)

Seasonal home range changes of the Sichuan snub-nosed monkey (Rhinopithecus roxellana) in the Qinling Mountains of China

The seasonal changes in home range and habitat use of the Sichuan snub-nosed monkey, Rhinopithecus roxellana, have been studied by radio tracking and direct observation in the Qinling Mountains of China. The home range size was 14.1 km(2) in spring, 9.5 km(2) in summer, 12.1 km(2) in autumn and 12.3 km(2) in winter; the total area used was 22.5 km(2). The area of the home range is closely correlated with the distribution and abundance of food resources. Seasonal change in the home range area is correlated with the phenology of the vegetation. An unusually large home range is a unique characteristic of this monkey.

A protein disulfide oxidoreductase from the archaeon Pyrococcus furiosus contains two thioredoxin fold units

Protein disulfide bond formation is a rate limiting step in protein folding and is catalyzed by enzymes belonging to the protein disulfide oxidoreductase superfamily, including protein disulfide isomerase (PDI) in eucarya and DsbA in bacteria. The first high resolution X-ray crystal structure of a protein disulfide oxidoreductase from the hyperthermophilic archaeon Pyrococcus furiosus reveals structural details that suggest a relation to eukaryotic PDI. The protein consists of two homologous structural units with low sequence identity. Each unit contains a thioredoxin fold with a distinct CXXC active site motif. The accessibilities of both active sites are rather different as are, very likely, their redox properties. The protein shows the ability to catalyze the oxidation of dithiols as well as the reduction of disulfide bridges.

The gateway to transcription: identifying, characterizing and understanding promoters in the eukaryotic genome

Eukaryotic transcriptional regulation requires the integration of complex signals by the transcriptional promoter. Distinct sequence elements, characteristic chromatin modifications and coordinated protein-DNA interactions at these sequences constitute a transcriptional regulatory code that remains poorly understood today. Here, we review recent experimental and computational advances that have enabled the identification and analysis of transcriptional promoters on an unprecedented scale, laying a foundation for systematic determination of the transcriptional regulatory networks in eukaryotic cells. The knowledge gained from these large-scale investigations has challenged some conventional concepts of promoter structure and function, and provided valuable insights into the complex gene regulatory mechanisms in a variety of organisms.

Peroxisome proliferator-activated receptor alpha inhibits hepatic S14 gene transcription. Evidence against the peroxisome proliferator-activated receptor alpha as the mediator of polyunsaturated fatty acid regulation of s14 gene transcription

The peroxisome proliferator-activated receptor (PPARalpha) has been implicated in fatty acid regulation of gene transcription. Lipogenic gene transcription is inhibited by polyunsaturated fatty acids (PUFA). We have used the PUFA-sensitive rat liver S14 gene as a model to examine the role PPARalpha plays in fatty acid regulation of hepatic lipogenic gene transcription. Both PPARalpha and the potent peroxisome proliferator, WY14643, inhibit S14CAT activity in transfected primary hepatocytes. WY14643 and PPARalpha target the S14 T3 regulatory region (TRR, -2.8 to -2.5 kilobases), a region containing 3 T3 response elements (TRE). Transfer of the TRR to the thymidine kinase (TK) promoter conferred negative control to the TKCAT gene following WY14643 and PPARalpha treatment. Gel shift analysis showed that PPARalpha, either alone or with RXRalpha, did not bind the S14TRR. However, PPARalpha interfered with TRbeta/RXRalpha binding to a TRE (DR+4). Functional studies showed that co-transfected RXRalpha, but not T3 receptor beta1 (TRbeta1), abrogated the inhibitory effect of PPARalpha on S14 gene transcription. These results suggest that WY14643 and PPARalpha functionally interfere with T3 regulation of S14 gene transcription by inhibiting TRbeta1/RXR binding to S14 TREs. Previous studies had established that the cis-regulatory targets of PUFA control were located within the proximal promoter region of the S14 gene, i.e. between -220 and -80 bp. Finding that the cis-regulatory elements for WY14643/PPARalpha and PUFA are functionally and spatially distinct argues against PPARalpha as the mediator of PUFA suppression of S14 gene transcription.

Single-and dual-energy CT with monochromatic synchrotron x-rays

We explored the potential for clinical research of computed tomography (CT) with monochromatic x-rays using the preclinical multiple energy computed tomography (MECT) system at the National Synchrotron Light Source. MECT has a fixed, horizontal fan beam with a subject apparatus rotating about a vertical axis; it will be used for imaging the human head and neck. Two CdWO4-photodiode array detectors with different spatial resolutions were used. A 10.5 cm diameter acrylic phantom was imaged with MECT at 43 keV and with a conventional CT (CCT) at 80 kVp: spatial resolution approximately equal to 6.5 line pairs (lp)/cm for both; slice height, 2.6 mm for MECT against 3.0 mm for CCT; surface dose, 3.1 cGy for MECT against 2.0 cGy for CCT. The resultant image noise was 1.5 HU for MECT against 3 HU for CCT. Computer simulations of the same images with more precisely matched spatial resolution, slice height and dose indicated an image-noise ratio of 1.4:1.0 for CCT against MECT. A 13.5 cm diameter acrylic phantom imaged with MECT at approximately 0.1 keV above the iodine K edge and with CCT showed, for a 240 micrograms I ml-1 solution, an image contrast of 26 HU for MECT and 13 and 9 HU for the 80 and 100 kVp CCT, respectively. The corresponding numbers from computer simulation of the same images were 26, 12, and 9 HU, respectively. MECT's potential for use in clinical research is discussed.

Long-term correction of diabetes in rats after lentiviral hepatic insulin gene therapy

AIMS/HYPOTHESIS

Type 1 diabetes results from the autoimmune destruction of pancreatic beta cells. Exogenous insulin therapy cannot achieve precise physiological control of blood glucose concentrations, and debilitating complications develop. Lentiviral vectors are promising tools for liver-directed gene therapy. However, to date, transduction rates in vivo remain low in hepatocytes, without the induction of cell cycling. We investigated long-term transgene expression in quiescent hepatocytes in vitro and determined whether the lentiviral delivery of furin-cleavable insulin to the liver could reverse diabetes in rats.

MATERIALS AND METHODS

To improve transduction efficiency in vitro, we optimised hepatocyte isolation and maintenance protocols and, using an improved surgical delivery method, delivered furin-cleavable insulin alone or empty vector to the livers of streptozotocin-induced diabetic rats by means of a lentiviral vector. Rats were monitored for changes in body weight and blood glucose, and intravenous glucose tolerance tests were performed. Expression of insulin was determined by RT-PCR, immunohistochemistry and electron microscopy.

RESULTS

We achieved long-term transgene expression in quiescent hepatocytes in vitro (87 +/- 1.2% transduction efficiency), with up to 60 +/- 3.2% transduction in vivo. We normalised blood glucose for 500 days-a significantly longer period than previously reported-making this the first successful study using a lentiviral vector. This procedure resulted in the expression of genes encoding several beta cell transcription factors, some pancreatic endocrine transdifferentiation, hepatic insulin storage in granules, and restoration of glucose tolerance. Liver function tests remained normal. Importantly, pancreatic exocrine transdifferentiation did not occur.

CONCLUSIONS/INTERPRETATION

Our data suggest that this regimen may ultimately be employed for the treatment of type 1 diabetes.

Monte Carlo simulation of dose distributions from a synchrotron-produced microplanar beam array using the EGS4 code system

Microbeam therapy is established as a general concept for brain tumour treatment. A synchrotron based x-ray source was chosen for experimental research into microbeam therapy, and therefore new simulations were essential for investigating the therapy parameters with a proper description of the synchrotron radiation characteristics. To design therapy parameters for tumour treatments, the newly upgraded LSCAT (Low energy SCATtering) package of the EGS4 Monte Carlo simulation code was adapted to develop an accurate self-written user code for calculating microbeam radiation dose profiles with a precision of 1 microm. LSCAT is highly suited to this purpose due to its ability to simulate low-energy x-ray transport with detailed photon interactions (including bound electron incoherent scattering functions, and linear polarized coherent scattering). The properties of the synchrotron x-ray microbeam, including its polarization, source spectrum and beam penumbra, were simulated by the new user codes. Two concentric spheres, an inner sphere, defined as a brain, and a surrounding sphere, defined as a skull, represented the phantom. The microbeam simulation was tested using a 3 x 3 cm array beam for small treatment areas and a 6 x 6 cm array for larger ones, with different therapy parameters, such as beam width and spacing. The results showed that the microbeam array retained an adequate peak-to-valley ratio, of five times at least, at tissue depths suitable for radiation therapy. Dose measurements taken at 1 microm resolution with an 'edge-on' MOSFET validated the basics of the user code for microplanar radiation therapy.

Interferon regulatory factor-1-induced apoptosis mediated by a ligand-independent fas-associated death domain pathway in breast cancer cells

Interferon (IFN) regulatory factor-1 (IRF-1) is a transcription factor that has apoptotic anti-tumor activity. In breast cancer cell types, IRF-1 is implicated in mediating apoptosis by both novel and established anti-tumor agents, including the anti-estrogens tamoxifen and faslodex. Here we demonstrate that in MDA468 breast cancer cells, apoptosis by IFN-gamma is mediated by IRF-1 and IFN-gamma, and IRF-1-induced apoptosis is caspase-mediated. IRF-1 induction results in cleavage of caspase-8, -3 and -7, and application of caspase inhibitors attenuate activated cleavage products. IRF-1-induced apoptosis involves caspase-8 since apoptosis is significantly decreased by the caspase-8-specific inhibitor IETD, c-FLIP expression and in caspase-8-deficient cancer cells. Furthermore, we demonstrate that IRF-1-induced apoptosis requires fas-associated death domain (FADD) since dominant-negative FADD expressing cells resist IRF-1-induced apoptosis and activated downstream products. Immunofluorescent studies demonstrate perinuclear colocalization of FADD and caspase-8. Despite the known role of FADD in mediating death-ligand induced apoptosis, neutralizing antibodies against classical death receptors do not inhibit IRF-1 induced apoptosis, and no secreted ligand appears to be involved since MDA468 coincubated with IRF-1 transfected cells do not apoptose. Therefore, we demonstrate that IRF-1 induces a ligand-independent FADD/caspase-8-mediated apoptosis in breast cancer cells.

Effects of fatty acids on hepatic gene expression

Polyunsaturated fatty acids (PUFA) have dramatic effects on hepatic lipid metabolism by regulating the transcription of specific genes encoding enzymes involved in glycolysis and lipogenesis. The S14 gene, a putative lipogenic protein, has been used as a model to define the molecular basis of PUFA action on hepatic gene expression. We have shown that PUFA-regulated hepatic transcription factors target cis-regulatory elements located between -220 and -80 bp upstream from the 5' end of the S14 gene. Peroxisomal proliferators (PP) also have dramatic effects on hepatic lipid metabolism through effects on gene expression. The mechanism of PP action is mediated, at least in part, through nuclear receptors, i.e. PP activated receptor (PPAR). We found that the potent PP, i.e. WY14,643, suppressed mRNAS14 and the activity of an S14CAT fusion gene in cultured primary hepatocytes. Preliminary mapping studies showed that WY14,643 cis-regulatory elements were located either within the S14 proximal promoter (-290 and +19), the S14 TRE (-2900 to -2500) or both regions. Gel shift analysis showed that PPAR did not bind S14 promoter elements. These studies suggest that PUFA- and PP-regulated factors may share common cis-acting elements within the S14 promoter. However, if PUFA control of S14 gene transcription is mediated by PPAR, this mechanism does not involve direct interaction of PPAR with the S14 proximal promoter.