bluuebunny/crossref_metadata_2025 huggingface dataset:
On achieving better than 1-A accuracy in a simulation of a large protein: Streptomyces griseus protease A.
Authors: Kitson D H , Avbelj F , Moult J , Nguyen D T , Mertz J E , Hadzi D , Hagler A T
Published: May 2006

Computational methods are frequently used to simulate the properties of proteins. In these studies accuracy is clearly important, and the improvement of accuracy of protein simulation methodology is one of the major challenges in the application of theoretical methods, such as molecular dynamics, to structural studies of biological molecules. Much effort is being devoted to such improvements. Here, we present an analysis of a 187-ps molecular dynamics simulation of the serine protease Streptomyces griseus protease A in its crystal environment. The reproduction of the experimental structure is considerably better than has been achieved in earlier simulations--the root mean square deviation of the simulated structure from the x-ray structure being less than 1 A, a significant step toward the goal of simulating proteins to within experimental error. The use of a longer cutoff with truncation rather than a switching function, inclusion of all crystalline water and the counterions in the crystallization medium, and use of the consistent valence force field characterize the differences in this calculation.
Engineered leucine zippers show that hemiphosphorylated CREB complexes are transcriptionally active.
Authors: Loriaux M M , Rehfuss R P , Brennan R G , Goodman R H
Published: May 2006

The ability of basic/leucine zipper transcription factors to form homo- and heterodimers potentially increases the diversity of signaling pathways that can impinge upon a single genetic element. The capacity of these proteins to dimerize in various combinations complicates the analysis of their functional properties, however. To simplify the functional analysis of CREB dimers, we mutated selected residues within the leucine zipper region to generate proteins that could only heterodimerize. These mutants allowed us to determine whether phosphorylation of both CREB subunits was necessary for transcriptional activation. Our results reveal that hemiphosphorylated CREB dimers are half as active as fully phosphorylated dimers. It is possible, therefore, that the degree of phosphorylation of CREB complexes could modulate the transcriptional responses of specific genes to cAMP.
Three-dimensional structure of a membrane-containing virus.
Authors: Paredes A M , Brown D T , Rothnagel R , Chiu W , Schoepp R J , Johnston R E , Prasad B V
Published: May 2006

The structure of Sindbis virus was determined by electron cryomicroscopy. The virion contains two icosahedral shells of viral-encoded proteins separated by a membrane bilayer of cellular origin. The three-dimensional structure of the ice-embedded intact Sindbis virus, reconstructed from electron images, unambiguously shows that proteins in both shells are arranged with the same icosahedral lattice of triangulation number T = 4. These studies also provide structural evidence of contact between the glycoprotein and the nucleocapsid protein across the membrane bilayer. The structural organization of Sindbis virus has profound implications for the morphogenesis of the alphaviruses. The observed interactions confirm stoichiometric and specific protein associations that may be crucial for virion stability and predict a mechanism for assembly.
A genetic method for defining DNA-binding domains: application to the nuclear receptor NGFI-B.
Authors: Wilson T E , Padgett K A , Johnston M , Milbrandt J
Published: May 2006

A method is described that allows for rapid and efficient generation of functional mutations in DNA-binding domains of proteins. The target DNA-binding domain is attached to the Gal4p transcriptional-activating domain and expressed in yeast. The binding site recognized by the target domain is placed upstream of a gene that produces a protein toxic to yeast cells, so that the chimeric protein activates its expression, providing a selection against DNA-binding domain function. The chimeric protein also activates expression of a gene necessary for histidine prototrophy, using a second DNA-binding domain included in the chimera (lexA), providing a selection against general activator mutations. Therefore, requiring growth in the absence of histidine focuses mutations to the target DNA-binding domain. This method was applied to the DNA-binding domain of the nuclear receptor NGFI-B. Nearly all mutations obtained concurred with previous studies of NGFI-B and other nuclear receptors, verifying the functional validity of the mutational profile obtained. In addition, by coupling this selection scheme with the two-hybrid system [Chien, C.-t., Bartel, P. L., Sternglanz, R. & Fields, S. (1991) Proc. Natl. Acad. Sci. USA 88, 9578-9582], mutations that alter protein interaction domains could also be obtained.
Unconventional processing of the 3' termini of the Epstein-Barr virus DNA polymerase mRNA.
Authors: Furnari F B , Adams M D , Pagano J S
Published: May 2006

Northern blot analysis of the Epstein-Barr virus DNA polymerase mRNA identified two discrete sizes of virally encoded polymerase transcripts, 5.08 kb detected in strains P3HR1, Raji, W-91, and FF-41 and 3.7 kb detected solely in the prototype B95-8 strain. 3' S1-nuclease mapping and analysis of cDNA sequence generated by RNA-based PCR demonstrated that the 3.7-kb polymerase mRNA from B95-8 terminates 484 base pairs downstream of the open reading frame in a region of the genome remarkable for its lack of an apparent polyadenylylation signal. Moreover, between the cleavage point and the poly(A) tract of the cDNAs are a series of inserted nucleotides, mostly adenosine and uridine residues of unknown origin. A similar analysis of the 3' terminus of the 5.0-kb mRNA from the other cell lines revealed that polyadenylylation occurs 1.4 kb downstream of the B95-8 terminus. This region is deleted in B95-8, which accounts for the alternate upstream terminus used in B95-8. Like the 3.7-kb terminus, the 5.0-kb terminus lacks a canonical polyadenylylation signal, but contains a rarely used UAUAAA sequence 32 bp upstream of the poly(A) tail. These results indicate that the mRNA encoded by the Epstein-Barr virus DNA polymerase gene is polyadenylylated at two different termini without the use of canonical signals, raising the possibility of involvement of a virus-encoded factor in 3' processing of this message.
A 1.5-megabase yeast artificial chromosome contig from human chromosome 10q11.2 connecting three genetic loci (RET, D10S94, and D10S102) closely linked to the MEN2A locus.
Authors: Lairmore T C , Dou S , Howe J R , Chi D , Carlson K , Veile R , Mishra S K , Wells S A , Donis-Keller H
Published: May 2006

The genetic loci RET, D10S94, and D10S102 from human chromosome 10q11.2 are very closely linked to a locus responsible for the multiple endocrine neoplasia type 2 (MEN2A and MEN2B) and medullary thyroid carcinoma (MTC1) familial cancer syndromes. We have constructed a 1.5-megabase contig consisting of six genomic yeast artificial chromosome clones which include these loci and define their physical order. A critical crossover event has been identified within the map interval; this event places the MEN2A locus centromeric to D10S102 and defines the orientation of the physical map on the chromosome. The orientation of the contig and order of the markers are centromere-RET-D10S94-D10S102-telomere. In addition, a microsatellite repeat polymorphism with a heterozygosity of 71% at the RET locus and a restriction fragment length polymorphism with a heterozygosity of 42% detected by a lambda clone from the D10S94 locus have been developed for high-resolution genetic linkage mapping and predictive diagnostic testing. These data place three important markers on a contiguous physical map, narrow the MEN2 disease locus interval, and provide a framework for further candidate gene identification efforts. Placement of these genetic loci along a clone-based map and continued expansion of the contig will also facilitate efforts to determine the relationship of physical to genetic distance near the centromeres of human chromosomes.
Cytokines, endotoxin, and glucocorticoids regulate the expression of inducible nitric oxide synthase in hepatocytes.
Authors: Geller D A , Nussler A K , Di Silvio M , Lowenstein C J , Shapiro R A , Wang S C , Simmons R L , Billiar T R
Published: May 2006

Nitric oxide (NO.) is a short-lived mediator which can be induced in a variety of cell types and produces many physiologic and metabolic changes in target cells. The inducible or high-output NO. synthase (NOS) pathway was first characterized in macrophages activated by lipopolysaccharide (LPS) and interferon gamma (IFN-gamma). Hepatocytes also express an inducible NOS following exposure to the combination of endotoxin (LPS) and tumor necrosis factor (TNF), interleukin 1 (IL-1), and IFN-gamma. In this study, to identify which of these cytokines, if any, was acting to induce the gene expression for hepatocyte NOS, we measured the levels of rat hepatocyte NOS mRNA by Northern blot analysis after stimulation by various combinations of endotoxin and cytokines in vitro. We found the mRNA for hepatocyte NOS to be a single band at approximately 4.5 kilobases which was maximally up-regulated (approximately 70-fold) by the combination of TNF, IL-1, IFN-gamma, and LPS. Abundance of NOS mRNA peaked 6-8 hr after stimulation and then declined by 25% at 24 hr. Unstimulated hepatocytes in vitro showed only a trace mRNA band after prolonged autoradiographic exposure. As single agents, TNF and IL-1 were the most effective inducers of hepatocyte NOS mRNA. Combinations of two or three stimuli revealed strong synergy between TNF, IL-1, and IFN-gamma. The increased mRNA levels correlated with elevated nitrogen oxide release and cGMP levels in the culture supernatants. Dexamethasone and cycloheximide inhibited induction of mRNA for hepatocyte NOS in a dose-dependent fashion. The addition of NG-monomethyl-L-arginine had no effect on mRNA levels but effectively blocked NO. formation. The inducible hepatocyte NOS mRNA was also detected in rat hepatocytes following chronic hepatic inflammation triggered by Corynebacterium parvum injection in vivo. These data demonstrate that the inducible NOS is functional in rat hepatocytes both in vitro and in vivo and that this pathway is under complex control. Endotoxin and inflammatory cytokines act synergistically to up-regulate gene expression for hepatocyte NOS, whereas glucocorticoids down-regulate the mRNA.
Genome mapping by nonrandom anchoring: a discrete theoretical analysis.
Authors: Zhang M Q , Marr T G
Published: May 2006

As part of our effort to construct a physical map of the genome of the fission yeast Schizosaccharomyces pombe, we have made theoretical predictions for the progress expected, as measured by the expected length fraction of island coverage and by the expected properties of the anchored islands such as the number and the size of islands. Our experimental strategy is to construct a random clone library and screen the library for clones having unique sequence at both ends. This scheme is essentially the same as the clone-limited double sequence-tagged-site selection scheme which was used in a computer simulation by Palazzolo et al. [Palazzolo, M. J., Sawyer, S. A., Martin, C. H., Smoller, D. A. & Hartl, D. L. (1991) Proc. Natl. Acad. Sci. USA 88, 8034-8038]. Both simulation and ongoing experiments in our laboratory have shown that the nonrandom anchoring method is far superior to random anchoring. In this paper, we propose a theoretical model to explain the simulated data and the experimental data.
On the nature of the protein folding code.
Authors: Rackovsky S
Published: May 2006

This paper investigates quantitatively the characteristics of the local folding code. The overlapping four-residue fragments which make up the amino acid sequences of 114 proteins are divided into classes on the basis of the physical properties of their constituent amino acids. The distribution of structural types associated with each class of sequence fragment is determined and compared with an ensemble of random structural distributions of the same size selected from the actual protein structures. A criterion is proposed, based on the relative entropies of the two types of distribution, and on a hypothesis as to the characteristics of fragments which code for local structure, that makes it possible to identify those four-residue sequence elements which encode specific time-averaged structure. It is determined that, by this criterion, only 60-70% of the four-residue fragments encode specific structures. It is suggested that the remaining sequence fragments intrinsically encode susceptibility to conformational alteration under the influence of long-range interactions and that this susceptibility is required for correct folding of the molecule. This feature introduces an inherent indeterminacy into the local folding code. The implications of this observation for the prediction of protein structure by various methods are briefly discussed.
Roles of the six peptide-binding pockets of the HLA-A2 molecule in allorecognition by human cytotoxic T-cell clones.
Authors: Matsui M , Hioe C E , Frelinger J A
Published: May 2006

To evaluate the contribution of the major histocompatibility complex class I pockets to the binding of self-peptides recognized by alloreactive cytotoxic T-lymphocyte (CTL) clones, we have constructed an extensive library of HLA-A2 mutants with different amino acid substitutions in each of the six pockets. When these mutants were tested in cytotoxicity assays with a panel of HLA-A2-specific alloreactive CTL clones, each CTL clone showed a unique pattern of reactivity, implying the different contributions of each pocket to binding individual peptides. We noted that the majority of the mutants in pocket B significantly affect recognition by the CTL clones. Unexpectedly, the mutations influencing allorecognition are found in all other pockets as well. Overall, this study demonstrates that each of the six peptide-binding pockets plays an important and distinct role in binding of self-peptides required for recognition of the HLA-A2 molecule by alloreactive CTLs.
Pleiotrophin transforms NIH 3T3 cells and induces tumors in nude mice.
Authors: Chauhan A K , Li Y S , Deuel T F
Published: May 2006

The pleiotrophin (PTN) gene (Ptn) encodes an 18-kDa protein that is highly conserved among mammalian species and that functions as a weak mitogen and promotes neurite-outgrowth activity in vitro. To further investigate the role PTN plays in regulating cell growth, we overexpressed the bovine PTN cDNA and now show that PTN phenotypically transforms NIH 3T3 cells, as evidenced by increased cell number at confluence, focus formation, anchorage-independent growth, and tumor formation in the nude mouse. The results demonstrate that the Ptn gene has the potential to regulate NIH 3T3 cell growth and suggest that PTN may influence abnormal cell growth in vivo.
Regulation of cysteine-rich intestinal protein by dexamethasone in the neonatal rat.
Authors: Levenson C W , Shay N F , Lee-Ambrose L M , Cousins R J
Published: May 2006

The cysteine-rich intestinal protein (CRIP) is an intestinal zinc-binding protein containing a single copy of a cysteine-rich domain known as the LIM motif. CRIP mRNA and protein levels increased in the rat small intestine throughout the suckling period, reaching highest levels by the late weanling stage. A similar developmental pattern of CRIP protein levels was also detected by an increase in zinc binding to CRIP-containing HPLC fractions of intestinal cytosol. Administration of the synthetic glucocorticoid hormone dexamethasone to neonates caused the precocious rise of CRIP mRNA and protein. In adult rats, CRIP mRNA levels were not significantly altered by dexamethasone. Maximal CRIP mRNA content was detected in cells from the mid-villus, as confirmed by expression of cryptdin mRNA. In this report we show the glucocorticoid regulation of the LIM motif-containing protein CRIP and suggest that glucocorticoid hormones play a role in developmental regulation of CRIP.
Regional expression and chromosomal localization of the delta opiate receptor gene.
Authors: Bzdega T , Chin H , Kim H , Jung H H , Kozak C A , Klee W A
Published: May 2006

The delta opiate receptor gene has been cloned from the mouse neuroblastoma-rat glioma hybrid cell NG108-15. The clone that we isolated is apparently identical to that reported by Evans et al. [Evans, C. J., Keith, D. E., Jr., Morrison, H., Magendzo, K. & Edwards, R. H. (1992) Science 258, 1952-1955] and essentially identical with that of Kieffer et al. [Kieffer, B. L., Befort, K., Gaveriaux-Ruff, C. & Hirth, C. G. (1992) Proc. Natl. Acad. Sci. USA 89, 12048-12052]. We have found full-length transcripts of the gene in mouse brain but in no other tissues examined. Within the brain the gene is expressed at low levels in many regions but transcripts are found in particularly large amounts in the anterior pituitary and pineal glands. Since these tissues are located outside the blood-brain barrier, opioid peptides easily can reach receptors in these areas from the blood. The gene, which is present as a single copy, has been mapped to the distal region of mouse Chromosome 4.
Chromosomal rearrangement segregating with adrenoleukodystrophy: a molecular analysis.
Authors: Sack G H , Alpern M , Webster T , Feil R P , Morrell J C , Chen G , Chen W , Caskey C T , Moser H W
Published: May 2006

The relationship between X chromosome-linked adrenoleukodystrophy and the red/green color pigment gene cluster on Xq28 was investigated in a large kindred. The DNA in a hemizygous male showed altered restriction fragment sizes compatible with at least a deletion extending from the 5' end of the color pigment genes. Segregation analysis using a DNA probe within the color pigment gene cluster showed significant linkage with adrenoleukodystrophy (logarithm of odds score of 3.19 at theta = 0.0). These data demonstrate linkage, rather than association, between a unique molecular rearrangement in the color pigment gene cluster and adrenoleukodystrophy. The DNA changes in this region are thus likely to be helpful for determining the location and identity of the responsible gene.
The hobo transposable element of Drosophila can be cross-mobilized in houseflies and excises like the Ac element of maize.
Authors: Atkinson P W , Warren W D , O'Brochta D A
Published: May 2006

The hobo transposable element from Drosophila melanogaster was found to be capable of excision, resulting in donor sites unlike those reported for any other transposable element currently known in animals. These empty sites most closely resemble those left by the transposable elements Ac and Tam3 in Zea mays and Antirrhinum majus, respectively. Like Ac and Tam3, the hobo element was found to function in a distantly related species, in this case the housefly Musca domestica. Hobo excision in M. domestica was found not to require the expression of hobo-encoded transposase but instead appears to be driven by an endogenous hobo transposase-like activity. DNA sequences displaying high homology to the hobo transposase gene were isolated from the genome of M. domestica and appear to be part of a mobile-element system related to hobo, Ac, and Tam3.
Mutant DnaK chaperones cause ribosome assembly defects in Escherichia coli.
Authors: Alix J H , Guérin M F
Published: May 2006

To determine whether the biogenesis of ribosomes in Escherichia coli is the result of the self-assembly of their different constituents or involves the participation of additional factors, we have studied the influence of a chaperone, the product of the gene dnaK, on ribosome assembly in vivo. Using three thermosensitive (ts) mutants carrying the mutations dnaK756-ts, dnaK25-ts, and dnaK103-ts, we have observed the accumulation at nonpermissive temperature (45 degrees C) of ribosomal particles with different sedimentation constants--namely, 45S, 35S, and 25S along with the normal 30S and 50S ribosomal subunits. This is the result of a defect not in thermostability but in ribosome assembly at the nonpermissive temperature. These abnormal ribosomal particles are rescued if the mutant cells are returned to 30 degrees C. Thus, the product of the dnaK gene is implicated in ribosome biogenesis at high temperature.
Diversified sequences of peptide epitope for same-RNA recognition.
Authors: Kim S , Ribas de Pouplana L , Schimmel P
Published: May 2006

We replaced an essential RNA-binding, 30-amino acid helix-loop in an Escherichia coli tRNA synthetase with an inactive and simplified "generic" sequence having 23 of the 30 amino acids as alanine and serine. Wild-type residues were restored in random combinations to generate a library with a sequence complexity of about 1.9 x 10(7). Active molecules were obtained by genetic selection at a frequency of approximately 1% and contained variants with as many as 11 alanine/serine replacements and a total of 17 alanine/serine residues. These variants have activities which are thermodynamically competitive with that of the native protein and therefore are functionally and, most likely, conformationally equivalent.
Determination of mRNA fate by different RNA polymerase II promoters.
Authors: Enssle J , Kugler W , Hentze M W , Kulozik A E
Published: May 2006

Translational stop mutations of the human beta-globin gene cause a reduction of cytoplasmic mRNA accumulation in thalassemia patients and in transfection models. The exact mechanism underlying this phenomenon has remained enigmatic but is known to be post-transcriptional. We have used transfected HeLa cells to study the expression of beta-globin mRNAs with nonsense or frameshift mutations within the three exons of this gene. Mutations in exons 1 or 2 reduce cytoplasmic mRNA accumulation whereas a mutation in exon 3 permits essentially normal expression. We report here that the post-transcriptional fate of mutated beta-globin mRNAs is differentially affected by the type of RNA polymerase II promoter driving expression. Replacement of the beta-globin promoter with the herpes simplex virus type 1 thymidine kinase gene promoter but not the cytomegalovirus immediate early promoter rescues the cytoplasmic accumulation of mutated mRNA to wild-type levels. This effect is shown to be independent of the absolute quantity and the kinetics of accumulation of mutated mRNA synthesized, and primer-extension analyses confirm that both viral promoters accurately utilize identical transcription start sites. These data thus reveal an unexpected property of RNA polymerase II promoters: determination of the post-transcriptional fate of the maturing mRNA, presumably by influencing alternative choices between as yet undefined processing and/or transport pathways.
Voltage-dependent potentiation of the activity of cardiac L-type calcium channel alpha 1 subunits due to phosphorylation by cAMP-dependent protein kinase.
Authors: Sculptoreanu A , Rotman E , Takahashi M , Scheuer T , Catterall W A
Published: May 2006

Barium currents mediated by the alpha 1 subunit of the cardiac L-type Ca channel expressed in Chinese hamster ovary (CHO) cells were increased up to 10-fold during dialysis of the cell with the catalytic subunit of cAMP-dependent protein kinase. After partial activation by exogenous kinase, the activity of the alpha 1 subunit was also reversibly potentiated up to 3.5-fold by prepulses to voltages in the range of 0 to +150 mV. Potentiation at +48 mV developed with a biphasic time course with time constants of 131 ms and 8 s. Reversal at -60 mV was biphasic with half-times of 12 ms and 100 ms and was blocked in the presence of the phosphatase inhibitor okadaic acid. Both the increase in calcium-channel activity during dialysis with kinase and the voltage-dependent potentiation were accompanied by shifts in the voltage dependence of activation to more negative membrane potentials. The increases in Ba current due to protein phosphorylation and to the dihydropyridine Ca channel agonist Bay K8644 were approximately additive. The results show that the alpha 1 subunit of the cardiac L-type Ca channel is sufficient for substantial modulation of Ca-channel activity by cAMP-dependent protein kinase and for potentiation by state-dependent protein phosphorylation. Voltage-dependent potentiation of the activity of the alpha 1 subunit may contribute to the increase in contractile force in response to increased rate of stimulation, the positive staircase effect in heart muscle.
Stimulation of Trypanosoma cruzi adenylyl cyclase by an alpha D-globin fragment from Triatoma hindgut: effect on differentiation of epimastigote to trypomastigote forms.
Authors: Fraidenraich D , Peña C , Isola E L , Lammel E M , Coso O , Añel A D , Pongor S , Baralle F , Torres H N , Flawia M M
Published: May 2006

A peptide from hindguts of the Triatoma hematophagous Chagas insect vector activates adenylyl cyclase activity in Trypanosoma cruzi epimastigote membranes and stimulates the in vitro differentiation of epimastigotes to metacyclic trypomastigotes. Hindguts were obtained from insects fed 2 days earlier with chicken blood. Purification was performed by gel filtration and HPLC on C18 and C4 columns. SDS/PAGE of the purified peptide showed a single band of about 10 kDa. The following sequence was determined for the 20 amino-terminal residues of this peptide: H2N-Met-Leu-Thr-Ala-Glu-Asp-Lys-Lys-Leu-Ile-Gln- Gln-Ala-Trp-Glu-Lys-Ala-Ala-Ser-His. This sequence is identical to the amino terminus of chicken alpha D-globin. On a Western blot, the peptide immunoreacted with a polyclonal antibody against chicken globin D. A synthetic peptide corresponding to residues 1-40 of the alpha D-globin amino terminus also stimulated adenylyl cyclase activity and promoted differentiation. This 125I-labeled synthetic peptide bound specifically to T. cruzi epimastigote cells. Activation of epimastigote adenylyl cyclase by the hemoglobin-derived peptide may play an important role in T. cruzi differentiation and consequently in the transmission of Chagas disease.
Direct identification of an endogenous peptide recognized by multiple HLA-A2.1-specific cytotoxic T cells.
Authors: Henderson R A , Cox A L , Sakaguchi K , Appella E , Shabanowitz J , Hunt D F , Engelhard V H
Published: May 2006

An endogenous peptide recognized by a murine T-cell clone specific for the human class I major histocompatibility complex-encoded molecule HLA-A2.1 was identified through the use of microcapillary high-performance liquid chromatography coupled with electrospray-ionization tandem mass spectrometry. The peptide was associated with HLA-A2.1 on both normal cells and the antigen-processing-mutant cell line T2. This observation demonstrates that a processing mechanism other than that involving the transporter associated with antigen processing (TAP) proteins 1 and 2 can produce peptides that can be recognized by T cells. The peptide was also recognized by four other independently derived murine HLA-A2.1-specific murine T-cell clones. This suggests that xenogeneic responses are directed at a restricted subset of major histocompatibility complex product-associated peptides. Finally, quantitation of this peptide in cell extracts using mass spectrometry showed it to be among the most dominant HLA-A2.1 associated species on human lymphoid cells. The potential relevance of this observation to models of alloreactivity will be discussed. The methodology described should be generally useful for the identification of peptide epitopes recognized by alloreactive, tumor-specific, and autoimmune T cells.
Mapping of interacting domains between the nucleocapsid protein and the phosphoprotein of vesicular stomatitis virus by using a two-hybrid system.
Authors: Takacs A M , Das T , Banerjee A K
Published: May 2006

Specific interaction between the nucleocapsid protein (N) and the phosphoprotein (P) of vesicular stomatitis virus (VSV), an important step in the life-cycle of the virus, was studied by using a two-hybrid system. Plasmids encoding P fused with the yeast GAL4 DNA-binding domain (pGALP) and N fused with the herpes simplex virus VP16 transactivating region (pVPN) were transfected into CHO cells along with a reporter plasmid encoding chloramphenicol acetyltransferase (CAT). The ability of N and P to associate in vivo was measured by activation of the CAT gene by the VP16 transactivating region. Transfection of plasmids pGALP and pVPN resulted in a high level of CAT activity, indicating that the N and P portions of the fusion proteins associated very strongly with each other. Progressive C-terminal deletions of the P protein revealed two regions that are important for association with the N protein: the N-terminal acidic domain and the C-terminal basic domain. Phosphorylation of P protein was not required for N-P association. Various deletions and mutations of the N protein revealed the C-terminal 5 amino acids (Val-Glu-Phe-Asp-Lys), in particular the amino acids Val-Glu-Phe, to be critical for N association with P. This two-hybrid system can be used in other viral systems to study the interaction between proteins involved in transcription and replication.
Altered protein binding to the octamer motif appears to be an early event in programmed neuronal cell death.
Authors: Wang S , Pittman R N
Published: May 2006

Electrophoretic mobility-shift assays were used to characterize binding of nuclear proteins to consensus sequences for Sp1, E2F, octamer, and cAMP responsive enhancer element (CRE) during neuronal death in vitro after removal of nerve growth factor (NGF). Molecular events occurring prior to cell death in terminally differentiated PC12 cells could be divided into three phases: (i) within 2 hr of removing NGF, binding to the octamer sequence decreased, (ii) after 5-7 hr an increase in binding to CRE occurred; and (iii) after 14 hr (the point at which 50% of the cells are committed to die) a decrease in binding to the Sp1 sequence occurred. Assays performed with extracts from sympathetic ganglia indicated that changes in binding to CRE and octamer motifs also occurred during the period of developmental cell death in vivo. Double-stranded oligonucleotides were delivered to neurons to act as dominant negative "promoters" unable to couple to transcriptional events but capable of binding and sequestering transcription factors. Double-stranded but not single-stranded octamer oligonucleotides increased cell death of primary cultures of sympathetic neurons. Most of the induced neuronal cell death could be blocked with NGF, which is consistent with oligonucleotides activating an endogenous death program rather than having a nonspecific toxic effect. Other double-stranded oligonucleotides as well as a mutant octamer oligonucleotide had little or no effect on cell death. These data are consistent with the hypothesis that cell death results from a cascade of cellular and molecular events and that an early event in programmed neuronal cell death is a decrease in binding of transcription factor(s) to octamer motif sequences.
Color, contrast sensitivity, and the cone mosaic.
Authors: Williams D , Sekiguchi N , Brainard D
Published: May 2006

This paper evaluates the role of various stages in the human visual system in the detection of spatial patterns. Contrast sensitivity measurements were made for interference fringe stimuli in three directions in color space with a psychophysical technique that avoided blurring by the eye's optics including chromatic aberration. These measurements were compared with the performance of an ideal observer that incorporated optical factors, such as photon catch in the cone mosaic, that influence the detection of interference fringes. The comparison of human and ideal observer performance showed that neural factors influence the shape as well as the height of the foveal contrast sensitivity function for all color directions, including those that involve luminance modulation. Furthermore, when optical factors are taken into account, the neural visual system has the same contrast sensitivity for isoluminant stimuli seen by the middle-wavelength-sensitive (M) and long-wavelength-sensitive (L) cones and isoluminant stimuli seen by the short-wavelength-sensitive (S) cones. Though the cone submosaics that feed these chromatic mechanisms have very different spatial properties, the later neural stages apparently have similar spatial properties. Finally, we review the evidence that cone sampling can produce aliasing distortion for gratings with spatial frequencies exceeding the resolution limit. Aliasing can be observed with gratings modulated in any of the three directions in color space we used. We discuss mechanisms that prevent aliasing in most ordinary viewing conditions.
Topography of the histone octamer surface: repeating structural motifs utilized in the docking of nucleosomal DNA.
Authors: Arents G , Moudrianakis E N
Published: May 2006

The histone octamer core of the nucleosome is a protein superhelix of four spirally arrayed histone dimers. The cylindrical face of this superhelix is marked by intradimer and interdimer pseudodyad axes, which derive from the nature of the histone fold. The histone fold appears as the result of a tandem, parallel duplication of the "helix-strand-helix" motif. This motif, by its occurrence in the four dimers, gives rise to repetitive structural elements--i.e., the "parallel beta bridges" and the "paired ends of helix I" motifs. A preponderance of positive charges on the surface of the octamer appears as a left-handed spiral situated at the expected path of the DNA. We have matched a subset of DNA pseudodyads with the octamer pseudodyads and thus have built a model of the nucleosome. In it, the two DNA strands coincide with the path of the histone-positive charges, and the central 12 turns of the double helix contact the surface of the octamer at the repetitive structural motifs. The properties of these complementary contacts appear to explain the preference of histones for double-helical DNA and to suggest a possible basis for allosteric regulation of nucleosome function.
Comparative spectroscopic, calorimetric, and computational studies of nucleic acid complexes with 2',5"-versus 3',5"-phosphodiester linkages.
Authors: Jin R , Chapman W H , Srinivasan A R , Olson W K , Breslow R , Breslauer K J
Published: May 2006

We have used a combination of spectroscopic, calorimetric, and computational techniques to characterize the properties of nucleic acid complexes with 2',5''- and 3',5''-phosphodiester linkages. Specifically, we have compared the properties of complexes formed by the association of 3',5'' single-stranded 16-mers of adenylic acid (A16) and thymidylic acid (T16) with the complexes formed by the corresponding single-stranded 16-mers with 2',5''-phosphodiester linkages (A*16 and T*16). Our results reveal the following differential features: (i) the 3',5'' strands form either a duplex or a triplex, depending on the sodium ion concentration, whereas the 2',5'' strands form either a triplex or no complex at all; (ii) the 2',5'' and 3',5'' triplexes exhibit significantly different CD spectra, suggesting that the two triplex states are conformationally nonequivalent; (iii) the 2',5'' triplex has a lower charge density than the 3',5'' triplex; (iv) the thermal stability of the 3',5'' triplex, as expected, is concentration dependent, whereas the thermal stability of the 2',5'' triplex is concentration independent; (v) relative to their component single strands, the 2',5'' triplex is thermodynamically much less stable than the 3',5'' triplex, despite being thermally more stable; (vi) the reduced thermodynamic stability of the 2',5'' triplex relative to the 3',5'' triplex is overwhelmingly enthalpic in origin. In the aggregate, our results reveal and characterize significant differences in the properties of complexes formed by the association of strands with identical base sequences but different phosphodiester linkages. We describe a structural model that is consistent with many of the differential properties observed. We also speculate on how these differential properties may have provided an evolutionary advantage for 3',5'' linkages and how the properties of 2',5'' complexes might be exploited in antisense strategies.
Strand-invasion of duplex DNA by peptide nucleic acid oligomers.
Authors: Peffer N J , Hanvey J C , Bisi J E , Thomson S A , Hassman C F , Noble S A , Babiss L E
Published: May 2006

Polyamide oligomers, termed peptide nucleic acids (PNAs), bind with high affinity to both DNA and RNA and offer both antisense and antigene approaches for regulating gene expression. When a PNA binds to a complementary sequence in a double-stranded DNA, one strand of the duplex is displaced, and a stable D-loop is formed. Unlike oligodeoxynucleotides for which binding polarity is determined by the deoxyribose sugar, the unrestrained polyamide backbone of the PNA could permit binding to a DNA target in an orientation-independent manner. We now provide evidence that PNAs can, in fact, bind to their complementary sequence in DNA independent of the DNA-strand polarity--that is, a PNA binds to DNA in both "parallel" and "antiparallel" fashion. With a mixed-sequence 15-mer PNA, kinetic studies of PNA.DNA interactions revealed that D-loop formation was rapid and the complex was stable for several hours. However, when measured either by gel-mobility-shift analysis or RNA polymerase II-elongation termination, D-loop formation was salt dependent, but PNA-strand dissociation was not salt dependent. We observed that D-loop-containing DNA fragments had anomalous gel mobilities that varied as a function of the position of the D-loop relative to the DNA termini. On the basis of permutation analysis, the decreased mobility of the PNA.DNA complex was attributed to a bend in the DNA at or near the D-loop.
Failure of a protective major histocompatibility complex class II molecule to delete autoreactive T cells in autoimmune diabetes.
Authors: Slattery R M , Miller J F , Heath W R , Charlton B
Published: May 2006

The association of major histocompatibility complex genes with autoimmune diseases is firmly established, but the mechanisms by which these genes confer resistance or susceptibility remain controversial. The controversy extends to the nonobese diabetic (NOD) mouse that develops disease similar to human insulin-dependent diabetes mellitus. The transgenic incorporation of certain class II major histocompatibility complex genes protects NOD mice from diabetes, and clonal deletion or functional silencing of autoreactive T cells has been proposed as the mechanism by which these molecules provide protection. We show that neither thymic deletion nor anergy of autoreactive T cells occurs in NOD mice transgenic for I-Ak. Autoreactive T cells are present, functional, and can transfer diabetes to appropriate NOD-recipient mice.
Brn-3.0: a POU-domain protein expressed in the sensory, immune, and endocrine systems that functions on elements distinct from known octamer motifs.
Authors: Gerrero M R , McEvilly R J , Turner E , Lin C R , O'Connell S , Jenne K J , Hobbs M V , Rosenfeld M G
Published: May 2006

Characterization of Brn-3.0 and identification of a highly related member (Brn-3.1) of the class IV POU-domain family suggest potential roles of Brn-3.0 in the development of retinal ganglion cells and sensory neurons, as well as potential roles in the pituitary gland and the immune system. Brn-3.0 is expressed in the pituitary gland and in a corticotroph cell line. A functional DNA response element has been identified in the proopiomelanocortin promoter. In contrast to previously described mammalian POU-domain proteins, Brn-3.0 binds relatively ineffectively to known octamer DNA motifs, but instead binds with high affinity to a distinct set of DNA elements, functioning as a transcriptional activator. Brn-3.0, Brn-3.1, and the Drosophila tI-POU share an N-terminal region of homology, referred to as the "POU-IV box," which is similar to a conserved functional domain in the c-myc gene family.
Antioncogenes and human cancer.
Authors: Knudson A G
Published: May 2006

The antioncogenes, or tumor suppressor genes, as negative regulators of cell division, stand in contrast to oncogenes. For most human cancers, the more frequently mutated genes are the antioncogenes, the principal exception being the leukemias and lymphomas. Persons heterozygous for germ-line mutations in antioncogenes are strongly predisposed to one or more kinds of cancer, and most dominantly inherited cancer is attributable to such heterozygosity. Seven antioncogenes have been cloned through the study of these persons, and several others have been mapped. An eighth one was mapped and cloned through the investigation of tumors and is not yet known in hereditary form. Three dominantly inherited forms of cancer are not attributable to mutations in antioncogenes. The corresponding nonhereditary forms of most cancers generally reveal abnormalities of the same antioncogenes that are found in the hereditary forms but may also show additional ones. Some cancers, especially the embryonal tumors of children, have a small number of antioncogene mutations; some others, such as most sarcomas, have more, and the common carcinomas have the most, reflecting a hierarchy of controls over growth of stem cell populations. Still more members of this gene category remain to be mapped and cloned through the study of cancer families and of tumors. The genes that have been cloned act at diverse points in the signal transduction pathway in cells, from the outer cell membranes to sites of gene transcription, in some cases as negative regulators of oncogene expression.
Cytokinin stimulates dihydropyridine-sensitive calcium uptake in moss protoplasts.
Authors: Schumaker K S , Gizinski M J
Published: May 2006

Ca2+ influx through dihydropyridine (DHP)-sensitive Ca2+ channels is thought to be an early event in cytokinin-induced bud formation in moss protonema because DHP antagonists inhibit bud formation in the presence of cytokinin and DHP agonists stimulate bud formation in the absence of cytokinin [Conrad, P. A. & Helper, P. K. (1988) Plant Physiol. 86, 684-687]. In the present study, we established the presence of a DHP-sensitive Ca2+ transport system by measuring 45Ca2+ influx into moss protoplasts. Ca2+ influx was stimulated by external KCl (up to 5 mM), indicating that transport is voltage-dependent. K(+)-induced Ca2+ influx was DHP-sensitive with > 50% inhibition at 500 nM nifedipine. Ca2+ influx was stimulated by increasing concentrations of the DHP Ca2+ channel agonist Bay K8644 with half-maximal effects at 25 nM; this stimulation was seen only in the absence of K+, suggesting that the agonist works preferentially on polarized membranes. Ca2+ influx was also inhibited by phenylalkylamines (verapamil) and benzothiazepines (diltiazem). The phytohormone 6-benzylaminopurine consistently stimulated Ca2+ influx with a Km value of 1 nM, whereas adenine, indoleacetic acid, and gibberellic acid had no effect on Ca2+ transport. The cytokinins kinetin and trans-zeatin caused a greater stimulation of Ca2+ influx and induced more bud formation than did 6-benzylaminopurine. These results indicate that Ca2+ is taken up into moss protoplasts through voltage-dependent DHP-sensitive Ca2+ channels on the plasma membrane and that one of the cytokinin effects in the induction of bud formation is regulation of this plasma membrane Ca2+ channel.
Theoretical basis for separation of multiple linked gene effects in mapping quantitative trait loci.
Authors: Zeng Z B
Published: May 2006

It is now possible to use complete genetic linkage maps to locate major quantitative trait loci (QTLs) on chromosome regions. The current methods of QTL mapping (e.g., interval mapping, which uses a pair or two pairs of flanking markers at a time for mapping) can be subject to the effects of other linked QTLs on a chromosome because the genetic background is not controlled. As a result, mapping of QTLs can be biased, and the resolution of mapping is not very high. Ideally when we test a marker interval for a QTL, we would like our test statistic to be independent of the effects of possible QTLs at other regions of the chromosome so that the effects of QTLs can be separated. This test statistic can be constructed by using a pair of markers to locate the testing position and at the same time using other markers to control the genetic background through a multiple regression analysis. Theory is developed in this paper to explore the idea of a conditional test via multiple regression analysis. Various properties of multiple regression analysis in relation to QTL mapping are examined. Theoretical analysis indicates that it is advantageous to construct such a testing procedure for mapping QTLs and that such a test can potentially increase the precision of QTL mapping substantially.
On the puzzling arrangement of the asymmetric MalT-binding sites in the MalT-dependent promoters.
Authors: Danot O , Raibaud O
Published: May 2006

The MalT-dependent promoters of the enterobacteria belong to a small family of positively regulated prokaryotic promoters in which the activator protein recognizes short asymmetric nucleotide sequences present in several locations and orientations. We demonstrate that active MalT-dependent semisynthetic promoters can be constructed by using a synthetic decanucleotide as the MalT site and random nucleotide sequences as connecting sequences, provided that the location and orientation of the sites are the same as in natural MalT-dependent promoters. Strikingly, the induced level of promoter activity and the induction factor of each semisynthetic promoter are identical to those of its natural counterpart, in spite of considerable differences in their nucleotide sequences. The study of these semisynthetic promoters confirms the importance of the structural motif formed by two MalT sites in a direct repeat. This motif is involved in promoter activation either alone or in conjunction with a third MalT site, proximal with respect to the transcription start site. In this latter configuration, the promoters are active irrespective of the orientation of the repeat, and they retain at least some activity when the distance between the repeat and the proximal site is increased, provided that the alignment along the axis of the helix is conserved.
Inhibition of protein synthesis alters the subcellular distribution of mRNA in neurons but does not prevent dendritic transport of RNA.
Authors: Kleiman R , Banker G , Steward O
Published: May 2006

This study evaluates whether protein synthesis plays a role in targeting RNA molecules to different subcellular domains within neurons. Transport of newly synthesized RNA (labeled with [3H]uridine) was examined in the presence of the protein synthesis inhibitors puromycin and cycloheximide. In situ hybridization was used to determine whether inhibition of protein synthesis altered the subcellular distribution of mRNAs. Transport of recently synthesized RNA was not disrupted after prolonged exposure to either inhibitor. However, inhibition of protein synthesis caused several mRNAs that are normally confined to the cell body to appear in dendrites. The distribution of mRNAs that are normally present in dendrites was unaffected. These findings suggest that protein synthesis is not required to translocate RNA into the dendrites but may play a role in restricting particular mRNAs to the neuronal cell body.