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PubMed2004

Nonperturbative modeling of two-photon absorption in a three-state system.

The physics of the two-photon absorption process is investigated for a three-state system. The density-matrix equations for the two-photon interaction are solved in the steady-state limit assuming that the pump laser radiation is monochromatic. Collisional broadening, saturation, and Stark shifting of the two-photon resonance are investigated in detail by numerical solution of the steady-state density-matrix equations. Analytical expressions for the saturation intensity and the Stark shift are derived for the case where the single-photon transitions between the intermediate state and the initial and final states are far from resonance with the pump laser. For this case, it is found that the direction of the Stark shift is dependent on the relative magnitudes of the dipole-moment matrix elements for the single-photon transitions that couple the intermediate state with the initial and final states. Saturation and Stark shifting are also investigated for the case where the single-photon transitions between the intermediate state and the initial and final states are close to resonance with the pump laser.

Journal Article↗

PubMed1978

The effect of evolution on homologous proteins: a comparison between the chromophore microenvironments of Italian water buffalo (Bos bubalus, L.) and sperm whale apomyoglobin.

The perturbing effect of guanidium hydrochloride and pH on the molecular structure of water buffalo apomyoglobin has been investigated by circular dichroism in the far and near ultraviolet and by fluorescence. In the wavelength region between 320 and 260 nm the circular dichroic spectrum of the globin is highly structured and the contributions of the aromatic chromophores have been resolved. Buffalo apomyoglobin undergoes a structural transition at neutral pH which involves elements of the secondary and tertiary structure, as indicated by changes of dichroic activity of the peptide and aromatic chromophores and the fluorescence of the two tryptophanyl residues. The possibility of charge-transfer complex between indole and imidazole is discussed. A major structural transition with abrupt unfolding takes place in the pH region between 5.6 and 4.3. Below pH 4.3 the peptide helical residues, which survive the acid transition, appear to be resistent to further acidification to pH 2.0 while tryptophanyl emission is quenched and shifted to longer wavelengths. A structural transition occurs also in alkali above pH 10, which has been detected by the same techniques. The relationships between buffalo and sperm whale apomyoglobin are discussed.

Animals↗

PubMed2005

Probing conformational changes in T7 RNA polymerase during initiation and termination by using engineered disulfide linkages.

During the transition from an initiation complex to an elongation complex (EC), the single-subunit bacteriophage T7 RNA polymerase (RNAP) undergoes dramatic conformational changes. To explore the significance of these changes, we constructed mutant RNAPs that are able to form disulfide bonds that limit the mobility of elements that are involved in the transition (or its reversal) and examined the effects of the crosslinks on initiation and termination. A crosslink that is specific to the initiation complex conformation blocks transcription at 5-6 nt, presumably by preventing isomerization to an EC. A crosslink that is specific to the EC conformation has relatively little effect on elongation or on termination at a class I terminator (T), which involves the formation of a stable stem-loop structure in the RNA. Crosslinked ECs also pause and resume transcription normally at a class II pause site (concatamer junction) but are deficient in termination at a class II terminator (PTH, which is found in human preparathyroid hormone gene), both of which involve a specific recognition sequence. The crosslinked amino acids in the EC lie close to the upstream end of the RNA-DNA hybrid and may prevent a movement of the polymerase that would assist in displacing or releasing RNA from a relatively unstable DNA-RNA hybrid in the paused PTH complex.

Bacteriophage T7↗

PubMed2000

The initial domestication of goats (Capra hircus) in the Zagros mountains 10,000 years ago.

Initial goat domestication is documented in the highlands of western Iran at 10,000 calibrated calendar years ago. Metrical analyses of patterns of sexual dimorphism in modern wild goat skeletons (Capra hircus aegagrus) allow sex-specific age curves to be computed for archaeofaunal assemblages. A distinct shift to selective harvesting of subadult males marks initial human management and the transition from hunting to herding of the species. Direct accelerator mass spectrometry radiocarbon dates on skeletal elements provide a tight temporal context for the transition.

Aging↗

PubMed2002

DMSO complexes of trivalent metal ions: first microsolvated trications outside of group 3.

The advent of electrospray ionization source opened the door to generation of multiply charged metal ions complexed with organic molecules. A significant amount of work on ligated dications has appeared over the past decade. In contrast, only several microsolvated tripositive ions have been reported, involving solely the few rare earths with the lowest third ionization energies (IEs) of all elements (<23 eV). Here trications of numerous trivalent metals outside of group 3 are shown to coordinate dimethyl sulfoxide (DMSO), an eminent aprotic solvent. These include both main group elements (Al, Ga, In, Bi) and transition metals (V, Fe, Cr) with the third IE up to 31 eV, which is 22 eV above the IE of DMSO. Fragmentation of M(3+)(DMSO)(n) for these metals (plus La, Yb, and Sc) has been characterized in detail using collision-induced dissociation (CID). A rich, highly element specific dissociation chemistry is observed, including the homolytic C-S cleavage in (+3) charge state and various charge-reduction processes, such as dissociative electron and proton transfer and heterolytic S=O cleavage with and without a concomitant proton transfer. Characteristic sizes for the charge reduction in M(3+)(DMSO)(n) and M(2+)(DMSO)(n) have been measured as a function of the relevant elemental IE. These reveal no intrinsic gap between the stabilities of dication and trication complexes, once the IE is adjusted for. This, in particular, suggests that even microsolvated tetracations may exist.

Journal Article↗

PubMed2004

Expression and localization of cartilage-specific matrix protein chondromodulin-I mRNA in salivary pleomorphic adenomas.

Pleomorphic adenoma is the most common epithelial tumor in the salivary glands. This tumor frequently exhibits "mesenchyme"-like components, including myxoid or chondroid areas. Recently, using immunohistochemical techniques, we reported that cartilage-specific matrix protein, chondromodulin-I (ChM-I), was deposited on the inter-territorial matrix of the chondroid area in salivary pleomorphic adenomas and that ChM-I, which is also a strong angio-inhibitory factor, plays an important role in the avascular nature of the chondroid area and the chondroid formation in this type of tumor. To elucidate which cells express ChM-I mRNA in pleomorphic adenomas, we examined the expression and localization of ChM-I mRNA in this type of tumor using an in situ hybridization technique. Immunoreactivity for ChM-I was observed in the inter-territorial matrix of the chondroid area, especially around the lacunae, and in the cytoplasm of neoplastic myoepithelial cells of the myxoid element of pleomorphic adenomas. On in situ hybridization analysis, strong signals for ChM-I mRNA were detected in the cytoplasm of the lacuna cells of the chondroid element, and moderate to marked signals were observed in the cytoplasm of the neoplastic myoepithelial cells of the myxoid element. Signals for ChM-I mRNA were also seen in the cytoplasm of the spindle-shaped neoplastic myoepithelial cells in the transitional areas between the myxoid and chondroid elements of this tumor. Signals for ChM-I mRNA were not seen in the inner ductal cells or the fibrous element. These findings indicate that lacuna cells and neoplastic myoepithelial cells express ChM-I mRNA and that mature ChM-I, which lacuna cells and neoplastic myoepithelial cells translate, is deposited in the chondroid matrix of pleomorphic adenomas. In conclusion, lacuna cells and neoplastic myoepithelial cells express ChM-I mRNA ectopically in pleomorphic adenoma, and this plays an important role in chondroid formation and hypovascularity in this type of tumor.

Adenoma, Pleomorphic↗

PubMed2006

Spatial extent of the singlet and triplet excitons in luminescent angular-shaped transition-metal diynes and polyynes comprising non-pi-conjugated group 16 main group elements.

A novel approach based on conjugation interruption has been developed and is presented for a series of luminescent and thermally stable chalcogen-bridged platinum(II) polyyne polymers trans-[{-Pt(PBu3)2C[triple bond]C(C6H4)E(C6H4)C[triple bond]C-}n] (E = O, S, SO, SO2). Particular attention was focused on the photophysical properties of these Group 10 polymetallaynes and comparison was made to their binuclear model complexes trans-[Pt(Ph)(PEt3)2C[triple bond]C(C6H4)E(C6H4)C[triple bond]CPt(Ph)(PEt3)2] and their closest Group 11 gold(I) and Group 12 mercury(II) neighbours, [MC[triple bond]C(C6H4)E(C6H4)C[triple bond]CM] (M = Au(PPh3), HgMe; E = O, S, SO, SO2). The regiochemical structures of these angular-shaped molecules were studied by NMR spectroscopy and single-crystal X-ray structural analyses. Upon photoexcitation, each one has an intense purple-blue fluorescence emission near 400 nm in dilute fluid solutions at room temperature. Harvesting of the organic triplet emissions harnessed through the strong heavy-atom effects of Group 10-12 transition metals was studied in detail. These metal-containing aryleneethynylenes spaced by chalcogen units were found to have large optical gaps and high-energy triplet states. The influence of metal- and chalcogen-based conjugation interrupters on the intersystem crossing rate and on the spatial extent of the lowest singlet and triplet excitons was fully elucidated. We discuss and compare the phosphorescence spectra of these transition-metal diynes and polyynes in terms of the nature of the metal centre, conjugated chain length and Group 16 spacer unit. Our work here indicates that high-energy triplet states in these materials intrinsically give rise to very efficient phosphorescence with fast radiative decays and one could readily observe room-temperature phosphorescence for the platinum polyynes.

Journal Article↗

PubMedDate not supplied

[Levels in the structural organization of Escherichia coli promoter DNA].

A number of additional structural elements were identified by statistic analysis of nucleotide sequences in promoters recognized by Escherichia coli RNA polymerase. Together with canonical hexanucleotides, these elements characterize different levels in the structural organization of promoter DNA. Sequence motifs exhibiting the highest statistical significance, which dominate in the contact regions with RNA polymerase alpha and sigma subunits, are considered as targets for specific interaction with RNA polymerase. A typical feature of these elements is the presence of easily deformable dinucleotides (TG, CA and TA) or tracts containing only A/T base pairs. Thus, we noticed that the frequency of occurrence of TA in the promoter DNA is essentially higher than the average value for the genome. Besides the regions of specific interaction with RNA polymerase, these dinucleotides are often located in the number of other sites periodically distributed along the promoter DNA. This preferred disposition suggests that deformable elements participate in the adaptive conformational transitions of the promoter DNA favoring optimal configuration of the transcription complex. Probably, the most important feature of promoter DNA revealed by statistic analysis is the presence of A/T-tracts regularly distributed in the wide range from -160 up to +75 relative to the transcription start point. Both of these spatially distributed elements (TA dinucleotides and A/T-tracts) are linked with canonical regions and, therefore, may contribute to the conformational or dynamic features of the transcription machinery. Having high statistic significance, these elements might be considered as additional factors discriminating the promoter DNA on the background of other nucleotide sequences in the genome.

Base Sequence↗

PubMed1998

Tyrosine hydroxylase-like immunoreactivity in the brain of the teleost fish Tinca tinca.

The distribution of tyrosine hydroxylase-like immunoreactivity has been studied in the central nervous system of the tench (Tinca tinca) using a monoclonal antibody and the avidin-biotin-immunoperoxidase technique. Immunoreactive elements were found in all brain subdivisions. Thus, catecholaminergic neurons and fibers were detected in most nuclei of the ventral telencephalon and in the pars centralis and lateralis of the dorsal telencephalon. The diencephalon was the brain subdivision where largest density of immunoreactive elements were found, mainly located in the periventricular region. The mesencephalon and metencephalon only demonstrated immunoreactive fibers, and no immunoreactive cell bodies were observed in these regions. The myelencephalon showed three groups of immunoreactive neurons located at isthmal level, in the central medullary area, and at the medullary-spinal cord transition area. The distribution of catecholaminergic elements in the tench brain revealed a general pattern shared by most teleosts. The number and distribution of catecholaminergic elements was similar to those described in other teleostean species in the caudal region of the brain. However, noticeable differences were found in areas related to the integration of different sensory information, specially in the telencephalon and diencephalon, suggesting a relationship among the functional level of each sensorial system and the complexity of the catecholaminergic innervation of their integration regions. Additionally, this study revealed the presence of an important number of cerebrospinal fluid-contacting cells in the organum paraventricularis expressing tyrosine hydroxylase that in most investigated teleostean species were tyrosine hydroxylase-immunonegative despite they contained catecholamines. This data argues for distinct evolutionary patterns in the hypothalamic catecholaminergic system among different teleostean species.

Animals↗

PubMed2005

A common mechanism for the perception of first-order and second-order apparent motion.

A common mechanism for perceiving first-order, luminance-defined, and second-order, texture-contrast defined apparent motion between two element locations is indicated by: (1) transitivity--whether or not motion is perceived is inter-changeably affected by activationally equivalent luminance and contrast changes at each location, (2) local integration--whether or not motion is perceived depends on the net activation change resulting from simultaneous background-relative luminance and background-relative contrast changes at the same element location, and (3) inseparability--apparent motion is not perceived through independent first- or second-order mechanisms when luminance and contrast co-vary at the same location. These results, which are predicted by the response characteristics of directionally selective cells in areas V1, MT, and MST, are not instead attributable to changes in the location of the most salient element (third-order motion), attentive feature tracking, or artifactual first-order motion. Their inconsistency with Lu and Sperling's [Lu, Z., Sperling, G. (1995a). Attention-generated apparent motion. Nature 377, 237, Lu, Z., Sperling, G. (2001). Three-systems theory of human visual motion perception: review and update. Journal of the Optical Society of America A 18, 2331] model, which specifies independent first- and second-order mechanisms, may be due to computational requirements particular to the motion of discrete objects with distinct boundaries defined by spatial differences in luminance, texture contrast, or both.

Contrast Sensitivity↗

PubMed2005

Characterization of an upstream regulatory element of adenovirus L1 poly (A) site.

The transition from early to late stage infection by adenovirus involves a change in mRNA expression from the adenovirus major late transcription unit (AdMLTU). This early to late switch centers around alternative selection of one of five poly (A) sites (L1-L5) that code for the major structural proteins of Adenovirus. During the early stage of infection, steady state mRNA is primarily derived from the L1 poly (A) site. During the late stage of infection, each of the MLTU poly (A) sites is represented in the steady state mRNA pool (Falck-Pedersen, E., Logan, J., 1989. Regulation of poly(A) site selection in adenovirus. J. Virol. 63 (2), 532-541.). Using transient transfection of a plasmid expressing Chloramphenicol Acetyl Transferase with a tandem poly (A) minigene system (L13) (DeZazzo, J.D., Falck-Pedersen, E., Imperiale, M.J., 1991. Sequences regulating temporal poly(A) site switching in the adenovirus major late transcription unit. Mol. Cell. Biol. 11 (12), 5977-5984; Prescott, J., Falck-Pedersen, E., 1994. Sequence elements upstream of the 3' cleavage site confer substrate strength to the adenovirus L1 and L3 polyadenylation sites. Mol. Cell. Biol. 14 (7), 4682-4693.), it has been demonstrated that the promoter-proximal L1 poly (A) site which is poorly recognized by the 3' end processing machinery, contains an upstream repressor element (URE) that influences steady state levels of mRNA (Prescott, J.C., Liu, L., Falck-Pedersen, E., 1997. Sequence-mediated regulation of adenovirus gene expression by repression of mRNA accumulation. Mol. Cell. Biol. 17 (4), 2207-2216.). In this study, we have further characterized the elements that mediate L1URE function. These studies indicate that the L1 upstream regulatory element (L1 URE) contains a complex RNA architecture that serves to repress gene expression through multiple sub-effectors. The L1URE functions when located upstream of a heterologous poly (A) site, and is able to strongly suppress steady state mRNA expression from the MLTU L3 poly (A) site or the murine beta-globin poly (A) site. In the tandem L13 mini-gene system, the L1URE is revealed to influence steady state mRNA stability, and subdomains within L1URE influence both gene expression and the steady state ratio of transcripts processed at proximal versus distal poly (A) sites. Transcript and gene repression mediated by the L1URE may provide a general strategy employed by adenovirus to block premature expression of late stage MLTU transcripts.

Adenoviridae↗

PubMed1998

RNA recognition by arginine-rich peptide motifs.

A ubiquitious class of RNA-binding proteins is distinguished by an arginine-rich motif. Such proteins function in transcription, translation, RNA trafficking, and packaging. Peptide models are derived from viral regulatory proteins, including the virulence factors Tat and Rev of mammalian immunodeficiency viruses. Structures of model peptide-RNA complexes exhibit diverse strategies of recognition based in each case on structural transitions. Induced RNA structures contain noncanonical elements such as purine-purine mismatches, base triples, and flipped bases. Such elements enlarge and extend the RNA major groove to create specific peptide-binding pockets and surfaces. The repertoire of bound peptide structures--beta-hairpin, alpha-helix, and helix-bend-helix-reflects the diversity of induced RNA architectures. This repertoire, reminiscent of primordial exon-encoded peptides, may recapitulate early events in the transition between RNA and protein worlds. Peptide-directed changes in modern RNA structures can provide a mechanism of signaling in higher-order RNA-protein assemblies.

Arginine↗

PubMed1979

[Histology of the pigmented granular rankenneuroma (author's transl)].

We report on a case of a 40 years old female patient with a lentil-sized tumor of the left pinna present since early childhood. Histologic examination revealed pigmented granular "rankenneuroma". The lesion is unencapsulated but fairly well marginated in the dermis. It is composed of varying numbers of spindle-shaped or polyhedral cells arranged in intertwining and parallel bands separated by strands of collagen. The fascicles follow the preexisting nerve truncs. All layers of the dermis may be involved, but only rarely is the superficial subcutaneous tissue invaded. The fascicles of the tumor are generally constructed in a similar fashion. In the center one see argyrophile granular alterated unpigmented cells- Those elements are surrounded by mostly bipolar cells containing varying amounts of melanin. Silverstaining shows transition from spindle-shaped cells to granular degenerated elements. It is thought that the tumor most likely originates from the proliferation of the granular degenerated Schwann cells. The characteristic feature of tumor parenchyme is the association of the granular Schwann cells with cutaneous melanoblasts.

Adult↗

PubMed2001

Uroporphyrinogen III synthase erythroid promoter mutations in adjacent GATA1 and CP2 elements cause congenital erythropoietic porphyria.

Congenital erythropoietic porphyria, an autosomal recessive inborn error of heme biosynthesis, results from the markedly deficient activity of uroporphyrinogen III synthase. Extensive mutation analyses of 40 unrelated patients only identified approximately 90% of mutant alleles. Sequencing the recently discovered erythroid-specific promoter in six patients with a single undefined allele identified four novel mutations clustered in a 20-bp region: (a) a -70T to C transition in a putative GATA-1 consensus binding element, (b) a -76G to A transition, (c) a -86C to A transversion in three unrelated patients, and (d) a -90C to A transversion in a putative CP2 binding motif. Also, a -224T to C polymorphism was present in approximately 4% of 200 unrelated Caucasian alleles. We inserted these mutant sequences into luciferase reporter constructs. When transfected into K562 erythroid cells, these constructs yielded 3 +/- 1, 54 +/- 3, 43 +/- 6, and 8 +/- 1%, respectively, of the reporter activity conferred by the wild-type promoter. Electrophoretic mobility shift assays indicated that the -70C mutation altered GATA1 binding, whereas the adjacent -76A mutation did not. Similarly, the -90C mutation altered CP2 binding, whereas the -86A mutation did not. Thus, these four pathogenic erythroid promoter mutations impaired erythroid-specific transcription, caused CEP, and identified functionally important GATA1 and CP2 transcriptional binding elements for erythroid-specific heme biosynthesis.

Alleles↗

PubMed2005

Lanthanide-transition metal coordination polymers based on multiple N- and O-donor ligands.

Lanthanide-transition metal (Ln-M) coordination polymers have attracted extensive interest because they exhibit novel physical properties originating from the interactions between distinct metal ions. This review mainly describes our recent work in the design of Ln-M coordination polymers through the assembly of different metal ions and organic ligands, especially the ligands with multiple N- and O-donor atoms. Many of these crystalline Ln-M materials exhibit intriguing structural motifs and interesting magnetic properties.

Crystallization↗

PubMed1999

Does trifluoroethanol affect folding pathways and can it be used as a probe of structure in transition states?

Nonaqueous co-solvents, particularly 2,2,2-trifluoroethanol (TFE), have been used as tools to study protein folding. By analyzing FKBP12, an alpha/beta-protein that folds with two-state kinetics, we have been able to address three key questions concerning the use of TFE. First, does TFE perturb the folding pathway? Second, can the observed changes in the rate of folding and unfolding in TFE be attributed to a change in free energy of a single state? Finally, can TFE be used to infer information on secondary structure formation in the transition state? Protein engineering experiments on FKBP12, coupled with folding and unfolding experiments in 0% and 9.6% TFE, conclusively show that TFE does not perturb the folding pathway of this protein. Our results also suggest that the changes in folding and unfolding rates observed in 9.6% TFE are due to a global effect of TFE on the protein, rather than the stabilization of any elements of secondary structure in the transition state. Thus, studies with TFE and other co-solvents can be accurately interpreted only when combined with other techniques.

Immunophilins↗

PubMed1999

Angiogenesis in carcinosarcomas of the uterus: differences in the microvessel density and expression of vascular endothelial growth factor between the epithelial and mesenchymal elements.

Carcinosarcoma of the uterus is a highly aggressive neoplasm. However, the angiogenesis of this neoplasm is still unknown. This is the first study to examine the differences in angiogenesis between the epithelial and mesenchymal elements of this biphasic neoplasm. Surgical specimens from 21 primary uterine carcinosarcomas were histopathologically evaluated, and then immunohistochemically analyzed for tumor angiogenesis, using an anti-vascular endothelial growth factor (VEGF) antibody. The microvessel density (MVD) was also measured in each element of these neoplasms, using anti-CD34 monoclonal antibody. The MVD in the epithelial element was found to be higher than that of the mesenchymal element in 20 of 21 (95.2%) primary tumors. The epithelial elements showed a higher MVD (mean, 81.6 +/- 41.1) than the mesenchymal elements (mean, 36.7 +/- 23.8) in these primary tumors (P < .0001). Moreover, the epithelial elements showed a higher VEGF expression (mean, 0.78 +/- 0.23) than the mesenchymal elements (mean, 0.37 +/- 0.20) (P < .0001). The tumors with lymph-vascular invasion showed a higher VEGF expression (n = 17; mean, 0.85 +/- 0.17) than the tumors without lymph-vascular invasion (n = 4, mean, 0.47 +/- 0.12) (P < .01). Microscopically, neither lymph-vascular space invasion nor metastatic tumors consisted of sarcoma alone in this series. In addition, a decrease in the VEGF expression was found in the transitional areas between carcinomatous and sarcomatous elements in all 10 homologous and 4 heterologous tumors evaluated. These results suggest that the tumor angiogenesis in the epithelial element may be more active than that of the mesenchymal element and also substantiated the high metastatic potential of the epithelial element in uterine carcinosarcoma. Based on these findings, carcinoma cells thus may play a key role in the angiogenesis of this biphasic neoplasm.

Aged↗

PubMed2003

Sum1 and Ndt80 proteins compete for binding to middle sporulation element sequences that control meiotic gene expression.

A key transition in meiosis is the exit from prophase and entry into the nuclear divisions, which in the yeast Saccharomyces cerevisiae depends upon induction of the middle sporulation genes. Ndt80 is the primary transcriptional activator of the middle sporulation genes and binds to a DNA sequence element termed the middle sporulation element (MSE). Sum1 is a transcriptional repressor that binds to MSEs and represses middle sporulation genes during mitosis and early sporulation. We demonstrate that Sum1 and Ndt80 have overlapping yet distinct sequence requirements for binding to and acting at variant MSEs. Whole-genome expression analysis identified a subset of middle sporulation genes that was derepressed in a sum1 mutant. A comparison of the MSEs in the Sum1-repressible promoters and MSEs from other middle sporulation genes revealed that there are distinct classes of MSEs. We show that Sum1 and Ndt80 compete for binding to MSEs and that small changes in the sequence of an MSE can yield large differences in which protein is bound. Our results provide a mechanism for differentially regulating the expression of middle sporulation genes through the competition between the Sum1 repressor and the Ndt80 activator.

Amino Acid Sequence↗