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PubMedDate not supplied

Duplex recognition by oligonucleotides containing 2'-deoxy-2'-fluoro-D-arabinose and 2'-deoxy-2'-fluoro-D-ribose. Intermolecular 2'-OH-phosphate contacts versus sugar puckering in the stabilization of triple-helical complexes.

To gain insight into the origins of the large binding affinity of RNA toward target duplexes, 2'-deoxy-2'-fluororibonucleic acid (2'F-RNA) and 2'-deoxy-2'-fluoroarabinonucleic acid (2'F-ANA) were tested for their ability to recognize duplex DNA, duplex RNA, and RNA-DNA hybrids. 2'F-RNA, 2'F-ANA, and the corresponding control single-stranded (ss) DNA strands were shown to form triple-helical complexes only with duplex DNA and hybrid DNA (Pu)-RNA (Py), but not with duplex RNA and hybrid RNA (Pu)-DNA (Py). In contrast, an RNA third strand recognized all four possible duplexes (DD, DR, RD, and RR) as previously demonstrated by Roberts and Crothers [(1992) Science 258, 1463-1466]. The 2'F-RNA (C3'-endo) strand exhibited significantly reduced affinity for duplexes compared to an unmodified RNA (C3'-endo) strand. These findings are consistent with the intermolecular 2'-OH-phosphate contact mechanism proposed by Escudé et al. [(1993) Nucleic Acids Res. 24, 5547-5553], as a ribo 2'-F atom should not interact with a negatively charged phosphate. In addition, they emphasize the role of the 2'-OH ribose as a general recognition and binding determinant of RNA. The 2'-F arabino modification (2'F-ANA, C2'-endo) led to a considerable increase in the binding affinity for duplex DNA, as compared to those of DNA and 2'F-RNA third strands. This is likely to be the result of a greater population of C2'-endo pucker of the 2'F-ANA compared to DNA. The enhancement observed for 2'F-ANA strands toward duplex DNA is comparable to that observed with 2'-OMe RNA. Since 2'F-ANA has been shown to be more resistant to nuclease degradation than DNA, these results are likely to stimulate experimental work on arabinose derivatives in laboratories concerned with targeting DNA sequences in vivo ("antigene" strategy).

Arabinose↗

PubMed1997

ECG compression and recognition using complete tree representation.

This paper deals with a novel method of Electrocardiogram (ECG) representation, compression and recognition using Complete Tree algorithm. The construction of Complete Tree is like overlaying a ECG waveform on a grid. The waveform is observed through the grid structure with vertical and horizontal grid lines. In addition to nodes created for each interval enclosed by that waveform on a quantisation level, nodes are also created for each point where the waveform cuts the vertical grid line between the current quantisation level and the next quantisation level. A leaf node represents the data sample of ECG at that position. For reconstruction of this ECG waveform, only the leaf nodes are used resulting in ECG compression. This representation is also useful in ECG pattern matching and recognition without reconstructing the original waveform. The ECGs with sampling rate of 500 sps are used. A compression ratio (CR) of 4.8:1 with percent RMS difference (PRD) of 8.45% is obtained. The reconstruction of original ECG waveform from its tree representation shows high fidelity in all its complexes of ECG. The results are compared with all other compression techniques such as AZTEC, TP, FAN, DPCM etc. By using Tree merging and splitting algorithms, the matching and recognition of ECG is implemented.

Algorithms↗

PubMed1997

[Neurocutaneous syndromes with vascular alterations].

There are several syndromes in which neurological and cutaneous alterations of vascular origin, among other symptoms, occur. The key point of this fact is that these cutaneous signs permit early diagnosis, thus helping in further recognition of more complex syndromes and preventing unnecessary, harmful and costly diagnostic procedures or having to wait until the appearance of neurological signs. Therefore, these diseases should be classified attending to the most notorious vascular lesions they show, though they may show other less frequent cutaneous vascular lesions. In this way, these syndromes can be classified as associated with nevus flammeus (Sturge-Weber, Shapiro-Shulman, Bonnet-Dechaume-Blanc, Cobb, Klippel-Trenaunay, Fegeler, Robert), cavernous hemangiomas (Maffucci, blue-rubber-bleb-nevus, Proteus, Bannayan-Zonana, Riley-Smith, familial cavernous angiomatosis, POEMS syndrome), capillary hemangiomas (Rubinstein-Tayabi, Coffin-Siris, PHACE syndrome), telangiectasia (congenital telangiectatic cutis marmorata, Rendu-Osler-Weber, ataxia telangiectasia, Cockayne, De Sanctis-Cacchione), livedo reticularis (Sneddon, Divry-van-Bogaert), angioqueratoma (Fabry disease, Fucosidosis) and hemangioblastoma (Von Hippel-Lindau). Though we have tried that these vascular lesions should be named as angiomas if they are malformations and hemangiomas if they are benign neoplasias, they are called following morphological aspects rather than other criteria, due to their unknown origin.

Brain Neoplasms↗

PubMed1989

Simian virus 40 DNA replication in vitro: identification of multiple stages of initiation.

A cell-free DNA replication system dependent upon five purified cellular proteins, one crude cellular fraction, and the simian virus 40 (SV40)-encoded large tumor antigen (T antigen) initiated and completed replication of plasmids containing the SV40 origin sequence. DNA synthesis initiated at or near the origin sequence after a time lag of approximately 10 min and then proceeded bidirectionally from the origin to yield covalently closed, monomer daughter molecules. The time lag could be completely eliminated by a preincubation of SV40 ori DNA in the presence of T antigen, a eucaryotic single-stranded DNA-binding protein (replication factor A [RF-A]), and topoisomerases I and II. In contrast, if T antigen and the template DNA were incubated alone, the time lag was only partially decreased. Kinetic analyses of origin recognition by T antigen, origin unwinding, and DNA synthesis suggest that the time lag in replication was due to the formation of a complex between T antigen and DNA called the T complex, followed by formation of a second complex called the unwound complex. Formation of the unwound complex required RF-A. When origin unwinding was coupled to DNA replication by the addition of a partially purified cellular fraction (IIA), DNA synthesis initiated at the ori sequence, but the template DNA was not completely replicated. Complete DNA replication in this system required the proliferating-cell nuclear antigen and another cellular replication factor, RF-C, during the elongation stage. In a less fractionated system, another cellular fraction, SSI, was previously shown to be necessary for reconstitution of DNA replication. The SSI fraction was required in the less purified system to antagonize the inhibitory action of another cellular protein(s). This inhibitor specifically blocked the earliest stage of DNA replication, but not the later stages. The implications of these results for the mechanisms of initiation and elongation of DNA replication are discussed.

Antigens, Viral, Tumor↗

PubMed1979

Endocrine tumors of the pancreas.

The identification and description of a widely dispersed group of cells of common origin and biochemical characteristics, APUD cells, has allowed a better understanding and classification of endocrine tumors of the pancreas. Similarly, it has enabled the relationships between the endocrine tumors of the multiple endocrine neoplasia type I syndrome and the endocrine tumors of the pancreas to be better appreciated. This has facilitated both diagnosis and management of these conditions. The pluripotentiality of the cells of the APUD system combined with the certain existence of many unidentified peptides suggests the likelihood of other undescribed pancreatic endocrine tumors. Many of these are probably part of the heterogenous group of neoplasms currently designated as carcinoids, since their secretory products and exact cell types are not known. The recognition of the physiologic characteristics and cells of origin of these peptides, amines or other bioactive agents will allow delineation of the symptom complex and the identification of further functional tumors of the pancreas. The development of plasma radioimmunoassays for the various hormones and the appreciation of the specific clinical syndromes related to each tumor have enabled earlier diagnosis. The understanding of the hormonal physiopathologic functions has led to the evolution of specific therapeutic maneuvers. Provocative tests have allowed increased precision of the differential diagnosis, while selective arteriography and pancreatic venous sampling have greatly enhanced the accuracy of topical localization. The role of operation in tumor removal is still prominent, but malignant and recurrent tumors may now also be controlled with specific pharmacotherapy or appropriate endocrine cytotoxic agents. The use of peptides with antagonistic actions or the administration of specific antibodies to the active tumor products are areas of therapy that require further exploration.

Adult↗

PubMed1995

[Basic concepts of pathology in Germany 1858 until today and progress in medicine].

The rise of scientific medicine in the 19th century had its origins mainly in Rudolf Virchows localistic cellular pathology. As a consequence the organism as a complex system was kept in the background. In recognition of this problem, concepts of pathology, emerging in 20th century, tried in vain to establish organismic theories of illness. Pathology remained deeply indebted to Virchows work. Deficits appeared even in 19th century, when treatment of patients was mainly focussed on practicability of cure, ignoring the social background. Therefore, it is not possible to speak about progress of pathology in general, for diagnostics depends also on individual mentality, the subject, and the situation of the time.

Animals↗

PubMedDate not supplied

Recognition between flexible protein molecules: induced and assisted folding.

This review focuses on a very important but little understood type of molecular recognition--the recognition between highly flexible molecular structures. The formation of a specific complex in this case is a dynamic process that can occur through sequential steps of mutual conformational adaptation. This allows modulation of specificity and affinity of interaction in extremely broad ranges. The interacting partners can interact together to form a complex with entirely new properties and produce conformational signal transduction at substantial distance. We show that this type of recognition is frequent in formation of different protein-protein and protein-nucleic acid complexes. It is also characteristic for self-assembly of protein molecules from their unfolded fragments as well as for interaction of molecular chaperones with their substrates and it can be the origin of 'protein misfolding' diseases. Thermodynamic and kinetic features of this type of dynamic recognition and the principles underlying their modeling and analysis are discussed.

Animals↗

PubMed1999

Selective association between a macrocyclic nickel complex and extrahelical guanine residues.

Nickel-dependent recognition and oxidation of guanine have been linked in part through the paramagnetic effects of nickel on the NMR of model oligonucleotide duplexes. Direct interaction between nickel and guanine N7 had originally been postulated from correlations between the efficiency of guanine oxidation and the environment surrounding its N7 position. (1)H and (31)P NMR spectra of DNA containing a single, isolated extrahelical guanine are consistent with selective binding of nickel to the N7 of this unique base over a background of nonspecific association to the phosphate backbone. The presence of a macrocyclic complex or simple salt of nickel did not detectably alter the structure of the duplex or extrahelical residue. Accordingly, nickel appeared to bind the extrahelical guanine N7 within the major groove as indicated by paramagnetic effects on the proton signals of nucleotides on the 5' but not 3' side of the nickel binding site. Similar (1)H NMR analysis of DNA containing a dynamic equilibrium of extrahelical guanine residues also suggested that the nickel complex did not affect the native distribution of structures. Oxidation of these sites by a nickel-mediated pathway consequently reflected their solvent accessibility in a general and metal-independent manner. The close proximity of the extrahelical guanines produced a composite of paramagnetic effects on each adjacent nucleotide resulting from both direct and proximal coordination of nickel.

Chromium Alloys↗

PubMed1994

Natural variants of cytotoxic epitopes are T-cell receptor antagonists for antiviral cytotoxic T cells.

It has been suggested that mutations within immunodominant cytotoxic T-lymphocyte (CTL) epitopes may be exploited by viruses to evade protective immune responses critical for clearance. Viral escape could originate from passive mechanisms, such as mutations within crucial CTL epitopes, either affecting major histocompatibility complex binding or T-cell antigen receptor (TCR) recognition. Additionally, it has recently been shown that substitutions of TCR contact sites can yield analogue peptides that can still interact with the T-cell receptor but be unable to deliver a full stimulatory signal, thus inducing anergy or acting as an antagonist for the TCR. We report here that hepatitis B virus isolates derived from two chronically infected patients display variant epitopes that act as natural TCR antagonists with the capacity to inhibit the CTL response to the wild-type epitope. During natural infection, TCR antagonist mutations of CTL epitopes could contribute to the development of viral persistence, especially if the antiviral CTL response is monospecific or the epitope is strongly immunodominant.

Amino Acid Sequence↗

PubMed1993

Recognition of vaccinia virus-encoded major histocompatibility complex class I antigens by virus immune cytotoxic T cells is independent of the polymorphism of the peptide transporters.

In the cytotoxic T-cell response to viruses, peptide antigens of cytoplasmic origin are presented at the cell surface by the highly polymorphic major histocompatibility complex (MHC) class I molecules to CD8+ T-lymphocyte receptors. Peptide transporter molecules and other MHC-linked gene products have been implicated in the generation and import of antigenic peptides into the lumen of the endoplasmic reticulum for assembly with MHC class I glycoproteins. These accessory molecules in the antigen-presentation pathway map to a polymorphic region in the class II MHC, and the possibility of their allele-specific selectivity in antigen presentation has been raised. Here we show that additional, functionally polymorphic components are not apparent in an in vitro mouse MHC class I-restricted cytotoxic T-cell response to vaccinia and influenza viruses. When the mouse H-2Kd molecule was expressed via a recombinant vaccinia virus in target cells of different mouse MHC haplotypes or cells of rat, Syrian hamster, monkey, and human origin, efficient Kd-restricted and vaccinia virus-specific lysis was observed as measured with bulk effectors and at the clonal level. In addition, human transporters efficiently processed peptides originating from influenza virus nucleoprotein and hemagglutinin antigens as recognized by mouse influenza immune cytotoxic T cells.

Animals↗

PubMed2001

Complex objects are represented in macaque inferotemporal cortex by the combination of feature columns.

Intrinsic signal imaging from inferotemporal (IT) cortex, a visual area essential for object perception and recognition, revealed that visually presented objects activated patches in a distributed manner. When visual features of these objects were partially removed, the simplified stimuli activated only a subset of the patches elicited by the originals. This result, in conjunction with extracellular recording, suggests that an object is represented by a combination of cortical columns, each of which represents a visual feature (feature column). Simplification of an object occasionally caused the appearance of columns that were not active when viewing the more complex form. Thus, not all the columns related to a particular feature were necessarily activated by the original objects. Taken together, these results suggest that objects may be represented not only by simply combining feature columns but also by using a variety of combinations of active and inactive columns for individual features.

Action Potentials↗

PubMed2002

[Acute confusional syndrome due to acute nicotine withdrawal].

Delirium or acute confusional state among hospitalized patients is a frequent and serious problem. It is characterized by acute onset symptoms, fluctuating course, impaired attention, unorganized thinking, and altered level of consciousness. Delirium, as a manifestation of acute nicotine withdrawal syndrome has been reported in the reviewed literature only in eight cases. We report the case of a heavy smoker admitted because of a reagudization of his chronic obstructive pulmonary disease. At the third day of nicotine abstinence, he developed delirium with a rapid improvement of his symptoms after treatment with a transdermal nicotine patch. This description suggests that in hospitalized heavy smokers who develop delirium with agitation, a simple trial with a nicotine patch can offer a dramatic therapeutic response in a few hours, constituting additionally a confirmatory test. The recognition of delirium as a manifestation of nicotine withdrawal could allow to determine the origin of symptoms and to apply the appropriate therapy, in certain complex cases that now remain undiagnosed.

Acute Disease↗

PubMed1997

Autoantibody selectively inhibits binding of von Willebrand factor to glycoprotein ib. Recognition site is located in the A1 loop of von Willebrand factor.

A 20-year-old man with severe von Willebrand disease recently presented a progressive bleeding tendency, characterized recurrent subcutaneous hemorrhages and cerebral hemorrhage. Mixing and infusion studies suggested the presence of an inhibitor directed against vWF:RCo activity of von Willebrand factor (vWF) without significant inhibition of the FVIII:C. The inhibitor was identified as an antibody of IgG class. The inhibitor inhibited the interaction of vWF in the presence of ristocetin and that of asialo-vWF with GPIb while it partially blocked botrocetin-mediated interaction of vWF to GPIb. The inhibitor reacted with native vWF, the 39/34 kDa fragment (amino acids [aa] 480/ 481-718) and the recombinant vWF fragment (MalE-rvWF508-704), but not with Fragment III-T2 (heavy chains, aa 273-511; light chains, aa 674-728). A synthetic peptide (aa 514-542) did not inhibit vWF-inhibitor complex formation. We conclude that this is the first auto-antibody of class IgG from human origin that recognizes the sequence in the A1 loop of vWF, resulting in a virtual absence of functional vWF and a concomitant severe bleeding tendency although recognition site is different from the residues 514-542 which is crucial for vWF-GPIb interaction.

Adult↗

PubMed2000

Specific recognition of parental terminal protein by DNA polymerase for initiation of protein-primed DNA replication.

The linear genome of Bacillus subtilis phage phi29 has a protein covalently linked to the 5' ends, called parental terminal protein (TP), and is replicated using a free TP as primer. The initiation of phage phi29 DNA replication requires the formation of a DNA polymerase/TP complex that recognizes the replication origins located at the genome ends. The DNA polymerase catalyzes the formation of the initiation complex TP-dAMP, and elongation proceeds coupled to strand displacement. The same mechanism is used by the related phage Nf. However, DNA polymerase and TP from phi29 do not initiate the replication of Nf TP-DNA. To address the question of the specificity of origin recognition, we took advantage of the initiation reaction enhancement in the presence of Mn(2+), allowing us to detect initiation activity in heterologous systems in which DNA polymerase, TP, and template TP-DNA are not from the same phage. Initiation was selectively stimulated when DNA polymerase and TP-DNA were from the same phage, strongly suggesting that specific recognition of origins is brought through an interaction between DNA polymerase and parental TP.

Bacteriophages↗

PubMed2005

The Ter mutation in the dead end gene causes germ cell loss and testicular germ cell tumours.

In mice, the Ter mutation causes primordial germ cell (PGC) loss in all genetic backgrounds. Ter is also a potent modifier of spontaneous testicular germ cell tumour (TGCT) susceptibility in the 129 family of inbred strains, and markedly increases TGCT incidence in 129-Ter/Ter males. In 129-Ter/Ter mice, some of the remaining PGCs transform into undifferentiated pluripotent embryonal carcinoma cells, and after birth differentiate into various cells and tissues that compose TGCTs. Here, we report the positional cloning of Ter, revealing a point mutation that introduces a termination codon in the mouse orthologue (Dnd1) of the zebrafish dead end (dnd) gene. PGC deficiency is corrected both with bacterial artificial chromosomes that contain Dnd1 and with a Dnd1-encoding transgene. Dnd1 is expressed in fetal gonads during the critical period when TGCTs originate. DND1 has an RNA recognition motif and is most similar to the apobec complementation factor, a component of the cytidine to uridine RNA-editing complex. These results suggest that Ter may adversely affect essential aspects of RNA biology during PGC development. DND1 is the first protein known to have an RNA recognition motif directly implicated as a heritable cause of spontaneous tumorigenesis. TGCT development in the 129-Ter mouse strain models paediatric TGCT in humans. This work will have important implications for our understanding of the genetic control of TGCT pathogenesis and PGC biology.

Alleles↗

PubMed1999

Nickel allergy in mice: enhanced sensitization capacity of nickel at higher oxidation states.

Attempts to induce contact hypersensitivity to nickel in mice using, e.g., Ni(II)Cl2 often failed. Here, we report that sensitization was achieved by injecting Ni(II)Cl2 in combination with either CFA or an irritant, such as SDS and PMA, or IL-12, or by administering nickel at higher oxidation states, i.e., Ni(III) and Ni(IV). Although Ni(II), given alone, was ineffective in T cell priming, it sufficed for eliciting recall responses in vivo and in vitro, suggesting that Ni(II) is able to provide an effective signal 1 for T cell activation, but is unable to provide an adequate signal 2 for priming. Immunization of mice with nickel-binding proteins pretreated with Ni(IV), but not with Ni(II), allowed them to generate nickel-specific CD4+ T cell hybridomas. Ni(II) sufficed for restimulation of T cell hybridomas; in this and other aspects as well, the hybridomas resembled the nickel-specific human T cell clones reported in the literature. Interestingly, restimulation of hybridomas did not require the original Ni(IV)-protein complex used for priming, suggesting either that the nickel ions underwent ligand exchange toward unknown self proteins or peptides or that nickel recognition by the TCR is carrier-independent. In conclusion, we found that Ni(III) and Ni(IV), but not Ni(II) alone, were able to sensitize naive T cells. Since both Ni(III) and Ni(IV) can be generated from Ni(II) by reactive oxygen species, released during inflammation, our findings might explain why in humans nickel contact dermatitis develops much more readily in irritated than in normal skin.

Animals↗

PubMed2005

Isolation and characterization of a protochordate histocompatibility locus.

Histocompatibility--the ability of an organism to distinguish its own cells and tissue from those of another--is a universal phenomenon in the Metazoa. In vertebrates, histocompatibility is a function of the immune system controlled by a highly polymorphic major histocompatibility complex (MHC), which encodes proteins that target foreign molecules for immune cell recognition. The association of the MHC and immune function suggests an evolutionary relationship between metazoan histocompatibility and the origins of vertebrate immunity. However, the MHC of vertebrates is the only functionally characterized histocompatibility system; the mechanisms underlying this process in non-vertebrates are unknown. A primitive chordate, the ascidian Botryllus schlosseri, also undergoes a histocompatibility reaction controlled by a highly polymorphic locus. Here we describe the isolation of a candidate gene encoding an immunoglobulin superfamily member that, by itself, predicts the outcome of histocompatibility reactions. This is the first non-vertebrate histocompatibility gene described, and may provide insights into the evolution of vertebrate adaptive immunity.

Animals↗

PubMed2001

Cooperativity in drug-DNA recognition: a molecular dynamics study.

NMR studies have shown that the minor groove-binding ligand Hoechst 33258 binds to the two T4/A4 tracts within the duplex d(CTTTTCGAAAAG)2 in a highly cooperative manner, such that in titration experiments no intermediate 1:1 complex can be detected. The NMR-derived structures of the free DNA and the 2:1 complex have been obtained, but can shed little light on what the origins of this cooperativity may be. Here we present the results of a series of molecular dynamics simulations on the free DNA, the 1:1 complex, and the 2:1 complex, which have been designed to enable us to calculate thermodynamic parameters associated with the molecular recognition events. The results of the molecular dynamics studies confirm that structural factors alone cannot explain the cooperativity observed, indeed when enthalpic and hydration factors are looked at in isolation, the recognition process is predicted to be slightly anticooperative. However, when changes in configurational entropy are taken into account as well, the overall free energy differences are such that the calculated cooperativity is in good agreement with that observed experimentally. The results indicate the power of molecular dynamics methods to provide reasonable explanations for phenomena that are difficult to explain on the basis of static models alone, and provide a nice example of the concept of "allostery without conformational change".

Bisbenzimidazole↗