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At least 721 records · Page 40Linked to original sources
PubMed2001

Functional characterization of Marek's disease virus (MDV) origin-binding protein (OBP): analysis of its origin-binding properties.

In previous studies, we identified a Marek's disease virus (MDV) origin-binding protein (OBP) gene that is highly homologous to the herpes simplex virus type 1 UL9 gene that encodes an OBP and functions as an initiator protein for viral DNA replication. In this study, a protein of 95 kDa was produced in coupled in vitro transcription-translation reaction with the plasmid containing the wild type MDV OBP gene. The in vitro synthesized protein was detected by immunoprecipitation with a penta-histidine specific monoclonal antibody. Further characterization of MDV OBP was accomplished using electrophoretic mobility shift assay (EMSA) with the in vitro expressed MDV OBP using a double-stranded (ds) 26-mer oligonucleotide as the probe, which was designed from the putative MDV OBP binding site present in the serotype 1 or 2 MDV replication origin. The EMSA results indicated that MDV OBP could form a protein-DNA complex with the ds 26-mer oligonucleotide designed from serotype 1 or 2 replication origin. A series of 26-mer oligonucleotides with two-base-pair (bp) substitution across the putative MDV OBP binding site were used in competitive EMSA to determine the recognition sequence for the MDV OBP. The results demonstrated that the recognition sequence for MDV OBP was the TTCGCACC that is a subset of a 9-bp element (CGTTCGCAC) conserved in the replication origins of alphaherpesviruses. Furthermore, the results of EMSA with a series of deletion mutants from the N-terminus of MDV OBP indicated that the origin-binding domain was located at the amino acids region 528 to 841 of the wild-type MDV OBP. Taken together, our results suggest that the MDV OBP gene encodes an OBP of MDV.

Amino Acid Sequence↗
PubMed2002

Atomic force microscopy reveals kinks in the p53 response element DNA.

p53 is a 53 kDa nuclear phosphoprotein. Its function as a tumor suppressor critically lies in its ability to recognize its target DNA response elements as a tetramer. Here, we report the structural theme intrinsic to the response element DNA that governs this recognition phenomenon. The intrinsic flexibility or dynamic bending between two distinctly different, but naturally occurring p53 response elements has been compared by ring closure. Results show that DNA binding sites containing helically phased d(CATG.CATG) tetra-nucleotide sequences at the centers of quasi-dyad symmetry in each half-response site are more intrinsically flexible (i.e. preferentially bent under axial stress) than their d(CTTG.CTTG) counterparts. Intriguingly, p53 binding sites containing these more flexible d(CATG.CATG) sequence elements also exhibit a stronger tendency for tetrameric binding of the p53 DNA binding domain peptide. Examination of the shapes of DNA microcircles obtained by circularization of oligomers constructed from such flexible p53 target DNA sequences in tandem using MacMode atomic force microscopy directly revealed sequence-specific kinks in solution. The tetra-nucleotide sequence d(CATG.CATG) is highly conserved in most functional p53 response elements. Consequently, we propose that the sequence-specific kinks originating from d(CATG.CATG) sequences could be a common structural theme in p53 response elements and as evident from the results reported here, could be a determinant of binding site recognition by the p53 protein and the subsequent stability of the p53-DNA complex.

Base Sequence↗
PubMed2000

Overview of CARMEM: a new dynamic quantitative cardiac model for ECG monitoring and its adaptation to observed signals.

Different approaches have been proposed in order to achieve knowledge integration for coronary care monitoring applications, usually in the form of expert systems. The clinical impact of these expert systems, which are based only on "shallow" knowledge, has not been remarkable due to the difficulties associated with the construction and maintenance of a complete knowledge base. Model-based systems represent an alternative to these problems because they allow efficient integration of the "deep" knowledge on the underlying physiological phenomena being monitored. In this work, a brief review of existing model-based systems for cardiac rhythm interpretation is presented, followed by the description of a new system for Cardiac Arrhythmia Recognition by Model-Based ECG Matching (CARMEM). Fundamental characteristics of CARMEM are presented; in particular, its ability to provide online parameter adaptation to simulate complex rhythms and to match observed ECG signals. The proposed model can be useful for the explanation of the origin of cardiac arrhythmias and contribute towards their robust characterization in the context of coronary care units.

Artificial Intelligence↗
PubMed2000

Viral carcinogenesis: revelation of molecular mechanisms and etiology of human disease.

The RNA and DNA tumor viruses have made fundamental contributions to two major areas of cancer research. Viruses were vital, first, to the discovery and analysis of cellular growth control pathways and the synthesis of current concepts of cancer biology and, second, to the recognition of the etiology of some human cancers. Transforming retroviruses carry oncogenes derived from cellular genes that are involved in mitogenic signalling and growth control. DNA tumor viruses encode oncogenes of viral origin that are essential for viral replication and cell transformation; viral oncoproteins complex with cellular proteins to stimulate cell cycle progression and led to the discovery of tumor suppressors. Viral systems support the concept that cancer development occurs by the accumulation of multiple cooperating events. Viruses are now accepted as bona fide etiologic factors of human cancer; these include hepatitis B virus, Epstein-Barr virus, human papillomaviruses, human T-cell leukemia virus type I and hepatitis C virus, plus several candidate human cancer viruses. It is estimated that 15% of all human tumors worldwide are caused by viruses. The infectious nature of viruses distinguishes them from all other cancer-causing factors; tumor viruses establish long-term persistent infections in humans, with cancer an accidental side effect of viral replication strategies. Viruses are usually not complete carcinogens, and the known human cancer viruses display different roles in transformation. Many years may pass between initial infection and tumor appearance and most infected individuals do not develop cancer, although immunocompromised individuals are at elevated risk of viral-associated cancers. Variable factors that influence viral carcinogenesis are reviewed, including possible synergy between viruses and environmental cofactors. The difficulties in establishing an etiologic role for a virus in human cancer are discussed, as well as the different approaches that proved viral links to cancer. Future directions for tumor virus studies are considered.

Cell Transformation, Viral↗
PubMedDate not supplied

Cytokines and allergic diseases: clinical aspects.

In recent years there has been an explosive expansion of knowledge relating to a family of proteins involved in the intercellular communication network of the immune system. These substances, referred to as cytokines, are importantly involved in the highly regulated complex sequence of events of cellular interaction that comprise immune responses. Atopic diseases, which afflict 20-30% of the general population, are now considered to be associated with a set of abnormal genetically regulated immune responses to foreign antigens, i.e., allergens. The atopic individuals is characterized by the excessive production of IgE antibody to allergens after inhalation, ingestion, and surface contact. There are now recognized over 19 major classes of cytokines, which have been organized into the following categories according to their major functional activities: 1) Acute phase reactants, promoting and mediating natural immunity (e.g., IL-1, IL-6, TNF, interferons alpha and beta, and IL-8); 2) Cytokines that mediate cellular growth and differentiation (e.g., IL-7, IL-4, IL-2, IL-5, IL-10, IL-12, IL-13); 3) Cytokines that act as hematopoietic growth factors (IL-3, GMCSF, IL-9, IL-11, stem cell factor); 4) Chemokines (alpha and beta major groups, DTG, RANTES); and 5) Cytokines that exert lymphocyte regulatory activity (EG, IFN-gamma, TGF). Of particular importance to allergic disease is the recent recognition of the regulation of helper immune function by two lineages of T helper cells, i.e., Th1 and Th2, by these cytokines. The Th2 hypothesis of allergy (4) considers atopy as a Th2-driven hypersensitivity reaction to allergens of complex genetic and environmental origins, in which the Th1 lineage, normally driven by IL-2, TNF, and IFN-gamma is deficient, and in which a predominant Th2 response is seen that is driven by IL-4, IL-13, IL-5, and IL-10. This knowledge is finding application in both the diagnosis and therapy of allergic diseases, through the measurement or use of cytokines, which may replace deficient quantities, or the use of anticytokines, which may neutralize elevated quantities of cytokines, events that collectively contribute to the immunologic imbalance characteristic of the allergic state. In the future, the application of cytokines will continue to find clinical application in allergic disease, and it behooves the clinical allergist-immunologist to keep abreast of the exciting new developments that are occurring in this field.

Cytokines↗
PubMed1992

Expansion of major histocompatibility complex-restricted antimelanoma cytotoxic T-cell lymphocyte clones with identical T-cell receptor from tumor-infiltrating lymphocytes.

Tumor-infiltrating lymphocytes (TILs) were isolated from a subcutaneous metastasis of melanoma and cytotoxic T-cell lymphocyte (CTL) lines were obtained by sensitizing in vitro four separate aliquots of TILs with autologous tumor cells and recombinant interleukin-2. All CTL lines were predominantly WT31+, CD3+, and CD8+ and displayed a preferential cytotoxic activity against the autologous tumor. T-cell receptor (TCR) composition was analyzed by using the polymerase chain reaction with 5' variable region (V alpha or V beta)-specific primers and 3' constant (C alpha or C beta) primers. The entire repertoire of the V alpha and V beta gene families tested was present in fresh TILs and in the CTL lines, although, in the latter, consistent quantitative variations in transcripts of several V alpha and V beta occurred. CTL clones that exhibited CD3-dependent and major histocompatibility complex-restricted killing of the autologous melanoma were isolated from the four TIL cultures. TCR analysis indicated that, independently from the culture of origin, only two combinations of V alpha and V beta gene families were present in the majority of these CTL clones. These V alpha and V beta gene families were not found in a panel of CTL clones that did not lyse the autologous tumor. This study indicates that recognition of melanoma antigens can strongly select for certain types of TCR-bearing T-lymphocytes.

Base Sequence↗
PubMed2001

T Lymphocytes infiltrating various tumour types express the MHC class II ligand lymphocyte activation gene-3 (LAG-3): role of LAG-3/MHC class II interactions in cell-cell contacts.

The product of the Lymphocyte Activation Gene-3 (LAG-3, CD223) is a high affinity MHC class II ligand expressed by activated CD4(+) and CD8(+) T cells, which can associate with the T cell receptor (TCR) and downregulate TCR signalling in vitro. We have also reported that a soluble mLAG-3Ig fusion protein works as a vaccine adjuvant in vivo in mice, enhancing Th1 and CD8 T cell responses. Here, we report that LAG-3 expression was found, using fluorescent activated cell sorting (FACS) analysis, on 11-48% of human tumour-infiltrating lymphocytes (TILs) isolated from eight freshly dissociated renal cell carcinomas (RCCs), and was restricted mostly to CD8(+) cells. Immunohistochemical analysis confirmed LAG-3 expression by TILs in 9/11 RCCs, as well as in tumours of different origins, such as melanomas (3/5) and lymphomas (7/7). Since not only antigen presenting cells (APCs), but also TILs themselves strongly express major histocompatibility complex (MHC) class II, we firstly investigated whether LAG-3/MHC class II T-T cell contacts might influence tumour cell recognition. However, cytotoxicity inhibition was not observed in two RCC-specific CD8(+) T cell clones in the presence of the LAG-3-specific MAb, and there was also no observed difference in the recognition of LAG-3-transfected or wild-type RCC by these cytotoxic T lymphocytes (CTLs). In contrast, MHC class II engagement by LAG-3Ig was found to enhance the capacity of immature dendritic cells to stimulate naive T cell proliferation and IL-12-dependent IFN-gamma production by T cells in vitro. These results therefore provide support for a role for TIL-expressed LAG-3 in the engagement of class II molecules on APCs, thereby contributing to APC activation and Th1/Tc1 commitment, without downregulating cytotoxicity.

Antigens, CD↗
PubMed1998

The herpes simplex virus type 1 origin binding protein. Specific recognition of phosphates and methyl groups defines the interacting surface for a monomeric DNA binding domain in the major groove of DNA.

The UL9 gene of herpes simplex virus type 1 (HSV-1) encodes an origin binding protein (OBP). It is an ATP-dependent DNA helicase and a sequence-specific DNA-binding protein. The latter function is carried out by the C-terminal domain of OBP (DeltaOBP). We have now performed a quantitative analysis of the interaction between DeltaOBP and its recognition sequence, GTTCGCAC, in oriS. Initially optimal conditions for binding were carefully determined. We observed that complexes with different electrophoretic mobilities were formed. A cross-linking experiment demonstrated that nonspecific complexes containing 2 or more protein monomers per DNA molecule were formed at high protein concentrations. The specific complex formed at low concentrations of DeltaOBP had an electrophoretic mobility corresponding to a 1:1 complex. We then demonstrated that the methyl groups of thymine in the major groove were essential for high affinity binding. Changes in the minor groove had considerably smaller effects. Ethylation interference experiments indicated that specific contacts were made between OBP and three phosphates in the recognition sequence. Finally, these observations were used to present a model of the surface of DNA that interacts with DeltaOBP in a sequence-specific manner.

Base Sequence↗
PubMed2004

Site-specific expression of polycomb-group genes encoding the HPC-HPH/PRC1 complex in clinically defined primary nodal and cutaneous large B-cell lymphomas.

Polycomb-group (PcG) genes preserve cell identity by gene silencing, and contribute to regulation of lymphopoiesis and malignant transformation. We show that primary nodal large B-cell lymphomas (LBCLs), and secondary cutaneous deposits from such lymphomas, abnormally express the BMI-1, RING1, and HPH1 PcG genes in cycling neoplastic cells. By contrast, tumor cells in primary cutaneous LBCLs lacked BMI-1 expression, whereas RING1 was variably detected. Lack of BMI-1 expression was characteristic for primary cutaneous LBCLs, because other primary extranodal LBCLs originating from brain, testes, and stomach were BMI-1-positive. Expression of HPH1 was rarely detected in primary cutaneous LBCLs of the head or trunk and abundant in primary cutaneous LBCLs of the legs, which fits well with its earlier recognition as a distinct clinical pathological entity with different clinical behavior. We conclude that clinically defined subclasses of primary LBCLs display site-specific abnormal expression patterns of PcG genes of the HPC-HPH/PRC1 PcG complex. Some of these patterns (such as the expression profile of BMI-1) may be diagnostically relevant. We propose that distinct expression profiles of PcG genes results in abnormal formation of HPC-HPH/PRC1 PcG complexes, and that this contributes to lymphomagenesis and different clinical behavior of clinically defined LBCLs.

Carrier Proteins↗
PubMed1988

Division of human helper T cells into two sets on the basis of the induction of anti-tumor cytotoxicity by phorbol ester and calcium ionophore.

Fourteen noncytotoxic human helper T cell clones were examined for autocrine proliferative responses and cytotoxicity to tumor cells after stimulation with 12-O-tetradecanoylphorbol 13-acetate (TPA) and ionomycin (Io). Although all clones responded to alloantigen, they could be divided into two groups based on their proliferative response or lack of it to TPA/Io. Nonresponders could not be converted to responder status by addition of interleukin (IL) 1 or indomethacin to the cultures. Responder status did not correlate with any of the following properties of the clones: originating donor, recognitive specificity, B cell helper activity, proliferative response to IL 2 or 4, lymphokine secretory capacity or density of expression of antigen receptors, CD4 or HLA class II molecules. Responder status did, however, correlate with the ability of TPA/Io to induce major histocompatibility complex-unrestricted cytolytic activity directed towards natural killer-resistant tumor cells. These results divide human helper cells into two types on the basis of induction of anti-tumor cytotoxicity.

Antigens, Differentiation, T-Lymphocyte↗
PubMed1998

Engrailed homeodomain-DNA complex at 2.2 A resolution: a detailed view of the interface and comparison with other engrailed structures.

We report the 2.2 A resolution structure of the Drosophila engrailed homeodomain bound to its optimal DNA site. The original 2.8 A resolution structure of this complex provided the first detailed three-dimensional view of how homeodomains recognize DNA, and has served as the basis for biochemical studies, structural studies and molecular modeling. Our refined structure confirms the principal conclusions of the original structure, but provides important new details about the recognition interface. Biochemical and NMR studies of other homeodomains had led to the notion that Gln50 was an especially important determinant of specificity. However, our refined structure shows that this side-chain makes no direct hydrogen bonds to the DNA. The structure does reveal an extensive network of ordered water molecules which mediate contacts to several bases and phosphates (including contacts from Gln50), and our model provides a basis for detailed comparison with the structure of an engrailed Q50K altered-specificity variant. Comparing our structure with the crystal structure of the free protein confirms that the N and C termini of the homeodomain become ordered upon DNA-binding. However, we also find that several key DNA contact residues in the recognition helix have the same conformation in the free and bound protein, and that several water molecules also are "preorganized" to contact the DNA. Our structure helps provide a more complete basis for the detailed analysis of homeodomain-DNA interactions.

Crystallography, X-Ray↗
PubMed2002

Rational design of peptide-based tumor vaccines.

Administration of synthetic peptides derived from proteins uniquely or overexpressed in tumor cells (tumor-associated antigens) can elicit tumor-specific immune responses in vivo. This is because cytotoxic T lymphocytes can recognize and lyse tumor cells that display peptides derived from tumor-associated antigens (TAAs) in the context of class I major histocompatibility complex (MHC) molecules. TAA peptides, in contrast to peptides of viral origin, generally bind weakly to the MHC molecule. In many cases, this explains the poor magnitude of T cell response directed at the tumor in vivo. Improving MHC binding as a strategy to upregulate antigen recognition can convert low affinity TAA peptides into useful tools in clinical trial settings. High-resolution structures of class I MHC molecules reported over the past two decades provided the framework for designing peptides that can induce optimal T cell response. This review will discuss the basic and clinical aspects of modifying native TAA peptides as tumor vaccines.

Animals↗
PubMed1996

The human leucocyte antigen complex: its role in colorectal cancer.

The human leucocyte antigen (HLA) is frequently altered in human tumours compared to the tissue from which they originate. The ability of the tumour to invade requires a change in the phenotype of the cell allowing it to advance and expand without restraint from adjacent tissue and the host immune system. One important regulator of tumour growth is cellular immunity. Antigen recognition by "T" cells occurs in the context of the HLA products. Changes in the HLA expression of a malignant tissue may directly influence immunosurveillance mechanisms, as these molecules play a central role in presenting potentially immunogenic peptides to "T" cells. To assess whether alteration in HLA expression is a critical step in the multistep origin of tumours, it is important to examine the HLA expression in premalignant precursor lesions of tumours and in tumours themselves. Our studies have recently reported a downregulation of HLA class I expression in colorectal cancers and adenomatous polyps when compared to normal appearing mucosa adjacent to the cancer. Our study on the class I antigen expression showed the presence of the antigen on all samples of control colonic epithelium. In sporadic adenomatous polyps of the colorectum, 21% (n = 7) of adenomas expressed levels of HLA that were comparable to controls, 51% (n = 17) expressed low levels, and in 28% (n = 9) the antigen was undetectable. Similarly, in colorectal adenocarcinomas the antigen was reduced even further with levels comparable to controls in 5% (n = 2) of tumours, reduced in 30% (n = 6) and undetectable in 65% (n = 13). This abnormality may result in the loss of immunosurveillance which could be one mechanism by which cancer cells can evade "T" cell control, thus resulting in invasion and metastasis.

Colon↗
PubMed1996

A nuclear cap-binding complex facilitates association of U1 snRNP with the cap-proximal 5' splice site.

The mechanism by which intron-containing RNAs are recognized by the splicing machinery is only partly understood. A nuclear cap-binding complex (CBC), which specifically recognizes the monomethyl guanosine cap structure carried by RNA polymerase II transcripts, has previously been shown to play a role in pre-mRNA splicing. Using a combination of splicing complex and psoralen cross-linking analysis we demonstrate that CBC is required for efficient recognition of the 5' splice site by U1 snRNP during formation of E (early) complex on a pre-mRNA containing a single intron. However, in a pre-mRNA containing two introns, CBC is not required for splicing of the cap distal intron. In this case, the presence of an intact polypyrimidine tract in the cap-proximal intron renders splicing of the cap-distal intron independent of CBC. These results support models in which the splice sites in a pre-mRNA are originally recognized by interactions spanning exons. The defects in splicing and U1 snRNP binding caused by CBC depletion can be specifically reversed by recombinant CBC. In summary, efficient recognition of the cap-proximal 5' splice site by U1 snRNP is facilitated by CBC in what may be one of the earliest steps in pre-mRNA recognition. Data in Colot et al. (this issue) indicate that this function of CBC is conserved in humans and yeast.

Base Sequence↗
PubMed1991

Evolution of the complement system.

The ancestral form of the alternative pathway of complement activation probably originated as a primitive independent immune system. Subsequent evolution of an adaptive immune response drove the specialization of the classical pathway to connect antibody-mediated nonself recognition to the complement-dependent effector mechanisms. In this article Timothy Farries and John Atkinson consider how the contemporary complexity arose by a succession of credible alterations at the genetic level, and the selective advantages provided at each step.

Biological Evolution↗
PubMed2005

Dinoflagellate cysts and hydrographical change in Gullmar Fjord, west coast of Sweden.

This high-resolution study of the latest Holocene dinoflagellate cyst record from Gullmar Fjord, on the west coast of Sweden, provides evidence for the recognition of two major dinoflagellate communities within the fjord over the last 85 years. These communities may have their origins with the history of cultural eutrophication within the region, but are more likely to be associated with the wider phenomenon of the North Atlantic Oscillation and/or the complex hydrographical response of the fjord to various changing climatic environments between 1915 and 1999. The changing dinoflagellate cyst populations are compared in detail with the many hydrographical parameters available from this well studied fjord with its long instrumental records. Indeed the dinoflagellate cysts fail to demonstrate a convincing ongoing eutrophication record for the fjord but do show a major change in the cyst assemblages at about 1969/1970 at a time when the NAO was changing from a negative phase to the present-day positive phase. Gullmar Fjord is important in the history of dinoflagellate cyst studies, being the site of the 1954 study by Erdtman in which viable cysts, produced within the phytoplankton, were first documented within the water column.

Animals↗
PubMed2002

Visual agnosia and prosopagnosia in childhood: a prospective case study.

Selective impairments in visual processing are well documented in adults but rarely reported in children. The few childhood cases reported are mostly retrospective accounts with little attention paid to developmental, assessment or management issues. We report a prospective case study of a boy with prosopagnosia and visual processing deficits of presumed developmental origin. At the age of 4 years, AL presented with a range of cognitive and visual recognition deficits. Subsequent assessments revealed an evolving pattern in visual recognition and dissociations between developing skills. At the age of 7 AL has impairments in early perceptual analysis, visual organisation and in complex visual processing. Although he can identify facial features and match faces he is unable to recognise familiar faces. His reading and spelling are developing normally. The nature of his deficits and his progress are discussed within a cognitive neuropsychological framework.

Achievement↗
PubMed2003

Effectiveness of the Rey-Osterrieth Complex Figure Test and the Meyers and Meyers recognition trial in the detection of suspect effort.

The Rey-Osterrieth Complex Figure Test (ROCFT) is a popular measure of visuoconstructive skills and visual memory. A recognition memory trial was recently developed by Meyers and Meyers (1995) and attached to the standard administration of the ROCFT. The addition of this recognition paradigm (comprised of 12 small designs from the original ROCFT stimulus interspersed among 12 foils) makes ROCFT a potentially useful instrument in capturing suspect effort because patients attempting to feign memory difficulties typically operate from the misconception that recognition memory is as impaired as free recall in brain injury and, as a result, suppress recognition performance. The ROCFT (copy, immediate recall [i.e., 3-min recall], and the recognition trial) was administered to four sets of participants: 58 patients with suspect effort; 23 neuropsychology clinic patients with verbal memory impairment, 17 clinic patients with visual memory impairment, and 30 clinic patients without memory impairment. Group comparisons revealed significant group differences in direct copy, immediate recall, and recognition scores of the ROCFT (p<.0001), with the suspect effort group displaying significantly lower performance on the copy and immediate recall scores than the verbal memory impaired and nonmemory impaired clinic patient groups, and significantly lower recognition scores than all three clinical groups. Furthermore, qualitative examination of the recognition trial revealed the presence of "atypical recognition errors" that were endorsed with significantly higher frequency by the suspect effort patients. A combination score incorporating the copy, true positive recognition, and atypical recognition error scores yielded a sensitivity of 74% while misclassifying only approximately 4% of verbal memory impaired clinic patients, 12% of visual memory impaired clinic patients, and 3% of nonmemory impaired clinic patients. Thus, the ROCFT+recognition trial show considerable potential for detecting noncredible effort.

Adolescent↗