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PubMed2005

Structure-function analysis of yeast tRNA ligase.

Trl 1 is an essential 827-amino-acid enzyme that executes the end-healing and end-sealing steps of tRNA splicing in Saccharomyces cerevisiae. Trl1 consists of two catalytic domains--an N-terminal adenylyltransferase/ligase component (amino acids 1-388) and a C-terminal 5'-kinase/cyclic phosphodiesterase component (amino acids 389-827)--that can function in tRNA splicing in vivo when expressed as separate polypeptides. Sedimentation analysis indicates that the ligase and kinase/CPD domains are monomeric proteins that do not form a stable complex in trans. To understand the structural requirements for the RNA ligase component, we performed a mutational analysis of amino acids that are conserved in Trl1 homologs from other fungi. Alanine scanning identified 23 new residues as essential for Trl1-(1-388) activity in vivo. Structure-activity relationships at these positions, and four essential residues defined previously, were clarified by introducing 50 different conservative substitutions. Lethal mutations of Lys114, Glu184, Glu266, and Lys284 abolished Trl1 adenylyltransferase activity in vitro. The essential elements embrace (1) putative equivalents of nucleotidyltransferase motifs I, Ia, III, IV, and V found in DNA ligases, T4 RNA ligase 2, and mRNA capping enzymes; (2) an N-terminal segment shared with the T4 RNA ligase 1 subfamily only; and (3) a constellation of conserved residues specific to fungal tRNA splicing enzymes. We identify yeastlike tRNA ligases in the proteomes of Leishmania and Trypanosoma. These findings recommend tRNA ligase as a target for antifungal and antiprotozoal drug discovery.

Amino Acid Motifs↗
PubMed2004

Genotyping and functional analysis of the D104N variant of human endostatin.

Endostatin is an endogenous inhibitor of angiogenesis derived from the extracellular matrix protein collagen XVIII. It has been reported that a variation at the 104 position (D104N) of human endostatin is associated with an increased risk of prostate cancer, potentially indicating that this protein variant is less active as an anti-angiogenic agent. Herein we reported the results of genotyping 389 patients with androgen independent prostate cancer (AIPC) and 352 normal control individuals for D104N endostatin. There was no significant association between the frequency of 104N endostatin and the incidence of AIPC in either Caucasian or African American patients compared to controls (15% Caucasian AIPC versus 13.7% in Caucasian controls, p=0.79; 7.4% African American AIPC versus 5.6% in African American controls, p=0.64). Actuarial analysis revealed no statistically significant association between incidence of the DN heterozygous genotype and survival (p=0.62 by logrank test). To study the functional significance of the D104N conversion, we have expressed and purified insoluble recombinant human 104D and 104N endostatin and compared their respective activities in human umbilical vein endothelial cell (HUVEC) tube formation assays. The 104N variant of human endostatin inhibited HUVEC tube formation at least as well as the wild-type form. We concluded that the D104N variation in human endostatin is neither clinically relevant nor suitable as a pharmacogenomic endpoint to assess the risk for developing AIPC.

Aged↗
PubMed1987

DNA sequence and functional analysis of an ARS-element from the zygomycete Absidia glauca.

A DNA fragment of mitochondrial origin from the mucoraceous fungus Absidia glauca promoting autonomous plasmid replication in Saccharomyces cerevisiae was sequenced and functionally characterised. We could show that the original mitochondrial insert cloned in Yip5 contains two regions with ARS activity which mutually inhibit each other. All plasmid derivatives replicating in yeast are rapidly lost during growth under non-selective conditions. In addition to one ARS consensus sequence with only one base substitution, the mitochondrial insert contains 18 related sequences with two base pair exchanges. With one exception all consensus sequences are preceded by sequence motifs strongly resembling ARS boxes.

Base Sequence↗
PubMed1977

A comparative study of infantile autism and specific developmental receptive language disorders. III. Discriminant function analysis.

A psychometric, observational, and interview study was undertaken with 47 boys, aged 4 1/2 to 10 years, with nonverbal IQs of 70+ and a severe developmental disorder of language comprehension. Separate discriminant function analyses, based on behavioral, language, or cognitive features, showed little overlap between clinically defined autistic and dysphasic subgroups. Moreover, the discrimination could be made as clearly on language or cognitive characteristics as on social or behavioral critera. Language abnormalities and behavioral features also intercorrelated within the autistic subgroup. It is concluded that autism and dysphasia differ in important ways and that a cognitive deficit is an essential part of the syndrome of autism.

Autistic Disorder↗
PubMed1993

Molecular cloning and functional analysis of Drosophila TAF110 reveal properties expected of coactivators.

The general transcription factor TFIID is a multiprotein complex containing the TATA-binding protein and several associated factors (TAFs), some of which may function as coactivators that are essential for activated, but not basal, transcription. Here we describe the isolation and characterization of the first gene encoding a TAF protein. The deduced amino acid sequence of TAF110 revealed the presence of several glutamine- and serine/threonine-rich regions reminiscent of the protein-protein interaction domains of the regulatory transcription factor Sp1 that are involved in transcription activation and multimerization. In both Drosophila cells and yeast, TAF110 specifically interacts with the glutamine-rich activation domains of Sp1. Moreover, purified Sp1 selectively binds recombinant TAF110 in vitro. These findings taken together suggest that TAF110 may function as a coactivator by serving as a site of protein-protein contact between activators like Sp1 and the TFIID complex.

Amino Acid Sequence↗
PubMedDate not supplied

Comparative functional analysis of lymphocytes and monocytes from plateletapheresis.

Large numbers (2.9 +/- 1.2 X 10(9)) of mononuclear cells can be obtained from incidental samples collected during routine plateletapheresis. We conducted studies comparing characteristics and functions of mononuclear cells derived from venous blood samples and from routine plateletapheresis in the same normal donors. Cell viability was similar in both samples (96 +/- 1% plateletapheresis vs 97 +/- 2% venous blood). Higher concentration of monocytes were observed in the plateletapheresis samples (32.3 +/- 6%) than in the venous blood (14.3 +/- 4%). The procedure of plateletapheresis does not seem to alter lymphocyte or monocyte function. Thus, the functional integrity of these cell populations was demonstrated in terms of natural killer cell activity, blastogenic response to mitogens, local graft-versus-host reactions, monocyte-mediated antibody-dependent cellular cytotoxicity against human red cells, monocyte-mediated tumor cell cytotoxicity, latex phagocytosis, and monocyte-dependent lymphocyte blastogenesis. We conclude that monocytes and lymphocytes obtained during routine plateletapheresis are functionally intact.

Antibody-Dependent Cell Cytotoxicity↗
PubMed2006

Functional analysis of AP-2 alpha and mu2 subunits.

The AP-2 adaptor complex plays a key role in cargo recognition and clathrin-coated vesicle formation at the plasma membrane. To investigate the functions of individual binding sites and domains of the AP-2 complex in vivo, we have stably transfected HeLa cells with wild-type and mutant small interfering RNA-resistant alpha and mu2 subunits and then used siRNA knockdowns to deplete the endogenous proteins. Mutating the PtdIns(4,5)P2 binding site of alpha, the phosphorylation site of mu2, or the YXXPhi binding site of mu2 impairs AP-2 function, as assayed by transferrin uptake. In contrast, removing the C-terminal appendage domain of alpha, or mutating the PtdIns(4,5)P2 binding site of mu2, has no apparent effect. However, adding a C-terminal GFP tag to alpha renders it completely nonfunctional. These findings demonstrate that there is some functional redundancy in the binding sites of the various AP-2 subunits, because no single mutation totally abolishes function. They also help to explain why GFP-tagged AP-2 never appears to leave the plasma membrane in some live cell imaging studies. Finally, they establish a new model system that can be used both for additional structure-function analyses, and as a way of testing tagged constructs for function in vivo.

Adaptor Protein Complex alpha Subunits↗
PubMed1995

Spinal cord monitoring of the ventral funiculus function. Analysis of spinal field potentials after galvanic vestibular stimulation.

STUDY DESIGN: This study was designed to examine the possibility of a new spinal cord monitoring method using galvanic vestibular stimulation to monitor the function of the ventral funiculus of the spinal cord. OBJECTIVES: To settle the problems of previous monitoring methods by using galvanic vestibular nerve stimulation, which is highly selective for monitoring the function of the ventral funiculus of the spinal cord. SUMMARY OF BACKGROUND DATA: Although various spinal cord monitoring methods have been used, there are still problems because potentials recorded by these methods do not reflect selectively the function of the ventral funiculus of the spinal cord, which is vulnerable during anterior spinal surgeries. METHODS: In anesthetized cats, field potentials evoked by galvanic stimulation of the labyrinth were recorded from the epidural space of the spinal cord. The origin of these potentials was determined by mapping field potentials from within the upper cervical spinal cord using a micropipette and by examining the effect of sectioning the brainstem on the evoked potentials. RESULTS: The spinal cord potentials evoked by galvanic stimulation between the bilateral labyrinths could be recorded from the epidural space, and these potentials mainly originated from the ventral and ventromedial funiculus of the spinal cord. The latency and intraspinal distribution of the evoked potentials and the effect of sectioning the medial longitudinal fascicle on the evoked potentials indicated that the earliest component of the evoked potentials reflects mainly the activity of the vestibulospinal tract. CONCLUSIONS: Recording spinal cord potentials evoked by galvanic vestibular stimulation from the epidural space appears to be a potential technique to monitor the functional state of the ventral funiculus during anterior spinal surgeries.

Animals↗
PubMed2006

Rubella virus pseudotypes and a cell-cell fusion assay as tools for functional analysis of the rubella virus E2 and E1 envelope glycoproteins.

The rubivirus Rubella virus contains the two envelope glycoproteins E2 and E1 as a heterodimeric spike complex embedded in its lipid envelope. The functions of both proteins, especially of E2, in the process of viral entry are still not entirely understood. In order to dissect E2 and E1 entry functions from post-entry steps, pseudotypes of lentiviral vectors based on Simian immunodeficiency virus were used. C-terminally modified E2 and E1 variants successfully pseudotyped lentiviral vector particles. This is the first report to show that not only E1, but also E2, is able to mediate infectious viral entry. Furthermore, a cell-cell fusion assay was used to further clarify membrane-fusion activities of E2 and E1 as one of the early steps of infection. It was demonstrated that the capsid protein, when coexpressed in cis, enhances the degree of E2- and E1-mediated cell-cell fusion.

Animals↗
PubMed2004

Identification and functional analysis of a locus for improvement of lodging resistance in rice.

We identified a new locus responsible for increased pushing resistance of the lower part of rice (Oryza sativa) and analyzed its physiological function to understand how to improve lodging resistance in rice. Quantitative trait loci (QTLs) controlling pushing resistance of the lower part were analyzed in a population of backcross inbred lines of japonica Nipponbare x indica Kasalath plants cut out at 40 cm to exclude the effect of the weight of the upper parts. Five QTLs for pushing resistance were detected; only one QTL from Kasalath on chromosome 5 (prl5) had a positive effect. The likelihood odds ratio curve of prl5 echoed that for lodging resistance by typhoon. We selected three near-isogenic lines (NILs) in which the chromosomal region of prl5 was substituted with that of Kasalath in the Nipponbare background. The dry weights and densities and the contents of accumulated carbohydrate in stems below 40 cm (lower stems) in each NIL were significantly higher than those of Nipponbare. There was no difference between Nipponbare and the NILs in yield, root characteristics, or the weights of the upper parts. Pushing resistance of the lower part and lodging resistance in the NILs were up to twice as high as in Nipponbare. These results suggest that prl5 might affect the characteristics of the lower stems of the NILs, thus increasing lodging resistance.

Carbohydrate Metabolism↗
PubMed1983

Immunoregulation in atopic dermatitis: functional analysis of T-B cell interactions and the enumeration of Fc receptor-bearing T cells.

Immune aberrations in atopic dermatitis (AD) are multiple and interrelated. We investigated immunoregulatory cell markers and functional interactions of purified T- and B-enriched cells in a pokeweed mitogen (PWM)-stimulated IgG production assay in patients with AD. Atopic mononuclear leukocytes and autologous recombinations of purified atopic T and B cells were hyporesponsive to PWM stimulation of IgG synthesis. When atopic B cells were cultured with normal T cells, they were still less responsive than normal B cells. Atopic T cells generated normal levels of suppression in three responder systems. Radioresistant T-cell help was also in the normal range whereas nonirradiated AD T cells produced slightly less help than normal T cells. We noted reduced levels of T lymphocytes with FcIgG receptors (T gamma) and found that T gamma reduction correlated inversely with log serum IgE. In the light of normal T suppression, we critically examined AD cell adherence and contamination at various steps in the T gamma assay to rule out technical causes of T gamma reduction in AD. Lowered T gamma cells in AD were not associated with circulating IgG immune complexes and subsequent blockade of the FcIgG receptors. Thus, we have identified defects in the numbers of an immunoregulatory T cell, and in the generation of PWM-responsive B cells. A model is proposed in which the alterations in atopic cyclic nucleotide metabolism of T-cell helpers could result in abnormalities of immunoregulatory T cells and PWM-recruitable B cells.

Adolescent↗
PubMedDate not supplied

Comparative functional analysis of the Bristow, Magnuson-Stack, and Putti-Platt procedures for recurrent dislocation of the shoulder.

Literature on anterior shoulder instability deals most often with elimination of recurrence following reconstruction. We analyzed the subjective function, loss of motion and shoulder strength of three operative procedures: Magnuson-Stack, Bristow, and Putti-Platt. A retrospective review of 27 patients, 9 in each surgical group, with no postoperative dislocations or on-going pain was performed. All patients were male, right hand dominant with the right shoulder affected. Average time of followup was 6.75 years (range, 4.2 to 10.3 years). All patients completed a questionnaire and had their range of motion measured by a hand-held goniometer and their shoulder strength tested on the Cybex II Dynomometer. Peak torque as a percent of body weight and side-to-side differences were calculated for six arm positions and compared to nine right hand dominant controls of similar age and recreational activity. Sixty percent returned to throwing sport. One Magnuson-Stack and Bristow patient felt full functional return to preinjury level. Three patients in each of these two groups returned to unmodified throwing sport whereas no Putti-Platt patient attained this level. Deficit of external rotation at shoulder neutral measured 4.7 degrees, Magnuson-Stack; 12.2 degrees, Bristow; and 21.8 degrees, Putti-Platt. At 90 degrees shoulder abduction, similar deficits in external rotation measured 6.4 degrees, 11.6 degrees, and 28.8 degrees respectively. These values were statistically significant employing analysis of variance. We compared the operative groups as a whole to the controls and compared the operative groups to each other.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗
PubMed1979

Functional analysis of the replicator structure of lambdoid bacteriophage DNAs.

In our hybrid-plasmid reconstruction analysis of lambda (lambdoid) DNA signal structures involved in phage DNA replication, we have detected a dual system alternatingly able to initiate a first primer-RNA synthesis. Both of them--the major, primase-dependent ori system and the minor and usually suppressed, RNA-polymerase-dependent oop system--act in conjunction with a common signal structure for inception of DNA synthesis. It appears that in situations such as this, where one has to deal with the existence of regular as well as backup systems serving the same function, straightforward conclusions are no longer possible in their genetic analysis. For example, even though the oop-DNA segment can be deleted entirely from bacteriophage lambda DNA without disturbing its ability to replicate, it may not be valid to conclude that the oop system has no function in DNA replication. Dual systems of this type or organization in general have also been observed previously for some other replicons such as the R-factors R6-5 and R6K (Timmis et al. 1978; Crosa et al., this volume) or the F factor (Helinski et al., this volume), and they may be more common than presently expected.

Bacteriophage lambda↗
PubMed1997

Functional analysis of glycosyltransferases encoded by the capsular polysaccharide biosynthesis locus of Streptococcus pneumoniae serotype 14.

Bacteria belonging to the species Streptococcus pneumoniae vary in their capsule. Presently, 90 capsular serotypes are known, all possessing their own specific polysaccharide structure. Little is known about the biosynthesis of these capsular polysaccharides. The cps locus of S. pneumoniae serotype 14 was cloned. So far, 7 open reading frames have been sequenced, cps14B to cps14H. The gene products are similar to proteins involved in bacterial polysaccharide biosynthesis, both of Gram-negative and -positive micro-organisms. Gene-specific mutants were created for cps14D to cps14H by insertional mutagenesis. All mutants no longer agglutinated with a monoclonal antibody against type 14 capsule polysaccharides. The biosynthetic function of cps14E and cps14G was determined by analysis of the intermediates in the synthesis of the oligosaccharide subunit, formed in membrane preparations of the wild-type and mutant strains and in membrane preparations of Escherichia coli expressing the pneumococcal glycosyltransferases. The enzyme encoded by cps14E is a glucosyl-1-phosphate transferase that links glucose to a lipid carrier, the first step in the biosynthesis of the type 14 repeating unit. The gene product of cps14G encodes a beta-1,4-galactosyltransferase, the enzyme responsible for the second step in the subunit synthesis, the transfer of galactose to lipid-linked glucose.

Amino Acid Sequence↗
PubMed1988

Structural and functional analysis of poly(ADP ribose) polymerase: an immunological study.

Poly(ADP ribose) polymerase (EC 2.4.2.30) was studied using monoclonal antibodies for three different epitopes on the enzyme. The epitopes were mapped in relation to the functional domains of the protein and the inhibitory properties of the antibodies. The intranuclear and interspecies immunoreactivity of the enzyme was also investigated. The epitope of antibody 2 was mapped to the 17 kDa fragment generated by chymotryptic digestion of the C-terminal 54 kDa NAD-binding domain. Antibody 9 binds to the N-terminal 29 kDa fragment of the DNA binding domain and inhibits the enzyme activity by 80%. This antibody was used to purify poly(ADP ribose) polymerase by immunoaffinity chromatography. The third antibody binds to a central 36 kDa fragment that possesses part of the DNA-binding domain and the automodification domain. This antibody increases the enzymatic activity by 30%. An analysis of the species cross-reactivity of the antibodies was carried out by immunoblot analysis of nuclear proteins. Antibody 10 binding was detected in rat FR3T3 cells, Chinese hamster ovary cells (CHO) and epidermoid carcinoma lung human cells (CALU-1). The other two antibodies are specific for the human and bovine enzymes. Western blot analysis showed the association of poly(ADP ribose) polymerase with residual nuclear material obtained after nuclease treatment and high-salt extraction. Immunofluorescence studies with the three different monoclonals demonstrated that accessibility of the epitopes varies in the nucleus.

Animals↗
PubMed2004

Isolation of murine hepatic lymphocytes using mechanical dissection for phenotypic and functional analysis of NK1.1+ cells.

AIM: To choose an appropriate methods for the isolation of hepatic lymphocytes between the mechanical dissection and the enzymatic digestion and investigate the effects of two methods on phenotype and function of hepatic lymphocytes. METHODS: Hepatic lymphocytes were isolated from untreated, poly (I:C)-stimulated or ConA-stimulated mice using the two methods, respectively. The cell yield per liver was evaluated by direct counting under microscope. Effects of digestive enzymes on the surface markers involved in hepatic lymphocytes were represented by relative change rate ((percentage of post-digestion -percentage of pre-digestion)/percentage of pre-digestion). Phenotypic analyses of the subpopulations of hepatic lymphocytes and intracellular cytokines were detected by flow cytometry. The cytotoxicity of NK cells from wild C57BL/6 or poly (I:C)-stimulated C57BL/6 mice was analyzed with a 4-h (51)Cr release assay. RESULTS: NK1.1(+) cell markers, NK1.1 and DX5, were significantly down-expressed after enzymatic digestion and their relative change rates were about 28% and 32%, respectively. Compared with the enzymatic digestion, the cell yield isolated from unstimulated, poly (I:C)-treated or ConA-treated mice by mechanical dissection was not significantly decreased. Hepatic lymphocytes isolated by the mechanical dissection comprised more innate immune cells like NK, NKT and gammadelta cells in normal C57BL/6 mice. After poly (I:C) stimulation, hepatic NK cells rose to about 35%, while NKT cells simultaneously decreased. Following ConA injection, the number of hepatic NKT cells was remarkably reduced to 3.67%. Higher ratio of intracellular IFN-gamma(+) (68%) or TNF-alpha(+) (15%) NK1.1(+) cells from poly (I:C)-treated mice was obtained using mechanical dissection method than control mice. There was no difference in viability between the mechanical dissection and the enzymatic digestion, and hepatic lymphocytes obtained with the two methods had similar cytotoxicity against YAC-1 cells. CONCLUSION: There is no difference in the cell yield and viability of the hepatic lymphocyte isolated with the two methods. The mechanical dissection, but not the enzymatic digestion, may be suitable for the phenotypic analysis of hepatic NK1.1(+) cell.

Animals↗
PubMed1998

Protein expression and functional analysis of the FHIT gene in human tumor cells.

BACKGROUND: The fragile histidine triad (FHIT) gene at chromosome 3p14.2 has been proposed to be a candidate tumor suppressor gene in human cancers. To test whether FHIT exhibits the functional properties of a tumor suppressor gene, we studied the expression of its protein (pFHIT) in human carcinoma cells and examined the ability of FHIT to inhibit the neoplastic phenotype of cancer cells. METHODS: Subcellular localization and patterns of protein expression in tumor cells were determined by immunohistochemical analysis and immunoblotting with the use of polyclonal anti-pFHIT antisera. In tumor cells with undetectable pFHIT, we examined the effect of recombinant pFHIT expression on morphology, growth rate, colony formation, and in vivo tumor formation. RESULTS: We demonstrated that pFHIT is a cytoplasmic 17-kd polypeptide whose expression could not be detected in 30 of 52 human carcinoma cell lines tested. We observed, however, that the stable overexpression of pFHIT did not alter cell morphology, inhibit colony formation, or inhibit cell proliferation in vitro. Furthermore, overexpression of pFHIT did not lead to altered cell cycle kinetics in dividing cells. The in vivo tumorigenicity of a tumor cell line that expressed high levels of recombinant pFHIT was equivalent to that of control transfectants and of parental cells. CONCLUSIONS: These results suggest that the replacement of pFHIT in human carcinoma cells does not suppress tumor cell growth and that this protein may be involved in tumorigenesis in ways that are distinct from the "classic" tumor suppressor paradigm.

Carcinoma, Small Cell↗
PubMed1997

Expression, purification, and functional analysis of the TyrR protein of Haemophilus influenzae.

The gene that was inferred to encode the TyrR protein of Haemophilus influenzae Rd was synthesized by polymerase chain reaction and inserted into a T7-based expression vector. Methods were developed to overexpress the TyrR protein of H. influenzae in Escherichia coli and to purify the protein on a large scale. Both in vitro and in vivo functional comparisons of the H. influenzae and E. coli TyrR proteins were carried out. The TyrR protein of H. influenzae was able to bind in vitro to an operator target upstream of the aroF-tyrA gene of E. coli. In the presence of [gamma-S]ATP, the DNA binding ability of the H. influenzae TyrR protein was drastically reduced. Despite the much shorter peptide chain length (318 amino acid residues vs 513), the TyrR protein of H. influenzae was as active in repressing the aroF promoter as the TyrR protein of E. coli. Repression by both proteins was enhanced in the presence of tyrosine; however, the transcriptional activation function associated with the TyrR protein of E. coli could not be detected when the H. influenzae TyrR protein was expressed in E. coli. By computer analysis, at least five operator targets for TyrR were identified within the genomic DNA of H. influenzae. These observations show that the assignment of function to the tyrR gene of H. influenzae was correctly made. Further studies of the H. influenzae TyrR protein in comparison to its E. coli counterpart should provide valuable mechanistic information on transcriptional regulation in this system.

Amino Acid Sequence↗