Biomedical subjects

Y X Fu

Publications and source records attributed to Y X Fu.

At least 73 records · Page 4Linked to original sources

PubMed1995

Decreased macrophage-mediated cytotoxicity in mammary-tumor-bearing mice is related to alteration of nitric-oxide production and/or release.

Peritoneal-exudate macrophages (PEM) from mammary-tumor-bearing mice have impaired cytotoxic activity against syngeneic and allogeneic tumor targets. The ability of PEM from normal and tumor-bearing mice to bind tumor targets was found to be similar in the presence or the absence of surrogate receptors, which enhanced the binding but not the killing of tumor targets by PEM from tumor-bearing mice, suggesting that other mechanisms are involved in their impaired cytolytic activity. Soluble and membrane-bound TNF-alpha, as well as H2O2, were found in higher amounts in PEM from tumor bearers upon stimulation with LPS, as compared with PEM from normal mice. However, tumor-bearers' macrophages displayed decreased capacity to produce and/or release nitric oxide, which could be reversed by the addition of increasing levels of IFN-gamma. These results indicate that the lack of macrophage cytotoxicity in mammary-tumor-bearing mice is related to impaired production and/or release of NO by these effector cells, possibly aggravated by the insufficient IFN-gamma production previously reported in these animals. Moreover, mammary-tumor progression results in dis-regulation of synthesis of macrophage-mediators, with over-production of molecules to which mammary-tumor cells are insensitive and deficient production of NO, the crucial molecule to which these cells appear to be highly sensitive.

Animals↗

PubMed1995

Statistical properties of segregating sites.

A mutation leading to a segregating site of a sample can be classified by the number of sequences in the sample that inherits the mutant nucleotide; it can also be classified by the frequencies of the two segregating nucleotides at the resulting segregating side. We define the size of a mutation to be the number of sequences in the sample that inherits the mutant nucleotide and the type of mutation (segregating site) to be the smallest value of the frequencies of segregating nucleotides. Each of these two classifications of mutations is analogous to allelic types in a sample of genes. Assuming the neutral Wright-Fisher model, we derived in this paper the mean and variance of the frequency of mutations of each size and type, and the covariance between the numbers of mutations of two different sizes and two different types. Potential applications of these results are discussed.

Analysis of Variance↗

PubMed1995

Classifying and counting linear phylogenetic invariants for the Jukes-Cantor model.

Linear invariants are useful tools for testing phylogenetic hypotheses from aligned DNA/RNA sequences, particularly when the sites evolve at different rates. Here we give a simple, graph theoretic classification for each phylogenetic tree T, of its associated vector space I(T) of linear invariants under the Jukes-Cantor one-parameter model of nucleotide substitution. We also provide an easily described basis for I(T), and show that if I is a binary (fully resolved) phylogenetic tree with n sequences at its leaves then: dim[I(T)] = 4n-F2n-2 where Fn is the nth Fibonacci number. Our method applies a recently developed Hadamard matrix-based technique to describe elements of I(T) in terms of edge-disjoint packings of subtrees in T, and thereby complements earlier more algebraic treatments.

Base Sequence↗

PubMed1995

Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites.

This paper presents a maximum likelihood approach to estimating the variation of substitution rate among nucleotide sites. We assume that the rate varies among sites according to an invariant+gamma distribution, which has two parameters: the gamma parameter alpha and the proportion of invariable sites theta. Theoretical treatments on three, four, and five sequences have been conducted, and computer program have been developed. It is shown that rho = (1 + theta alpha)/(1 + alpha) is a good measure for the rate heterogeneity among sites. Extensive simulations show that (1) if the proportion of invariable sites is negligible, i.e., theta = 0, the gamma parameter alpha can be satisfactorily estimated, even with three sequences; (2) if the proportion of invariable sites is not negligible, the heterogeneity rho can still be suitably estimated with four or more sequences; and (3) the distances estimated by the proposed method are almost unbiased and are robust against violation of the assumption of the invariant + gamma distribution.

Computer Simulation↗

PubMed1994

Recognition of trophoblasts by gamma delta T cells.

The juxtaposition of maternal and fetal tissues in the hemochorial placenta has led to speculation that maternal recognition of fetal Ags present on trophoblasts might play an important role in reproductive biology. We report here for the first time such recognition of trophoblasts by T lymphocyte hybridomas representative of certain cells present in the maternal decidua. Trophoblast recognition is TCR dependent and is mediated by members of the V gamma 1+ subset of gamma delta T lymphocytes, a population that we previously have shown to be associated with heat shock protein-60 reactivity. Recognition occurred in experiments in which trophoblast clones or freshly prepared trophoblasts were used and requires cell-cell interaction. Although the maternal-fetal immune relationship typically has been cast in terms of an allograft, the T cell recognition of trophoblasts as described herein is not MHC-restricted, inasmuch as freshly prepared trophoblasts from beta 2-microglobulin-deficient mice were found to be stimulatory. Furthermore, the trophoblast ligand that mediates this recognition is probably a conserved mammalian molecule, because a human trophoblast cell line is also stimulatory. Our findings suggest a novel form of T cell recognition, and may provide an enhanced understanding of the maternal-fetal immune relationship.

Animals↗

PubMed1994

Immune protection and control of inflammatory tissue necrosis by gamma delta T cells.

Host defenses against experimental listeriosis in mice involve neutrophils, macrophages, NK cells, and alpha beta T cells. Recently gamma delta T cells have also been implicated in antilisterial resistance. However, their specific role has remained unclear. Here we show that efficient resistance to infection by this bacterium depends on the functions of both alpha beta and gamma delta T cells in both primary and secondary responses. We also present evidence that these functions are complementary. In the livers of alpha beta T cell-depleted mice, bacteria grow to large numbers within hepatocytes but are infrequently found extracellularly. Granulomatous lesions are more frequent and somewhat larger than in normal controls, but remain focal. Neutrophils are absent from liver lesions in these mice. In contrast, the livers of gamma delta T cell-depleted mice contain many extracellular bacteria, but do not show hepatocytes containing large numbers of Listeria. Liver lesions in gamma delta T cell-depleted mice are far more extensive than in normal controls or in alpha beta T cell-depleted mice, and contain large numbers of neutrophils. Particularly in secondary listeriosis, gamma delta T cell-depleted mice show vast coalescent areas of necrotic liver parenchyma within 48 h after infection. Because the bacterial numbers in gamma delta T cell-depleted mice remain lower than in alpha beta T cell-depleted mice, increased mortality in the former may be in part caused by liver failure. We conclude that gamma delta T cells are required to control inflammatory reactivity and to prevent excessive liver damage during the immune response to Listeria monocytogenes.

Animals↗

PubMed1994

Allelic differences in TCR gamma-chains alter gamma delta T cell antigen reactivity.

Mouse gamma delta T cell hybridomas from various strains that express a TCR-V gamma 1/V delta 6 respond weakly to an autologous Ag and more strongly to a short segment of the mycobacterial heat shock protein-60 (HSP-60). However, V gamma 1/V delta 6 hybridomas derived from AKR mice show greatly reduced or absent responses to these stimuli. To determine whether the lack of response in these AKR hybridomas is caused by polymorphisms found in the expressed AKR gamma and TCR-delta genes or, instead, stems from other genes in AKR, we crossed an AKR mouse with a responder mouse, C57BL/10 (B10), and prepared hybridomas from F1 progeny. Expression of an AKR V gamma 1-J gamma 4-C gamma 4 gene correlated with nonresponsiveness, whereas expression of a B10 V gamma 1-J gamma 4-C gamma 4 gene in most hybridomas ensured responses to both self Ag and the HSP-60 peptide. An allelic difference in the expressed V gamma 6 gene was irrelevant to these responses. Moreover, transfection of a functional B10 V gamma 1-J gamma 4-C gamma 4 gene into an F1 hybridoma variant that had lost the AKR version of this gene restored responses. The allelic gamma gene products differ at nine amino acids in the V region, and three amino acids in the C region. In addition, the AKR C gamma 4 region contains a 16-amino acid insertion. We propose that amino acid differences among those encoded by the AKR V gamma 1-J gamma 4-C gamma 4 gene are responsible for the lack of response, and reduce the ability of the TCR-gamma delta to bind the relevant Ag.

Alleles↗

PubMed1994

Structural requirements for peptides that stimulate a subset of gamma delta T cells.

Hybridomas representing the V gamma 1-positive subset of murine gamma delta T cells secrete lymphokines in response to synthetic peptides representing a short segment of the mycobacterial 60-kDa heat shock protein (HSP-60). Here we show the TCR dependency of this response by transfection of productively rearranged TCR genes derived from an HSP-60 reactive gamma delta T cell hybridoma. We also have defined structural requirements for the stimulatory peptide. The smallest HSP-60 peptide capable of stimulating these hybridomas is seven amino acids long, representing positions 181-187, and having the sequence FGLQLEL. Amino acid-substituted derivatives of this peptide, and another containing the same core, p180-190, revealed amino acids essential for stimulatory activity. Phenylalanine in position 181 and leucine in position 183 seem to be required for stimulation of all HSP-60 reactive cells, whereas others are only required by some. Clonal differences in the responses to these peptides provide indirect evidence for cognate TCR-peptide interactions. The smallest stimulatory peptide, p181-187, represents an area not well conserved among HSP-60 molecules of other species, and stimulates a mycobacteria-specific response unlike the earlier observed cross-reactive responses of the same hybridomas with longer HSP-60 peptides derived from mycobacteria and other species (our manuscript in preparation). We propose that the TCR-dependent multiclonal gamma delta T cell response to HSP-60 peptides and derivatives, which in some ways resembles superantigen responses and in other ways resembles responses to conventional Ag, may be a separate, third type of Ag response by T cells.

Amino Acid Sequence↗

PubMed1994

A phylogenetic estimator of effective population size or mutation rate.

A new estimator of the essential parameter theta = 4Ne mu from DNA polymorphism data is developed under the neutral Wright-Fisher model without recombination and population subdivision, where Ne is the effective population size and mu is the mutation rate per locus per generation. The new estimator has a variance only slightly larger than the minimum variance of all possible unbiased estimators of the parameter and is substantially smaller than that of any existing estimator. The high efficiency of the new estimator is achieved by making full use of phylogenetic information in a sample of DNA sequences from a population. An example of estimating theta by the new method is presented using the mitochondrial sequences from an American Indian population.

DNA, Mitochondrial↗

PubMed1994

Estimating effective population size or mutation rate using the frequencies of mutations of various classes in a sample of DNA sequences.

Mutations resulting in segregating sites of a sample of DNA sequences can be classified by size and type and the frequencies of mutations of different sizes and types can be inferred from the sample. A framework for estimating the essential parameter theta = 4Nu utilizing the frequencies of mutations of various sizes and types is developed in this paper, where N is the effective size of a population and mu is mutation rate per sequence per generation. The framework is a combination of coalescent theory, general linear model and Monte-Carlo integration, which leads to two new estimators theta xi and theta eta as well as a general Watterson's estimator theta K and a general Tajima's estimator theta tau. The greatest strength of the framework is that it can be used under a variety of population models. The properties of the framework and the four estimators theta K, theta tau, theta xi and theta eta are investigated under three important population models: the neutral Wright-Fisher model, the neutral model with recombination and the neutral Wright's finite-islands model. Under all these models, it is shown that theta xi is the best estimator among the four even when recombination rate or migration rate has to be estimated. Under the neutral Wright-Fisher model, it is shown that the new estimator theta xi has a variance close to a lower bound of variances of all unbiased estimators of theta which suggests that theta xi is a very efficient estimator.

Base Sequence↗

PubMed1994

The infectivity of gametocytes of Plasmodium falciparum from patients treated with artemisinin.

Twenty-seven patients with gametocytes of Plasmodium falciparum (PF) were divided into groups A, B, and C. A daily dose of 1200 mg artemisinin was given for 5 days to group A, a state dose of 750 mg of mefloquine to group B and a single dose of 750 mg mefloquine combined with 45 mg primaquine to group C. After treatment, the gametocyte count was taken daily, and infectivity of the gametocytes to Anopheles dirus via membrane feeding was also studied. Results showed that in group A, the density of gametocyte and infectivity were significantly reduced on days 4, 7, 14 and 21 after treatment; In group B, the gametocytes were significantly reduced on days 7, 14 and 21 and infectivity was significantly cut down on days 14 and 21 after medication. In group C, gametocytes disappeared in 5 out of 9 patients with failure of infecting mosquitoes in all 9 patients on day 4 after treatment. These indicate that artemisinin can effectively influence the infectivity of gametocytes of PF. Artemisinin is much better in blocking the transmission of PF malaria than mefloquine.

Animals↗

PubMed1993

Evidence that murine V gamma 5 and V gamma 6 gamma delta-TCR+ lymphocytes are derived from a common distinct lineage.

Murine V gamma 5 and V gamma 6+ T lymphocytes develop sequentially in the thymus during fetal and newborn life, giving rise to intraepithelial lymphocytes of the epidermis and female reproductive tract. In analyzing a panel of gamma delta T cell hybridomas derived from various tissues, we found that all V gamma 6+ cells tested (n = 25) expressed V gamma 5-C gamma 1 mRNA, whereas none of a panel of V gamma 6- cells analyzed (n = 33) expressed this mRNA. V gamma 6 mRNA was rare in V gamma 5+ cells (1 of 9), and absent in all other gamma delta T cells (n = 10). These findings suggest that most, if not all, V gamma 6-TCR+ lymphocytes arise from precursor cells that have previously rearranged the V gamma 5 gene, and indicate that V gamma 5 and V gamma 6+ lymphocytes belong to a common, distinct lineage that does not give rise to other gamma delta T cells.

Animals↗

PubMed1993

In vivo response of murine gamma delta T cells to a heat shock protein-derived peptide.

Recent results suggested that a large subset of heat shock protein HSP-60 reactive peripheral lymphoid gamma delta T cells preexists in normal adult mice, all members of which respond to a single segment of this common HSP. However, the experimental evidence supporting this idea involved in vitro peptide responses of gamma delta T-cell hybridomas generated from unprimed spleen cells. Here, we report an attempt to elicit a gamma delta T-cell response in vivo by stimulation of adult C57BL/10 mice with HSP-60 or an HSP-60-derived peptide fragment comprising amino acids 180-196 of mycobacterial HSP-60. Whereas no gamma delta T-cell response was detectable in mice injected with the intact protein, stimulation with the peptide altered the reactive gamma delta T-cell population in vivo. These changes were detected among hybridomas generated with cells restimulated in vitro and included a large increase in hybridizable gamma delta T cells, a nearly maximal increase in the relative frequency of HSP-60-reactive cells, and structural changes in expressed T-cell receptors of HSP-60-reactive cells. Interestingly, we failed to elicit a detectable alpha beta T-cell response to the particular peptide stimulatory for gamma delta T cells, although at least three other HSP-60 epitopes were recognized. Our data show that normal gamma delta T cells can respond in vivo to small peptide antigens. The gamma delta T-cell response to the HSP-60-derived peptide studied here is apparently independent of antigen-specific alpha beta T-cell reactivity.

Animals↗

PubMed1993

Statistical tests of neutrality of mutations.

Mutations in the genealogy of the sequences in a random sample from a population can be classified as external and internal. External mutations are mutations that occurred in the external branches and internal mutations are mutations that occurred in the internal branches of the genealogy. Under the assumption of selective neutrality, the expected number of external mutations is equal to theta = 4Ne mu, where Ne is the effective population size and mu is the rate of mutation per gene per generation. Interestingly, this expectation is independent of the sample size. The number of external mutations is likely to deviate from its neutral expectation when there is selection while the number of internal mutations is less affected by the presence of selection. Statistical properties of the numbers of external mutations and of internal mutations are studied and their relationships to two commonly used estimates of theta are derived. From these properties, several new statistical tests based on a random sample of DNA sequences from the population are developed for testing the hypothesis that all mutations at a locus are neutral.

Analysis of Variance↗

PubMed1993

Maximum likelihood estimation of population parameters.

One of the most important parameters in population genetics is theta = 4Ne mu where Ne is the effective population size and mu is the rate of mutation per gene per generation. We study two related problems, using the maximum likelihood method and the theory of coalescence. One problem is the potential improvement of accuracy in estimating the parameter theta over existing methods and the other is the estimation of parameter lambda which is the ratio of two theta's. The minimum variances of estimates of the parameter theta are derived under two idealized situations. These minimum variances serve as the lower bounds of the variances of all possible estimates of theta in practice. We then show that Watterson's estimate of theta based on the number of segregating sites is asymptotically an optimal estimate of theta. However, for a finite sample of sequences, substantial improvement over Watterson's estimate is possible when theta is large. The maximum likelihood estimate of lambda = theta 1/theta 2 is obtained and the properties of the estimate are discussed.

Biological Evolution↗

PubMed1992

Heat shock protein Hsp60-reactive gamma delta cells: a large, diversified T-lymphocyte subset with highly focused specificity.

Previously, we detected a subset of gamma delta T cells in the newborn mouse thymus that responded to the mycobacterial heat shock protein Hsp60, as well as with what seemed to be a self-antigen. All of these cells expressed V gamma 1, most often in association with V delta 6+. It was not clear, however, whether similar, mature gamma delta cells with Hsp60 reactivity are common outside of the thymus, or rather, whether they are largely eliminated during development. From the data presented here, we estimate that gamma delta cells responding to Hsp60 comprise 10-20% of normal splenic and lymph node gamma delta T cells. Such cells, derived from adult spleen, always express a V gamma 1-J gamma 4-C gamma 4 gamma chain, although not all cells with this gamma chain show Hsp60 reactivity. Many of these V gamma 1+ cells also express V delta 6-J delta 1-C delta, though fewer than in V gamma 1+ cells from the newborn thymus. Extensive diversity is evident in both the gamma and delta chain junctional amino acids of the receptors of these cells, indicating that they may largely develop in the thymus of older animals or undergo peripheral expansion. Finally, we found that all such cells responding to both a putative self-antigen and to mycobacterial Hsp60 respond to a 17-amino acid synthetic peptide representing amino acids 180-196 of the Mycobacterium leprae Hsp60 sequence. This report demonstrates that a large subset of Hsp60-reactive peripheral lymphoid gamma delta T cells preexists in normal adult mice, all members of which respond to a single segment of this common heat shock protein.

Animals↗

PubMed1992

Regulation of leukocyte binding to endothelial tissues by tumor-derived GM-CSF.

The adherence of leukocytes to endothelial cells is the first step in the migration of these cells into tumor tissues. Specific binding to the endothelial cells by leukocytes is mediated by the development and maintenance of adhesion molecules on the endothelium; however, the mechanisms of leukocyte traffic into tumors and of their interactions with neoplastic tissue are not clearly understood. The infiltration of leukocytes occurs in most spontaneous and transplanted solid tumors and we have previously reported that not only are murine mammary tumors heavily infiltrated by leukocytes but tumor-derived factors alter the development and function of leukocytes in tumor-bearing mice. We now present evidence that a tumor-derived cytokine, namely granulocyte-macrophage-colony-stimulating factor, appears to be of importance in the regulation of leukocyte binding to endothelial cells. The data suggest that tumor-derived factors may influence leukocyte trafficking within tumor tissue.

Animals↗

PubMed1992

Construction of linear invariants in phylogenetic inference.

An analytical method is presented for constructing linear invariants. All linear invariants of a k-species tree can be derived from those of (k-1)-species trees using this method. The new method is simpler than that of Cavender, which relies on numerical computations. Moreover, the new method provides a convenient tool to study the relationships between linear invariants of the same tree or of different trees. All linear invariants of trees of up to five species are derived in this study. For four species, there are 16 independent linear invariants for each of the three possible unrooted trees, 14 of which are shared by two unrooted trees and 12 of these are shared by all three unrooted trees; the last types of linear invariants can be used to construct tests on the assumptions about nucleotide substitutions. The number of linear invariants for a tree is found to increase rapidly with the number of species.

Base Sequence↗