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91.
There is considerable interest in identifying and characterizing block-like patterns of linkage disequilibrium (LD; haplotype blocks) in the human genome as these may facilitate the identification of complex disease genes via genome-wide association studies. Although recombination hot-spots have been suggested as the primary mechanism to explain the block-like pattern of LD, other forces, such as genetic drift, may also be important. To this end, we have studied the effect of various recombination models on patterns of LD by using extensive simulations. As expected, haplotype blocks were observed under a model allowing recombination hot-spots. However, we also observed similar block-like patterns in the models where recombination crossovers are randomly and uniformly distributed, and we demonstrate that these blocks are generated by genetic drift. We caution that genetic drift may be an alternative mechanism (in addition to recombination hot-spots) that can lead to block-like patterns of LD. Our findings highlight the necessity of characterizing haplotype blocks in world-wide populations. 相似文献
92.
Chakraborty M Abrams SI Camphausen K Liu K Scott T Coleman CN Hodge JW 《Journal of immunology (Baltimore, Md. : 1950)》2003,170(12):6338-6347
CD8(+) CTL play important roles against malignancy in both active and passive immunotherapy. Nonetheless, the success of antitumor CTL responses may be improved by additional therapeutic modalities. Radiotherapy, which has a long-standing use in treating neoplastic disease, has been found to induce unique biologic alterations in cancer cells affecting Fas gene expression, which, consequently, may influence the overall lytic efficiency of CTL. Here, in a mouse adenocarcinoma cell model, we examined whether exposure of these tumor cells to sublethal doses of irradiation 1) enhances Fas expression, leading to more efficient CTL killing via Fas-dependent mechanisms in vitro; and 2) improves antitumor activity in vivo by adoptive transfer of these Ag-specific CTL. Treatment of carcinoembryonic Ag-expressing MC38 adenocarcinoma cells with irradiation (20 Gy) in vitro enhanced Fas expression at molecular, phenotypic, and functional levels. Furthermore, irradiation sensitized these targets to Ag-specific CTL killing via the Fas/Fas ligand pathway. We examined the effect of localized irradiation of s.c. growing tumors on the efficiency of CTL adoptive immunotherapy. Irradiation caused up-regulation of Fas by these tumor cells in situ, based on immunohistochemistry. Moreover, localized irradiation of the tumor significantly potentiated tumor rejection by these carcinoembryonic Ag-specific CTL. Overall, these results showed for the first time that 1) regulation of the Fas pathway in tumor cells by irradiation plays an important role in their sensitization to Ag-specific CTL; and 2) a combination regimen of tumor-targeted irradiation and CTL promotes more effective antitumor responses in vivo, which may have implications for the combination of immunotherapy and radiation therapy. 相似文献
93.
Liu J Chakraborty C Graham CH Barbin YP Dixon SJ Lala PK 《Experimental cell research》2003,286(1):138-151
The serine protease urokinase-type plasminogen activator (uPA) promotes matrix degradation by many cell types, including the invasive extravillous trophoblast (EVT) of the human placenta. The noncatalytic amino-terminal end of uPA binds to uPA receptors (uPARs) expressed by these cells. A highly polarized expression of uPAR-bound uPA at the migration front of EVT cells in situ suggests a functional role of uPA:uPAR interaction in EVT cell migration. The present study examined whether uPA stimulates EVT cell migration, independent of proteolytic function, and investigated some of the signaling pathways involved. Using in vitro-propagated EVT cells in Transwell migration assays, both uPA and its noncatalytic amino-terminal fragment (ATF) were shown to stimulate migration through multiporous polycarbonate (pore size 8 microm) membranes. A uPAR-blocking antibody inhibited basal and ATF-stimulated migration. Migration was found to be stimulated by hypoxic conditions, which upregulates uPAR expression; this stimulation was abrogated with the uPAR-blocking antibody, indicating the role of endogenous uPA in EVT cell migration. Spectrofluorometric measurement of cytosolic calcium in cells treated with uPA and ATF demonstrated a rapid rise in [Ca2+](i), which was prevented by pretreatment of cells with thapsigargin, indicating a release from intracellular stores. Both basal and ATF-mediated migratory responses were suppressed in the presence of selective pharmacological inhibitors LY294002, U73122, and U0126, implicating the respective roles of phosphatidinylinositol 3-kinase (PI 3-K), phospholipase C (PLC), and MEK1/2 in basal and ATF-stimulated migratory capacity. Taken together, these results demonstrate that uPA:uPAR interaction stimulates EVT cell migration, independent of uPA enzymatic activity, using the mitogen-activated protein kinase pathway and calcium signaling events including the participation of PI 3-K and PLC. These findings are relevant to clinical conditions of aberrant trophoblast migration, including spontaneous abortion, preeclampsia, and choriocarcinoma. 相似文献
94.
AIMS: The influence of carbon-nitrogen and nitrogen-phosphorus ratios of input fertilizers, and that of pond water, on the growth of heterotrophic and phosphate-solubilizing bacteria of water and sediment, was examined in relation to fertilizer mineralization indices using different modes of fertilization through inorganic and organic sources. METHODS AND RESULTS: The first experiment used carbon-nitrogen-phosphorus ratios varying from 12 : 2 : 1 to 151 : 6 : 1, applied at the rate of 0.043 g l(-1) week(-1), whereas in the second ratios varied from 25.6 : 6.2 : 1 to 150 : 12 : 1 applied once at the rate of 3.33 g l(-1). Different fertilizers (cattle dung, poultry droppings, urea, single superphosphate and starch) were mixed in different proportions to achieve the desired carbon-nitrogen-phosphorus ratio. The heterotrophic and phosphate-solubilizing populations were more responsive to an early manuring phase than later, implying that pond fertilization was microbiologically more dynamic in the earlier phase. The carbon-nitrogen and nitrogen-phosphorus ratios of 11.8 (88.6 : 7.5) and 7.5 (7.5 : 1), respectively, of input fertilizers favoured growth of both heterotrophic and phosphate-solubilizing bacterial populations much better than the other ratios tested. Likewise, water carbon-nitrogen and nitrogen-phosphorus ratios of 11.9 and 3.34 induced bacterial growth. The carbon-nitrogen ratios of 12.63 (101 : 8) (input fertilizer)-4.54 (water), and nitrogen-phosphorus ratios of 8 (8 : 1) (input fertilizer)-2.93 (water), gave gross primary productivity values higher than the remaining ratios, exhibiting overall curvilinear relationships. The values of gross primary productivity were the direct function of values of fertilizer mineralization indices for carbon, nitrogen and phosphorus. CONCLUSION: It is concluded that the mixed fertilizer (carbon-nitrogen-phosphorus-88.6 : 7.5 : 1) comprising cattle dung (95%), poultry droppings (2.5%), urea (2%) and single superphosphate (0.5%), applied at the rate of 23,000 kg ha(-1) year(-1), was a suitable cost-effective fertilization option for aquaculture practices. SIGNIFICANCE AND IMPACT OF THE STUDY: As chemical fertilizers are expensive and cause some adverse effects on the soil structure, composition, microflora and other characteristics of the pond, mixed combinations of inorganic and organics with narrow range of carbon-nitrogen-phosphorus ratio can be suitable and cost-effective fertilization tools in aquaculture practices, which is to be linked with the microbial activities of the pond. 相似文献
95.
Genetic diversity and population history of the red panda (Ailurus fulgens) as inferred from mitochondrial DNA sequence variations 总被引:9,自引:0,他引:9
The red panda (Ailurus fulgens) is one of the flagship species in worldwide conservation and is of special interest in evolutionary studies due to its taxonomic uniqueness. We sequenced a 236-bp fragment of the mitochondrial D-loop region in a sample of 53 red pandas from two populations in southwestern China. Seventeen polymorphic sites were found, together with a total of 25 haplotypes, indicating a high level of genetic diversity in the red panda. However, no obvious genetic divergence was detected between the Sichuan and Yunnan populations. The consensus phylogenetic tree of the 25 haplotypes was starlike. The pairwise mismatch distribution fitted into a pattern of populations undergoing expansion. Furthermore, Fu's F(S) test of neutrality was significant for the total population (F(S) = -7.573), which also suggests a recent population expansion. Interestingly, the effective population size in the Sichuan population was both larger and more stable than that in the Yunnan population, implying a southward expansion from Sichuan to Yunnan. 相似文献
96.
Kenny-Moynihan MB DeRose PB Gal AA Chakraborty H Cohen C 《Analytical and quantitative cytology and histology / the International Academy of Cytology [and] American Society of Cytology》2001,23(4):313-320
OBJECTIVE: To compare nuclear DNA by flow (FCM) and image cytometry (ICM) in thymic neoplasms and to relate results to clinical outcome. STUDY DESIGN: DNA ploidy of 44 thymomas and 6 thymic carcinomas was studied by FCM and ICM of single nuclear suspensions from paraffin blocks. RESULTS: By FCM, 33 thymomas (75%) and one thymic carcinoma (17%) were diploid; 6 thymomas (14%) and 4 thymic carcinomas (67%) were aneuploid. By ICM, 36 thymomas (82%) were diploid; 7 thymomas (16%) and 6 thymic carcinomas (100%) were aneuploid. Mean follow-up in 44 cases was 46.2 months (range, 1-162). Ten patients with persistent/recurrent disease included four with thymic carcinoma, who died of the disease (two aneuploid by both techniques, two aneuploid by ICM with unsatisfactory/diploid FCM). Four had invasive thymoma and recurrence after 13-150 months (two diploid and two aneuploid by both methods), one had diploidy and noninvasive thymoma that recurred at 92 months, and one had an epithelial thymoma that recurred at 144 months (aneuploid by FCM, diploid by ICM). CONCLUSION: The results obtained in this preliminary, retrospective study show a high concordance between FCM and ICM; aneuploidy correlated with poor outcome by both methodologies. While these findings are encouraging, larger numbers of cases will be needed to define the role of FCM and ICM in predicting outcome in thymic tumors. 相似文献
97.
Active site geometry of oxalate decarboxylase from Flammulina velutipes: Role of histidine-coordinated manganese in substrate recognition 总被引:2,自引:0,他引:2 下载免费PDF全文
Chakraborty S Chakraborty N Jain D Salunke DM Datta A 《Protein science : a publication of the Protein Society》2002,11(9):2138-2147
Oxalate decarboxylase (OXDC) from the wood-rotting fungus Flammulina velutipes, which catalyzes the conversion of oxalate to formic acid and CO(2) in a single-step reaction, is a duplicated double-domain germin family enzyme. It has agricultural as well as therapeutic importance. We reported earlier the purification and molecular cloning of OXDC. Knowledge-based modeling of the enzyme reveals a beta-barrel core in each of the two domains organized in the hexameric state. A cluster of three histidines suitably juxtaposed to coordinate a divalent metal ion exists in both the domains. Involvement of the two histidine clusters in the catalytic mechanism of the enzyme, possibly through coordination of a metal cofactor, has been hypothesized because all histidine knockout mutants showed total loss of decarboxylase activity. The atomic absorption spectroscopy analysis showed that OXDC contains Mn(2+) at up to 2.5 atoms per subunit. Docking of the oxalate in the active site indicates a similar electrostatic environment around the substrate-binding site in the two domains. We suggest that the histidine coordinated manganese is critical for substrate recognition and is directly involved in the catalysis of the enzyme. 相似文献
98.
Agrawal R Chandrashekhar R Mishra AK Ramadevi J Sharma Y Aggarwal RK 《Journal of biosciences》2002,27(3):251-259
τ-Crystallin is a taxon-specific structural protein found in eye lenses. We present here the cloning and sequencing of complete
τ-crystallin cDNA from the embryonic lens ofCrocodylus palustris and establish it to be identical to the α-enolase gene from non-lenticular tissues. Quantitatively, the τ-crystallin was
found to be the least abundant crystallin of the crocodilian embryonic lenses. Crocodile τ-crystallin cDNA was isolated by
RT-PCR using primers designed from the only other reported sequence from duck and completed by 5′- and 3′-rapid amplification
of cDNA ends (RACE) using crocodile gene specific primers designed in the study. The complete τ-crystallin cDNA of crocodile
comprises 1305 bp long ORF and 92 and 409 bp long untranslated 5′- and 3′-ends respectively. Further, it was found to be identical
to its putative counterpart enzyme α-enolase, from brain, heart and gonad, suggesting both to be the product of the same gene.
The study thus provides the first report on cDNA sequence of τ-crystallin from a reptilian species and also re-confirms it
to be an example of the phenomenon of gene sharing as was demonstrated earlier in the case of peking duck. Moreover, the gene
lineage reconstruction analysis helps our understanding of the evolution of crocodilians and avian species. 相似文献
99.
Distribution of recombination crossovers and the origin of haplotype blocks: the interplay of population history,recombination, and mutation 总被引:31,自引:0,他引:31 下载免费PDF全文
Recent studies suggest that haplotypes are arranged into discrete blocklike structures throughout the human genome. Here, we present an alternative haplotype block definition that assumes no recombination within each block but allows for recombination between blocks, and we use it to study the combined effects of demographic history and various population genetic parameters on haplotype block characteristics. Through extensive coalescent simulations and analysis of published haplotype data on chromosome 21, we find that (1) the combined effects of population demographic history, recombination, and mutation dictate haplotype block characteristics and (2) haplotype blocks can arise in the absence of recombination hot spots. Finally, we provide practical guidelines for designing and interpreting studies investigating haplotype block structure. 相似文献
100.
Restoration of TGF-beta regulation of plasminogen activator inhibitor-1 in Smad3-restituted human choriocarcinoma cells 总被引:6,自引:0,他引:6
Xu G Chakraborty C Lala PK 《Biochemical and biophysical research communications》2002,294(5):1079-1086
Proliferation, migration, and invasiveness of the normal placental extravillous trophoblast (EVT) cells are negatively regulated by transforming growth factor-beta (TGF-beta), whereas malignant EVT (JAR and JEG-3 choriocarcinoma) cells are resistant to TGF-beta. These malignant cells were found to have lost the expression of Smad3. Present study examined whether Smad3 restitution in JAR cells could restore TGF-beta response. We produced a stable Smad3 cDNA-transfected clone (JAR-smad3/c) which exhibited further upregulation of Smad3 in the presence of TGF-beta1. Since anti-invasive effects of TGF-beta in the normal EVT cells were shown to be mediated in part by plasminogen activator inhibitor-1 (PAI-1) and urokinase-type plasminogen activator (uPA), we compared the expression of PAI-1 and uPA in the normal EVT, JAR, and JAR-smad3/c cells in the presence or absence of TGF-beta1. The basal levels of PAI-1 mRNA and secreted PAI-1 and uPA proteins were found to be very low in JAR and JAR-smad3/c cells, as compared to the normal EVT cells. However, TGF-beta1 upregulated PAI-1 and downregulated uPA in JAR-smad3/c cells, but not in JAR cells. Thus, resistance of choriocarcinoma cells to anti-invasive effects of TGF-beta may, at least in part, be due to loss of Smad3 expression. 相似文献