Biomedical subjects

P Shen

Publications and source records attributed to P Shen.

At least 19 recordsLinked to original sources

PubMed2001

Origins and divergence of the Roma (gypsies).

The identification of a growing number of novel Mendelian disorders and private mutations in the Roma (Gypsies) points to their unique genetic heritage. Linguistic evidence suggests that they are of diverse Indian origins. Their social structure within Europe resembles that of the jatis of India, where the endogamous group, often defined by profession, is the primary unit. Genetic studies have reported dramatic differences in the frequencies of mutations and neutral polymorphisms in different Romani populations. However, these studies have not resolved ambiguities regarding the origins and relatedness of Romani populations. In this study, we examine the genetic structure of 14 well-defined Romani populations. Y-chromosome and mtDNA markers of different mutability were analyzed in a total of 275 individuals. Asian Y-chromosome haplogroup VI-68, defined by a mutation at the M82 locus, was present in all 14 populations and accounted for 44.8% of Romani Y chromosomes. Asian mtDNA-haplogroup M was also identified in all Romani populations and accounted for 26.5% of female lineages in the sample. Limited diversity within these two haplogroups, measured by the variation at eight short-tandem-repeat loci for the Y chromosome, and sequencing of the HVS1 for the mtDNA are consistent with a small group of founders splitting from a single ethnic population in the Indian subcontinent. Principal-components analysis and analysis of molecular variance indicate that genetic structure in extant endogamous Romani populations has been shaped by genetic drift and differential admixture and correlates with the migrational history of the Roma in Europe. By contrast, social organization and professional group divisions appear to be the product of a more recent restitution of the caste system of India.

DNA, Mitochondrial↗

PubMed2001

Comparison of soluble and immobilized acetate for removing Pb from contaminated soil.

Five lead (Pb) contaminated soils were used in a laboratory and modeling study to examine the effects of soluble and immobilized acetate on Pb removal from a contaminated soil as a function of pH. Soluble acetate was added as sodium acetate; immobilized acetate was added in the form of a cation exchange resin. For comparative purposes, Pb adsorption with no acetate also was measured as a function of pH. A surface complexation modeling framework was used to interpret experimental data. Experimental results showed the cation exchange resin was much more effective than soluble acetate in removing Pb from soils due to a strong affinity of the resin for Pb. In addition, concentrations of soluble Pb in resin/soil slurry were very low, minimizing the pollution threat if discharged. As deduced from modeling studies, soluble acetate performed poorly compared to the resin, in part, due to adsorption of the soluble PbAc(+) complex. The effectiveness of both soluble and immobilized acetate was diminished below pH 4 as a result of competition by H(+) for acetate. Modeling results based on resin affinity for Pb compare well with experimental data for resin/soil mixtures, suggesting that Pb partitioning in resin/soil mixtures may be predicted reasonably well if soil/Pb and resin/Pb partitioning are known. Thus, the modeling approach may be used as a screening tool to determine the performance of alternative resins.

Acetates↗

PubMed2001

Global analysis of ATM polymorphism reveals significant functional constraint.

ATM, the gene that is mutated in ataxia-telangiectasia, is associated with cerebellar degeneration, abnormal proliferation of small blood vessels, and cancer. These clinically important manifestations have stimulated interest in defining the sequence variation in the ATM gene. Therefore, we undertook a comprehensive survey of sequence variation in ATM in diverse human populations. The protein-encoding exons of the gene (9,168 bp) and the adjacent intron and untranslated sequences (14,661 bp) were analyzed in 93 individuals from seven major human populations. In addition, the coding sequence was analyzed in one chimpanzee, one gorilla, one orangutan, and one Old World monkey. In human ATM, 88 variant sites were discovered by denaturing high-performance liquid chromatography, which is 96%-100% sensitive for detection of DNA sequence variation. ATM was compared to 14 other autosomal genes for nucleotide diversity. The noncoding regions of ATM had diversity values comparable to other genes, but the coding regions had very low diversity, especially in the last 29% of the protein sequence. A test of the neutral evolution hypothesis, through use of the Hudson/Kreitman/Aguadé statistic, revealed that this region of the human ATM gene was significantly constrained relative to that of the orangutan, the Old World monkey, and the mouse, but not relative to that of the chimpanzee or the gorilla. ATM displayed extensive linkage disequilibrium, consistent with suppression of meiotic recombination at this locus. Seven haplotypes were defined. Two haplotypes accounted for 82% of all chromosomes analyzed in all major populations; two others carrying the same D126E missense polymorphism accounted for 33% of chromosomes in Africa but were never observed outside of Africa. The high frequency of this polymorphism may be due either to a population expansion within Africa or to selective pressure.

Africa↗

PubMed2001

Lymphatic mapping improves staging during laparoscopic colectomy for cancer.

BACKGROUND: Recently, lymphatic mapping (LM) of the sentinel lymph node (SN) has been coupled with ultrastaging methods to diagnose nodal micrometastases from colorectal cancer (CRC). We have developed a technique for LM at the time of laparoscopic colon resection (LCR). METHODS: Between August 1996 and February 2000, 11 patients with small early-stage CRC underwent laparoscopic LM and LCR. The primary tumor/polyp site was visualized through a colonoscope and either tattooed preoperatively with a carbon dye (India ink), or stained intraoperatively by peritumoral injection of isosulfan blue dye. Immediately after intraoperative injection of blue dye, efferent lymphatic channels were visualized through the laparoscope and followed to the SN. Each blue-stained SN was marked with a suture or clip. RESULTS: In all 11 cases, laparoscopic LM identified between one and three SN draining the primary tumor. LM added ~15-20 min to the operating time. The SN correctly reflected the nodal status of the entire specimen in all cases. In the one node-positive case, micrometastases were found only in an SN and only after cytokeratin immunohistochemistry (CK-IHC). In four cases, LM demonstrated unexpected primary lymphatic drainage that prompted an increase in the margins of resection. CONCLUSIONS: LM during laparoscopic colectomy for CRC may be useful to mark the primary tumor site and to demonstrate lymphatic drainage that can alter the margins of resection. Focused examination of SN identifies occult micrometastases that up-stage CRC.

Aged↗

PubMed2001

Effects of cis arrangement of chromatin insulators on enhancer-blocking activity.

Chromatin boundary elements or insulators are believed to regulate gene activity in complex genetic loci by organizing specialized chromatin structures. Here, we report that the enhancer-blocking activity of the Drosophila suHw insulator is sensitive to insulator copy number and position. Two tandem copies of suHw were ineffective in blocking various enhancers from a downstream promoter. Moreover, an enhancer was blocked more effectively from a promoter by two flanking suHw insulators than by a single intervening one. Thus, insulators may modulate enhancer-promoter interactions by interacting with each other and facilitating the formation of chromatin loop domains.

Animals↗

PubMed2001

The Werner syndrome gene and global sequence variation.

We have identified a dense set of markers useful in association studies involving the Werner syndrome (WRN) gene. The homozygotic disruption of the WRN gene is the cause of Werner disease. In addition, this gene is likely to be involved in many complex traits, such as aging, or at least some of the traits and diseases related to age. To investigate the genetic variation associated with the WRN gene, a sample of 93 individuals representing all the continents was analyzed by denaturing high-performance liquid chromatography. A systematic survey of all 35 exons and flanking regions identified 58 single-nucleotide polymorphisms, 15 of which fall in the coding region and cause 11 missense mutations. The resulting global nucleotide diversity was 5.226 x 10(-4), with a slight difference between coding and noncoding regions.

Alleles↗

PubMed2001

Drosophila neuropeptide F mediates integration of chemosensory stimulation and conditioning of the nervous system by food.

The conserved neuropeptide Y (NPY) signaling pathway has been strongly implicated in the stimulation of food uptake in vertebrates as well as in the regulation of food conditioned foraging behaviors of Caenorhabditis elegans. Using in situ RNA hybridization and immunocytochemistry, we report the neuronal network of Drosophila neuropeptide F (dNPF), a human NPY homologue, in the larval central nervous system and its food-dependent modifications. We provide indications that gustatory stimulation by sugar, but not its ingestion or metabolism, is sufficient to trigger long-term, dose-dependent alterations of the dNPF neuronal circuit through both dnpf activation and increased synaptic transmission. Our results strongly suggest that the dNPF neuronal circuit is an integral part of the sensory system that mediates food signaling, providing the neural basis for understanding how invertebrate NPY regulates food response.

Animals↗

PubMed2001

Dermal versus intraparenchymal lymphoscintigraphy of the breast.

BACKGROUND AND OBJECTIVE: Dermal and intraparenchymal (IP) injections of radiocolloid have been used for lymphoscintigraphic identification of the sentinel node (SN) in breast cancer. Because of our institute's extensive experience with dermal and IP lymphoscintigraphy for melanoma and breast cancer, we compared patterns of lymphatic migration after both types of injections to identify any differences in drainage patterns or SN identification. METHODS: Lymphoscintigrams (n = 31) after dermal injections in 30 patients with primary cutaneous melanoma on the breast were compared with lymphoscintigrams after IP injections in 97 consecutive patients with breast cancer. In each case, 400 microCi of filtered 99mTc-sulfur colloid was injected in four quadrants around the tumor or in the biopsy cavity. All lymphoscintigrams were reviewed for patterns of migration and SN location. RESULTS: Five of 31 (16%) dermal injections demonstrated bilateral axillary migration (n = 3) or a suprasternal SN (n = 2), neither of which was found with IP injections. Conversely, 3 of 97 (3%) IP injections demonstrated direct supraclavicular (n = 2) or costal margin (n = 1) nodes (P = .006), neither of which was found with dermal injections. Low axillary SNs were noted after 26 (84%) dermal and 93 (96%) IP injections (P = .037). The incidence of extra-axillary SNs was 26% (8 of 31) in the dermal group but only 5% (5 of 97) in the IP group (P = .0027). CONCLUSION: There is a significant difference in lymphatic drainage and SN localization between dermal and IP lymphoscintigraphy. This finding has implications for injection techniques when lymphatic mapping of the SN is undertaken to stage a breast carcinoma.

Axilla↗

PubMed2001

A convenient and rapid method for genetic transformation of E. coli with plasmids.

A convenient and rapid method for the genetic transformation of Escherichia coli with plasmids is proposed. By mixing the recipient cells and plasmid DNA and spreading them directly on selective medium plates containing Ca2+, the so-called 'plate transformation' could achieve almost the same transformation efficiency as the classical transformation method with calcium. The whole protocol takes only about 2 min, its simplicity compared favorably, not only to the usual protocol, but also to all other documented modifications.

Calcium Chloride↗

PubMed2001

The phylogeography of Y chromosome binary haplotypes and the origins of modern human populations.

Although molecular genetic evidence continues to accumulate that is consistent with a recent common African ancestry of modern humans, its ability to illuminate regional histories remains incomplete. A set of unique event polymorphisms associated with the non-recombining portion of the Y-chromosome (NRY) addresses this issue by providing evidence concerning successful migrations originating from Africa, which can be interpreted as subsequent colonizations, differentiations and migrations overlaid upon previous population ranges. A total of 205 markers identified by denaturing high performance liquid chromatography (DHPLC), together with 13 taken from the literature, were used to construct a parsimonious genealogy. Ancestral allelic states were deduced from orthologous great ape sequences. A total of 131 unique haplotypes were defined which trace the microevolutionary trajectory of global modern human genetic diversification. The genealogy provides a detailed phylogeographic portrait of contemporary global population structure that is emblematic of human origins, divergence and population history that is consistent with climatic, paleoanthropological and other genetic knowledge.

Africa↗

PubMed2001

Antibody-antigen interactions measured by surface plasmon resonance: global fitting of numerical integration algorithms.

The interactions between adenylate kinase (AK) and a monoclonal antibody against AK (McAb3D3) were examined by means of optical biosensor technology, and the sensograms were fitted to four models using numerical integration algorithms. The interaction of a solution of McAb3D3 with immobilized AK follows a double exponential function and the data fitted well to an inhomogeneous ligand model. The interaction of a solution AK with immobilized McAb3D3 follows a single exponential function and the data fitted well to a pseudo-first order reaction model. The true association constants of AK binding to McAb3D3 in solution were obtained from competition BIAcore measurements. The difference in results obtained with solid-phase BIAcore and competition BIAcore may be due to rebinding of the dissociated analyte to the immobilized surface. The results obtained with BIAcore are compared to those obtained by ELISA methods. We suggest that the best method for analysis of BIAcore data is direct, global fitting of sensorgrams to numerical integration algorithms corresponding to the different possible models for binding.

Adenylate Kinase↗

PubMed2001

Remineralization of enamel subsurface lesions by sugar-free chewing gum containing casein phosphopeptide-amorphous calcium phosphate.

Casein phosphopeptide-amorphous calcium phosphate nanocomplexes (CPP-ACP) exhibit anticariogenic potential in laboratory, animal, and human in situ experiments. The aim of this study was to determine the ability of CPP-ACP in sugar-free chewing gum to remineralize enamel subsurface lesions in a human in situ model. Thirty subjects in randomized, cross-over, double-blind studies wore removable palatal appliances with six human-enamel half-slabs inset containing sub-surface demineralized lesions. The appliances were inserted immediately before gum-chewing for 20 min and then retained for another 20 min. This was performed four times per day for 14 days. At the completion of each treatment, the enamel half-slabs were paired with their respective demineralized control half-slabs, embedded, sectioned, and subjected to microradiography and densitometric image analysis, for measurement of the level of remineralization. The addition of CPP-ACP to either sorbitol- or xylitol-based gum resulted in a dose-related increase in enamel remineralization, with 0.19, 10.0, 18.8, and 56.4 mg of CPP-ACP producing an increase in enamel remineralization of 9, 63, 102, and 152%, respectively, relative to the control gum, independent of gum weight or type.

Adult↗

PubMed2001

Genomic context modulates insulator activity through promoter competition.

Chromatin insulators regulate gene expression by preventing inappropriate enhancer-promoter interactions. Our previous study showed that insulators do not merely function as rigid blockers, rather their activities are quantitative and selective. We have investigated the factors and mechanisms that determine the effectiveness of the suHw insulator in transgenic Drosophila. We show that the suHw-mediated blockage of the AE1 enhancer from a downstream promoter depends on the ability of the promoter to compete for AE1. Promoters that are highly competitive for the enhancer are blocked less effectively. Moreover, blockage of AE1 from its cognate ftz promoter can range from virtually complete to non-detectable, depending on the property of the neighboring upstream promoter. A highly competitive neighboring promoter enhances the suHw-mediated blockage, whereas a less competitive promoter reduces the insulator effectiveness. The influence on insulator effectiveness by both the interacting and the neighboring competing promoters correlates with their ability to compete for the enhancer, which was previously shown to depend on core promoter sequences. Our findings suggest a mechanism at the level of gene organization that modulates insulator effectiveness through promoter competition. The dependence of insulator function on its cis contexts may provide it with more regulatory flexibility while imposing organizational restraints on eukaryotic gene complexes.

Animals↗

PubMed2000

Population genetic implications from sequence variation in four Y chromosome genes.

Some insight into human evolution has been gained from the sequencing of four Y chromosome genes. Primary genomic sequencing determined gene SMCY to be composed of 27 exons that comprise 4,620 bp of coding sequence. The unfinished sequencing of the 5' portion of gene UTY1 was completed by primer walking, and a total of 20 exons were found. By using denaturing HPLC, these two genes, as well as DBY and DFFRY, were screened for polymorphic sites in 53-72 representatives of the five continents. A total of 98 variants were found, yielding nucleotide diversity estimates of 2.45 x 10(-5), 5. 07 x 10(-5), and 8.54 x 10(-5) for the coding regions of SMCY, DFFRY, and UTY1, respectively, with no variant having been observed in DBY. In agreement with most autosomal genes, diversity estimates for the noncoding regions were about 2- to 3-fold higher and ranged from 9. 16 x 10(-5) to 14.2 x 10(-5) for the four genes. Analysis of the frequencies of derived alleles for all four genes showed that they more closely fit the expectation of a Luria-Delbrück distribution than a distribution expected under a constant population size model, providing evidence for exponential population growth. Pairwise nucleotide mismatch distributions date the occurrence of population expansion to approximately 28,000 years ago. This estimate is in accord with the spread of Aurignacian technology and the disappearance of the Neanderthals.

Aged↗

PubMed2000

Recent common ancestry of human Y chromosomes: evidence from DNA sequence data.

We consider a data set of DNA sequence variation at three Y chromosome genes (SMCY, DBY, and DFFRY) in a worldwide sample of human Y chromosomes. Between 53 and 70 chromosomes were fully screened for sequence variation at each locus by using the method of denaturing high-performance liquid chromatography. The sum of the lengths of the three genes is 64,120 bp. We have used these data to study the ancestral genealogy of human Y chromosomes. In particular, we focused on estimating the expected time to the most recent common ancestor and the expected ages of certain mutations with interesting geographic distributions. Although the geographic structure of the inferred haplotype tree is reminiscent of that obtained for other loci (the root is in Africa, and most of the oldest non-African lineages are Asian), the expected time to the most recent common ancestor is remarkably short, on the order of 50,000 years. Thus, although previous studies have noted that Y chromosome variation shows extreme geographic structure, we estimate that the spread of Y chromosomes out of Africa is much more recent than previously was thought. We also show that our data indicate substantial population growth in the effective number of human Y chromosomes.

Biological Evolution↗

PubMed2000

Nanometer-size alpha-PbO(2)-type TiO(2) in garnet: A thermobarometer for ultrahigh-pressure metamorphism

A high-pressure phase of titanium dioxide (TiO(2)) with an alpha-PbO(2)-type structure has been identified in garnet of diamondiferous quartzofeldspathic rocks from the Saxonian Erzgebirge, Germany. Analytical electron microscopy indicates that this alpha-PbO(2)-type TiO(2) occurred as an epitaxial nanometer-thick slab between twinned rutile bicrystals. Given a V-shaped curve for the equilibrium phase boundary of alpha-PbO(2)-type TiO(2) to rutile, the stabilization pressure of alpha-PbO(2)-type TiO(2) should be 4 to 5 gigapascals at 900 degrees to 1000 degrees C. This suggests a burial of continental crustal rocks to depths of at least 130 kilometers. The alpha-PbO(2)-type TiO(2) may be a useful pressure and temperature indicator in the diamond stability field.

Journal Article↗

PubMed2000

Cloning and overexpression of a tyrosinase gene mel from Pseudomonas maltophila.

The tyrosinase gene (mel), which is responsible for melanin formation, was isolated by shotgun cloning of SalI fragments of Pseudomonas maltophila DNA. A 0.7-kb SalI fragment in the recombinant plasmid pWSY8 imparted the ability to synthesize melanin to an Escherichia coli host HB101. The nucleotide sequence of this DNA fragment revealed an open reading frame of 504 bp, encoding a protein of 169 amino acids. The fragment containing the mel gene was then cloned into an expression plasmid pPAS1 under the control of a promoter isolated from the host, P. maltophilia AT18. This strain increased the melanin production by 70.6% compared with the strain HB101/pWSY8, in which the cloned mel gene was under the control of the lac promoter from the vector pUC18.

Amino Acid Sequence↗

PubMed2000

Is adjuvant radiotherapy necessary after positive lymph node dissection in head and neck melanomas?

INTRODUCTION: Postoperative radiotherapy (PR) has been recommended in patients with advanced head and neck melanomas to improve regional control. This study examined the incidence of cervical recurrence among patients who did not receive PR after surgical management of node-positive head and neck melanomas. METHODS: A computerized search of a database listing more than 10,000 patients with melanoma prospectively acquired between 1971 and 1998 identified 217 patients with pathologically positive nodes who had undergone regional lymph node dissection (RLND). Of these patients, 21 had received PR and 196 had not. RESULTS: Median follow-up after RLND was 20 months for nonsurvivors and 32 months for survivors. The overall incidence of cervical recurrence was 14% (27/196). The 5-year cervical recurrence-free survival rate was 83%. Five-year cervical recurrence-free survival rates were 69% vs. 87% for patients with vs. without extranodal disease (P = .004), 96% vs. 81% for patients with nonpalpable vs. palpable nodes (P = .0761), and 82% vs. 91% for patients with one to three positive nodes vs. more than three positive nodes (P = .256). Multivariate analysis, which included the timing of nodal disease presentation and the effect of systemic adjuvant therapy, identified extranodal disease as the only independent predictor of cervical recurrence (P = .034). Cervical recurrence was significantly related to the subsequent occurrence of distant relapse. CONCLUSIONS: The low incidence of cervical recurrence after RLND in patients with node-positive head and neck melanomas does not justify the routine use of PR. The only subset of patients who may benefit from PR are those with extranodal disease.

Adolescent↗