Biomedical subjects

Ying Li

Publications and source records attributed to Ying Li.

At least 289 records · Page 16Linked to original sources

PubMed2003

Effects of hydrogen peroxide upon nicotinamide nucleotide metabolism in Escherichia coli: changes in enzyme levels and nicotinamide nucleotide pools and studies of the oxidation of NAD(P)H by Fe(III).

DNA is damaged in vivo by the Fenton reaction mediated by Fe2+ and cellular reductants such as NADH, which reduce Fe3+ to Fe2+ and allow the recycling of iron. To study the response of Escherichia coli to such cycling, the activities of several enzymes involved in nicotinamide nucleotide metabolism were measured following an H2O2 challenge. NADPH-dependent peroxidase, NADH/NADP+ transhydrogenase, and glucose-6-phosphate dehydrogenase were most strongly induced, increasing 2.5-3-fold. In addition, the cellular ratios of NADPH to NADH increased 6- or 92-fold 15 min after exposure to 0.5 or 5 mm H2O2, respectively. In vitro, NADH was oxidized by Fe3+ up to 16-fold faster than NADPH, despite their identical reduction potentials. To understand this rate difference, the interactions of Fe3+ and Ga3+ with NAD(P)H were examined by 1H, 13C, and 31P NMR spectroscopy. Association with NADH occurred primarily with adenine at N7 and the amino group, but for NADPH, strong metal interactions also occurred at the 2'-phosphate group. Interaction of M3+ (Fe3+ or Ga3+) with the adenine ring would bring it into close proximity to the redox-active nicotinamide ring in the folded form of NAD(P)H, but interaction of M3+ with the 2'-phosphate group would avoid this close contact. In addition, as determined by absorbance spectroscopy, the energy of the charge-transfer species was significantly higher for the Fe3+.NADPH complex than for the Fe3+.NADH complex. We therefore suggest that upon exposure to H2O2 the NADH pool is depleted, and NADPH, which is less reactive with Fe3+, functions as the major nicotinamide nucleotide reductant.

Enzymes↗

PubMed2003

Serotonin regulates rhythmic whisking.

Many rodents explore their environment by rhythmically palpating objects with their mystacial whiskers. These rhythmic whisker movements ("whisking"; 5-9 Hz) are thought to be regulated by an unknown brainstem central pattern generator (CPG). We tested the hypothesis that serotonin (5-HT) inputs to whisking facial motoneurons (wFMNs) are part of this CPG. In response to exogenous serotonin, wFMNs recorded in vitro fire rhythmically at whisking frequencies, and selective 5-HT2 or 5-HT3 receptor antagonists suppress this rhythmic firing. In vivo, stimulation of brainstem serotonergic raphe nuclei evokes whisker movements. Unilateral infusion of selective 5-HT2 or 5-HT3 receptor antagonists suppresses ipsilateral whisking and substantially alters the frequencies and symmetry of whisker movements. These findings suggest that serotonin is both necessary and sufficient to generate rhythmic whisker movements and that serotonergic premotoneurons are part of a whisking CPG.

Animals↗

PubMed2003

Single amino acid mutations, but not common polymorphisms, decrease the activity of CYP1B1 against (-)benzo[a]pyrene-7R-trans-7,8-dihydrodiol.

Genetic differences that underlie inter-individual variation in the metabolism of common carcinogens are important potential sources of cancer susceptibility. Cytochrome P450 1B1 (CYP1B1), a central enzyme in the activation of the ubiquitous environmental carcinogen benzo[a]pyrene (B[a]P), has several genetic variants. This study investigated six rare mutations and four common polymorphisms for their effects on B[a]P metabolism. Five missense mutations associated with congenital glaucoma (Gly61Glu, Gly365Trp, Asp374Asn, Pro437Leu and Arg469Tryp) dramatically decreased the capacity of CYP1B1 to convert (-)benzo[a]pyrene-7R-trans-7,8-dihyrodiol (B[a]P-7,8-diol) to (+/-)benzo[a]pyrene-r-7,t-8-dihydrodiol-9,10-epoxides. These five mutations resulted in enzymes with 3-12% of normal activity when assayed in vitro using an Saccharomyces cerevisiae microsomal expression system. A 10 bp deletion mutation produced no detectable protein or activity. In contrast, proteins containing all possible combinations of four common single nucleotide polymorphisms (Arg48Gly, Ala199Ser, Val432Leu, Asn453Ser) had modest effects on B[a]P-7,8-diol metabolism. Michaelis-Menten analysis suggested that two alleles, Arg48, Ala119, Val432, Ser453 (RAVS) and Arg48, Ala119, Leu432, Ser453 (RALS), have KM values 2-fold lower than Arg48, Ala119, Val432, Ser453 (RAVN): 1.4+/-0.3 and 1.3+/-0.4 microM, respectively, compared with 2.8+/-0.8 microM (P<0.05). However, these differences could not be confirmed with direct measurements of rate at low substrate concentration. There were no significant differences for either of two other kinetic parameters, kcat or kcat/KM. Allele frequency analysis in three populations reveals the Ser453 variant is rare among those of Asian (<1%) and African ancestry (<4%), and more common in individuals of European ancestry (16%). Haplotypes containing the Ser453 variant were uncommon; only RALS was detectable in our small populations. The RALS allele occurred between 0.5% in Asians and 15% in Europeans. Our study demonstrates that rare, disease-associated mutations in CYP1B1 significantly decrease the enzyme's metabolism of B[a]P-7,8-diol; however, our results do not identify any major differences in this metabolism due to four common single amino acid polymorphisms.

Aryl Hydrocarbon Hydroxylases↗

PubMed2003

DNA helicase Srs2 disrupts the Rad51 presynaptic filament.

Mutations in the Saccharomyces cerevisiae gene SRS2 result in the yeast's sensitivity to genotoxic agents, failure to recover or adapt from DNA damage checkpoint-mediated cell cycle arrest, slow growth, chromosome loss, and hyper-recombination. Furthermore, double mutant strains, with mutations in DNA helicase genes SRS2 and SGS1, show low viability that can be overcome by inactivating recombination, implying that untimely recombination is the cause of growth impairment. Here we clarify the role of SRS2 in recombination modulation by purifying its encoded product and examining its interactions with the Rad51 recombinase. Srs2 has a robust ATPase activity that is dependent on single-stranded DNA (ssDNA) and binds Rad51, but the addition of a catalytic quantity of Srs2 to Rad51-mediated recombination reactions causes severe inhibition of these reactions. We show that Srs2 acts by dislodging Rad51 from ssDNA. Thus, the attenuation of recombination efficiency by Srs2 stems primarily from its ability to dismantle the Rad51 presynaptic filament efficiently. Our findings have implications for the basis of Bloom's and Werner's syndromes, which are caused by mutations in DNA helicases and are characterized by increased frequencies of recombination and a predisposition to cancers and accelerated ageing.

Adenosine Triphosphatases↗

PubMed2003

Stimulation of human DNA polymerase epsilon by MDM2.

The human DNA polymerase epsilon catalytic subunit consists of a 140-kDa N-terminal domain that contains the catalytic activity and a 120-kDa C-terminal domain that binds to the other subunits and to exogenous peptides, including PCNA and MDM2. We report here that recombinant human MDM2 purified from insect cells or Escherichia coli stimulated the activity of DNA polymerase epsilon up to 10- and 40-fold, respectively, but not those of DNA polymerase beta or Klenow fragment of E.coli DNA polymerase I. Kinetic studies indicated that MDM2 increased the maximum velocity of the reaction, but did not change substrate affinities. The stimulation depended upon the interaction of the N-terminal 166 amino acid residues of MDM2 with the C-terminal domain of the full-length catalytic subunit, since the deletion of 166 amino acids from N-terminal of MDM2 or the removal of the C-terminal domain of DNA polymerase epsilon by trypsin digestion or competition for binding to it by the addition of excess C-terminal fragment eliminated the stimulation. Since DNA polymerase epsilon appears to be involved in DNA replication, recombination and repair synthesis, we suggest that MDM2 binding to DNA polymerase epsilon might be part of a reconfiguration process that allows DNA polymerase epsilon to associate with repair/recombination proteins in response to DNA damage.

Animals↗

PubMed2003

Cystatin E1 and E2, new members of male reproductive tract subgroup within cystatin type 2 family.

The family of type 2 cystatin proteins is a class of cysteine proteinase inhibitors that function as potent inhibitors of papain-like cysteine proteinases. Recent studies have suggested that cystatins in the male reproductive tract subgroup may perform functions distinct from those of typical cystatins. The objective of the present study was to identify and characterize the expression of new gene members of the cystatin family 2 in mouse male reproductive tissues. Two new members of cystatin family 2, named mouse Cystatin E1 and mouse Cystatin E2 (mCST E1 and mCST E2, respectively), were identified in mice by searching the National Center for Biotechnology Information database for proteins containing homology to known type 2 cystatins. Human CST E1 has recently been reported independently under the name CST 11. The deduced amino acid sequences of these genes have significant homology with the family 2 cystatins, including four conserved cysteine residues at the C-terminus. Similar to other male reproductive subgroup cystatins, the inhibitory motifs are not well conserved in these genes. Northern blot analyses showed that both genes were highly expressed only in the epididymis. In situ hybridization demonstrated that both genes were restricted in their expression to the epithelial cells of the caput and that the highest expression was localized to the initial segment of caput epididymis. Northern blot analyses and in situ hybridization showed that both mCST E1 and E2 mRNA decreased after castration, and treatment with testosterone propionate (T) did not maintain expression of these genes. In fact, T treatment further repressed the expression of these genes in the epididymis following castration. Efferent ductule ligation resulted in a dramatic decrease of epididymal expression of mCST E1 and E2. The expression of mCST E1 mRNA was up-regulated by 17 beta-estradiol (E) administration for 7 days postcastration, whereas no recovery of mCST E1 mRNA level was detected after 14 days of E treatment. Combined E and T (E+T) treatment for 1 and 2 wk reduced the mCST E1 transcripts. The expression of mCST E2 mRNA was maintained by E administration for both 7 and 14 days after castration, whereas treatment of both T and E repressed the expression of mCST E2. Although both mCST E1 and E2 share significant homology with family 2 cystatins, including similar distribution in tissues and localization in epididymis, these genes may have different functions, because their regulation involves different hormones and, probably, other testicular factors.

Amino Acid Sequence↗

PubMed2003

Identification and cloning of two isoforms of human high-temperature requirement factor A3 (HtrA3), characterization of its genomic structure and comparison of its tissue distribution with HtrA1 and HtrA2.

In the present study, we identified an additional member of the human high-temperature requirement factor A (HtrA) protein family, called pregnancy-related serine protease or HtrA3, which was most highly expressed in the heart and placenta. We cloned the full-length sequences of two forms (long and short) of human HtrA3 mRNA, located the gene on chromosome 4p16.1, determined its genomic structure and revealed how the two mRNA variants are produced through alternative splicing. The alternative splicing was also verified by Northern blotting. Four distinct domains were found for the long form HtrA3 protein: (i) an insulin/insulin-like growth factor binding domain, (ii) a Kazal-type S protease-inhibitor domain, (iii) a trypsin protease domain and (iv) a PDZ domain. The short form is identical to the long form except it lacks the PDZ domain. Comparison of all members of human HtrA proteins, including their isoforms, suggests that both isoforms of HtrA3 represent active serine proteases, that they may have different substrate specificities and that HtrA3 may have similar functions to HtrA1. All three HtrA family members showed very different mRNA-expression patterns in 76 human tissues, indicating a specific function for each. Interestingly, both HtrA1 and HtrA3 are highly expressed in the placenta. Identification of the tissue-specific function of each HtrA family member is clearly of importance.

Alternative Splicing↗

PubMed2003

Molecular cloning and characterization of rat chemokine-like factor 1 and 2.

Chemokine-like factor 1(CKLF1) is a newly cloned cytokine with three RNA splicing isoforms. It has chemotactic activities on leukocytes and plays an important role in skeletal muscle regeneration. Here we have isolated two rat homologues of human chemokine-like factors by expressed sequence tag assembly, which are designated as rat chemokine-like factor 1 and 2 (rat CKLF1, CKLF2). The full-length cDNAs of rat CKLF1 and -2 contain 523 and 682 nucleotides and the open reading frames encoding 98 and 151 amino acids, respectively. Rat CKLF1 and -2 share about 54.1 and 59.6% homologies with human CKLF1 and -2 at the amino acid level; both rat CKLF1 and -2 contain a CX3C motif at their C-terminal regions while human CKLFs have a CC motif at the same regions. Rat CKLFs are highly expressed in testis, while human CKLFs have a broad expression spectrum across multiple tissues. Recombinant rat CKLF1 can be secreted into the cell culture supernatants and has chemotactic effects on neutrophils, macrophages and lymphocytes, which is similar to human CKLF1, while recombinant rat CKLF2 has weaker chemotactic effects on these cells. These findings show that rat CKLFs have similar bioactivity with human CKLFs, although they are different in tissue distribution and contain different characteristic motifs.

Amino Acid Sequence↗

PubMed2003

Synthesis and cytotoxicity of dihydroartemisinin ethers containing cyanoarylmethyl group.

A new type of ether of dihydroartemisinin containing cyano and aryl groups was prepared and tested for cytotoxicity to A549, P388, L1210 and HT29 cells using the MTT assay. 12k and 12l were the most cytotoxic compounds. 13 lacking the peroxy group showed a 1000-fold less potency than 12l. Similarly, the inactive compound 14 indicated that the position of cyano groups was also important. Flow cytometry data showed that the compounds caused an accumulation of P388 cells in the G(1)-phase of the cell cycle.

Animals↗

PubMed2003

Recoil-limited laser cooling of 87Sr atoms near the Fermi temperature.

A dynamic magneto-optical trap, which relies on the rapid randomization of population in Zeeman substates, has been demonstrated for fermionic strontium atoms on the 1S0-3P1 intercombination transition. The obtained sample, 1x10(6) atoms at a temperature of 2 microK in the trap, was further Doppler cooled and polarized in a far-off resonant optical lattice to achieve 2 times the Fermi temperature.

Journal Article↗

PubMed2003

A novel three-dimensional coordination polymer constructed with mixed-valence dimeric copper(I,II) units.

A novel three-dimensional coordination polymer with a mixed-valence localized copper(I,II) dimeric unit, [Cu2(4-pya)3]n (4-pya = 4-pyridinecarboxylate), was hydrothermally synthesized via a simultaneous in-situa redox and hydrolysis reaction of Cu(II) and 4-cyanopyridine and crystallographically characterized to be a twofold interpenetrated three-dimensional coordination network with a cubic [Cu16(4-pya)12] building unit.

Journal Article↗

PubMed2003

Transplantation of olfactory ensheathing cells into spinal cord lesions restores breathing and climbing.

One of the most devastating effects of damage to the upper spinal cord is the loss of the ability to breathe; patients suffering these injuries can be kept alive only with assisted ventilation. No known method for repairing these injuries exists. We report here the return of supraspinal control of breathing and major improvements in climbing after the application of a novel endogenous matrix transfer method. This method permits efficient transfer and retention of cultured adult rat olfactory ensheathing cells when transplanted into large lesions that destroy all tracts on one side at the upper cervical level of the adult rat spinal cord. This demonstrates that transplantation can produce simultaneous repair of two independent spinal functions.

Animals↗

PubMed2003

Metal ion binding and enzymatic mechanism of Methanococcus jannaschii RNase HII.

RNase H degrades the RNA moiety in DNA:RNA hybrid in a divalent metal ion dependent manner. It is essential to understand the role of metal ion in enzymatic mechanism. One of the key points in this study is how many metal ions are involved in the enzyme catalysis. Accordingly, either one-metal binding mechanism or two-metal binding mechanism is proposed. We have studied the thermodynamic properties of four metal ions (Mg(2+), Mn(2+), Ca(2+), and Ba(2+)) binding to Methanococcus jannaschii RNase HII using isothermal titration calorimetry. All of the four metal ions were found to bind Mj RNase HII with 1:1 stoichiometry in the absence of substrate. Together with enzymatic activity assay data, we propose that only one metal ion binding to the enzyme in catalytic process. We also studied the pH dependence of metal binding and enzyme activity and found that at pH 6.5, Mg(2+) did not bind to the enzyme without the substrate but still activated the enzyme to about 2% of its maximum activity (in 10 mM Mn(2+) at pH 8). This implies that the substrate may also be incorporated in metal ion binding and help to position the metal ion. To find which acidic residues correspond to metal ion binding, we also studied the binding thermodynamics and enzymatic activity assay of four mutants: D7N, E8Q, D112N, and D149N in the presence of Mn(2+). The thermodynamic parameters are least affected for the D149N mutant, which has a very low enzymatic activity. This indicates that Asp149 is essential for the enzymatic activity. On the basis of all these observations, we suggest a metal binding model in which D7, E8, and D112 bind the metal ion and D149 activates a water molecule to attack the P-O bond in the RNA chain of the substrate.

Archaeal Proteins↗

PubMed2003

Inability to detect cell free fetal DNA in the urine of normal pregnant women nor in those affected by preeclampsia associated HELLP syndrome.

OBJECTIVE: Recent reports have indicated that cell-free fetal DNA can be detected in the urine of pregnant women. We attempted to reproduce those data. METHODS: Urine samples were collected from 18 normal pregnant women (11 with a male fetus). Urinary DNA was examined by Y-chromosome-specific nested polymerase chain reaction (PCR) or real-time PCR. Samples were also examined from two pregnancies complicated by HELLP (hemolysis, elevated liver enzymes, and low platelets) syndrome, which had very high levels of cell-free fetal DNA in the maternal plasma. To validate our data, a quantitative comparison of different DNA extraction procedures used in the previous reports was performed. RESULTS: In no instance were we able to detect any fetal DNA in maternal urine, although copious quantities of cell-free fetal DNA were present in the maternal plasma of those pregnancies affected by HELLP syndrome. Our quantitative analysis of the various extraction procedures used indicated that the commercial column elution method we used was comparable, if not superior, to the noncommercial methods used in previous reports. CONCLUSION: Our data strongly suggest that cell-free fetal DNA is not readily detectable in maternal urine, even under conditions known to increase kidney permeability.

Chromosomes, Human, Y↗

PubMed2003

The buccinator musculomucosal island flap for partial tongue reconstruction.

BACKGROUND: Ideal tongue reconstruction after partial or total glossectomy should be accomplished with like tissue. The buccinator musculomucosal island flap is similar to lingual tissue, consisting of thin, pliable mucosa of mucus production, with high cell renewal rate and minimal scar formation, excellent color, contour, texture match, and buccinator muscle fibers over the flap's entire length, providing tongual muscle reconstruction without a conspicuous donor site. STUDY DESIGN: The buccinator musculomucosal island flap, based on the facial artery and vein, is designed in a shuttle or in a fish-mouth fashion, encompassing the oral commissure anteriorly. If the flap design is made in a three-leaf shape, a larger flap will be obtained without an oral corner deformity or mouth opening difficulty. The flap is safe and simple to raise. The pedicle of the flap is longer and quite reliable and has a wide range of applicability. The flap may be used for reconstruction of the partial glossectomy defect (tongual defect was not more than half a tongue). The surgeon must know about possible anatomic variations, especially in the venous system, and plan to raise a contralateral buccinator musculomucosal island flap if homolateral facial vascular variation jeopardizes the flap's survival. RESULTS: The flap was successfully used for partial tongue reconstruction in 16 patients, and all flaps have survived without complications. Satisfactory results (including configuration and function of the neotongue) were achieved. Electromyographic studies performed on one patient with half glossectomy revealed reinnervation of the muscle in the flap with active motion of the reconstructed tongue. CONCLUSION: The buccal musculomucosal island flap based on the facial artery and vein is a better reconstruction option with the same or similar kind of tissue as the tongue and, with the addition of the reinnervated flap, offers the potential for improved physiologic motion.

Adult↗

PubMed2003

The crystal structure of the bifunctional primase-helicase of bacteriophage T7.

Within minutes after infecting Escherichia coli, bacteriophage T7 synthesizes many copies of its genomic DNA. The lynchpin of the T7 replication system is a bifunctional primase-helicase that unwinds duplex DNA at the replication fork while initiating the synthesis of Okazaki fragments on the lagging strand. We have determined a 3.45 A crystal structure of the T7 primase-helicase that shows an articulated arrangement of the primase and helicase sites. The crystallized primase-helicase is a heptamer with a crown-like shape, reflecting an intimate packing of helicase domains into a ring that is topped with loosely arrayed primase domains. This heptameric isoform can accommodate double-stranded DNA in its central channel, which nicely explains its recently described DNA remodeling activity. The double-jointed structure of the primase-helicase permits a free range of motion for the primase and helicase domains that suggests how the continuous unwinding of DNA at the replication fork can be periodically coupled to Okazaki fragment synthesis.

Bacteriophage T7↗

PubMed2003

Chryseobacterium miricola sp. nov., a novel species isolated from condensation water of space station Mir.

Classification of strain W3-B1, which was isolated from condensation water in the Russian space laboratory Mir, was investigated by a polyphasic taxonomic approach. Cells of strain W3-B1 were nonmotile, asporogenous, gram-negative slender rods with rounded ends. 16S rRNA gene sequence analysis indicated that organism should be placed in the genus Chryseobacterium. This organism contains menaquinone MK-6 as the predominent isoprenoid quinone and 3-OH iso 17:0 (40%), iso 15:0 (33%) as the major fatty acids. Phylogenetically, the nearest relative of strain W3-B1 is Chryseobacterium meningosepticum with sequence similarity of 98.4%, but DNA-DNA hybridization resulted in similarity values of only 52.3%. The G+C mol% is 34.6 mol%. Based upon results obtained by morphological, biochemical, chemotaxonomic, and molecular methods, strain W3-B1 was clearly distinguishable from other Chryseobacterium species. For these reasons, a novel species of family Flavobacteriaceae is proposed; strain W3-B1(T) (= GTC 862(T) = JCM 11413(T) = DSM 14571(T)) is the type strain.

Base Composition↗

PubMed2003

The optimization of HPLC-UV conditions for use with FTIR detection in the analysis of B vitamins.

The water-soluble vitamins thiamine (B(1)), riboflavin (B(2)), pantothenic acid (B(5)), and pyridoxine (B(6)) are separated by high-performance liquid chromatography. The mobile phase, column temperature, and flow rate are optimized so that the chromatograph can be used with a Fourier-transform infrared (FTIR) detector. Reproducibility, linearity, and detection limits are evaluated for method validation. Finally, this method is successfully transferred to liquid chromatography-FTIR with a standard mixture.

Chromatography, High Pressure Liquid↗