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Biomedical subjects

D Shi

Publications and source records attributed to D Shi.

At least 19 recordsLinked to original sources
PubMed2001

Projection structure and molecular architecture of OxlT, a bacterial membrane transporter.

The major facilitator superfamily (MFS) represents the largest collection of evolutionarily related members within the class of membrane 'carrier' proteins. OxlT, a representative example of the MFS, is an oxalate-transporting membrane protein in Oxalobacter formigenes. From an electron crystallographic analysis of two-dimensional crystals of OxlT, we have determined the projection structure of this membrane transporter. The projection map at 6 A resolution indicates the presence of 12 transmembrane helices in each monomer of OxlT, with one set of six helices related to the other set by an approximate internal two-fold axis. The projection map reveals the existence of a central cavity, which we propose to be part of the pathway of oxalate transport. By combining information from the projection map with related biochemical data, we present probable models for the architectural arrangement of transmembrane helices in this protein superfamily.

Amino Acid Sequence↗
PubMed2001

Crystallization and preliminary X-ray crystallographic studies of wild-type human ornithine transcarbamylase and two naturally occurring mutants at position 277.

Wild-type human ornithine transcarbamylase (OTCase) and two mutants (R277Q and R277W) that cause 'late-onset' hyperammonemia were crystallized and a preliminary structure determination was carried out. The unliganded wild-type enzyme crystallizes in the cubic space group I23, with unit-cell parameters a = b = c = 203.4 A. R277Q crystallizes in two crystal forms under the same crystallization conditions. One crystal form is isomorphous to that of unliganded wild-type crystals, with unit-cell parameters a = b = c = 202.2 A. The second form also belongs to a cubic space group, P4(3)32, but has unit-cell parameters a = b = c = 139.8 A. R277W crystals are isomorphous to the second crystal form of R277Q, with unit-cell parameters a = b = c = 138.7 A. None of these crystal forms is isomorphous to other crystal forms of OTCase that have been studied. The structures in both crystal forms have been solved using molecular replacement. In the first crystal form there are two monomers in the asymmetric unit, corresponding to a solvent content of 75%. Because of its high molecular and crystal symmetry and the presence of non-crystallographic symmetry, this structure could not be solved with AMoRe or X-PLOR, but was solved successfully with COMO. There is only one monomer in the asymmetric unit in the second crystal form, corresponding to a solvent content of 62%. This structure was successfully solved with AMoRe.

Crystallization↗
PubMed2001

Human ornithine transcarbamylase: crystallographic insights into substrate recognition and conformational changes.

Two crystal structures of human ornithine transcarbamylase (OTCase) complexed with the substrate carbamoyl phosphate (CP) have been solved. One structure, whose crystals were prepared by substituting N-phosphonacetyl-L-ornithine (PALO) liganded crystals with CP, has been refined at 2.4 A (1 A=0.1 nm) resolution to a crystallographic R factor of 18.4%. The second structure, whose crystals were prepared by co-crystallization with CP, has been refined at 2.6 A resolution to a crystallographic R factor of 20.2%. These structures provide important new insights into substrate recognition and ligand-induced conformational changes. Comparison of these structures with the structures of OTCase complexed with the bisubstrate analogue PALO or CP and L-norvaline reveals that binding of the first substrate, CP, induces a global conformational change involving relative domain movement, whereas the binding of the second substrate brings the flexible SMG loop, which is equivalent to the 240s loop in aspartate transcarbamylase, into the active site. The model reveals structural features that define the substrate specificity of the enzyme and that regulate the order of binding and release of products.

Amino Acid Sequence↗
PubMed2001

Surface water phosphorus dynamics in rice fields receiving fertiliser and manure phosphorus.

A long-term randomised block field experiment was established in 1997 to study the dynamics of total P and dissolved P in the surface waters of rice fields receiving two application rates of fertiliser P and one rate of combined fertiliser and manure P. Preliminary results from the first two crops show that concentrations of both total P and dissolved P in the surface waters increased significantly following P application, especially during the first 2 weeks after application. P concentrations subsequently declined sharply within about 10 days, then declined steadily and remained almost constant from about 1 month after application. The initial increase in P concentration of surface waters was higher with increasing rate of fertiliser P, and the P concentration at the highest fertiliser rate peaked within about 1 week of application. The elevated P concentrations following fertiliser P application declined more rapidly than those following the combined application of fertiliser and manure P. When fertiliser and manure P were applied together, about 7 days later the surface water P concentrations were significantly higher than when the same rate of P (or double) was applied as fertiliser only. Disturbance of the surface soil by hand harrowing further increased the P concentrations in surface waters, with a subsequent decline to a steady value after about 1 week. Application of P fertiliser to the high P status soil in this experiment gave no crop yield response and may have increased the risk of pollution of adjacent surface waters through drainage from heavy rainfall events during the rice growing season. Therefore, fertiliser P should not be applied to such soils. If, however, fertiliser or manure P is applied, the application should be made during the dry winter to reduce P losses. Manure should be applied with particular care because of the higher risk of P losses to surface water arising from the relatively long period of high P concentrations in surface waters and the potential for greater release of P to field surface waters from the soil. Hand harrowing should also be avoided during wet weather to protect water quality.

Animals↗
PubMed2001

Visualizing filamentous actin on lipid bilayers by atomic force microscopy in solution.

The surface structure of actin filaments (F-actin) was visualized at high resolution, by atomic force microscopy (AFM) in aqueous solution, in large paracrystals prepared on positively charged lipid monolayers. The increased stability of these closely packed specimens allowed us to show that both the long pitch (38 nm) and the monomer (5.8 nm) can be directly resolved by AFM in the contact mode. The right-handed helical surface, distinguishable in high resolution images, was compared with reconstructed models based on electron microscopy. The height of the rafts, a measure of the actin filament diameter, was 10 +/- 1 nm, whereas the smaller inter-filament distance, 8 +/- 1 nm, was consistent with interdigitation of the filaments. The 10 +/- 1 nm F-actin diameter is in good agreement with the results of fibre X-ray diffraction. As such specimens are relatively easy to prepare without specialized equipment, this method may allow the study of the thin filaments in which F-actin-associated proteins are also present.

Actin Cytoskeleton↗
PubMed2000

An epidemiological and ecological study of human alveolar echinococcosis transmission in south Gansu, China.

Human alveolar echinococcosis (AE) is usually a rare, highly pathogenic zoonotic disease, transmitted across the northern hemisphere between fox and rodent hosts. In China the first cases were described in 1965; however very few epidemiological studies have been undertaken since. Following identification in 1991 of a serious focus of human AE in south Gansu province, detailed village-based community and ecological studies were carried out between 1994 and 1997. Hepatic ultrasound mass screening with serological testing (five tests) identified 84/2482 new AE cases (3%). An overall prevalence of 4.1% (135/3331) was recorded for the area when previous cases were also included. Based on a seropositive result only, without an ultrasound scan indication, no additional AE cases were identified. Of the evolutive AE cases, 96% were seropositive in at least one test, while up 15-20% of individuals who exhibited hepatic calcified lesions and 12-15% exhibiting hepatic nodular lesions were seropositive for specific Em2 or Em18 antibodies. Village (n=31) human AE prevalence rates varied from 0 to 15.8%. Questionnaire analysis indicated that total number of dogs owned over a period was a risk factor (P<0.006), but not a history of red fox hunting (P>0.6). Rodent ecology studies revealed an association between density indices of voles (Microtus limnophilus) and village AE prevalence rates, on the one hand, and village landscape characterised by a ratio of scrub/grassland to total area above 50% (P<0.005). Long-term transmission of Echinococcus multilocularis and risk of zoonotic infection of south Gansu farmers may be related ultimately to a process of deforestation driven by agriculture. This in turn probably results in creation of optimal peri-domestic habitats for rodents that serve as intermediate host species (such as M. limnophilus) and subsequent development of a peri-domestic cycle involving dogs.

Adult↗
PubMed2000

Crystal structure of human ornithine transcarbamylase complexed with carbamoyl phosphate and L-norvaline at 1.9 A resolution.

The crystal structure of human ornithine transcarbamylase (OTCase) complexed with carbamoyl phosphate (CP) and L-norvaline (NOR) has been determined to 1.9-A resolution. There are significant differences in the interactions of CP with the protein, compared with the interactions of the CP moiety of the bisubstrate analogue N-(phosphonoacetyl)-L-ornithine (PALO). The carbonyl plane of CP rotates about 60 degrees compared with the equivalent plane in PALO complexed with OTCase. This positions the side chain of NOR optimally to interact with the carbonyl carbon of CP. The mixed-anhydride oxygen of CP, which is analogous to the methylene group in PALO, interacts with the guanidinium group of Arg-92; the primary carbamoyl nitrogen interacts with the main-chain carbonyl oxygens of Cys-303 and Leu-304, the side chain carbonyl oxygen of Gln-171, and the side chain of Arg-330. The residues that interact with NOR are similar to the residues that interact with the ornithine (ORN) moiety of PALO. The side chain of NOR is well defined and close to the side chain of Cys-303 with the side chains of Leu-163, Leu-200, Met-268, and Pro-305 forming a hydrophobic wall. C-delta of NOR is close to the carbonyl oxygen of Leu-304 (3.56 A), S-gamma atom of Cys-303 (4.19 A), and carbonyl carbon of CP (3.28 A). Even though the N-epsilon atom of ornithine is absent in this structure, the side chain of NOR is positioned to enable the N-epsilon of ornithine to donate a hydrogen to the S-gamma atom of Cys-303 along the reaction pathway. Binding of CP and NOR promotes domain closure to the same degree as PALO, and the active site structure of CP-NOR-enzyme complex is similar to that of the PALO-enzyme complex. The structures of the active sites in the complexes of aspartate transcarbamylase (ATCase) with various substrates or inhibitors are similar to this OTCase structure, consistent with their common evolutionary origin.

Aspartate Carbamoyltransferase↗
PubMed2000

In vitro bioactive behavior of hydroxylapatite-coated porous Al(2)O(3).

To produce bioactive materials for bone substitutes, two major deposition methods, suspension method and thermal deposition method, were employed to develop bioactive, mechanically strong, and porous ceramics. Hydroxylapatite (HA) has been uniformly coated onto inner pore surfaces of reticulated alumina substrates. It has been found that the in vitro bioactivity of HA coatings was affected by both structural crystallinity and specific surface area. Well-crystallized HA heat-treated at high temperatures has resulted in reduced bioactivity. The bio-reaction rate was found to increase with the surface area of HA. We have found that the stability of the well-crystallized HA is associated with the high driving force required for the formation of hydroxy-carbonate apatite (HCA) phase.

Aluminum Oxide↗
PubMed2000

Cryoatomic force microscopy of filamentous actin.

Cryoatomic force microscopy (cryo-AFM) was used to image phalloidin-stabilized actin filaments adsorbed to mica. The single filaments are clearly shown to be right-handed helical structures with a periodicity of approximately 38 nm. Even at a moderate concentration ( approximately 10 microg/ml), narrow, branched rafts of actin filaments and larger aggregates have been observed. The resolution achieved is sufficient to resolve actin monomers within the filaments. A closer examination of the images shows that the branched rafts are composed of up to three individual filaments with a highly regular lateral registration with a fixed axial shift of approximately 13 nm. The implications of these higher-order structures are discussed in terms of x-ray fiber diffraction and rheology of actin gels. The cryo-AFM images also indicate that the recently proposed model of left-handed F-actin is likely to be an artifact of preparation and/or low-resolution AFM imaging.

Actin Cytoskeleton↗
PubMed2000

Role of frizzled 7 in the regulation of convergent extension movements during gastrulation in Xenopus laevis.

Wnt signalling plays a crucial role in the control of morphogenetic movements. We describe the expression and functional analyses of frizzled 7 (Xfz7) during gastrulation in Xenopus. Low levels of Xfz7 transcripts are expressed maternally during cleavage stages; its zygotic expression strongly increases at the beginning of gastrulation and is predominantly localized to the presumptive neuroectoderm and deep cells of the involuting mesoderm. Overexpression of Xfz7 in the dorsal equatorial region affects the movements of convergent extension and delays mesodermal involution. It alters the correct localization, but not the expression, of mesodermal and neural markers. These effects can be rescued by extra-Xfz7, which is a secreted form of the receptor that also weakly inhibits convergent extension when overexpressed. This suggests that the wild-type and truncated receptors have opposing effects when coexpressed and that overexpression of Xfz7 causes an increased signalling activity. Consistent with this, Xfz7 biochemically and functionally interacts with Xwnt11. In addition, Dishevelled, but not (&bgr;)-catenin, synergizes with Xfz7 to affect convergent extension. Furthermore, overexpression of Xfz7 and Xwnt11 also affects convergent extension in activin-treated animal caps, and this can be efficiently reversed by coexpression of Cdc42(T17N), a dominant negative mutant of the small GTPase Cdc42 known as a key regulator of actin cytoskeleton. Conversely, Cdc42(G12V), a constitutively active mutant, rescues the effects of extra-Xfz7 on convergent extension in a dose-dependent manner. That both gain-of-function and loss-of-function of both frizzled and dishevelled produce the same phenotype has been well described in Drosophila tissue polarity. Therefore, our results suggest an endogenous role of Xfz7 in the regulation of convergent extension during gastrulation.

Adaptor Proteins, Signal Transducing↗
PubMed1999

Images of oligomeric Kv beta 2, a modulatory subunit of potassium channels.

The Shaker type voltage-gated potassium (K+) channel consists of four pore-forming Kv alpha subunits. The channel expression and kinetic properties can be modulated by auxiliary hydrophilic Kv beta subunits via formation of heteromultimeric Kv alpha-Kv beta complexes. Because each (Kv alpha)4 could recruit more than one Kv beta subunit and different Kv beta subunits could potentially interact, the stoichiometry of alpha-beta and beta-beta complexes is therefore critical for understanding the functional regulation of Shaker type potassium channels. We expressed and purified Kv beta 2 subunit in Sf9 insect cells. The purified Kv beta 2, examined by atomic force and electron microscopy techniques, is found predominately as a square-shaped tetrameric complex with side dimensions of 100 x 100 A2 and height of 51 A. Thus, Kv beta 2 is capable of forming a tetramer in the absence of pore-forming alpha subunits. The center of the Kv beta 2 complex was observed to be the most heavily stained region, suggesting that this region could be part of an extended tubular structure connecting the inner mouth of the ion permeation pathway to the cytoplasmic environment.

Amino Acid Sequence↗
PubMed1999

Coating of hydroxyapatite on porous alumina substrate through a thermal decomposition method.

A thin film of hydroxyapatite (HA) was uniformly coated onto a highly porous substrate of alumina through the thermal decomposition method. Calcium 2-ethyl hexanoate and bis(2-ethyhexyl) phosphite were used as starting materials. Scanning electron microscopy, X-ray diffraction, and infrared spectroscopy were used to characterize the chemical and structural evolution of the coating. In vitro tests were conducted to evaluate the reactivity of the synthetic HA. It was found that the sintering process greatly influenced the in vitro behavior of HA. High temperature sintering may reduce the reactivity of HA, suggesting that the reactivity is structure dependent.

Aluminum Oxide↗
PubMed1999

Crystal structure of bullfrog M ferritin at 2.8 A resolution: analysis of subunit interactions and the binuclear metal center.

Ferritins concentrate and store iron as a mineral in all bacterial, plant, and animal cells. The two ferritin subunit types, H or M (fast) and L (slow), differ in rates of iron uptake and mineralization and assemble in vivo to form heteropolymeric protein shells made up of 24 subunits; H/L subunit ratios reflect cell specificity of H and L subunit gene expression. A diferric peroxo species that is the initial reaction product of Fe(II) in H-type ferritins, as well as in ribonucleotide reductase (R2) and methane monooxygenase hydroxylase (MMOH), has recently been characterized, exploiting the relatively high accumulation of the peroxo intermediate in frog H-subunit type recombinant ferritin with the M sequence. The stability of the diferric reaction centers in R2 and MMOH contrasts with the instability of diferric centers in ferritin, which are precursors of the ferric mineral. We have determined the crystal structure of the homopolymer of recombinant frog M ferritin in two crystal forms: P4(1)2(1)2, a = b = 170.0 A and c = 481.5 A; and P3(1)21, a = b = 210.8 A and c = 328.1 A. The structural model for the trigonal form was refined to a crystallographic R value of 19.0% (Rfree = 19.4%); the two structures have an r.m.s.d. of approximately 0.22 A for all C alpha atoms. Comparison with the previously determined crystal structure of frog L ferritin indicates that the subunit interface at the molecular twofold axes is most variable, which may relate to the presence of the ferroxidase site in H-type ferritin subunits. Two metal ions (Mg) from the crystallization buffer were found in the ferroxidase site of the M ferritin crystals and interact with Glu23, Glu58, His61, Glu103, Gln137 and, unique to the M subunit, Asp140. The data suggest that Gln137 and Asp140 are a vestige of the second GluxxHis site, resulting from single nucleotide mutations of Glu and His codons and giving rise to Ala140 or Ser140 present in other eukaryotic H-type ferritins, by additional single nucleotide mutations. The observation of the Gln137xxAsp140 site in the frog M ferritin accounts for both the instability of the diferric oxy complexes in ferritin compared to MMOH and R2 and the observed kinetic variability of the diferric peroxo species in different H-type ferritin sequences.

Amino Acid Sequence↗
PubMed1999

Expression of gp145trkB in the early stage of Schwann cell tube formation.

We investigated the expression of tyrosine kinase receptors (trkBs) and their ligand, brain-derived neurotrophic factor (BDNF), in isolated sciatic nerve segments of rat in a silicone chamber model devoid of axonal contact, using an immunohistochemical technique. The receptor gp 95trkB was not detected during the first 3 weeks but was strongly expressed in the nerve stumps on day 21. In contrast, gp 145trkB immunoreactivity was readily detected in the Schwann cells in the nerve stumps between days 1 and 7 after isolation. Immunohistochemical analysis using anti-S-100 antibody demonstrated that Schwann cell tube formation within the silicone chamber had been completed by the third week, which suggested that gp 95trkB began to be produced by Schwann cells after completion of Schwann cell tube formation. Considering the low level of BDNF production during the first week, molecules other than BDNF may be ligands for gp 145trkB in the silicone chamber model devoid of axonal contact.

Animals↗
PubMed1999

Karyological and dental identification of Microtus limnophilus in a large focus of alveolar echinococcosis (Gansu, China).

A study of voles (Arvicolidae, Rodentia) from Gansu (China) designed to identify a potential host of Echinococcus multilocularis, responsible for human alveolar echinococcosis, leads to a general analysis of Microtus limnophilus population karyotypes, M1 of M. oeconomus populations from all of Eurasia and of M. limnophilus of Mongolia. The Microtus of Gansu belonging to the nominal subspecies M. limnophilus limnophilus (2n = 38; NF = 58) differs markedly in size and shape of M1 from the M. limnophilus of Mongolia, which must therefore be considered as a new subspecies M. limnophilus of malygini nov. ssp. (2n = 38; NF = 60) and the M. oeconomus of Mongolia should be ranked as M. oeconomus kharanurensis nov. ssp. (2n = 30; NF = 60).

Animals↗