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Biomedical subjects

W Shi

Publications and source records attributed to W Shi.

At least 37 records · Page 2Linked to original sources

Structures of purine nucleoside phosphorylase from Mycobacterium tuberculosis in complexes with immucillin-H and its pieces.

A structural genomics comparison of purine nucleoside phosphorylases (PNPs) indicated that the enzyme encoded by Mycobacterium tuberculosis (TB-PNP) resembles the mammalian trimeric structure rather than the bacterial hexameric PNPs. The crystal structure of M. tuberculosis PNP in complex with the transition-state analogue immucillin-H (ImmH) and inorganic phosphate was solved at 1.75 A resolution and confirms the trimeric structure. Binding of the inhibitor occurs independently at the three catalytic sites, unlike mammalian PNPs which demonstrate negative cooperativity in ImmH binding. Reduced subunit interface contacts for TB-PNP, compared to the mammalian enzymes, correlate with the loss of the cooperative inhibitor binding. Mammalian and TB-PNPs both exhibit slow-onset inhibition and picomolar dissociation constants for ImmH. The structure supports a catalytic mechanism of reactant destabilization by neighboring group electrostatic interactions, transition-state stabilization, and leaving group activation. Despite an overall amino acid sequence identity of 33% between bovine and TB-PNPs and almost complete conservation in active site residues, one catalytic site difference suggests a strategy for the design of transition-state analogues with specificity for TB-PNP. The structure of TB-PNP was also solved to 2.0 A with 9-deazahypoxanthine (9dHX), iminoribitol (IR), and PO(4) to reconstruct the ImmH complex with its separate components. One subunit of the trimer has 9dHX, IR, and PO(4) bound, while the remaining two subunits contain only 9dHX. In the filled subunit, 9dHX retains the contacts found in the ImmH complex. However, the region of IR that corresponds to the oxocarbenium ion is translocated in the direction of the reaction coordinate, and the nucleophilic phosphate rotates away from the IR group. Loose packing of the pieces of ImmH in the catalytic site establishes that covalent connectivity in ImmH is required to achieve the tightly bound complex.

Actinomycetales↗

Genetic locus in mice that blocks development of atherosclerosis despite extreme hyperlipidemia.

The genes contributing to the common forms of atherosclerosis are largely unknown. One approach to dissecting complex traits such as atherosclerosis is to use animal models, such as the mouse, to map and characterize the genetic loci involved. We now report the identification of a locus for aortic lesion formation on mouse chromosome 6 that exhibits a highly significant lod score of 6.7 in a genetic cross between the susceptible strain, C57BL/6J, and the resistant strain, CAST/Ei. The locus was confirmed by constructing a congenic strain in which the chromosome 6 segment from CAST/Ei was transferred to a C57BL/6J background in a series of backcrosses. The congenic strain was almost completely resistant to diet-induced atherosclerosis. The chromosome 6 segment was also transferred onto the background of an LDL receptor-null mutation and resulted again in almost complete resistance to aortic lesion formation. This locus also influenced insulin levels but did not affect plasma lipoprotein levels, blood pressure, or body fat. The chromosome 6 gene, which we call Artles (for arterial lesions), did not affect endothelial cell responses to oxidized LDL, but lesion formation was partially reduced through bone marrow transplantation. The locus contains the candidate gene peroxisome proliferator-activated receptor-gamma, and the congenic mice exhibited significantly reduced expression of peroxisome proliferator-activated receptor-gamma.

Animals↗

A transition-state analogue reduces protein dynamics in hypoxanthine-guanine phosphoribosyltransferase.

Hypoxanthine-guanine phosphoribosyltransferase (HGPRT) is the key enzyme in purine base salvage in humans and in purine auxotrophs, including Plasmodium falciparum, the leading cause of malaria. Hydrogen/deuterium (H/D) exchange into amide bonds, quantitated by on-line HPLC and mass spectrometry, has been used to compare the dynamic and conformational properties of human HGPRT alone, the HGPRT-GMP-Mg(2+) complex, the HGPRT-IMP-MgPPi <==> HGPRT-Hx-MgPRPP equilibrating mixture, and the transition-state analogue complex HGPRT-ImmGP-MgPPi. The rate and extent of H/D exchange of 26 peptic peptides, spanning 91% of the primary structure, have been monitored. Human HGPRT has 207 amide H/D exchange sites. After 1 h in D2O, HGPRT alone exchanges 160, HGPRT-GMP-Mg(2+) exchanges 154, the equilibrium complex exchanges 139, and the transition-state analogue complex exchanges 126 of these amide protons. H/D exchange rates are correlated with structure for peptides in (1) catalytic site loops, (2) a connected peptide of the subunit interface of the tetramer, and (3) a loop buried in the catalytic site. Structural properties related to H/D exchange are defined from crystallographic studies of the HGPRT-GMP-Mg(2+) and HGPRT-ImmGP-MgPPi complexes. Transition-state analogue binding strengthens the interaction between subunits and tightens the catalytic site loops. The solvent exchange dynamics in specific peptides correlates with hydrogen bond patterns, solvent access, crystallographic B-factors, and ligand exchange rates. Solvent exchange reveals loop dynamics in the free enzyme, Michaelis complexes, and the complex with the bound transition-state analogue. Proton transfer paths, rather than dynamic motion, are required to explain exchange into a buried catalytic site peptide in the complex with the bound transition-state analogue.

Amino Acid Sequence↗

MinK-related peptide 1: A beta subunit for the HCN ion channel subunit family enhances expression and speeds activation.

The HCN family of ion channel subunits underlies the currents I(f) in heart and I(h) and I(q) in the nervous system. In the present study, we demonstrate that minK-related peptide 1 (MiRP1) is a beta subunit for the HCN family. As such, it enhances protein and current expression as well as accelerating the kinetics of activation. Because MiRP1 also functions as a beta subunit for the cardiac delayed rectifier I(Kr), these results suggest that this peptide may have the unique role of regulating both the inward and outward channels that underlie cardiac pacemaker activity. The full text of this article is available at http://www.circresaha.org.

Animals↗

Functional soluble CD100/Sema4D released from activated lymphocytes: possible role in normal and pathologic immune responses.

CD100/Sema4D is a 150-kd transmembrane protein that belongs to the semaphorin family. The interaction of CD100 with CD72 is critical for the immune system. In CD100-deficient mice, the production of specific antibodies against T-cell-dependent antigens is severely impaired, but not against T-cell-independent antigens. Here, a functional soluble CD100 protein (sCD100) released from activated lymphocytes is reported. sCD100 was detected in culture supernatants of activated lymphocytes. Either affinity-purified from supernatants of activated T-cells, or produced as a recombinant sCD100 protein consisting of the extracellular region of the mouse CD100 fused to the human IgG1 Fc (CD100-Fc), sCD100 significantly enhanced CD40-induced B-cell responses. Furthermore, sCD100 was detected either in sera of mice immunized with T-cell-dependent antigens, or in sera of MRL/lpr mice, but not in sera of mice immunized with T-cell-independent antigens. A significant correlation was observed between the level of sCD100 and the titer of autoantibodies in the serum of MRL/lpr mice. This study's findings suggest a potential role for sCD100 in immune responses, including production of antibody, and autoimmune diseases. (Blood. 2001;97:3498-3504)

Animals↗

Pulmonary hypoplasia in mice lacking tumor necrosis factor-alpha converting enzyme indicates an indispensable role for cell surface protein shedding during embryonic lung branching morphogenesis.

Many membrane-bound protein precursors, including cytokines and growth factors, are proteolytically shed to yield soluble intercellular regulatory ligands. The responsible protease, tumor necrosis factor-alpha converting enzyme (TACE/ADAM-17), is a transmembrane metalloprotease-disintegrin that cleaves multiple cell surface proteins, although it was initially identified for the enzymatic release of tumor necrosis factor-alpha (TNF-alpha). Mammalian lung growth and development are tightly controlled by cytokines and peptide growth factors. However, the biological function of the cell shedding mechanism during lung organogenesis is not understood. We therefore evaluated the role of TACE as a "sheddase" during lung morphogenesis by analyzing the developmental phenotypes of lungs in mice with an inactive TACE gene in both in vivo and ex vivo organ explant culture. Neonatal TACE-deficient mice had visible respiratory distress and their lungs failed to form normal saccular structures. These newborn mutant lungs had fewer peripheral epithelial sacs with deficient septation and thick-walled mesenchyme, resulting in reduced surface for gas exchange. At the canalicular stage of E16.5, the lungs of TACE mutant mice were impaired in branching morphogenesis, inhibited in epithelial cell proliferation and differentiation, and delayed in vasculogenesis. Embryonic TACE knockout mouse lungs (E12) branched poorly compared to wild-type lungs, when placed into serumless organ culture. Gene expression of both surfactant protein-C and aquaporin-5 were inhibited in cultured TACE-mutant embryonic lungs, indicating defects in both branching and peripheral epithelial cytodifferentiation in the absence of TACE protein. Furthermore, both the hypoplastic phenotype and the delayed cytodifferentiation in TACE-deficient lungs were rescued by exogenous addition of soluble stimulatory factors including either TNF-alpha or epidermal growth factor in embryonic lung culture. Thus, the impaired lung branching and maturation without TACE suggest a broad role for TACE in the processing of multiple membrane-anchored proteins, one or more of which is essential for normal lung morphogenesis. Taken together, our data indicate that the TACE-mediated proteolytic mechanism which enzymatically releases membrane-tethered proteins plays an indispensable role in lung morphogenesis, and its inactivation leads to abnormal lung development.

ADAM Proteins↗

Testosterone inhibits early atherogenesis by conversion to estradiol: critical role of aromatase.

The effects of testosterone on early atherogenesis and the role of aromatase, an enzyme that converts testosterone to estrogens, were assessed in low density lipoprotein receptor-deficient male mice fed a Western diet. Castration of male mice increased the extent of fatty streak lesion formation in the aortic origin compared with testes-intact animals. Administration of anastrazole, a selective aromatase inhibitor, to testes-intact males increased lesion formation to the same extent as that observed with orchidectomized animals. Testosterone supplementation of orchidectomized animals reduced lesion formation when compared with orchidectomized animals receiving the placebo. This attenuating effect of testosterone was not observed when the animals were treated simultaneously with the aromatase inhibitor. The beneficial effects of testosterone on early atherogenesis were not explained by changes in lipid levels. Estradiol administration to orchidectomized males attenuated lesion formation to the same extent as testosterone administration. Aromatase was expressed in the aorta of these animals as assessed by reverse transcription-PCR and immunohistochemistry. These results indicate that testosterone attenuates early atherogenesis most likely by being converted to estrogens by the enzyme aromatase expressed in the vessel wall.

Animals↗

Point mutant mice with hypersensitive alpha 4 nicotinic receptors show dopaminergic deficits and increased anxiety.

Knock-in mice were generated that harbored a leucine-to-serine mutation in the alpha4 nicotinic receptor near the gate in the channel pore. Mice with intact expression of this hypersensitive receptor display dominant neonatal lethality. These mice have a severe deficit of dopaminergic neurons in the substantia nigra, possibly because the hypersensitive receptors are continuously activated by normal extracellular choline concentrations. A strain that retains the neo selection cassette in an intron has reduced expression of the hypersensitive receptor and is viable and fertile. The viable mice display increased anxiety, poor motor learning, excessive ambulation that is eliminated by very low levels of nicotine, and a reduction of nigrostriatal dopaminergic function upon aging. These knock-in mice provide useful insights into the pathophysiology of sustained nicotinic receptor activation and may provide a model for Parkinson's disease.

Animals↗

Transition state structure of purine nucleoside phosphorylase and principles of atomic motion in enzymatic catalysis.

Immucillin-H [ImmH; (1S)-1-(9-deazahypoxanthin-9-yl)-1,4-dideoxy-1,4-imino-D-ribitol] is a 23 pM inhibitor of bovine purine nucleoside phosphorylase (PNP) specifically designed as a transition state mimic [Miles, R. W., Tyler, P. C., Furneaux, R. H., Bagdassarian, C. K., and Schramm, V. L. (1998) Biochemistry 37, 8615-8621]. Cocrystals of PNP and the inhibitor are used to provide structural information for each step through the reaction coordinate of PNP. The X-ray crystal structure of free ImmH was solved at 0.9 A resolution, and a complex of PNP.ImmH.PO(4) was solved at 1.5 A resolution. These structures are compared to previously reported complexes of PNP with substrate and product analogues in the catalytic sites and with the experimentally determined transition state structure. Upon binding, ImmH is distorted to a conformation favoring ribosyl oxocarbenium ion formation. Ribosyl destabilization and transition state stabilization of the ribosyl oxocarbenium ion occur from neighboring group interactions with the phosphate anion and the 5'-hydroxyl of the ribosyl group. Leaving group activation of hypoxanthine involves hydrogen bonds to O6, N1, and N7 of the purine ring. Ordered water molecules provide a proton transfer bridge to O6 and N7 and permit reversible formation of these hydrogen bonds. Contacts between PNP and catalytic site ligands are shorter in the transition state analogue complex of PNP.ImmH.PO(4) than in the Michaelis complexes of PNP.inosine.SO(4) or PNP.hypoxanthine.ribose 1-PO(4). Reaction coordinate motion is dominated by translation of the carbon 1' of ribose between relatively fixed phosphate and purine groups. Purine and pyrimidine phosphoribosyltransferases and nucleoside N-ribosyl hydrolases appear to operate by a similar mechanism.

Animals↗

Sulfonated acrylamide copolymers as pseudo-stationary phases in electrokinetic chromatography.

Sulfonated copolymers were synthesized, characterized and used as separation media in electrokinetic chromatography. The polymers used were synthesized from AMPS (2-acrylamido-2-methyl-1-propanesulfonic acid) and LMAm (lauryl methacrylamide) in different mole ratios (from 100:0 to 60:40). Electrophoretic mobilities and methylene selectivities were calculated, which showed the expected correlation with the monomer ratios. The chemical selectivities for the separation of nine solutes by the copolymers were compared with that of sodium lauryl sulfate micelles, showing significant differences. No significant difference in chemical selectivities was observed for copolymers with different monomer ratios. No significant change of hydrophobic microdomain of copolymers was found in background buffers with different ionic strength values, based on the investigation of the retention factors, methylene selectivities and polymer effective mobilities. No change of hydrophobic microdomain of the copolymer solutions was found at copolymer concentrations from 0.17 to 3% (w/v), however, plots of k' versus polymer concentration suggested a different copolymer phase at lower concentrations (from 0 to 0.1%, w/v) from that at higher concentrations (from 0.17 to 3%, w/v). The copolymer with AMPS-LMAm (80:20) could be chosen as optimum copolymer as far as the methylene selectivity, peak symmetry and polymer mobility were concerned.

Acrylamides↗

Increased T cell autoreactivity in the absence of CD40-CD40 ligand interactions: a role of CD40 in regulatory T cell development.

Mutations in the CD40 ligand (CD40L) gene lead to X-linked immunodeficiency with hyper-IgM, which is often associated with autoimmune diseases. To determine the contribution of defective CD40-CD40L interactions to T cell autoreactivity, we reconstituted CD40-CD40L interactions by transferring T cells from CD40-deficient mice to syngenic athymic nude mice and assessed autoimmunity. T cells from CD40-deficient mice triggered autoimmune diseases accompanied with elevations of various autoantibodies, while those from wild-type mice did not. In CD40-deficient mice, the CD25(+) CD45RB(low) CD4(+) subpopulation which regulates T cell autoreactivity was markedly reduced. CD40-deficient APCs failed to induce T regulatory cells 1 producing high levels of an inhibitory cytokine, IL-10 in vitro. Furthermore, autoimmune development was inhibited when T cells from CD40-deficient mice were cotransferred with CD45RB(low) CD4(+) T cells from wild-type mice or with T regulatory cells 1 induced on CD40-expressing APCs. Collectively, our results indicate that CD40-CD40L interactions contribute to negative regulation of T cell autoreactivity and that defective interactions can lead to autoimmunity.

Animals↗

Analysis of the frequencies of HLA-A, B, and C alleles and haplotypes in the five major ethnic groups of the United States reveals high levels of diversity in these loci and contrasting distribution patterns in these populations.

The HLA system is the most polymorphic of all human genetic systems. The frequency of HLA class I alleles and their linkage disequilibrium patterns differ significantly among human populations as shown in studies using serologic methods. Many DNA-defined alleles with identical serotypes may have variable frequencies in different populations. We typed HLA-A, B, and C loci at the allele level by PCR-based methods in 1,296 unrelated subjects from five major outbred groups living in the U.S.A (African, AFAM; Caucasians, CAU; Asian, ORI; Hispanic, HIS, and North American Natives, NAI). We detected 46, 100 and 32 HLA-A, B, and C alleles, respectively. ORI and HIS presented more alleles at each of these loci. There was lack of correlation between the levels of heterozygosity and the number of alleles detected in each population. In AFAM, heterozygosity (>90%) is maximized at all class I loci. HLA-A had the lowest heterozygosity in all populations but CAU. Tight LD was observed between HLA-B and C alleles. AFAM had weaker or nonexistent associations between alleles of HLA-A and B than other populations. Analysis of the genetic distances between these and other populations showed a close relationship between specific US populations and a population from their original continents. ORI exhibited the largest genetic distance with all the other U.S. groups and were closer to NAI. Evidence of admixture with CAU was observed for AFAM and HIS. HIS also had significant frequencies of AFAM and Mexican Indian alleles. Differences in both LD and heterozygosity levels suggest distinct evolutionary histories of the HLA loci in the geographical regions from where the U.S. populations originated.

Alleles↗

Atomic motion in enzymatic reaction coordinates.

Atomic excursions of reactants in enzymatic catalytic sites can be estimated from high-resolution crystal structures of enzyme complexes with substrates, transition state analog inhibitors and products. Transition state structures, defined from kinetic isotope effect studies, are compared to crystallographic structures to validate the properties of the transition state analog. Atomic excursions in enzymatic catalytic sites can differ from those in solution and define the role of the enzymatic catalyst in directing atomic motion.

Animals↗

Association of p53, p16, and vascular endothelial growth factor protein expressions with the prognosis and metastasis of gallbladder cancer.

BACKGROUND: Tumor suppressor genes were studied in gallbladder disease including cancer for correlation. VEGF (vascular endothelial growth factor) expression was assessed against Nevin staging and metastasis of gallbladder carcinoma. The importance of p53, p16, and VEGF in gallbladder cancer was estimated. STUDY DESIGN: Twenty-four gallbladder carcinomas, 20 gallbladder adenomas, and 18 chronic cholecystitis specimens were immunohistochemically and histopathologically investigated for the relation of p53, p16, and VEGF to Nevin staging and pathologic grading. RESULTS: The expression rate of abnormal p53 in gallbladder carcinomas was significantly higher than that in gallbladder adenoma and chronic cholecystitis (p = 0.003, p = 0.014). The expression rate of abnormal p53 in Nevin staging S1, S2, S3 gallbladder carcinoma was significantly higher than that in S4, S5 (p = 0.01). Abnormal p16 was highest in carcinoma, next in adenoma, and lowest in chronic cholecystitis (p = 0.031, p = 0.017). Gallbladder carcinoma expressed VEGF far more often than adenoma or cholecystitis (p = 0.001); VEGF-positive rates were lower in S1, S2, S3 than S4, S5 by Nevin staging of gallbladder cancer (p = 0.044). CONCLUSION: Mutation of p53 and p16 genes might correlate with progression of of gallbladder carcinoma. Analysis of p53 and p16 can estimate the prognosis of gallbladder cancer. VEGF expression correlates with Nevin staging in gallbladder cancer.

Adenoma↗

Synthesis and quantitative structure-activity relationships of new 2,5-disubstituted-1,3,4-oxadiazoles.

Fourteen new 2,5-disubstituted-1,3,4-oxadiazoles, namely (i) six 2-[2,2-dimethyl-3-(2,2-dichlorovinyl)-cyclopropyl]-5-substituted-1,3,4-oxadiazoles and (ii) eight 2-substituted-phenoxymethyl-5-substituted-aryl-1,3,4-oxadiazoles, were synthesized and evaluated for their insect growth regulatory activity against second-instar larvae of armyworm (Pseudaletia separata Walker). Two of these compounds (7 and 8) showed good insecticidal activities, with LC(50) values of 14.33 and 15.85 microg/mL, respectively. Steric parameters (e.g., the molecular length d and the ratio of the nonpolar surface area and polar surface area V(1)/V(2)) and semiempirical quantum parameters (e.g., the molecular total energy E(t) and the lowest unoccupied molecular orbital energy E(LUMO) and so on) of these compounds, as well as those of six other 2,5-disubstituted-1,3,4-oxadiazoles reported, were acquired by the molecular modeling method and the PM3-SCF-MO method, respectively. With the help of the synthons' activity contribution method based on the Free-Wilson approach in its Fujita-Ban variant, quantitative structure-activity relationships were studied by regressing half-lethal concentrations against the above parameters.

Animals↗

Three new MHC haplotypes in broiler breeder chickens.

Six distinct serotypes of the chicken B blood group system (which encodes the major histocompatibility complex) were identified in a commercial broiler breeder line (Line C). The B serotypes were compared by B-G restriction fragment length polymorphism (RFLP) analysis, allele-specific PCR typing test for B-LBII family genes and nucleotide sequence analysis of expressed B-F and B-LBII family genes. The results indicated the existence of seven distinct B haplotypes. Nucleotide sequence analysis demonstrated that three of the Line C haplotypes encode new B-F and B-LB alleles.

Alleles↗

Functional analysis of salt-inducible proline transporter of barley roots.

We cloned a cDNA encoding Hordeum vulgare Proline Transporter (HvProT) from salt-stressed barley roots by differential display. HvProT was 2,161 bp long and had an open reading frame encoding 450 amino acids. The deduced amino acid sequence of HvProT was similar to those of proline transporter proteins of rice (65.7%), Arabidopsis (57.7%) and tomato (42.0%). Northern blot analysis showed that the transcript level of HvProT was induced in roots at 30 min after 200 mM NaCl treatment and its peak was observed at 3 h. However, the transcript level was very low in leaves and did not increase by salt stress. The expression level of Delta(1)-pyrroline-5-carboxylate synthetase (P5CS), encoding a key enzyme of proline synthesis, was induced later than HvProT by salt stress. A transport assay using a yeast with mutation in proline uptake revealed that HvProT was a transporter with high affinity for L-proline (K(m) = 25 microM). HvProT was found to be a unique transporter with high affinity for L-proline. Since its transport activity was dependent on the pH gradient, HvProT was suggested to be a H(+)/amino acid symporter. In situ hybridization analysis showed that the HvProT mRNA was strongly expressed in root cap cells under salt stress. HvProT might play an important role in the transport of proline to root tip region urgently upon salt stress.

1-Pyrroline-5-Carboxylate Dehydrogenase↗

Prolongation of corneal allograft survival using cyclosporine in a polylactide-co-glycolide polymer.

PURPOSE: To test for prolongation of corneal transplant survival with cyclosporine in a polymer placed in the anterior chamber of corneal allograft recipients. METHODS: Wistar inbred rats with vascularized corneas were recipients of corneal allografts from Sprague-Dawley donor rats. Grafted rats were randomized into six groups: untreated control animals, cyclosporine-polymer anterior chamber recipients, cyclosporine-polymer subconjunctival recipients, cyclosporine-olive oil drop recipients, polymer-only anterior chamber recipients, and autografted Wistar rats. Grafts were examined by slit lamp every 3 days and the clinical condition scored. The cyclosporine concentration in the aqueous humor was assayed at 1, 2, and 4 weeks. At 2 and 4 weeks after transplantation, the eyes were collected for histopathologic evaluation of the grafts. RESULTS: The median survival time of untreated corneal allografts was 8.2 +/- 1.48 days for grafts treated with topical cyclosporine, 8.5 +/- 1.50 days for polymer-only anterior chamber implants, 10.6 +/- 1.90 days for 1% cyclosporine drops, 11.4 +/- 2.50 days for grafts given subconjunctival cyclosporine-polymer, 17 +/- 3.05 days for grafts given cyclosporine-polymer implants in the anterior chamber, and more than 3 months in autografted rats. There was a statistically significant difference ( p < 0.05) between the survival time of the allografts in the animals treated with the cyclosporine-polymer in the anterior chamber compared with the other groups of graft recipients. Significantly higher concentrations of cyclosporine were found in the eyes given an anterior chamber implant of cyclosporine-polymer than in the other treatment groups or the untreated rats. The cyclosporine-polymer implants placed in the anterior chamber induced a transient inflammatory response in transplanted eyes. CONCLUSIONS: Cyclosporine-polymer placed in the anterior chamber significantly prolongs corneal allograft survival in a high-risk corneal graft rejection. This intraocular delivery system may be a valuable adjunct for the suppression of immune graft rejection in high-risk recipients of corneal transplants.

Animals↗