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Structural characterization of argingipain, a novel arginine-specific cysteine proteinase as a major periodontal pathogenic factor from Porphyromonas gingivalis.

Argingipain, so termed due to its peptide cleavage specificity at arginine residue, is a unique extracellular cysteine proteinase produced by the anaerobic rod Porphyromonas gingivalis, which is known as a major pathogenic factor of the progressive periodontal disease (T. Kadowaki, M. Yoneda, K. Okamoto, K. Maeda, and K. Yamamoto (1994) J. Biol. Chem. 269, 21371-21378). The catalytic specificity and functional importance of this enzyme prompted us to elucidate its structural features. A DNA fragment for argingipain was selectively amplified by polymerase chain reaction using mixed oligonucleotide primers designed from the NH2-terminal amino acid sequence of the purified enzyme. Although the extracellular mature enzyme was shown to have an apparent molecular mass of 44 kDa in gels, the nucleotide sequence of the isolated gene revealed a single gene coding for a 109-kDa precursor of argingipain. The deduced amino acid sequence exhibited no significant similarity to the sequences of representative members of the cysteine protease family. The precursor contained four functional domains: the NH2-terminal signal peptide required for the inner membrane transport; the NH2-terminal prosequence, which is assumed to stabilize the precursor structure; the proteinase domain; and the COOH-terminal hemagglutinin domain, which appears to be essential for extracellular secretion of the proteinase domain. Experiments involving the addition of the argingipain inhibitors to the culture medium of P. gingivalis suggested that the maturation of argingipain occurs intracellularly via an autocatalytic cleavage of the pro-argingipain propeptide.

Adhesins, Bacterial

Secretory IgA, IgG, and IgM immunoglobulins isolated simultaneously from colostral whey by selective thiophilic adsorption.

In order to evaluate the collective contribution of immunoglobulins to gastrointestinal and immune system development in newborn infants, it would be advantageous to develop a simple and rapid procedure for the selective and quantitative removal of all immunoglobulin classes from colostrum and milk. Toward this end, the major immunoglobulin classes typically present in colostrum (IgM, sIgA, and IgG) have been isolated simultaneously by selective removal from a porcine colostral whey model system using a single-step, preparative scale procedure termed thiophilic adsorption. At neutral pH, the salt-promoted thiophilic affinity of immunoglobulins for the synthetic sulfone-thioether ligands exploits a common (as yet unknown) structural feature of immunoglobulins. The adsorption and recovery procedures operate efficiently under mild buffer conditions permitting the subsequent comparative biochemical analyses of individual immunoglobulin classes for structural and functional heterogeneity. Thus, 1 liter columns of thiophilic adsorbent (T-gel) were employed to obtain pure, structurally intact immunoglobulins from 1 liter batches of porcine colostral whey. The identity and purity of the isolated immunoglobulins were determined under both structure-stabilizing ('native') conditions and denaturing conditions using high-performance size-exclusion chromatography, sucrose density gradient centrifugation, immunodiffusion techniques, SDS-polyacrylamide gradient gel electrophoresis with immunoblotting identification procedures, and two-dimensional electrophoresis. This is the first procedure known to us that allows for the simultaneous one-step isolation (under homologous conditions) of various immunoglobulins with preserved quaternary structure and apparent biological activity.

Adsorption

Dynamics of microtubules from erythrocyte marginal bands.

Microtubules can adjust their length by the mechanism of dynamic instability, that is by switching between phases of growth and shrinkage. Thus far this phenomenon has been studied with microtubules that contain several components, that is, a mixture of tubulin isoforms, with or without a mixture of microtubule-associated proteins (MAPs), which can act as regulators of dynamic instability. Here we concentrate on the influence of the tubulin component. We have studied MAP-free microtubules from the marginal band of avian erythrocytes and compared them with mammalian brain microtubules. The erythrocyte system was selected because it represents a naturally stable aggregate of microtubules; second, the tubulin is largely homogeneous, in contrast to brain tubulin. Qualitatively, erythrocyte microtubules show similar features as brain microtubules, but they were found to be much less dynamic. The critical concentration of elongation, and the rates of association and dissociation of tubulin are all lower than with brain microtubules. Catastrophes are rare, rescues frequent, and shrinkage slow. This means that dynamic instability can be controlled by the tubulin isotype, independently of MAPs. Moreover, the extent of dynamic behavior is highly dependent on buffer conditions. In particular, dynamic instability is strongly enhanced in phosphate buffer, both for erythrocyte marginal band and brain microtubules. The lower stability in phosphate buffer argues against the hypothesis that a cap of tubulin.GDP.Pi subunits stabilizes microtubules. The difference in dynamics between tubulin isotypes and between the two ends of microtubules is preserved in the different buffer systems.

Animals

[Features of mutated changes of genomic RNA of cold-adapted and hr-variants of influenza group A virus, detected by RNA:RNA hybridization].

The presence of mutations in the majority of the genes of cold-adapted strains A/Leningrad/134/17/57 (H2N2), A/Leningrad/134/47/57 (H2N2) and A/PR/8/59/1 (H1N1) of influenza A virus has been demonstrated by the RNA-RNA hybridization with the subsequent electrophoresis of double-stranded RNA in 7.5% polyacrylamide gel. The strains were cultivated 17, 47 and 59 passages in the chicken embryos at 25 degrees C. In the genomes of variants passaged in chicken embryos at optimal temperature of incubation 36 degrees C (hr-variants) the used technique permits identification of a single mutant gene. The obtained data suppose the attenuation of cold-adapted vaccine strains of influenza A virus and their high genetic stability to be a result of selection of the variants obtaining multiple mutations in the genome during passaging of the virions at cold temperature. The attenuation of hr-variants is defined by 1-2 mutations (first of all in HA-gene) that makes understandable their inability to serve as donors for recombinant live influenza vaccines construction.

Antigens, Viral

[Retinal pigment epithelial detachment].

The vast majority of cases of AMD involve widespread disease with visible neovascularization, "occult" neovascularization, and serous as well as hemorrhagic detachments of the RPE. Accurate interpretation of the clinical and fluorescein angiographic findings in PEDs is difficult. The most noteworthy problem is the recognition of the presence and extent of associated neovascularization. Definitive guidelines for laser photocoagulation treatment of these PEDs have not yet been established. Large-scale, sophisticated clinical trials are needed to assess the efficacy and safety of laser treatment for this important manifestation of exudative AMD. Until these investigations are completed, certain cases of PEDs may be selected for laser treatment by one of three treatment techniques. A grid pattern photocoagulation to a serous PED may be carried out when there is no demonstrable or suspected underlying SRN and there is persistence and progression of the detachment with associated visual decline. Total photocoagulation of the PED which is suspected of having neovascularization can also be carried out if the fovea can be spared. Finally, photocoagulation of extrafoveal neovascularization beneath or at the margin of a PED can be performed in an attempt to obliterate the neovascularization, resolve the exudative manifestations, and stabilize or improve the vision. Only experienced retinal specialists who are well trained in the recognition of the complex clinical and fluorescein angiographic features of PEDs should attempt to treat these unusual and complicated cases.

Aging

Immunotoxins: is there a clinical value?

Drug targeting is an attractive new approach to killing malignant cells, thereby leaving normal tissue unharmed. A decisive breakthrough was the advent of hybridoma technology, making monoclonal antibodies (MoAb) available in limitless supply. To construct reagents with selectivity for certain tumor cells, MoAbs or Fab' fragments were chemically linked to ribosome-damaging toxins derived from plants or bacteria like ricin, abrin, saporin, Pseudomonas exotoxin (PE), and diphtheria toxin (DT) to form immunotoxins, which combined the selectivity of the carrier moiety with the potency of the toxin moiety. The first generation of these immunotoxins showed impressive results in vitro but in most cases disappointing antitumour effects in animals or humans. By contrast, the second generation of immunotoxins, consisting of either A chain immunotoxins with a greatly improved stability in vivo or so-called 'blocked' ricin immunotoxins, have been demonstrated to be extremely effective in several animal models. Preliminary results of the current clinical trials suggest a possible clinical use of immunotoxins in leukemia and lymphoma patients. Genetically engineered fusion toxins have become available, which consist of a growth factor or a cytokine fused to a toxin moiety. In this paper, we will review the features of the three groups of immunotoxins which are most frequently used, i.e., ricin A chain and similar immunotoxins, blocked ricin immunotoxins, and recombinant toxins constructed with Pseudomonas exotoxin or diphtheria toxin.

Clinical Trials as Topic

Nature and distribution of sites of temperature-sensitive folding mutations in the gene for the P22 tailspike polypeptide chain.

Temperature-sensitive folding (tsf) mutations in gene 9 of bacteriophage P22 interfere with the folding and association of the tailspike polypeptide chain at restrictive temperature. We report here the location and amino acid substitutions for 24 independent tsf mutants. The distribution of these and previously identified mutations is distinctly non-random; all of the 32 unambiguous sites of tsf mutations are located in the central 350 residues of the 666 residue tailspike polypeptide chain. No ts mutation has been found among the N-terminal 140 amino acids, and none among the C-terminal 170 amino acids. Since the physiological defect in these mutants is the destabilization of an early intermediate in the folding pathway, the localization of the mutants suggests that the central region of the chain is critical for formation or stabilization of this early intermediate. The majority of amino acids that served as sites for the tsf mutations were hydrophilic residues. Sixty percent of the replacements of these residues represented charge changes. This probably reflects the selection for mutant sites at the mature protein surface where the substitutions can be best tolerated without interfering with function. None of the sites of tsf mutations were at aromatic residues, and only one proline site was found. Substitutions at these residues may cause lethal folding defects which are not recovered as tsf mutants. The local sequences at tsf sites resemble those reported for turns. Structural studies identify beta-sheet as the dominant secondary structure. These mutations may disrupt the formation of conformational features of beta-sheets which are repeated, such as turns, associations between pairs of strands, or sheet/sheet packing interactions. Such a model accounts for the occurrence of tsf mutations with similar defective phenotypes at multiple positions along the chain.

Amino Acids

Chemical ecology: a view from the pharmaceutical industry.

Biological diversity reflects an underlying molecular diversity. The molecules found in nature may be regarded as solutions to challenges that have been confronted and overcome during molecular evolution. As our understanding of these solutions deepens, the efficiency with which we can discover and/or design new treatments for human disease grows. Nature assists our drug discovery efforts in a variety of ways. Some compounds synthesized by microorganisms and plants are used directly as drugs. Human genetic variations that predispose to (or protect against) certain diseases may point to important drug targets. Organisms that manipulate molecules within us to their benefit also may help us to recognize key biochemical control points. Drug design efforts are expedited by knowledge of the biochemistry of a target. To supplement this knowledge, we screen compounds from sources selected to maximize molecular diversity. Organisms known to manipulate biochemical pathways of other organisms can be sources of particular interest. By using high throughput assays, pharmaceutical companies can rapidly scan the contents of tens of thousands of extracts of microorganisms, plants, and insects. A screen may be designed to search for compounds that affect the activity of an individual targeted human receptor, enzyme, or ion channel, or the screen might be designed to capture compounds that affect any step in a targeted metabolic or biochemical signaling pathway. While a natural product discovered by such a screen will itself only rarely become a drug (its potency, selectivity, bioavailability, and/or stability may be inadequate), it may suggest a type of structure that would interact with the target, serving as a point of departure for a medicinal chemistry effort--i.e., it may be a "lead." It is still beyond our capability to design, routinely, such lead structures, based simply upon knowledge of the structure of our target. However, if a drug discovery target contains regions of structure homologous to that in other proteins, structures known to interact with those proteins may prove useful as leads for a medicinal chemistry effort. The specificity of a lead for a target may be optimized by directing structural variation to specificity-determining sites and away from those sites required for interaction with conserved features of the targeted protein structure. Strategies that facilitate recognition and exploration of sites at which variation is most likely to generate a novel function increase the efficiency with which useful molecules can be created.

Animals

A prominent feature of the conversion of P-450 to P-420 of cytochrome P-450B1 among the cytochrome P-450 isozymes.

Conversion of cytochrome P-450 to P-420 was observed with the use of three isozymes of P-450, P-450PB, P-450MC and P-450B1. The last one, which was isolated and characterized in our laboratories, is the cytochrome P-450 with high affinity for cytochrome b5. Of these isozymes, cytochrome P-450B1 is predominantly fast in the rate of conversion from P-450 to P-420 in the reduced state under carbon monoxide. p-Nitroanisole, which is the substrate of P-450B1 for demethylation, accelerated the conversion, whereas the effects of the compound on the rate of conversion of the other P-450S were small. The effect of cholate on the conversion was distinct and rapid but not very selective among the isozymes. Stabilization with glycerol for prevention of the conversion was found to be effective, for any of these isozymes. No remarkable difference was observed in the stability of the oxidized state among these isozymes when detected in the CO-reduced form. The rates of the reaction from the oxidized to the CO-reduced form were measured with these isozymes. The rate of P-450B1 was the highest in both the medium with glycerol and that without glycerol. Circular dichroism was measured with respect to conversion of P-450 to P-420. The absorption at 450 nm was related to the significant circular dichroism, while the increased absorption at 420 nm due to the conversion was not accompanied by distinct circular dichroism. These data support the concept that the heme vicinity of cytochrome P-450B1 is more labile in the structure of the reduced form under carbon monoxide than those of the other isozymes.

Animals

Megamimivirus double-stranded DNA linear genomes flanked by highly diverse terminal inverted repeats.

UNLABELLED: Giant viruses have fundamentally expanded our understanding of virology by challenging the conventional boundaries of both virion size and genome complexity. However, the scarcity of isolates has left many of their unique biological features unexplored. Here, we report the isolation and characterization of four new giant virus species belonging to the subfamily Megamimivirinae, sampled from distinct environments across China. Among these, Megavirus daqingense is the first giant virus isolated from an oil reservoir; it exhibits virion stability under high salinity, chloroform exposure, and elevated temperatures, suggesting fitness adaptations to subsurface conditions. Using a hybrid sequencing approach that integrates short- and long-read technologies, we assembled complete linear genomes for all four isolates, each flanked by long terminal inverted repeats (TIRs). Comparative genomic and synteny analyses identified 29 distinct TIRs from 46 megamimivirus genomes. Gene content within these TIRs was highly diverse, with no orthologous proteins conserved across all repeats. Furthermore, TIR genes experienced weaker purifying selection than those in non-TIR regions (i.e., the genomic regions excluding the TIRs), consistent with their role as drivers of genome plasticity. Notably, we discovered for the first time that identical tRNA genes are shared between TIRs and non-TIR regions of eukaryotic viruses. Collectively, our work provides insights into the structural and evolutionary complexity of megamimiviruses, revealing TIRs as reservoirs of genetic diversity and hotspots for gene transfer, thereby playing a pivotal role in shaping the dynamic architecture of giant virus genomes. IMPORTANCE: Terminal inverted repeats (TIRs) are critical structural elements at the termini of linear genomes essential for fundamental processes such as recombination, replication, and integration across diverse organisms. However, the inherent limitations of short-read sequencing technologies have left the complete structure, diversity, and evolutionary significance of long TIRs in giant viruses unexplored. In this study, we leverage hybrid sequencing and comparative genomic analyses to unveil the complexity of TIRs across the subfamily Megamimivirinae. We demonstrate that TIRs are dynamic genomic hotspots characterized by remarkable gene diversity and unexpected conservation of specific tRNA genes. These findings establish TIRs as key drivers of genome plasticity, serving as hotspots for horizontal gene transfer and genetic innovation. By resolving the long-hidden terminal structures of megamimivirus genomes, this work provides a foundational framework for understanding how TIRs shape the evolution of giant viruses and, more broadly, advances our understanding of genome architecture in large DNA viruses.

Megavirus

Sequences directing dihydrolipoamide dehydrogenase (E3) binding are located on the 2-oxoglutarate dehydrogenase (E1) component of the mammalian 2-oxoglutarate dehydrogenase multienzyme complex.

Sequences located in the N-terminal region of the high M(r) 2-oxoglutarate dehydrogenase (E1) enzyme of the mammalian 2-oxoglutarate dehydrogenase multienzyme complex (OGDC) exhibit significant similarity with corresponding sequences from the lipoyl domains of the dihydrolipoamide acetyltransferase (E2) and protein X components of eukaryotic pyruvate dehydrogenase complexes (PDCs). Two additional features of this region of E1 resemble lipoyl domains: (i) it is readily released by trypsin, generating a small N-terminal peptide with an apparent M(r) value of 10,000 and a large stable 100,000 M(r) fragment (E1') and (ii) it is highly immunogenic, inducing the bulk of the antibody response to intact E1. This 'lipoyl-like' domain lacks a functional lipoamide group. Selective but extensive degradation of E1 with proteinase Arg C or specific conversion of E1 to E1' with trypsin both cause loss of overall OGDC function although the E1' fragment retains full catalytic activity. Removal of this small N-terminal peptide promotes the dissociation of dihydrolipoamide dehydrogenase (E3) from the E2 core assembly and also affects the stability of E1 interaction. Thus, structural roles which are mediated by a specific gene product, protein X in PDC and possibly also the E2 subunit, are performed by similar structural elements located on the E1 enzyme of the OGDC.

Amino Acid Sequence

Conformational study of a nine residue fragment of the antigenic loop of foot-and-mouth disease virus.

The nine-residue peptide Ac-TASARGDLA-NHMe was selected as model peptide in order to understand the conformational features of the antigenic loop of foot-and-mouth disease virus (FMDV). A throughout exploration of the conformational space has been carried out by means of molecular dynamics (MD) and energy minimization. The calculations have been carried out using the AMBER force field. Solvent effects have been included by an effective dielectric constant of epsilon = 4r. The lowest energy conformation presents a secondary structure constituted by an alpha-helix at the N-terminal end followed by two gamma-turns in the central region. The rest of the accessible minima found present also a high tendency to form gamma-turns. Finally, a 100 ps MD trajectory calculation at 298 K suggest a stability of the secondary structure elements of the lowest energy conformation.

Amino Acid Sequence

Proton NMR characterization of isomeric sulfmyoglobins: preparation, interconversion, reactivity patterns, and structural features.

The preparations of sulfmyoglobin (sulf-Mb) by standard procedures have been found heterogeneous by 1H NMR spectroscopy. Presented here are the results of a comprehensive study of the factors that influence the selection among the three dominant isomeric forms of sperm whale sulf-Mb and their resulting detailed optical and 1H NMR properties as related to their detectability and structural properties of the heme pocket. A single isomer is formed initially in the deoxy state; further treatment in any desired oxidation/ligation state can yield two other major isomers. Acid catalysis and chromatography facilitate formation of a second isomer, particularly in the high-spin state. At neutral pH, a third isomer is formed by a first-order process. The processes that alter oxidation/ligation state are found to be reversible and are judged to affect only the metal center, but the three isomeric sulf-Mbs are found to exhibit significantly different ligand affinity and chemical stability. The present results allow, for the first time, a rational approach for preparing a given isomeric sulf-Mb in an optimally pure state for subsequent characterization by other techniques. While optical spectroscopy can distinguish the alkaline forms, only 1H NMR clearly distinguishes all three ferric isomers. The ring current shifts in the carbonyl complexes of reduced sulf-Mb complexes support saturation for a pyrrole in each isomer. The hyperfine shift patterns in the various oxidation/spin states of sulf-Mbs indicate relatively small structural alteration, and the proximal and distal sides of the heme suggest that peripheral electronic effects are responsible for the differentially reduced ligand affinities for the three isomeric sulf-Mbs. The first 1H NMR spectra of sulfhemoglobins are presented, which indicate a structure similar to that of the initially formed sulf-Mb isomer but also suggest the presence of a similar molecular heterogeneity as found for sulf-Mb, albeit to a smaller extent.

Animals

Variation in spotting among the close relatives of the butterfly, Maniola jurtina.

A study of spotting in seven related butterfly species in the genera Maniola and Pyronia has been initiated, in the hope of complementing previous work on Maniola jurtina. Marked individual variability has been found in six of the species. Stability of spotting over large areas has not been prominent, but a high degree of apparent geographical variability has been found in four species. Sometimes this has taken the form of clines and sometimes of quantal steps. Some of the quantal changes coincide with the appearance of different "subspecies". Among the incomplete data presented, parallel geographical variation in different species has not been an obvious feature. There have not been enough samples to test for temporal variation in spotting.

Animals

Suppression of potato spindle tuber viroid replication and symptom expression by mutations which stabilize the pathogenicity domain.

Nucleotides within the pathogenicity domain of potato spindle tuber viroid (PSTVd) are known to play an important role in regulating symptom expression, but the underlying molecular mechanism is unknown. In order to determine more precisely how structural features within the pathogenicity domain regulate symptom expression, we have characterized a series of mutations that progressively stabilize premelting region 1 and the rest of the "virulence modulating" region. The structural effects of these mutations were monitored by temperature gradient gel electrophoresis of circularized RNA transcripts, and their biological effects were assessed by quantitative bioassays in tomato. Closure of a 4-nucleotide loop within the premelting region 1 virtually abolished PSTVd infectivity, especially when a nearby 2-nucleotide loop was also closed. Although RNA transcripts containing less stabilizing mutations were readily infectious, none of the four single and one double substitutions examined were stably maintained in vivo. The pattern of spontaneous, apparently compensatory sequence changes observed in the progeny suggests that PSTVd variants with less stable secondary structures enjoy a selective advantage. Mutations which stabilize the pathogenicity domain of PSTVd in vitro also suppressed symptom expression, but at least one other mutation having no obvious structural effects was associated with a similar phenotype. Conformational stability appears to be only one of several factors regulating PSTVd replication and pathogenicity.

Base Sequence

Patterns of myelination in the opossum superior colliculus with additional reference to the optic tract.

Patterns of myelination have been studied in the optic tract and the superior colliculus (SC), with special reference to the optic layer, in the opossum Didelphis marsupialis. Myelination in the optic tract starts far in precedence of eye opening and follows a rostrocaudal gradient. Myelination in the SC presents the following features: it proceeds according to a general inside-out pattern and follows both rostro-caudal and latero-medial gradients in the optic layer, and it accelerates in the SC optic layer soon after systematic exposure to visual input. The data presented here, together with other available information, suggest that myelination in the opossum optic tract starts in parallel with the stabilization in the number of optic fibers, and advances in the rostro-caudal mode common to most eutherian mammals, and also that myelogenesis in the SC neither correlates necessarily with, nor recapitulates, the sequence of acquisition of GFAP-positive astrocytes in a given set of layers. Changes in the rate of myelination in the optic layer after exposure to visual input are regionally-selective, and seem compatible with the recruitment of thin axons into the myelogenetic cycle rather than with the thickening of pre-existing myelin sheaths. It is concluded that the SC is a favorable structure for the study of the differentiation of glial cells, particularly in species with an extended time course of maturation such as the opossum.

Animals

Determination of the secondary structure of selected melittin analogues with different haemolytic activities.

In earlier studies, we have reported that minor modifications in the amino acid sequence of melittin result in dramatic changes in its biological activity. In the current study, we have investigated the secondary structure of melittin analogues with either increased or decreased haemolytic activity in order to further our understanding of the structural features involved in the binding and/or insertion of peptides into a phospholipid membrane from solution. This was accomplished by analysing the c.d. spectra of the analogues in solutions of various ionic strength and, separately, in the presence of micelles. These studies permit the assessment of the effect of small sequence modifications (i.e. single amino acid omission or substitution) on the self-association-induced secondary structure of melittin in aqueous solution, as well as its binding affinity to micelles. It was found that amphipathicity, as well as interchain distances and the orientation of hydrophobic residues, were involved in the induction of stabilized structures.

Amino Acid Sequence

Medical therapy of VIPomas.

VIP-secreting tumors are rare, but they produce a dramatic clinical picture, the most prominent feature of which is profuse, watery diarrhea and hypokalemia. A definitive diagnosis is aided by the determination of plasma VIP concentrations through the use of the sensitive radioimmunoassays that are now available. Intestinal secretion resulting from the direct action of VIP on the intestinal epithelial cell receptors accounts for the loss of fluid and electrolytes in patients with VIPoma. The hypokalemia is the result of passive and VIP-induced active secretion of potassium by colonic epithelial cells. Surgery is the most definitive treatment of VIPoma; pharmacotherapy is extremely important in controlling symptoms and stabilizing the patient prior to surgery. Sandostatin and glucocorticoids are well established agents in the management of the secretory diarrhea; other pharmacologic agents, including clonidine, indomethacin, phenothiazines, lithium carbonate, and propranolol, may be helpful in selected patients but require further study. The most potent and promising drug for the treatment of VIPoma is a new peptidomimetic agent--Sandostatin. This metabolically stable synthetic analogue of somatostatin appears, in part, to inhibit the release of VIP from the tumor and the secretion of chloride by the intestine. In addition to controlling the diarrhea, it may have a direct effect on the tumor in reducing its size.

Adenoma, Islet Cell