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PubMed2005

Competition between two kinds of correlations in literary texts.

A theory of additive Markov chains with long-range memory is used to describe the correlation properties of coarse-grained literary texts. The complex structure of the correlations in the texts is revealed. Anti-persistent correlations at small distances, L approximately < 300, and persistent ones at L approximately > 300 define this non-trivial structure. For some concrete examples of literary texts, the memory functions are obtained and their power-law behavior at long distances is disclosed. This property is shown to be a cause of self-similarity of texts with respect to the decimation procedure.

Journal Article↗

PubMed2004

State transitions in Chlamydomonas reinhardtii. The role of the Mehler reaction in state 2-to-state 1 transition.

The light intensity-dependent transition to state 1 of dark-adapted anaerobic state 2 Chlamydomonas reinhardtii cells is stimulated by oxygen and by other electron acceptors for photosystem I, such as oxaloacetate and methylviologen. This suggests that the transition to state 1 requires the oxidation of the intersystem chain by photosystem I photochemistry. On the other hand, the mere oxidation in the dark of the chain-by addition of O2-leads only to a slow and incomplete transition. The light-driven stimulation by O2 of the state 1 transition is saturated at an O2 concentration of 15 to 20 microm, definitely higher than that of respiration. We suggest that this may represent the affinity for oxygen of the Mehler reaction, a conclusion that is confirmed by the observations that mitochondrial respiration is apparently not involved in modulating state 2-to-state 1 transition. The catalysis of the state 2-to-state 1 transition upon illumination of anaerobically adapted algae might represent, therefore, a relevant physiological role of this process in C. reinhardtii.

Algal Proteins↗

PubMed1999

Molecular co-crystals of 2-aminothiazole derivatives.

A series of molecular adducts of 2-aminothiazole derivatives - 2-aminothiazole, 2-amino-2-thiazoline and 2-aminobenzothiazole with the carboxylic-acid-substituted heterocyclics indole-2-carboxylic acid, N-methylpyrrole-2-carboxylic acid and thiophene-2-carboxylic acid - have been prepared and characterized using X-ray powder diffraction and in five cases by single-crystal X-ray diffraction methods. These five compounds are the adducts of 2-amino-2-thiazolium with indole-2-carboxylate [(C(3)H(7)N(2)S)(+)(C(9)H(6)NO(2))(-)], and N-methylpyrrole-2-carboxylate [(C(3)H(7)N(2)S)(+)-(C(6)H(6)NO(2))(-)], 2-aminobenzothiazolium with indole-2-carboxylate [(C(7)H(7)N(2)S)(+)(C(9)H(6)NO(2))(-)], N-methylpyrrole-2-carboxylate [(C(7)H(7)N(2)S)(+)(C(6)H(6)NO(2))(-)] and thiophene-2-carboxylate [(C(7)H(7)N(2)S)(+)(C(5)H(3)O(2)S)(-)]. All complexes involve proton transfer, as indicated by IR spectroscopy, while the five crystal structures display similar hydrogen-bonding patterns with the dominant interaction being an R(2)(2)(8) graph set dimer association between carboxylate groups and the amine/heterocyclic nitrogen sites. Futhermore, in each case a subsiduary interaction between an amino proton and a carboxylate oxygen completes a linear hydrogen-bonded chain. In addition to this, the indole-2-carboxylate molecules in the adduct structure with 2-amino-2-thiazolium form associated dimers which add to the hydrogen-bonding network.

Journal Article↗

PubMed1999

Interactive 3-D virtual colonoscopy system.

We describe a low-cost three-dimensional (3-D) virtual colonoscopy system that is a noninvasive technique for examining the entire colon and can assist physicians in detecting polyps inside the colon. Using the helical CT data and proposed techniques, we can three-dimensionally reconstruct and visualize the inner surface of the colon. We generate high resolution of video views of the colon interior structures as if the viewer's eyes were inside the colon. The physicians can virtually navigate inside the colon in two different modes: interactive and automatic navigation, respectively. For automatic navigation, the flythrough path is determined a priori using the 3-D thinning and two-pass tracking schemes. The whole colon is spatially subdivided into several cells, and only potentially visible cells are taken into account during rendering. To further improve rendering efficiency, potentially visible cells are rendered at different levels of detail. Additionally, a chain of bounding volume in each cell is used to avoid penetrating through the colon during navigation. In comparison with previous work, the proposed system can efficiently accomplish required preprocessing tasks and afford adequate rendering speeds on a low-cost PC system.

Automation↗

PubMed2002

Side-chain modeling with an optimized scoring function.

Modeling side-chain conformations on a fixed protein backbone has a wide application in structure prediction and molecular design. Each effort in this field requires decisions about a rotamer set, scoring function, and search strategy. We have developed a new and simple scoring function, which operates on side-chain rotamers and consists of the following energy terms: contact surface, volume overlap, backbone dependency, electrostatic interactions, and desolvation energy. The weights of these energy terms were optimized to achieve the minimal average root mean square (rms) deviation between the lowest energy rotamer and real side-chain conformation on a training set of high-resolution protein structures. In the course of optimization, for every residue, its side chain was replaced by varying rotamers, whereas conformations for all other residues were kept as they appeared in the crystal structure. We obtained prediction accuracy of 90.4% for chi(1), 78.3% for chi(1 + 2), and 1.18 A overall rms deviation. Furthermore, the derived scoring function combined with a Monte Carlo search algorithm was used to place all side chains onto a protein backbone simultaneously. The average prediction accuracy was 87.9% for chi(1), 73.2% for chi(1 + 2), and 1.34 A rms deviation for 30 protein structures. Our approach was compared with available side-chain construction methods and showed improvement over the best among them: 4.4% for chi(1), 4.7% for chi(1 + 2), and 0.21 A for rms deviation. We hypothesize that the scoring function instead of the search strategy is the main obstacle in side-chain modeling. Additionally, we show that a more detailed rotamer library is expected to increase chi(1 + 2) prediction accuracy but may have little effect on chi(1) prediction accuracy.

Algorithms↗

PubMed1984

Structure-activity relationships of retinoids in the morphogenesis of cutaneous appendages in the chick embryo.

We have evaluated the efficacy of 13 analogues of retinoic acid (retinoids) in producing in vivo feathers on the normally scaly foot integument (ptilopody) of the chick embryo. The retinoids were dissolved in dimethylsulfoxide and injected at doses from 1.25-250 micrograms into the amniotic cavity of embryos of 10 days of incubation. The results showed that the production of ptilopody requires specific retinoids, namely, those incorporating a free trans carboxylic end group. Indeed, the esterification of this acid end group (retinoid ethyl ester) leads to a delay in the effect of the product. Its substitution by an alcohol (retinol) or an aldehyde group (retinal), or its isomerization, leads to inactive products. The esterification by acetic acid of the alcohol terminal group of retinol leads to a moderately active compound (retinyl acetate). By contrast, modifications of the ring do not interfere with the efficacy of the retinoid, and modifications of the side chain by addition of one or two supplementary rings lead to an increase of the activity.

Animals↗

PubMed2006

Dieldrin resistance in the malaria vector Anopheles gambiae in Ghana.

Anopheles gambiae Giles s.s. (Diptera: Culicidae) is one of the principal vectors of malaria in the Ashanti region of central Ghana. High levels of resistance to dieldrin were recorded in a wild-caught sample from Obuasi (south of Kumasi) as well as a laboratory colony established using material from the wild population. Cytogenetic analysis of wild-caught and laboratory samples revealed chromosomal polymorphism for inversions 2La and 2Rb. Although inversion 2La has previously been shown to be associated with dieldrin resistance in certain other laboratory strains originating from West Africa, there was no obvious association between inversion karyotype assortment and the resistance phenotype in the Obuasi population. In addition, polymerase chain reaction analysis indicated the presence of the alanine296 to glycine mutation in the GABA (gamma amino-butyric acid) receptor (which has been mapped to a chromosomal position within inversion 2La). This mutation has previously been shown to be associated with dieldrin resistance in the same An. gambiae laboratory strains of West African origin. Our data show only a weak association between the dieldrin resistance phenotype and the presence of this mutation, suggesting that another dieldrin resistance mechanism is operational in the Obuasi population. Biochemical and synergist exposure assays suggest a metabolic component, probably mediated by monooxygenase P450 enzymes. We conclude that dieldrin resistance in the An. gambiae population of the Obuasi region occurs at a high level - most likely in the absence of selection - and that control of the resistance phenotype is polyfactorial and must include components other than mutations in the GABA receptor locus.

Animals↗

PubMed1990

Transglutaminase-catalyzed modifications of SV-IV, a major protein secreted from the rat seminal vesicle epithelium.

One of the major proteins secreted from the rat seminal vesicle epithelium, namely SV-IV, was shown to act in vitro as acyl donor and acceptor substrate for transglutaminase from both guinea pig liver and rat anterior prostate secretory fluid. Electrophoretic and chromatographic experiments indicated that the enzyme catalyzed the formation of multiple modified forms of SV-IV. In the absence of small Mr amines, transglutaminase was able to produce at least six different molecular forms of the protein, half of which possessed an Mr higher than that of native SV-IV. These findings suggested that a variable number of intermolecular, and perhaps intramolecular, crosslinks were formed between one or both glutamine residues and one or more lysine residues occurring in the SV-IV polypeptide chain. In addition, at least three modified forms of the protein were produced by transglutaminase in the presence of high concentrations of spermidine, thus indicating the formation of different (gamma-glutamyl)polyamine derivatives of SV-IV. Rabbit uteroglobin and rat anterior prostate secretory protein(s) were also shown to be able to covalently bind spermidine in the presence of the enzyme. The possible biological significance of transglutaminase-mediated modifications of SV-IV, as well as of other proteins occurring in the mammal seminal fluid, are discussed.

Animals↗

PubMed2005

Synthesis and X-ray crystal structure study of the hydroxyurea and hydantoin derivatives of L-valine.

The novel hydroxyurea 5 derivative of L-valine was prepared by aminolysis of N-(1-benzotriazolecarbonyl)-L-valine cyclohexanemethylamide 4 with hydroxylamine. The corresponding hydantoin derivative 6 was synthesized by base catalyzed cyclization of the amide 4. The exact stereostructure of hydantoin derivative 6 has been determined by X-ray crystal structure analysis. The chiral atom of the hydantoin ring in 6 has S configuration what is in agreement with its configuration in the starting L-valine. The molecules of 6 are joined into infinite chains by N-H...O intermolecular hydrogen bond. The infinite chains are additionally linked by two C-H...O hydrogen bonds, thus forming two-dimensional network. The hydantoin derivative of L-valine 6 and its L-leucine analogue LH have similar packing arrangements, so they are homostructural.

Crystallography, X-Ray↗

PubMed1976

Two forms of RNA polymerase B in yeast. Proteolytic conversion in vitro of enzyme BI into BII.

Special care to prevent proteolysis during yeast RNA polymerase B purification leads to the appearance of two forms of enzymes, BI and BII, with different molecular weight (465 000) and 435 000, respectively). The two forms of enzyme can be separated by ion-exchange chromatography or polyacrylamide gel electrophoresis. Their subunit structures were compared by sodium dodecylsulfate gel electrophoresis, the only observed difference between the two enzymes is in the molecular weight of the heaviest subunit which is 220 000 for enzyme BI and 180 000 for enzyme BII. Otherwise, the two enzymes have seven common subunits of molecular weights 150 000, 45 000, 26 000, 22 500, 14 500, 12 500 and 9000. Two additional polypeptide chains of 32 000 and 16 500 Mr are dissociated from the enzyme upon polyacrylamide gel electrophoresis or DEAE Sephadex chromatography. The largest subunit of enzyme BI (Mr 220 000) can be specifically cleaved in vitro by a yeast protease extract, generating a polypeptide chain indistinguishable from the largest subunit of enzyme BII. This proteolytic cleavage of enzyme BI in vitro is inhibited by phenylmethylsulfonyl fluoride and does not significantly change the activity of the enzyme with single-stranded or double-stranded DNA as template. The precursor-product relationship of the different forms of class B RNA polymerases in eukaryotic cells is discussed.

Amanitins↗

PubMed1987

Characterization of three constituent chains of collagen type VI by peptide sequences and cDNA clones.

Pepsin-solubilized collagen VI was prepared from human placenta and used to separate three constituent chains for determining partial amino acid sequences. Antibodies raised against the chains assisted in the identification and purification of several cDNA clones from three expression lambda gt11 libraries. Most of the clones hybridized to either a 3.5-kb or 4.2-kb mRNA species which by matching peptide and nucleotide sequences could be identified as coding for the alpha 2(VI) or alpha 1(VI) chain, respectively. Other clones hybridized to either an 8.5-kb mRNA which very likely encoded the alpha 3(VI) chain or to an unknown 2.0-kb mRNA. Northern blots revealed a considerable variation in the mRNA levels for each collagen VI chain in both skin and cornea fibroblasts and in several tumor cell lines. Limited sequence data generated from peptides and cDNA clones demonstrated a characteristic cysteine pattern at the junction between N-terminal globular domain and triple helix in all three chains. In addition, the data showed occasional interruptions of triplet sequences within the triple-helical domain and the presence of two Arg-Gly-Asp sequences which are potential cell-binding structures.

Amino Acid Sequence↗

PubMed1992

Biosynthesis and intracellular transport of alpha-2,6-sialyltransferase in rat hepatoma cells.

We investigated biosynthesis, intracellular transport and release of beta-galactoside alpha-2,6-sialyltransferase in a dexamethasone-inducible rat hepatoma cell line. Confluent cells were induced by 10 microM dexamethasone for 24 h, and metabolically labelled with [35S]methionine/cysteine, followed by immunoprecipitation of sialyltransferase and electrophoretic/fluorographic analysis. The 35S-labelled enzyme was synthesized as a 46-kDa precursor, converted to an intermediate 47-kDa form after 1 h, and gradually to a mature form of 48 kDa within the following 3 h. By means of either tunicamycin inhibition of N-glycosylation or cleavage of N-glycans from isolated sialyltransferase using N-glycosidase F, the sizes of the precursor and the mature form were reduced to 41 kDa and 43 kDa, respectively. After a 4-h chase, treatment with endoglycosidase H revealed two distinct molecular forms of sialyltransferase, bearing either two N-acetyllactosamine-type or one oligomannose-type and one N-acetyllactosamine-type N-linked sugar chain. In addition, sialyltransferase became sensitive to neuraminidase digestion after a 4-h chase. The half-life of intracellular [35S]sialyltransferase was estimated at 3 h. A soluble form was detectable in the supernatant, 2 h after the pulse. Only 12% of the initially labelled sialyltransferase was found in the medium after 12 h, while 73% of the enzyme was degraded intracellularly. To characterize a possible intracellular degradation site, we studied intracellular transport in the presence of either secretion-blocking or acidotropic agents or protease inhibitors. Degradation was significantly delayed by all treatments. Our results show that sialyltransferase follows the secretory pathway as a membrane protein and is retained at a late Golgi stage. We suggest that the bulk of sialyltransferase in rat hepatoma cells is diverted to a post-Golgi degradation pathway. This route contrasts with the post-Golgi trafficking of beta-1,4-galactosyltransferase in HeLa cells, which is constitutively secreted [Strous, G. J. A. M. & Berger, E. G. (1982) J. Biol. Chem. 257, 7623-7628].

Animals↗

PubMed2005

Comparison of standard phenotypic assays with a PCR method to discriminate Candida albicans and C. dubliniensis.

In 1995, Candida dubliniensis was described as a new species in the genus Candida. Its close relationship to C. albicans has proved problematic in the identification of C. dubliniensis in clinical specimens. The objective of this study was to determine if reproducible differentiation between both species can be obtained by phenotypic assays. Therefore, 100 strains from 86 patients with the ability to produce chlamydospores were examined with different methods including API ID 32 C, colour development on CHROMagar, chlamydospore formation on Staib agar, growth at different temperatures and germ tube formation at 39 degrees C. Additionally, polymerase chain reaction (PCR) was used as gold standard. Six of the investigated strains were C. dubliniensis. The results suggest that there is still no single phenotypic method satisfactory to distinguish between C. albicans and C. dubliniensis.

Agar↗

PubMed1997

Fingerprinting of Salmonella enterica subsp. enterica serovar Enteritidis by ribotyping.

OBJECTIVE: To carry out an epidemiologic evaluation of Salmonella enterica subsp. enterica serovar Enteritidis outbreaks in households and small communities by means of rRNA gene restriction pattern analysis (ribotyping). METHODS: One hundred Enteritidis isolates dating from 1989 to 1994 which could be allocated epidemiologically to different sources or to small community outbreaks were investigated with ribotyping, a fingerprinting method in which bacterial DNA is hybridized with the biotin-labeled plasmid pKK 3535 containing a ribosomal RNA operon of Escherichia coli to determine the ribosomal RNA gene restriction patterns. RESULTS: Four different ribotyping patterns were found with the restriction endonuclease Smal and nine with Sphl. Ribotypes of isolates which could be allocated epidemiologically to a common source usually corresponded. Almost 60% of the Enteritidis infections had the ribotyping pattern Sphl-A. In contrast, this pattern was not found in any of the five Enteritidis strains isolated in 1989. The suspicion that Enteritidis phage type 4 infections are caused by consumption of insufficiently heated eggs is supported by the fact that the ribotyping pattern Sph1-A was found in isolates from eggs and from human specimens. CONCLUSIONS: As patterns Sphl-A and Smal-J appeared in 58% and 75% of the isolates, respectively, ribotyping cannot be used for the differentiation between various outbreaks with these two patterns. In cases where the Enteritidis strains showed less frequent patterns, ribotyping seems to be a practical tool for the identification of infection chains. In addition newly appearing ribotyping patterns can give information about the epidemiologic development of Enteritidis infection.

Journal Article↗

PubMed1998

Mechanisms of force inhibition by halothane and isoflurane in intact rat cardiac muscle.

1. We investigated the mechanisms underlying the negative inotropic effect of the volatile anaesthetics halothane and isoflurane using twenty-two intact, right ventricular trabeculae of rat. [Ca2+]1 was measured qualitatively using either fluo-3 or fura-2, loaded into the cytosol via the acetoxymethyl (AM) ester form. Diastolic sarcomere length was adjusted to 2.1-2.2 micrograms and experiments were performed at 21-23 degrees C. 2. Halothane (0.25-3%) and isoflurane (0.48-4%) produced dose-dependent decreases in the amplitudes of the intracellular Ca2+ transients and twitch force. When the fluorescent Ca2+ indicator signals were corrected for changes in autofluorescence, neither volatile anaesthetic significantly changed diastolic [Ca2+]. 3. The ability of halothane and isoflurane to induce Ca2+ release from the sarcoplasmic reticulum of quiescent trabeculae was examined. When the superfusate was Ca2+ ad Na+ free (thereby preventing Na(+)-Ca2+ exchange and Ca2+ influx), 2% halothane, but not 4% isoflurane, evoked a transient increase in [Ca2+]i. 4. Halothane and isoflurane produced reversible, dose-dependent changes in cellular autofluorescence, the pattern of which was consistent with an increase in concentration of the reduced forms of nicotinamide adenine nucleotides and flavoproteins. This observation supports the putative inhibitory action of volatile anaesthetics at the site of Complex I of the mitochondrial electron transport chain. 5. Addition of the fatty acid hexanoate, a substrate that can be metabolized in the face of Complex I inhibition, did not appreciably attenuate the anaesthetic-induced negative inotropy; however, it greatly diminished autofluorescence changes. 6. To determine whether direct actions of the volatile anaesthetics on the contractile system contributed to the negative inotropy, external [Ca2+] was varied to modulate the amplitude of the Ca2+ transient. In the presence of 2% halothane or 4% isoflurane, restoration of the peak Ca2+ transient to control levels did not restore peak force. Moreover, halothane (1%) and isoflurane (16%) each reduced maximal Ca2(+)-activated force (attained using ryanodine tetani and a high external [Ca2+]) by around 15%. 7. We conclude that the negative inotropic actions of halothane and isoflurane on intact cardiac muscle reflect both reduced availability of Ca2+ and decreased responsiveness of the contractile system to Ca2+. The inhibitory action of the volatile anaesthetics on mitochondrial function does not contribute significantly to the negative inotropy but may lead to changes in cellular autofluorescence and misinterpretation of fluorescent Ca2+ indicator signals.

Anesthetics, General↗

PubMed2006

Expression of prothrombin, thrombin and its receptors in human scars.

The coagulation system is thought to play a pivotal role during the initial phase of wound healing, but mechanisms and cells involved are only partly understood. We have therefore examined human scars for the expression of thrombin, its precursor prothrombin and the thrombin receptors, thrombomodulin (TM) and protease-activated receptor-1 (PAR-1), compared with normal skin. Biopsies of scars were obtained from primary excision sites of melanoma patients (n = 20) and were compared with normal skin distant from the scar (n = 10), using immunohistochemistry. In addition, polymerase chain reaction analyses were performed on scar versus normal tissue and on cultured keratinocytes, fibroblasts and endothelial cells before and after stimulation with selected cytokines known to be active in wound healing. Normal epidermis was stained for prothrombin, thrombin, TM and PAR-1, and dermal tissue was stained only for TM and PAR-1. In scar tissue, thrombin and TM were upregulated in the epidermis and all four molecules in the dermis, independent of the age of the scars. In tissue extracts, mRNA expression of PAR-1 and prothrombin expression were, however, unchanged and TM even slightly decreased in scars, compared with normal skin. On analysis of cultured cells, keratinocytes expressed mRNA for PAR-1, TM and prothrombin, endothelial cells for PAR-1 and TM, and fibroblasts for PAR-1. An upregulation of PAR-1 mRNA was induced in fibroblasts on exposure to tumor necrosis factor-alpha (TNF-alpha), while it remained unchanged in endothelial cells in response to TNF-alpha. A downregulation of TM was induced in endothelial cells on exposure to TNF-alpha. These findings, showing a marked modulation of thrombin, PAR-1 and TM even in older human scar tissue, suggest that the coagulation system is not only involved during clotting, but also during the inflammatory and tissue remodelling phases of wound healing.

Cells, Cultured↗

PubMed2005

Periodontal status and preterm low birth weight: a case control study.

BACKGROUND: Previous studies have suggested that periodontal disease may be an important risk factor for preterm low birth weight. However, the link between periodontal health status of pregnant women and preterm low birth weight is contentious, as recent studies found no association between periodontitis and pregnancy outcome. OBJECTIVE: The aim of this study was to investigate this potential link in a German Caucasian population. METHODS: Fifty-nine pregnant women with a high risk for a preterm low birth weight infant (suffering from preterm contractions, cases, group 1) as well as 42 control women with no preterm contractions during pregnancy and having an infant appropriate for date and weight (>or= 37 weeks gestation, >or= 2500 g, group 2) were examined. Clinical periodontal status was recorded on a full mouth basis. Subgingival plaque samples were taken and periodontal pathogens were identified by polymerase chain reaction. Additionally, interleukin-1 beta level in gingival crevicular fluid was analysed. RESULTS: The mean percentage of sites showing moderate to advanced attachment loss (>or=3 mm) was low in all study groups (group 1: 9.9 +/- 11.2%; group 2:10.6 +/- 14.1%, respectively). No significant differences between the groups in any aspects of the studied periodontitis parameters could be detected. Using a logistic regression model controlling for known preterm low birth weight risk factors, no periodontitis-associated factors increased risk for preterm contractions or preterm low birth weight. The odds ratio (OR) was 1.19 for preterm contractions, the 95% confidence interval (CI) 0.46; 3.11 and 0.73 for preterm low birth weight; 95% CI: 0.13; 4.19, respectively. CONCLUSION: In this population, periodontitis was not a detectable risk factor for preterm low birth weight in pregnant women.

Adolescent↗

PubMed2006

Polarized apical sorting of guanylyl cyclase C is specified by a cytosolic signal.

Receptor guanylyl cyclases respond to ligand stimulation by increasing intracellular cGMP, thereby initiating a variety of cell-signaling pathways. Furthermore, these proteins are differentially localized at the apical and basolateral membranes of epithelial cells. We have identified a region of 11 amino acids in the cytosolic COOH terminus of guanylyl cyclase C (GCC) required for normal apical localization in Madin-Darby canine kidney (MDCK) cells. These amino acids share no significant sequence homology with previously identified cytosolic apical sorting determinants. However, these amino acids are highly conserved and are sufficient to confer apical polarity to the interleukin-2 receptor alpha-chain (Tac). Additionally, we find two molecular weight species of GCC in lysates prepared from MDCK cells over-expressing GCC but observe only the fully mature species on the cell surface. Using pulse-chase analysis in polarized MDCK cells, we followed the generation of this mature species over time finding it to be detectable only at the apical cell surface. These data support the hypothesis that selective apical sorting can be determined using short, cytosolic amino acid motifs and argue for the existence of apical sorting machinery comparable with the machinery identified for basolateral protein traffic.

Amino Acid Sequence↗