Rule of antibody structure: the primary structure of a human monoclonal IgA1-immunoglobulin (myeloma protein Tro), III. Isolation and characterization of the tryptic peptides of the H-chain (author's transl)]

The reduced and either aminothylated or carboxymethylated H-chain of the monoclonal IgA1 immunoglobulin Tro was digested with trypsin. The tryptic peptides were isolated by gel and ion-exchange chromatography. Because of different methods of alkylation, the cysteine-containing peptides could be obtained in two forms and showed additional overlaps. Sequence studies performed with these fragments elucidated the primary structure of the protein.     

Letter: Fragments of polyproline-like structure from a structural protein, cuticlin

Cuticlin is a proline-rich protein isolated from the cuticle of Ascaris lumbricoides. The protein was digested by pronase and fragments very rich in proline were isolated from the digest. Proline accounted for about three-quarters of the total amino acids in the fragments. The number average molecular weight of the fragments was about 3200. The optical rotatory dispersion and circular dichroism measurements indicated that the fragments formed a conformation similar to poly-l-proline II in aqueous solution.     

Adsorption of IgG onto hydrophobic teflon. Differences between the F(ab) and F(c) domains

The effect of differences in the degree of hydrophobicity of protein patches/fragments on the adsorption behaviour of the protein is investigated. The adsorption isotherm of a monoclonal mouse anti-human immunoglobulin G (isotype 2b) onto hydrophobic Teflon particles is measured using a depletion method. The adsorption-induced denaturation of the immunoglobulin as a function of the adsorbed amount is studied by differential scanning calorimetry, and the corresponding rearrangements in the secondary structure of the whole IgG molecule and its F(ab) and F(c) fragments are determined by circular dichroism spectroscopy. The effects of adsorption on the F(ab) and F(c) fragments in the intact IgG molecule occur independently. Adsorption of the whole IgG molecule leads to denaturation of the F(ab) fragments, whereas the F(c) fragment remains unperturbed; adsorption of the isolated fragments results in structural changes in both F(ab) and F(c). The surface hydrophobicity of the isolated fragments was studied by HPLC. These experiments support the hypothesis that differences in the degree of denaturation between F(ab) and F(c) are due to the higher degree of hydrophobicity of the F(ab) fragment. The adsorption-induced changes in the secondary structure are more prominent for the isolated fragments as compared to intact IgG. This is ascribed to the higher flexibility of the isolated fragment, as compared to the fragment in the whole molecule.     

Antigenic structure of rabies virus glycoprotein: ordering and immunological characterization of the large CNBr cleavage fragments.

After rabies virus glycoprotein was treated with CNBr, the peptide mixture was fractionated by preparative sodium dodecyl sulfate-polyacrylamide gel electrophoresis. CNBr-cleaved peptide fragments were resolved into seven peptide bands under reducing conditions and six peptide bands under nonreducing conditions. The isolated nonreduced polypeptides were further analyzed by electrophoresis under reducing conditions. The N-terminal amino acid sequences were determined for the peptides in each of the isolated bands. The sequence data identified eight CNBr peptides and allowed the peptide fragments to be ordered within the deduced amino acid sequence of the glycoprotein. Analysis of the nonreduced CNBr peptides revealed two conformations of the glycoprotein. Two CNBr peptide fragments were specifically immunoprecipitated with a hyperimmune anti-rabies glycoprotein serum. These two and one other CNBr peptide induced the production of rabies virus-neutralizing antibodies, indicating the existence of at least three distinct antigenic sites on the rabies virus glycoprotein.     

An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics

A systematic evaluation of the value and potential of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure has been undertaken. The reproducibility and robustness of the method has been assessed using environmental DNA samples isolated directly from PCB-polluted or pristine soil, and subsequent polymerase chain reaction (PCR) amplification of total community 16S rDNA. An initial investigation to assess the variability both within and between different polyacrylamide gel electrophoresis (PAGE) runs showed that almost identical community profiles were consistently produced from the same sample. Similarly, very little variability was observed as a result of variation between replicate restriction digestions, PCR amplifications or between replicate DNA isolations. Decreasing concentrations of template DNA produced a decline in both the complexity and the intensity of fragments present in the community profile, with no additional fragments detected in the higher dilutions that were not already present when more original template DNA was used. Reducing the number of cycles of PCR produced similar results. The greatest variation between profiles generated from the same DNA sample was produced using different Taq DNA polymerases, while lower levels of variability were found between PCR products that had been produced using different annealing temperatures. Incomplete digestion by the restriction enzyme may, as a result of the generation of partially digested fragments, lead to an overestimation of the overall diversity within a community. The results obtained indicate that, once standardized, T-RFLP analysis is a highly reproducible and robust technique that yields high-quality fingerprints consisting of fragments of precise sizes, which, in principle, could be phylogenetically assigned, once an appropriate database is constructed.     

The primary structure of the hemoglobins of a southern hemisphere lamprey (Mordacia mordax, Cyclostomata)

Mordacia mordax is a southern hemisphere lamprey belonging to Mordaciidae, a primitive family of Cyclostomata. Adult erythrocytes contain three monomeric hemoglobins which can be easily separated by cellulose acetate electrophoresis and isolated by ion-exchange chromatography. The N-terminal regions, and the tryptic peptides from each chain were submitted to automated Edman degradation; the alignment of the fragments was obtained by homology with the other Petromyzonoidea hemoglobins hitherto sequenced. Our results confirm the phylogenic distance between lampreys and hag-fish hemoglobins. As was observed for Petromyzon marinus species, two hemoglobins of Mordacia mordax are very close, as they differ only at 7 positions.     

Effects of cytochalasin B on pancreatic acinar cell structure and secretion

Summary The effects of cytochalasin B (CB) on pancreatic structure and amylase release were studied by use of pancreatic fragments, isolated acini and isolated acinar cells. In pancreatic fragments and isolated acini CB caused the disappearance of microfilaments underlying the apical plasma membrane, loss of apical microvilli and luminal swelling, the last of which was greatly enhanced by addition of protein secretagogues. CB had no effect on basal amylase release but inhibited bethanechol-stimulated amylase in both fragments and acini. Isolated acinar cells, while retaining overall polarity, had lost most of the apical specialization including the microfilament and microvillous complex. Cells were still able to release amylase in response to bethanechol but this release was not affected by CB. The only structural effect of CB on isolated cells was margination of zymogen granules against the plasma membrane. This was, however, not accompanied by increased amylase release. It is concluded that microfilaments are important in maintaining the pancreatic acinar structure. Interference with this structure by CB leads to inhibition of bethanechol-stimulated amylase release. Microfilaments, however, may not play a direct role in secretion.Supported by NIH grant GM-19998 from the United States Public Health Service. — We are indebted to Dr. John Heuser for advice throughout this project and assistance in the preparation of rapidly frozen acini, and to M. Lee for technical assistance     

A fine structure physical map of the short arm of chromosome 5.

A series of somatic cell hybrids that retain abnormal chromosomes 5 from 11 different persons with deletions or translocations involving 5p have been isolated. One hundred twenty DNA fragments isolated from a genomic library enriched for sequences from 5p were regionally localized by Southern blot analysis of the hybrid cell deletion mapping panel, including five DNA fragments that reveal restriction fragment length polymorphisms. The fine structure physical map of 5p together with the identification of additional polymorphic loci will facilitate the construction of a complete linkage map of this region. In addition, DNA fragments localized to a region near the 5p15.2-5p15.3 border, which appears to be the segment of 5p that is critical in producing the phenotype associated with the cri du chat syndrome when it is rendered hemizygous by deletion, will be useful in a molecular and DNA level analysis of this deletion syndrome.     

The structure of the termini of the DNA of Epstein-Barr virus.

We have studied the DNA of Epstein-Barr virus (EBV) isolated from the B95-8 strain of that virus (Miller and Lipman, 1973). When EBV DNA is partially digested with lambda-exonuclease and allowed to reanneal, up to 50% of the full-length molecules circularize. The arrangements of nucleotide sequences containing the terminal repeats identified in this circularization experiment have been determined. Those fragments of viral DNA generated by digestion with restriction endonucleases which are terminal and contain the terminal repeats have been identified by their sensitivity to digestion of full-length DNA by lambda-exonuclease and by virtue of their being partially homologous to one another. The population of DNA molecules in the B95-8 strain of EBV was found to be nonuniform. The nonuniformity results from different molecules having different numbers of a 0.37 megadalton terminal repeat at each end. About 70% of molecules have four terminal repeats at one end, while four equal classes, each comprising approximately 25% of the population, have one, two, three or four repeats at the other end. The arrangements of nucleotide sequences identified as being terminal in virion DNA were studied in the intracellular circular viral DNA of cells transformed by a single particle on EBV. All fragments produced by digestion with endonucleases and scored as being terminal in virion DNA were absent from intracellular circular DNA. An additional fragment was identified in the digests of intracellular DNA of each transformed clone. The molecular weights of the new fragments equal the sum of the molecular weights of two terminal fragments which are joined upon intracellular circularization of viral DNA.     

The primary structure of the Chloroflexus aurantiacus reaction-center polypeptides

The complete nucleotide sequence of two Chloroflexus aurantiacus reaction-center genes has been obtained. The amino acid sequence deduced from the first gene showed 40% similarity to the L subunit of the Rhodobacter sphaeroides reaction center. This L subunit was 310 amino acids long and had an approximate molecular mass of 35 kDa. The second gene began 17 bases downstream from the first gene. The amino acid sequence deduced from it (307 amino acids; 34950 Da) was 42% similar to the M subunit of the Rhodobacter sphaeroides reaction center. 20% of the deduced primary structure were confirmed through automated Edman degradation of cyanogen bromide peptide fragments or N-chlorosuccinimide peptide fragments isolated from the purified reaction-center complex or from the individual subunits. The peptides were isolated by preparative gel electrophoresis combined with molecular sieve chromatography in the presence of a mixture of formic acid, acetonitrile, 2-propanol and water. This method appeared to be applicable to the isolation of other hydrophobic proteins and their peptides.     

Similarity in structure and function of the 3′-terminal region of the four brome mosaic viral RNAs

A 3′-terminal fragment, about 160 nucleotides long, was cleaved by limited nuclease digestion from each of the four RNA components of brome mosaic virus, and purified by two cycles of gel electrophoresis. These fragments accepted tyrosine in reactions catalyzed by wheat germ aminoacyl-tRNA synthetase. Analyses of nuclease digests suggested that the sequences of the fragments from brome mosaic virus RNA 3 and 4 were identical and that the fragments from RNA 1 and 2 differed from that of RNA 4 only in the positions of two and one nucleotides, respectively. A fragment isolated in a similar way from cowpea chlorotic mottle virus was similar in size to the brome mosaic virus RNA fragments, accepted tyrosine in the presence of wheat germ aminoacyl-tRNA synthetase, but had a substantially different nucleotide sequence.     

The covalent structure of hepatic microsomal epoxide hydrolase. I. Isolation and characterization of the cyanogen bromide fragments

Microsomal epoxide hydrolase was purified to homogeneity from phenobarbital-induced rabbit liver for the purpose of determining the complete amino acid sequence. All of the expected 11 cyanogen bromide fragments of epoxide hydrolase were isolated by a combination of gel filtration and high pressure liquid chromatography. Each was characterized by its amino acid composition and NH2-terminal amino acid sequence. The complete amino acid sequences of the eight small fragments, from 5-29 residues, were determined.     

Type VI collagen. Studies on its localization, structure, and biosynthetic form with monoclonal antibodies

Monoclonal antibodies were prepared by immunization with whole tissue and were selected for their reactivity with extracellular matrices in tissue immunofluorescence. Two such antibodies were used to isolate the corresponding antigen from pepsin extracts of human placental tissue by immunochromatography. In each case, polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate showed that the isolated material was composed of four polypeptides of Mr between 57,000 and 85,000 that were disulfide-bonded into a high molecular weight aggregate. Amino acid analyses showed that the isolated material was partly collagenous. The material was shown to be antigenically related to previously isolated peptic fragments of type VI collagen and it shared their unique structure as revealed by electron microscopy. Based on these findings, it was concluded that the isolated material was a form of type VI collagen. In immunofluorescence, the monoclonal antibodies localized type VI collagen throughout the connective tissue and in the extracellular matrix of cultured fibroblasts. Polypeptides presumably comprising the intact form of this collagen were isolated from cultures of metabolically radiolabeled fibroblast cell cultures using the two monoclonal antibodies. The isolated material consisted of two polypeptides of Mr 240,000 and 140,000 that were extensively disulfide cross-linked. Four additional monoclonal antibodies bound the same radioactive polypeptides from fibroblast cultures, but only one of them reacted with the fragments isolated from pepsin-digested placenta. Since all six antibodies were originally selected based on tissue immunofluorescence, and therefore react with the tissue form of the protein, the tissue form appears to be more similar to the polypeptides detected in fibroblast cultures than to the pepsin-resistant fragments. Since these monoclonal antibodies apparently recognize different parts of the molecule, they will be useful for further study of the structure and function of the intact form of type VI collagen.     

Genetic analysis reveals population structure and recent migration within the highly fragmented range of the Cross River gorilla (Gorilla gorilla diehli)

Recently developed methods of individual-based analysis of genetic data allow an unprecedented opportunity to understand the relationships among fragmented populations. By defining population structure and identifying migrant individuals, such analyses can provide a framework to aid in evaluating the threats posed by inbreeding and reduced genetic variability as a consequence of limited gene flow among fragments. Here we investigate population structure in the critically endangered Cross River gorilla (Gorilla gorilla diehli) by applying a suite of individual-based analyses to data obtained from between one-quarter and one-third of the estimated total population through the use of noninvasively collected DNA samples. The population structure inferred using data from 11 autosomal microsatellite loci was broadly consistent with geography and habitat fragmentation, but showed no simple isolation-by-distance effects. In contrast to previous field surveys, which suggested that all gorilla localities were isolated from one another, we infer low levels of gene flow and identify migrants between habitat fragments as well as individuals of admixed ancestry, suggesting persistent recent reproductive contact between many of the localities. These results are encouraging for the conservation of the Cross River gorilla population. Conservation efforts should strive to maintain connectivity between subpopulations that are still in migratory contact and attempt to restore connectivity where it has been lost.     

Secondary structure of the large subunit ribosomal RNA from Escherichia coli, Zea mays chloroplast, and human and mouse mitochondrial ribosomes.

Short base-paired RNA fragments, and fragments containing intra-RNA cross-links, were isolated from E. coli 23S rRNA or 50S ribosomal subunits by two-dimensional gel electrophoresis. The interactions thus found were used as a first basis for constructing a secondary structure model of the 23S rRNA. Sequence comparison with the 23S rDNA from Z. mays chloroplasts, as well as with the 16S (large subunit) rDNA from human and mouse mitochondria, enabled the experimental model to be improved and extrapolated to give complete secondary structures of all four species. The structures are organized in well-defined domains, with over 450 compensating base changes between the two 23S species. Some ribosomal structural "'switches" were found, one involving 5S rRNA.     

Composition of the photosystems and chloroplast structure in extreme shade plants

Chloroplasts were isolated from leaves of three species of tropical rainforest plants, Alocasia macrorrhiza, Cordyline rubra and Lomandra longifolia; these species are representative of extreme “shade” plants. It was found that shade plant chloroplasts contained 4–5 times more chlorophyll than spinach chloroplasts. Their chlorophyll a/chlorophyll b ratio was 2.3 compared with 2.8 for spinach. Electron micrographs of leaf sections showed that the shade plant chloroplasts contained very large grana stacks. The total length of partitions relative to the total length of stroma lamellae was much higher in Alocasia than in spinach chloroplasts. Freeze-etching of isolated chloroplasts revealed both the small and large particles found in spinach chloroplasts.

Despite their increased chlorophyll content, low chlorophyll a/chlorophyll b ratio, and large grana, the shade plant chloroplasts were fragmented with digitonin to yield small fragments (D-144) highly enriched in Photosystem I, and large fragments (D-10) enriched in Photosystem II. The degree of fragmentation of the shade plant chloroplasts was remarkably similar to that of spinach chloroplasts, except that the subchloroplast fragments from the shade plants had lower chlorophyll a/chlorophyll b ratios than the corresponding fragments from spinach. The D-10 fragments from the shade plants had chlorophyll a/chlorophyll b ratios of 1.78-2.00 and the D-144 fragments ratios of 3.54–4.07. We conclude that Photosystems I and II of the shade plants have lower proportions of chlorophyll a to chlorophyll b than the corresponding photosystems of spinach. The lower chlorophyll a/chlorophyll b ratio of shade plant chloroplasts is not due to a significant increase in the ratio of Photosystem II to Photosystem I in these chloroplasts.

The extent of grana formation in higher plant chloroplasts appears to be related to the total chlorophyll content of the chloroplast. Grana formation may simply be an means of achieving a higher density of light-harvesting assemblies and hence a more efficient collection of light quanta.     

Rule of antibody structure: the primary structure of a human monoclonal IgA1-immunoglobulin (Myeloma protein Tro). IV. Isolation and characterization of the chymotryptic peptides of the H-chain (author's transl)]

The preceeding papers dealth with the purification and characterization of IgA immunoglobulin Tro and its H- and L-chains, the separation and characterization of the cyanogen bromide fragments and the isolation of the tryptic splitting products of the H-chain. In this paper the chymotryptic peptides of the H-chain are presented. All chymotryptic peptides were isolated and purified parallel to the isolation of tryptic peptides. On the basis of these overlapping splitting products the arrangement of the tryptic peptides in the protein could be determined. These and other splitting products listed in this paper contributed to the complete sequence determination of of the H-chain.     

Evaluation of the effect of late blight-resistant potato plants on the structure of bacterial associations in soil

We studied the compositions of microbial associations isolated from soils where nontransgenic and transgenic late blight-resistant lines of potato varieties Lugovskoi, Charodei, and Golubizna had been grown. The analysis was based on denaturing gradient gel electrophoresis of total amplificates of 16S rRNA gene fragments and analysis of clone libraries of nifH gene fragments. Neither method revealed significant differences in the structure of the microbial associations isolated from soils with control or transgenic plants. The minor differences detected in the microflora ranges were no greater than those in the rhizospheres of different nontransgenic potato varieties.     

Subunit structure of dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex from bovine kidney

The pyruvate dehydrogenase complex has been isolated from bovine kidney mitochondria under special anti-proteolytic conditions yielding preparations with a specific activity of up to 20 U/mg protein. Dihydrolipoamide acetyltransferase resolved from the complex was subjected to limited proteolysis resulting in the formation of two major fragments with apparent molecular weights of 36000 and 28000. The fragments were isolated by extraction from dodecyl sulfate polyacrylamide gels and were both shown to possess enzymatic activity for acetyl transfer. Acetylation studies indicated that each fragment contains one protein-bound lipoyl group. It is concluded that the kidney dihydrolipoamide acetyltransferase subunit consists of two homologous if not identical domains. A model is suggested where the acetyltransferase core of the mammalian pyruvate dehydrogenase complex is made up of 30 polypeptide chains whose 60 domains could be arranged in pentagonal dodecahedron symmetry quite similar as proposed for the 60 subunit structure of the acetyltransferase core.