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PubMedDate not supplied

Construction and characterization of a BAC library from a gynogenetic channel catfish Ictalurus punctatus.

A bacterial artificial chromosome (BAC) library was constructed by cloning HindIII-digested high molecular weight DNA from a gynogenetic channel catfish, Ictalurus punctatus, into the vector pBeloBAC11. Approximately 53,500 clones were arrayed in 384-well plates and stored at -80 degrees C (CCBL1), while clones from a smaller insert size fraction were stored at -80 degrees C without arraying (CCBL2). Pulsed-field gel electrophoresis of 100 clones after NotI digestion revealed an average insert size of 165 kb for CCBL1 and 113 kb for CCBL2. Further characterization of CCBL1 demonstrated that 10% of the clones did not contain an insert. CCBL1 provides a 7.2-fold coverage of the channel catfish haploid genome. PCR-based screening demonstrated that 68 out of 74 unique loci were present in the library. This represents a 92% chance to find a unique sequence. These libraries will be useful for physical mapping of the channel catfish genome, and identification of genes controlling major traits in this economically important species.

Animals↗
PubMed1989

The rat melanin-concentrating hormone messenger ribonucleic acid encodes multiple putative neuropeptides coexpressed in the dorsolateral hypothalamus.

The melanin-concentrating hormone (MCH) is a cyclic neuropeptide, first isolated from salmon pituitary glands, which regulates melanin dispersion in the skin and perhaps the activity of the pituitary-adrenal axis in teleost fish. We have recently purified and characterized rat MCH (rMCH) and report here the cloning and sequencing of specific MCH cDNA isolated from a rat hypothalamic library. The sequence of rMCH found by DNA sequencing confirms the sequence deduced from the purified peptide. rMCH is located at the C-terminus of a protein precursor of 165 amino acid residues. Comparison of the amino acid sequence of prepro-MCH and that of the Aplysia peptide-A prohormone suggests that these proteins as well as other precursors may be evolutionarily related. Besides rMCH, two putative neuropeptides, termed NGE and NEI, might be generated from the same precursor. The rMCH precursor shared sequence identities with human GH-releasing factor and mammalian CRF in the regions encoding NGE and NEI. By immunohistochemical studies we have established that the amidated C-terminus of NEI is recognized by some alpha MSH and rat CRF antisera and that the C-terminal portion of NGE is responsible for the cross-reactivity revealed with one hGRF-(1-37) antiserum. Our results explain the staining of a discrete population of dorso-lateral hypothalamic neurons by heretofore seemingly unrelated antisera and provide evidence for the production of multiple novel neuropeptides from a common precursor.

Animals↗
PubMed1997

Characterization of an intronic promoter of a cyclic adenosine 3',5'-monophosphate (cAMP)-specific phosphodiesterase gene that confers hormone and cAMP inducibility.

In the Sertoli cell, FSH stimulates transcription of a cAMP-phosphodiesterase (PDE) gene (PDE4D) and accumulation of corresponding mRNA and PDE protein. The regulation of this PDE gene is an important component of the desensitization state induced by this hormone. Given the ubiquitous nature of this regulation controlling cAMP levels, the molecular basis for the PDE4D induction was further investigated. FSH stimulation of the Sertoli cell causes the accumulation of only two of the four known PDE4D mRNAs (PDE4D1 and PDE4D2). The promoter controlling the expression of these two messages was identified and characterized. An EcoRI fragment containing a coding exon as well as 5'-upstream sequence of the PDE4D1/2 mRNA was isolated from rat genomic libraries and sequenced. No TATA box was identified, but GC-rich regions were present upstream of the putative translation start site. RNAse protection and PCR analysis indicated the presence of at least two distinct cap sites. This genomic region had promoter activity when transfected both in Sertoli and MA-10 cells. Deletion mutation indicated that basal promoter activity was contributed by regions upstream of both cap sites. Transcription from this promoter was activated by FSH and (Bu)2cAMP, and elements responsible for cAMP regulation were present upstream from the second cap site. These data demonstrate that an intronic promoter that is cAMP- and hormone-inducible directs the expression of these truncated PDE proteins.

3',5'-Cyclic-AMP Phosphodiesterases↗
PubMed2005

Diversity of the microeukaryotic community in sulfide-rich Zodletone Spring (Oklahoma).

The microeukaryotic community in Zodletone Spring, a predominantly anaerobic sulfide and sulfur-rich spring, was examined using an 18S rRNA gene cloning and sequencing approach. The majority of the 288 clones sequenced from three different locations at Zodletone Spring belonged to the Stramenopiles, Alveolata, and Fungi, with members of the phylum Cercozoa, order Diplomonadida, and family Jakobidae representing a minor fraction of the clone library. No sequences suggesting the presence of novel kingdom level diversity were detected in any of the three libraries. A large fraction of stramenopile clones encountered were monophyletic with either members of the genus Cafeteria (order Bicosoecida) or members of the order Labyrinthulida (slime nets), both of which have so far been encountered mainly in marine habitats. The majority of the observed fungal clone sequences belonged to the ascomycetous yeasts (order Saccharomycetales), were closely related to yeast genera within the Hymenobasidiomycetes (phylum Basidiomycetes), or formed a novel fungal lineage with several previously published or database-deposited clones. To determine whether the unexpected abundance of fungal sequences in Zodletone Spring clone libraries represents a general pattern in anaerobic habitats, we generated three clone libraries from three different anaerobic settings (anaerobic sewage digester, pond sediment, and hydrocarbon-exposed aquifer sediments) and partially sequenced 210 of these clones. Phylogenetic analysis indicated that clone sequences belonging to the kingdom Fungi represent a significant fraction of all three clone libraries, an observation confirmed by phospholipid fatty acid and ergosterol analysis. Overall, this work reveals an unexpected abundance of Fungi in anaerobic habitats, describes a novel, yet-uncultured group of Fungi that appears to be widespread in anaerobic habitats, and indicates that several of the previously considered marine protists could also occur in nonmarine habitats.

Ecosystem↗
PubMed2003

Estimating the diversity of peptide populations from limited sequence data.

MOTIVATION: Combinatorial libraries of peptides such as those displayed on the surface of a bacteriophage particle have become widely used tools for characterizing protein-protein and protein-small molecule interactions. The quality of a library frequently depends on its completeness, or diversity-the proportion of possible sequences actually present in the library. The diversity of these libraries is frequently quoted on the basis of phage titers that provide little information about their completeness. RESULTS: Here, an analytical expression for diversity is introduced and a method for estimating the diversity of a peptide library from the sequences of a limited number of the members of the library is demonstrated. The diversities of a number of computationally constructed and actual peptide libraries are estimated using this method.

Algorithms↗
PubMed1992

Elongation factor 3 (EF-3) from Candida albicans shows both structural and functional similarity to EF-3 from Saccharomyces cerevisiae.

As with many other fungi, including the budding yeast Saccharomyces cerevisiae, the dimorphic fungus Candida albicans encodes the novel translation factor, elongation factor 3 (EF-3). Using a rapid affinity chromatography protocol, EF-3 was purified to homogeneity from C. albicans and shown to have an apparent molecular mass of 128 kDa. A polyclonal antibody raised against C. albicans EF-3 also showed cross-reactivity with EF-3 from S. cerevisiae. Similarly, the S. cerevisiae TEF3 gene (encoding EF-3) showed cross-hybridization with genomic DNA from C. albicans in Southern hybridization analysis, demonstrating the existence of a single gene closely related to TEF3 in the C. albicans genome. This gene was cloned by using a 0.7 kb polymerase chain reaction-amplified DNA fragment to screen to C. albicans gene library. DNA sequence analysis of 200 bp of the cloned fragment demonstrated an open reading frame showing 51% predicted amino acid identity between the putative C. albicans EF-3 gene and its S. cerevisiae counterpart over the encoded 65-amino-acid stretch. That the cloned C. albicans sequence did indeed encode EF-3 was confirmed by demonstrating its ability to rescue an otherwise non-viable S. cerevisiae tef3:HIS3 null mutant. Thus EF-3 from C. albicans shows both structural and functional similarity to EF-3 from S. cerevisiae.

Amino Acid Sequence↗
PubMed1998

Cloning, sequencing, and expression of a human brain ecto-apyrase related to both the ecto-ATPases and CD39 ecto-apyrases1.

An extracellular ATPase (E-type ATPase) clone was isolated from a human brain cDNA library and sequenced. The transcript shows similarity to the previously published chicken smooth muscle and rat brain ecto-ATPase cDNAs, human CD39L1 cDNA (putative human ecto-ATPase), and mammalian CD39 (lymphoid cell activation antigen, ecto-apyrase, ATPDase, ATP-diphosphohydrolase) cDNAs. The full-length human brain cDNA encodes a 529 amino acid glycoprotein with a putative membrane spanning region near each terminus, with the majority of the protein found extracellularly. Expression of this clone in mammalian COS-1 cells yielded NaN3-sensitive ATPase and ADPase activity detectable both on intact cells and cell membrane preparations. The nucleotide hydrolysis ratio of the expressed protein is approx. 2.75:1 (ATPase:ADPase activity), classifying it as an ecto-apyrase. However, this hydrolysis ratio is intermediate between that observed for the ecto-ATPases and the CD39 ecto-apyrases (L. Plesner, Int. Rev. Cytol. 158 (1995) 141-214). Quantitative analyses of amino acid identities and similarities between this ecto-apyrase and other vertebrate E-type ATPases suggest that this human brain enzyme is nearly equally related to the ecto-ATPases and the CD39s, and phylogenetic analysis suggests that it could be an ancestral enzyme from which both ecto-ATPases and CD39 ecto-apyrases are derived.

Adenosine Triphosphatases↗
PubMed1996

Structure of the phenylalanine hydroxylase gene in Drosophila melanogaster and evidence of alternative promoter usage.

The complete Drosophila melanogaster phenylalanine hydroxylase gene isolated from a genomic library was sequenced. Gene structure consisted of five exons covering a region of around 3 kb. Position of introns in the C-terminal domain was conserved with mammalian aromatic amino acid hydroxylase genes. Putative promoter sequences in the 5'UTR and intron 1 were identified. A novel transcript was detected differing from that previously reported by the inclusion of a part of the intron 1 sequence. It could be produced using an alternative promoter. The deduced open reading frame would code a protein with a small difference at the N-terminus. Expression of the alternative transcripts was examined throughout development.

Amino Acid Sequence↗
PubMed2004

DNA-templated organic synthesis and selection of a library of macrocycles.

The translation of nucleic acid libraries into corresponding synthetic compounds would enable selection and amplification principles to be applied to man-made molecules. We used multistep DNA-templated organic synthesis to translate libraries of DNA sequences, each containing three "codons," into libraries of sequence-programmed synthetic small-molecule macrocycles. The resulting DNA-macrocycle conjugates were subjected to in vitro selections for protein affinity. The identity of a single macrocycle possessing known target protein affinity was inferred through the sequence of the amplified DNA template surviving the selection. This work represents the translation, selection, and amplification of libraries of nucleic acids encoding synthetic small molecules rather than biological macromolecules.

Amides↗
PubMed1999

Genetic control of the humoral responses to xenografts. III. Identification of the immunoglobulin V(H) genes responsible for encoding rat immunoglobin G xenoantibodies to hamster heart grafts.

BACKGROUND: We have previously reported that the early phases of the immune response of rats to hamster xenografts are characterized by the production of IgM xenoantibodies encoded by a restricted group of Ig germline V(H) genes (V(H)HAR family). In the later phases of the reaction, an IgM to IgG isotype switch occurs and our study examines the structure of the rearranged V(H)HAR genes used to encode IgG antibodies after this isotype switch. METHODS: A quantitative polymerase chain reaction was used to investigate the changes in the levels of V(H)HAR+ IgG mRNA seen after xenotransplantation. cDNA libraries specific for V(H)HAR+ Iggamma chain were established from total RNA extracted from splenocytes of naive rats and xenograft recipients of hamster hearts at days 4, 8, 21, and 28 posttransplantation. Colony filter hybridization was used to estimate the relative frequency of the use of individual V(H)HAR+ IgG subclasses. Selected IgG clones from day 21 cDNA libraries were sequenced and analyzed for VH-D-J(H) gene usage and antibody combining site structure. RESULTS: The level of mRNA for V(H)HAR+ IgG increased 6-fold in xenograft recipients at day 21 post-transplantation when compared with naive animals. The relative frequency of isotype usage for V(H)HAR+ IgG1 antibodies alone increased from 22.3% at day 0 to 37.4% at day 21 PTx. Ten IgG clones from the day 21 cDNA libraries have been sequenced for the rearranged V(H)-D-J(H) genes. Thirty percent (3/10) of these IgG clones used V(H)HAR genes for the coding of heavy chain variable region with limited numbers of nucleic acid substitutions (>98% identity with their germline progenitors) although others demonstrated increased variation in nucleotide sequences (95-97% identity) when compared with germline V(H) genes. Analysis of the canonical binding site structure from the predicted amino acid sequences demonstrated that the majority of IgG clones (9/10) displayed a similar pattern of conserved configurations for their combining sites. CONCLUSIONS: The change in IgM to IgG antibody production in the later stages of the humoral immune response of rats to hamster xenografts is associated with an IgM to IgG isotype switch and an increased production of antibodies of the IgG1 isotype. Rat anti-hamster IgG xenoantibodies continue to express the V(H)HAR family of V(H) genes, many in their original germline configuration, to encode antibody recognition of the hamster target antigens. There are, however, a majority of antibodies for which the V(H) genes express evidence of increased nucleic acid sequence variation when compared to currently available germline sequences. The source of this variation is not known but may represent the expression of as yet unidentified germline genes and/or the introduction of T cell-driven somatic mutations. Despite the appearance of this variation, the unusual level of conservation in key antigen binding sites within the V(H) region suggests the variation, independent of its origin, may have a limited influence on the restricted nature of the host antibody response to xenografts.

Acute Disease↗
PubMed1991

Molecular cloning and expression of a protein-tyrosine phosphatase showing homology with transcription factors Fos and Jun.

A cDNA clone coding for a protein-tyrosine phosphatase (PTPase) was isolated from a rat spleen cDNA library. Nucleotide sequence of the clone showed an open reading frame coding for a polypeptide of 363 amino acids. Expression of this clone in E. coli in an expression vector showed PTPase activity. The non-catalytic region of this PTPase located at the carboxy terminus shows homology with the basic domains of transcription factors Fos and Jun. Northern blot analysis showed that a 1.7 kb transcript was present in many tissues and cells, the highest level being in macrophages. This PTPase is a rat homolog of human T-cell PTPase although it shows 3 large deletions in the carboxy terminal non-catalytic region.

Amino Acid Sequence↗
PubMed1994

Alcohol dehydrogenase of class IV (sigma sigma-ADH) from human stomach. cDNA sequence and structure/function relationships.

Human stomach mucosa contains a characteristic alcohol dehydrogenase (ADH) enzyme, sigma sigma-ADH. Its cDNA has been cloned from a human stomach library and sequenced. The deduced amino acid sequence shows 59-70% identities with the other human ADH classes, demonstrating that the stomach enzyme represents a distinct structure, constituting class IV, coded by a separate gene, ADH7. The amino acid identity with the rat stomach class IV ADH is 88%, which is intermediate between constant and variable dehydrogenases. This value reflects higher conservation than for the classical liver enzymes of class I, compatible with a separate functional significance of the class IV enzyme. Its enzymic features can be correlated with its structural characteristics. The residues lining the substrate-binding cleft are bulky and hydrophobic, similar to those of the class I enzyme; this explains the similar specificity of both classes, compatible with the origin of class IV from class I. Position 47 has Arg, in contrast to Gly in the rat class IV enzyme, but this Arg is still associated with an extremely high activity (kcat = 1510 min-1) and weak coenzyme binding (KiaNAD+ = 1.6 mM). Thus, the strong interaction with coenzyme imposed by Arg47 in class I is probably compensated for in class IV by changes that may negatively affect coenzyme binding: Glu230, His271, Asn260, Asn261, Asn363. The still higher activity and weaker coenzyme binding of rat class IV (kcat = 2600 min-1, KiaNAD = 4 mM) can be correlated to the exchanges to Gly47, Gln230 and Tyr363. An important change at position 294, with Val in human and Ala in rat class IV, is probably responsible for the dramatic difference in Km values for ethanol between human (37 mM) and rat (2.4 M) class IV enzymes.

Alcohol Dehydrogenase↗
PubMed1991

Identification and characterization of rat intestinal keratins. Molecular cloning of cDNAs encoding cytokeratins 8, 19, and a new 49-kDa type I cytokeratin (cytokeratin 21) expressed by differentiated intestinal epithelial cells.

In the previous paper (Quaroni, A., Calnek, D., Quaroni, E., and Chandler, J.S. (1991) J. Biol. Chem. 266, 11923-11931) we describe the use of a panel of "antikeratin" monoclonal antibodies to study cytokeratin distribution in rat intestinal epithelium. In the present paper we describe the use of three antikeratin monoclonal antibodies to identify and recovery cDNA clones expressing immunologically specific fusion proteins from a rat intestinal cDNA library. DNA sequence analysis identified each cDNA encoded epitope including the carboxyl-terminal portions of cytokeratins 8 and 19 (as cataloged by Moll, R., Franke, W.W., and Schiller, D.L. (1982) Cell 31, 11-24) recognized by antibodies RK4 and RK7, respectively. In addition, antibody RK5 was used to recover a cDNA clone (pRK5) encoding a portion of a 48-kDa keratin-related protein with unique tissue and cellular distribution, designated cytokeratin 21. Translation of cDNA-selected mRNAs yielded individual proteins which could be resolved and identified by their specific immunoreactivities. The pRK5 cDNA was used to recover a larger (approximately 1.3 kilobase pairs) cDNA clone (KB2) from an independent cDNA library for DNA sequence analysis and for the recovery of additional overlapping cDNA clones. The resulting cDNA sequence (1519 base pairs) contains the complete coding region of cytokeratin 21 (49,387 daltons). The predicted amino acid sequence of cytokeratin 21 confirms its identity as a novel type I cytokeratin expressed predominantly in the intestinal epithelium.

Amino Acid Sequence↗
PubMed1994

Clone Q379 immunoscreened from a Chinese HCV cDNA lambda gt11 library.

A Chinese HCV cDNA clone, designated as Q379, 379 nucleotides in length, was selected by recombinant immunoscreening from a random-primed Chinese HCV lambda gt11 library. DNA sequencing demonstrated that Q379 situated from positions 7314 to 7695 at NS5 region corresponded with the American prototype HCV nucleotide sequence. The homologies of Q379 with the equivalent sequences of the prototype were found to be 72.8% in nucleotides and 73.8% in amino acids, respectively. Hydrophobicity profile shows that Q379-encoded polypeptide (126 amino acid residues) contains two hydrophilic areas. This Chinese HCV clone would be valuable in basic and clinical studies of Chinese HCV infection.

Amino Acid Sequence↗
PubMed2006

Phylogenetic comparisons of bacterial communities from serpentine and nonserpentine soils.

I present the results of a culture-independent survey of soil bacterial communities from serpentine soils and adjacent nonserpentine comparator soils using a variety of newly developed phylogenetically based statistical tools. The study design included site-based replication of the serpentine-to-nonserpentine community comparison over a regional scale ( approximately 100 km) in Northern California and Southern Oregon by producing 16S rRNA clone libraries from pairs of samples taken on either side of the serepentine-nonserpentine edaphic boundary at three geographical sites. At the division level, the serpentine and nonserpentine communities were similar to each other and to previous data from forest soils. Comparisons of both richness and Shannon diversity produced no significant differences between any of the libraries, but the vast majority of phylogenetically based tests were significant, even with only 50 sequences per library. These results suggest that most samples were distinct, consisting of a collection of lineages generally not found in other samples. The pattern of results showed that serpentine communities tended to be more similar to each other than they were to nonserpentine communities, and these differences were at a lower taxonomic scale. Comparisons of two nonserpentine communities generally showed differences, and some results suggest that the geographical site may control community composition as well. These results show the power of phylogenetic tests to discern differences between 16S rRNA libraries compared to tests that discard DNA data to bin sequences into operational taxonomic units, and they stress the importance of replication at larger scales for inferences regarding microbial biogeography.

Bacteria↗