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1.
An empirical method for the evaluation of the quality of genomic DNA libraries. 总被引:1,自引:0,他引:1
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An empirical method is presented that enables one to determine, with only a relatively small investment of time and materials, whether a lambda genomic DNA library will be a productive source of clones carrying specific sequences. The method provides an indication of the abundance of the sequences in library DNA and indicates whether major DNA rearrangements have occurred during library construction and amplification. 相似文献
2.
T Meshulam H Herscovitz D Casavant J Bernardo R Roman R P Haugland G S Strohmeier R D Diamond E R Simons 《The Journal of biological chemistry》1992,267(30):21465-21470
The interrelationships between activation of phospholipases and neutrophil stimulus-induced Ca2+ responses remain unclear. We report here that immune complexes activate a phosphatidylcholine-specific phospholipase A in a neutrophil only after the cytoplasmic Ca2+ transient has been initiated in the same cell, while chemotactic peptide activation does not proceed via such a phospholipase A-mediated mechanism. Measurements of [Ca2+] changes and of phosphatidylcholine-specific phospholipase A activity were made by flow cytometry, using Indo-1 for Ca2+ indication, and a new fluorescent probe, bis-BODIPY-phosphatidylcholine, localized in the inner leaflet of the plasma membrane, to measure phospholipase A activation. Both 100 nM formyl-methionyl-leucyl-phenylalanine (with or without cytochalasin B) and 60 micrograms/ml insoluble immune complexes elicited cytoplasmic Ca2+ transients, but only insoluble immune complexes stimulated phospholipase A activation in a subpopulation of cells exhibiting an elevation of [Ca2+]in. Phospholipase A activation followed the Ca2+ transient, starting, in each cell, after [Ca2+]in had begun to decrease as Ca2+ redistributed in the activated cell. The products of this phospholipase activation were confirmed by thin layer chromatography. We conclude that neutrophils respond to immune complexes with an elevated cytoplasmic Ca(2+)-requiring phosphatidylcholine-specific phospholipase A activation and to chemotactic peptides by a different mechanism. 相似文献
3.
The aromatic di-alanine repeat is a novel 12-amino acid-long motif constituting alternate small and large hydrophobic residues that mediate the close packing of alpha-helices. A hidden Markov model profile was constructed from the motifs initially described in Soluble N-ethyl maleimide-sensitive factor attachment proteins (SNAP), a family of soluble proteins involved in intracellular membrane fusion. Scanning different sets of protein sequences showed unambiguously that this profile defines a structural motif independent of the tetratrico peptide repeat, another widespread alpha-helical motif. In addition to SNAP, aromatic di-alanine repeats are found in selective LIM homeodomain binding proteins (SLB) and in proteins from the Pyrococcus and Archaeoglobus prokaryotes. 相似文献
4.
Gavin AJ Scheetz TE Roberts CA O'Leary B Braun TA Sheffield VC Soares MB Robinson JP Casavant TL 《Bioinformatics (Oxford, England)》2002,18(9):1162-1166
MOTIVATION: In gene discovery projects based on EST sequencing, effective post-sequencing identification methods are important in determining tissue sources of ESTs within pooled cDNA libraries. In the past, such identification efforts have been characterized by higher than necessary failure rates due to the presence of errors within the subsequence containing the oligo tag intended to define the tissue source for each EST. RESULTS: A large-scale EST-based gene discovery program at The University of Iowa has led to the creation of a unique software method named UITagCreator usable in the creation of large sets of synthetic tissue identification tags. The identification tags provide error detection and correction capability and, in conjunction with automated annotation software, result in a substantial improvement in the accurate identification of the tissue source in the presence of sequencing and base-calling errors. These identification rates are favorable, relative to past paradigms. AVAILABILITY: The UITagCreator source code and installation instructions, along with detection software usable in concert with created tag sets, is freely available at http://genome.uiowa.edu/pubsoft/software.html CONTACT: tomc@eng.uiowa.edu 相似文献
5.
EST-based gene discovery in pig: virtual expression patterns and comparative mapping to human 总被引:3,自引:0,他引:3
Christopher K. Tuggle Jon A. Green Carolyn Fitzsimmons Rami Woods Randall S. Prather Sergei Malchenko Bento M. Soares Tamara Kucaba Keith Crouch Christina Smith Dylan Tack Natalie Robinson Brian O'Leary Todd Scheetz Thomas Casavant Daniel Pomp Brad J. Edeal Yuandan Zhang Max F. Rothschild Kevin Garwood William Beavis 《Mammalian genome》2003,14(8):565-579
A molecular understanding of porcine reproduction is of biological interest and economic importance. Our Midwest Consortium has produced cDNA libraries containing the majority of genes expressed in major female reproductive tissues, and we have deposited into public databases 21,499 expressed sequence tag (EST) gene sequences from the 3 end of clones from these libraries. These sequences represent 10,574 different genes, based on sequence comparison among these data, and comparison with existing porcine ESTs and genes indicate as many as 4652 of these EST clusters are novel. In silico analysis identified sequences that are expressed in specific pig tissues or organs and confirmed the broad expression in pig for many genes ubiquitously expressed in human tissues. Furthermore, we have developed computer software to identify sequence similarity of these pig genes with their human counterparts, and to extract the mapping information of these human homologues from genome databases. We demonstrate the utility of this software for comparative mapping by localizing 61 genes on the porcine physical map for Chromosomes (Chrs) 5, 10, and 14.
The following Accession numbers were assigned to our deposited sequences: BF701840 – BF704551, BF708383, BF708386 – BF713604, BG322266 – BG322271, BI398567 – BI405235, BQ597354 – BQ605166. 相似文献
6.
Isolation and characterization of autotrophic, hydrogen-utilizing, perchlorate-reducing bacteria 总被引:2,自引:0,他引:2
Shrout JD Scheetz TE Casavant TL Parkin GF 《Applied microbiology and biotechnology》2005,67(2):261-268
Recent studies have shown that perchlorate (ClO4
–) can be degraded by some pure-culture and mixed-culture bacteria with the addition of hydrogen. This paper describes the isolation of two hydrogen-utilizing perchlorate-degrading bacteria capable of using inorganic carbon for growth. These autotrophic bacteria are within the genus Dechloromonas and are the first Dechloromonas species that are microaerophilic and incapable of growth at atmospheric oxygen concentrations. Dechloromonas sp. JDS5 and Dechloromonas sp. JDS6 are the first perchlorate-degrading autotrophs isolated from a perchlorate-contaminated site. Measured hydrogen thresholds were higher than for other environmentally significant, hydrogen-utilizing, anaerobic bacteria (e.g., halorespirers). The chlorite dismutase activity of these bacteria was greater for autotrophically grown cells than for cells grown heterotrophically on lactate. These bacteria used fumarate as an alternate electron acceptor, which is the first report of growth on an organic electron acceptor by perchlorate-reducing bacteria. 相似文献
7.
Paula Augustus Kelly Casavant Natalie Troxel Randy Rieches Fred Bercovitch 《Zoo biology》2006,25(5):383-390
We analyzed 35 years of data from a captive breeding program of cheetahs to determine basic reproductive life history characteristics of females. Breeding females ranged in age from 2.7–10.5 years. Sixteen females and over 13 males produced 129 cubs in 36 litters, with an average litter size of 3.6. Older females produced significantly fewer cubs per litter than younger females, but cub survivorship was comparable across female ages. Sex ratio was balanced at birth and 71% of infants survived the weaning period. Given that the reproductive output of captive cheetahs in our study is similar to that in other zoologic institutions and to cheetahs in the wild, we suggest that reproductive deficits in captive cheetahs arise from the inability of some pairs to breed, due to a lack of mating preference, rather than from a species‐wide problem. Zoo Biol 0:1–8, 2006. © 2006 Wiley‐Liss, Inc. 相似文献
8.
Letavic MA Bronk BS Bertsche CD Casavant JM Cheng H Daniel KL George DM Hayashi SF Kamicker BJ Kolosko NL Norcia LJ Oberton VD Rushing MA Santoro SL 《Bioorganic & medicinal chemistry letters》2002,12(19):2771-2774
The stereoselective synthesis of two novel series of tribasic macrocyclic antibiotics with potent in vitro activity against Pasteurella multocida and Escherichia coli strains of bacteria is described. The in vitro activity can be significantly influenced by the nature of the substituents on the C-4" aminoalcohol, with the stereochemistry of the C-4" alcohol playing a less critical role. The effect of substitution and stereochemistry on the in vivo activity in a murine model of respiratory infection is also described. 相似文献
9.
Background
Protein translocation across the membrane of the Endoplasmic Reticulum (ER) is the first step in the biogenesis of secretory and membrane proteins. Proteins enter the ER by the Sec61 translocon, a proteinaceous channel composed of three subunits, α, β and γ. While it is known that Sec61α forms the actual channel, the function of the other two subunits remains to be characterized.Results
In the present study we have investigated the function of Sec61β in Drosophila melanogaster. We describe its role in the plasma membrane traffic of Gurken, the ligand for the Epidermal Growth Factor (EGF) receptor in the oocyte. Germline clones of the mutant allele of Sec61β show normal translocation of Gurken into the ER and transport to the Golgi complex, but further traffic to the plasma membrane is impeded. The defect in plasma membrane traffic due to absence of Sec61β is specific for Gurken and is not due to a general trafficking defect.Conclusion
Based on our study we conclude that Sec61β, which is part of the ER protein translocation channel affects a post-ER step during Gurken trafficking to the plasma membrane. We propose an additional role of Sec61β beyond protein translocation into the ER. 相似文献10.