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  • 1
    Publication Date: 2017-09-08
    Description: Northern bobwhite ( Colinus virginianus ; hereafter bobwhite) and scaled quail ( Callipepla squamata ) populations have suffered precipitous declines across most of their US ranges. Illumina-based first- (v1.0) and second- (v2.0) generation draft genome assemblies for the scaled quail and the bobwhite produced N50 scaffold sizes of 1.035 and 2.042 Mb, thereby producing a 45-fold improvement in contiguity over the existing bobwhite assembly, and ≥90% of the assembled genomes were captured within 1313 and 8990 scaffolds, respectively. The scaled quail assembly (v1.0 = 1.045 Gb) was ~20% smaller than the bobwhite (v2.0 = 1.254 Gb), which was supported by kmer-based estimates of genome size. Nevertheless, estimates of GC content (41.72%; 42.66%), genome-wide repetitive content (10.40%; 10.43%), and MAKER-predicted protein coding genes (17,131; 17,165) were similar for the scaled quail (v1.0) and bobwhite (v2.0) assemblies, respectively. BUSCO analyses utilizing 3023 single-copy orthologs revealed a high level of assembly completeness for the scaled quail (v1.0; 84.8%) and the bobwhite (v2.0; 82.5%), as verified by comparison with well-established avian genomes. We also detected 273 putative segmental duplications in the scaled quail genome (v1.0), and 711 in the bobwhite genome (v2.0), including some that were shared among both species. Autosomal variant prediction revealed ~2.48 and 4.17 heterozygous variants per kilobase within the scaled quail (v1.0) and bobwhite (v2.0) genomes, respectively, and estimates of historic effective population size were uniformly higher for the bobwhite across all time points in a coalescent model. However, large-scale declines were predicted for both species beginning ~15–20 KYA.
    Electronic ISSN: 2160-1836
    Topics: Biology
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  • 2
    Publication Date: 2013-11-10
    Description: Circadian clocks regulate numerous physiological processes that vary across the day-night (diurnal) cycle, but if and how the circadian clock regulates the adaptive immune system is mostly unclear. Interleukin-17-producing CD4(+) T helper (T(H)17) cells are proinflammatory immune cells that protect against bacterial and fungal infections at mucosal surfaces. Their lineage specification is regulated by the orphan nuclear receptor RORgammat. We show that the transcription factor NFIL3 suppresses T(H)17 cell development by directly binding and repressing the Rorgammat promoter. NFIL3 links T(H)17 cell development to the circadian clock network through the transcription factor REV-ERBalpha. Accordingly, TH17 lineage specification varies diurnally and is altered in Rev-erbalpha(-/-) mice. Light-cycle disruption elevated intestinal T(H)17 cell frequencies and increased susceptibility to inflammatory disease. Thus, lineage specification of a key immune cell is under direct circadian control.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4165400/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4165400/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yu, Xiaofei -- Rollins, Darcy -- Ruhn, Kelly A -- Stubblefield, Jeremy J -- Green, Carla B -- Kashiwada, Masaki -- Rothman, Paul B -- Takahashi, Joseph S -- Hooper, Lora V -- R01 DK070855/DK/NIDDK NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2013 Nov 8;342(6159):727-30. doi: 10.1126/science.1243884.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24202171" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Basic-Leucine Zipper Transcription Factors/genetics/*metabolism ; CLOCK Proteins/genetics ; Cell Differentiation/*genetics ; Cell Lineage/genetics ; Circadian Clocks/genetics/*immunology ; *Gene Expression Regulation ; Germ-Free Life ; HEK293 Cells ; Humans ; Intestine, Small/immunology/microbiology ; Jurkat Cells ; Mice ; Mice, Inbred C57BL ; Mice, Mutant Strains ; Nuclear Receptor Subfamily 1, Group D, Member 1/genetics/metabolism ; Nuclear Receptor Subfamily 1, Group F, Member 3/*genetics ; Promoter Regions, Genetic ; Th17 Cells/*cytology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2013-11-22
    Description: Human body-surface epithelia coexist in close association with complex bacterial communities and are protected by a variety of antibacterial proteins. C-type lectins of the RegIII family are bactericidal proteins that limit direct contact between bacteria and the intestinal epithelium and thus promote tolerance to the intestinal microbiota. RegIII lectins recognize their bacterial targets by binding peptidoglycan carbohydrate, but the mechanism by which they kill bacteria is unknown. Here we elucidate the mechanistic basis for RegIII bactericidal activity. We show that human RegIIIalpha (also known as HIP/PAP) binds membrane phospholipids and kills bacteria by forming a hexameric membrane-permeabilizing oligomeric pore. We derive a three-dimensional model of the RegIIIalpha pore by docking the RegIIIalpha crystal structure into a cryo-electron microscopic map of the pore complex, and show that the model accords with experimentally determined properties of the pore. Lipopolysaccharide inhibits RegIIIalpha pore-forming activity, explaining why RegIIIalpha is bactericidal for Gram-positive but not Gram-negative bacteria. Our findings identify C-type lectins as mediators of membrane attack in the mucosal immune system, and provide detailed insight into an antibacterial mechanism that promotes mutualism with the resident microbiota.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160023/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160023/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mukherjee, Sohini -- Zheng, Hui -- Derebe, Mehabaw G -- Callenberg, Keith M -- Partch, Carrie L -- Rollins, Darcy -- Propheter, Daniel C -- Rizo, Josep -- Grabe, Michael -- Jiang, Qiu-Xing -- Hooper, Lora V -- C06 RR30414/RR/NCRR NIH HHS/ -- F32 DK100074/DK/NIDDK NIH HHS/ -- GM093271/GM/NIGMS NIH HHS/ -- R01 DK070855/DK/NIDDK NIH HHS/ -- R01 NS040944/NS/NINDS NIH HHS/ -- R01 NS40944/NS/NINDS NIH HHS/ -- R01GM088745/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2014 Jan 2;505(7481):103-7. doi: 10.1038/nature12729. Epub 2013 Nov 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA. ; Department of Cell Biology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA. ; Department of Biological Sciences, University of Pittsburgh, and Joint Carnegie Mellon University-University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, Pennsylvania 15261, USA. ; Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA. ; Department of Biochemistry and Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA. ; 1] Department of Biological Sciences, University of Pittsburgh, and Joint Carnegie Mellon University-University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, Pennsylvania 15261, USA [2] Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California 94143, USA. ; 1] Department of Cell Biology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA [2]. ; 1] Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA [2] The Howard Hughes Medical Institute, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA [3].〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24256734" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Bacterial Agents/chemistry/immunology/*metabolism/pharmacology ; Antigens, Neoplasm/chemistry/immunology/*metabolism ; Biomarkers, Tumor/antagonists & inhibitors/chemistry/immunology/*metabolism ; Cell Membrane Permeability/drug effects ; Cryoelectron Microscopy ; Crystallography, X-Ray ; Gram-Negative Bacteria/drug effects/immunology/metabolism ; Humans ; Immunity, Mucosal/drug effects/immunology ; Intestines/*chemistry/immunology/microbiology ; Lectins, C-Type/antagonists & inhibitors/chemistry/immunology/*metabolism ; Lipopolysaccharides/pharmacology ; Listeria monocytogenes/drug effects/immunology/metabolism ; Microbial Viability/drug effects ; Models, Molecular ; Peptidoglycan/metabolism ; Phospholipids/metabolism ; Porins/antagonists & inhibitors/chemistry/*metabolism ; Symbiosis
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
    ISSN: 1520-6882
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Analytical chemistry 51 (1979), S. 633-637 
    ISSN: 1520-6882
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 6
    ISSN: 1432-184X
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Aeromonas species were recovered from over 27% of 183 chlorinated drinking water samples collected during an 18-month period. Sixteen of 20 isolates tested elicited a cytotoxic response by Y-1 mouse adrenal cells. None of the strains was either enterotoxigenic by the rabbit ligated ileal loop assay, exhibited piliation, or showed significant mannose resistant adherence to human buccal cells. TheAeromonas isolates were further identified to beA. sobria and were resistant to ampicillin and susceptible to chloramphenicol, kanamycin, streptomycin, and tetracycline. Total coliform levels did not correlate withAeromonas densities in distribution water. With 85% of the samplings,Aeromonas occurred in distribution water when no coliforms were detectable by either the membrane filter or most-probable-number techniques. A significant correlation (P〈.001) existed between standard plate count levels andAeromonas.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Springer
    European journal of clinical pharmacology 33 (1987), S. 391-396 
    ISSN: 1432-1041
    Keywords: metyrapone ; acetaminophen ; analgesic intoxication ; pharmacokinetics ; drug interaction ; healthy volunteers
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology , Medicine
    Notes: Summary This study examined the effect of metyrapone on the elimination rate of acetaminophen and on the apparent formation rate of acetaminophen metabolites in man. Metyrapone treatment, 1.5 g, increased the half-life of acetaminophen, decreased the fraction of the dose recovered in the urine as the glucuronide and increased the fraction of the dose recovered in urine as the sulfate and mercapturate conjugates. The apparent rate constant for the formation of acetaminophen glucuronide was significantly decreased by metyrapone while the apparent rate constants for the formation of the sulfate and mercapturic acid metabolites were unchanged or slightly increased, respectively. These data indicate that metyrapone inhibits acetaminophen glucuronidation and possibly enhances the oxidation of acetaminophen to its quantitatively minor yet highly toxic reactive metabolite. The extent to which the parallel pathways of acetaminophen elimination are also affected by inhibitors of cytochrome P-450-mediated oxidation will limit the efficacy of these types of potential antidotes for the treatment of acetaminophen overdose.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    Springer
    European journal of clinical pharmacology 50 (1996), S. 391-397 
    ISSN: 1432-1041
    Keywords: Keywords Codeine ; Scalp hair; disposition
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology , Medicine
    Notes: Abstract Objective: We studied the dose-proportion and time-course relationships for the incorporation of codeine into human hair after the administration of three different doses. Subjects: Male volunteers, with dark hair, were given oral codeine either as a single dose of 60 mg (n = 7) or 120 mg (n = 12), or as multiple doses of 30 mg 3 times daily for 5 days (n = 7) (450 mg total dose). Methods: Blood and urine were collected for various times for up to 72 h after dosing. Scalp hair was collected initially by plucking (up to 4 weeks) and later by cutting for up to 10 weeks. Plasma, urine, proximal 1 cm of hair and distal hair were each analyzed for codeine and its metabolites by positive-ion chemical ionization ion trap gas chromatography/mass spectrometry. Results: Codeine was detected in the proximal 1 cm of hair within 30 min of an oral 120-mg dose. Codeine was not detected in the distal hair segment until 3 weeks after receiving a dose of codeine. Codeine was detected in distal hair segments for at least 10 weeks at 30 pg mg−1 hair following a single 120 mg codeine dose and at 90 pg mg−1 hair following 30 mg codeine 3 times a day for 5 days. Morphine or the glucuronides of codeine or morphine were not detected in the hair specimens of these subjects. Conclusion: Codeine is rapidly distributed into the germanitive elements of hair in a dose-proportional manner. A portion of the codeine remains bound as the hair grows and can be detected in distal hair for up to 10 weeks after a single dose.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    Amsterdam : Elsevier
    International Journal of Non-Linear Mechanics 27 (1992), S. 265-277 
    ISSN: 0020-7462
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    Amsterdam : Elsevier
    International Journal of Non-Linear Mechanics 27 (1992), S. 405-412 
    ISSN: 0020-7462
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Type of Medium: Electronic Resource
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