Johnson SL

References (20)

Title : Development of a neuroprotective potential algorithm for medicinal plants - Liu_2016_Neurochem.Int_100_164
Author(s) : Liu W , Ma H , DaSilva NA , Rose KN , Johnson SL , Zhang L , Wan C , Dain JA , Seeram NP
Ref : Neurochem Int , 100 :164 , 2016
Abstract : Medicinal plants are promising candidates for Alzheimer's disease (AD) research but there is lack of systematic algorithms and procedures to guide their selection and evaluation. Herein, we developed a Neuroprotective Potential Algorithm (NPA) by evaluating twenty-three standardized and chemically characterized Ayurvedic medicinal plant extracts in a panel of bioassays targeting oxidative stress, carbonyl stress, protein glycation, amyloid beta (Abeta) fibrillation, acetylcholinesterase (AChE) inhibition, and neuroinflammation. The twenty-three herbal extracts were initially evaluated for: 1) total polyphenol content (Folin-Ciocalteu assay), 2) free radical scavenging capacity (DPPH assay), 3) ferric reducing antioxidant power (FRAP assay), 4) reactive carbonyl species scavenging capacity (methylglyoxal trapping assay), 5) anti-glycative effects (BSA-fructose, and BSA-methylglyoxal assays) and, 6) anti-Abeta fibrillation effects (thioflavin-T assay). Based on assigned index scores from the initial screening, twelve extracts with a cumulative NPA score >/=40 were selected for further evaluation for their: 1) inhibitory effects on AChE activity, 2) in vitro anti-inflammatory effects on murine BV-2 microglial cells (Griess assay measuring levels of lipopolysaccharide-induced nitric oxide species), and 3) in vivo neuroprotective effects on Caenorhabditis elegans post induction of Abeta1-42 induced neurotoxicity and paralysis. Among these, four extracts had a cumulative NPA score >/=60 including Phyllanthus emblica (amla; Indian gooseberry), Mucuna pruriens (velvet bean), Punica granatum (pomegranate) and Curcuma longa (turmeric; curcumin). These extracts also showed protective effects on H2O2 induced cytotoxicity in differentiated cholinergic human neuronal SH-SY5Y and murine BV-2 microglial cells and reduced tau protein levels in the SH-SY5Y neuronal cells. While published animal data support the neuroprotective effects of several of these Ayurvedic medicinal plant extracts, some remain unexplored for their anti-AD potential. Therefore, the NPA may be utilized, in part, as a strategy to help guide the selection of promising medicinal plant candidates for future AD-based research using animal models.
ESTHER : Liu_2016_Neurochem.Int_100_164
PubMedSearch : Liu_2016_Neurochem.Int_100_164
PubMedID: 27693453

Title : Genomic sequences of six botulinum neurotoxin-producing strains representing three clostridial species illustrate the mobility and diversity of botulinum neurotoxin genes - Smith_2015_Infect.Genet.Evol_30_102
Author(s) : Smith TJ , Hill KK , Xie G , Foley BT , Williamson CH , Foster JT , Johnson SL , Chertkov O , Teshima H , Gibbons HS , Johnsky LA , Karavis MA , Smith LA
Ref : Infect Genet Evol , 30 :102 , 2015
Abstract : The whole genomes for six botulinum neurotoxin-producing clostridial strains were sequenced to provide references for under-represented toxin types, bivalent strains or unusual toxin complexes associated with a bont gene. The strains include three Clostridium botulinum Group I strains (CDC 297, CDC 1436, and Prevot 594), a Group II C. botulinum strain (Eklund 202F), a Group IV Clostridium argentinense strain (CDC 2741), and a Group V Clostridium baratii strain (Sullivan). Comparisons of the Group I genomic sequences revealed close relationships and conservation of toxin gene locations with previously published Group I C. botulinum genomes. The bont/F6 gene of strain Eklund 202F was determined to be a chimeric toxin gene composed of bont/F1 and bont/F2. The serotype G strain CDC 2741 remained unfinished in 20 contigs with the bont/G located within a 1.15Mb contig, indicating a possible chromosomal location for this toxin gene. Within the genome of C. baratii Sullivan strain, direct repeats of IS1182 insertion sequence (IS) elements were identified flanking the bont/F7 toxin complex that may be the mechanism of bont insertion into C. baratii. Highlights of the six strains are described and release of their genomic sequences will allow further study of unusual neurotoxin-producing clostridial strains.
ESTHER : Smith_2015_Infect.Genet.Evol_30_102
PubMedSearch : Smith_2015_Infect.Genet.Evol_30_102
PubMedID: 25489752
Gene_locus related to this paper: 9clot-a0a0c1u9k6

Title : Complete genome sequences for 59 burkholderia isolates, both pathogenic and near neighbor - Johnson_2015_Genome.Announc_3_
Author(s) : Johnson SL , Bishop-Lilly KA , Ladner JT , Daligault HE , Davenport KW , Jaissle J , Frey KG , Koroleva GI , Bruce DC , Coyne SR , Broomall SM , Li PE , Teshima H , Gibbons HS , Palacios GF , Rosenzweig CN , Redden CL , Xu Y , Minogue TD , Chain PS
Ref : Genome Announc , 3 : , 2015
Abstract : The genus Burkholderia encompasses both pathogenic (including Burkholderia mallei and Burkholderia pseudomallei, U.S. Centers for Disease Control and Prevention Category B listed), and nonpathogenic Gram-negative bacilli. Here we present full genome sequences for a panel of 59 Burkholderia strains, selected to aid in detection assay development.
ESTHER : Johnson_2015_Genome.Announc_3_
PubMedSearch : Johnson_2015_Genome.Announc_3_
PubMedID: 25931592

Title : Finished Genome Sequence of Bacillus cereus Strain 03BB87, a Clinical Isolate with B. anthracis Virulence Genes - Johnson_2015_Genome.Announc_3_0
Author(s) : Johnson SL , Minogue TD , Teshima H , Davenport KW , Shea AA , Miner HL , Wolcott MJ , Chain PS
Ref : Genome Announc , 3 : , 2015
Abstract : Bacillus cereus strain 03BB87, a blood culture isolate, originated in a 56-year-old male muller operator with a fatal case of pneumonia in 2003. Here we present the finished genome sequence of that pathogen, including a 5.46-Mb chromosome and two plasmids (209 and 52 Kb, respectively).
ESTHER : Johnson_2015_Genome.Announc_3_0
PubMedSearch : Johnson_2015_Genome.Announc_3_0
PubMedID: 25593267
Gene_locus related to this paper: bacco-g2th77 , 9burk-a0a0d5v6j6 , 9burk-a0a0d5vg46 , bacmb-a0a0b6amr7 , 9gamm-a0a0b6d7n3 , 9gamm-a0a0e1n4r5 , 9gamm-c6yvf8 , 9burk-a0a0d5lcs9

Title : Draft Genome Sequence of Enterobacter cloacae Strain S611 - Wang_2014_Genome.Announc_2_
Author(s) : Wang D , Han CS , Dichosa AE , Gleasner CD , Johnson SL , Daligault HE , Davenport KW , Li PE , Pierson EA , Pierson LS, 3rd
Ref : Genome Announc , 2 : , 2014
Abstract : We report draft genomes of Enterobacter cloacae strain S611, an endophytic bacterium isolated from surface-sterilized germinating wheat seeds. We present the assembly and annotation of its genome, which may provide insights into the metabolic pathways involved in adaptation.
ESTHER : Wang_2014_Genome.Announc_2_
PubMedSearch : Wang_2014_Genome.Announc_2_
PubMedID: 25502660
Gene_locus related to this paper: entcl-v5ata3

Title : Complete Genome Sequence of Bacillus thuringiensis Serovar Israelensis Strain HD-789 - Doggett_2013_Genome.Announc_1_e01023
Author(s) : Doggett NA , Stubben CJ , Chertkov O , Bruce DC , Detter JC , Johnson SL , Han CS
Ref : Genome Announc , 1 : , 2013
Abstract : Bacillus thuringiensis is an important microbial insecticide for controlling agricultural pests. We report the finished genome sequence of Bacillus thuringiensis serovar israelensis strain HD-789, which contains genes encoding 7 parasporal crystals consisting of Cry4Aa3, Cry4Ba5 (2 genes), Cry10Aa3, Cry11Aa3, Cry60Ba3, and Cry60Aa3, plus 3 Cyt toxin genes and 1 hemagglutinin gene.
ESTHER : Doggett_2013_Genome.Announc_1_e01023
PubMedSearch : Doggett_2013_Genome.Announc_1_e01023
PubMedID: 24309743
Gene_locus related to this paper: bacce-BC2171 , bacce-BC2337 , bacce-BC4102

Title : Draft Genome Sequence of Pseudomonas putida Strain S610, a Seed-Borne Bacterium of Wheat - Wang_2013_Genome.Announc_1_e01048
Author(s) : Wang D , Han CS , Dichosa AE , Gleasner CD , Johnson SL , Daligault HE , Davenport KW , Li PE , Pierson EA , Pierson LS, 3rd
Ref : Genome Announc , 1 : , 2013
Abstract : We report the genome sequence of a seed-borne bacterium, Pseudomonas putida strain S610. The size of the draft genome sequence is approximately 4.6 Mb, which is the smallest among all P. putida strains sequenced to date.
ESTHER : Wang_2013_Genome.Announc_1_e01048
PubMedSearch : Wang_2013_Genome.Announc_1_e01048
PubMedID: 24371199
Gene_locus related to this paper: psepu-PIP , psepu-v6jk66 , psepu-v6j3y1

Title : Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome - Fitzsimons_2013_Genome.Res_23_878
Author(s) : Fitzsimons MS , Novotny M , Lo CC , Dichosa AE , Yee-Greenbaum JL , Snook JP , Gu W , Chertkov O , Davenport KW , McMurry K , Reitenga KG , Daughton AR , He J , Johnson SL , Gleasner CD , Wills PL , Parson-Quintana B , Chain PS , Detter JC , Lasken RS , Han CS
Ref : Genome Res , 23 :878 , 2013
Abstract : The majority of microbial genomic diversity remains unexplored. This is largely due to our inability to culture most microorganisms in isolation, which is a prerequisite for traditional genome sequencing. Single-cell sequencing has allowed researchers to circumvent this limitation. DNA is amplified directly from a single cell using the whole-genome amplification technique of multiple displacement amplification (MDA). However, MDA from a single chromosome copy suffers from amplification bias and a large loss of specificity from even very small amounts of DNA contamination, which makes assembling a genome difficult and completely finishing a genome impossible except in extraordinary circumstances. Gel microdrop cultivation allows culturing of a diverse microbial community and provides hundreds to thousands of genetically identical cells as input for an MDA reaction. We demonstrate the utility of this approach by comparing sequencing results of gel microdroplets and single cells following MDA. Bias is reduced in the MDA reaction and genome sequencing, and assembly is greatly improved when using gel microdroplets. We acquired multiple near-complete genomes for two bacterial species from human oral and stool microbiome samples. A significant amount of genome diversity, including single nucleotide polymorphisms and genome recombination, is discovered. Gel microdroplets offer a powerful and high-throughput technology for assembling whole genomes from complex samples and for probing the pan-genome of naturally occurring populations.
ESTHER : Fitzsimons_2013_Genome.Res_23_878
PubMedSearch : Fitzsimons_2013_Genome.Res_23_878
PubMedID: 23493677
Gene_locus related to this paper: 9stre-k0zi65

Title : Draft Genome Sequence of a Mucoid Isolate of Pseudomonas aeruginosa Strain C7447m from a Patient with Cystic Fibrosis - Yin_2013_Genome.Announc_1_e00837
Author(s) : Yin Y , Withers TR , Johnson SL , Yu HD
Ref : Genome Announc , 1 : , 2013
Abstract : Alginate overproduction by Pseudomonas aeruginosa, or mucoidy, plays an important role in the pathogenesis of chronic lung infections in cystic fibrosis (CF) patients. Here we report the draft genome sequence of a clinical isolate of mucoid P. aeruginosa strain C7447m from a CF patient with chronic lung infection.
ESTHER : Yin_2013_Genome.Announc_1_e00837
PubMedSearch : Yin_2013_Genome.Announc_1_e00837
PubMedID: 24115552
Gene_locus related to this paper: pseae-PA1558 , pseae-PA2927 , pseae-PA3695 , pseae-PA5080

Title : Draft Genome Sequences of Two Alginate-Overproducing Variants of Pseudomonas aeruginosa, PAO1-VE2 and PAO1-VE13 - Yin_2013_Genome.Announc_1_e01031
Author(s) : Yin Y , Withers TR , Niles RM , Johnson SL , Yu HD
Ref : Genome Announc , 1 : , 2013
Abstract : The small envelope protein MucE and the sensor kinase KinB are a positive and negative alginate regulator, respectively. Here, we announce the draft genome sequences of the alginate-overproducing variants Pseudomonas aeruginosa PAO1-VE2 (PAO1 with constitutive expression of mucE) and PAO1-VE13 (PAO1 with kinB inactivated). Both mutants were generated from a transposon mutagenesis screen.
ESTHER : Yin_2013_Genome.Announc_1_e01031
PubMedSearch : Yin_2013_Genome.Announc_1_e01031
PubMedID: 24336371
Gene_locus related to this paper: pseae-PA1558 , pseae-PA2927 , pseae-PA3695 , pseae-PA5080

Title : Complete Genome Sequence of the Encephalomyelitic Burkholderia pseudomallei Strain MSHR305 - Stone_2013_Genome.Announc_1_e00656
Author(s) : Stone JK , Johnson SL , Bruce DC , Detter JC , Mayo M , Currie BJ , Gelhaus HC , Keim P , Tuanyok A
Ref : Genome Announc , 1 :e00656 , 2013
Abstract : We describe the complete genome sequence of Burkholderia pseudomallei MSHR305, a clinical isolate taken from a fatal encephalomyelitis case, a rare form of melioidosis. This sequence will be used for comparisons to identify the genes that are involved in neurological cases.
ESTHER : Stone_2013_Genome.Announc_1_e00656
PubMedSearch : Stone_2013_Genome.Announc_1_e00656
PubMedID: 23969058
Gene_locus related to this paper: burma-a5tq93 , burma-q62mq7

Title : Draft Genome Sequence of a Stable Mucoid Strain of Pseudomonas aeruginosa PAO581 with a mucA25 Mutation - Yin_2013_Genome.Announc_1_e00834
Author(s) : Yin Y , Withers TR , Govan JR , Johnson SL , Yu HD
Ref : Genome Announc , 1 : , 2013
Abstract : A mutation in the mucA gene, which encodes a negative regulator of alginate production in Pseudomonas aeruginosa, is the main mechanism underlying the conversion to mucoidy in clinical isolates from patients with cystic fibrosis (CF). Here, we announce the draft genome sequence of the stable alginate-overproducing mucoid strain P. aeruginosa PAO581 with a mucA25 mutation, a derivative from the nonmucoid strains P. aeruginosa PAO381 and PAO1.
ESTHER : Yin_2013_Genome.Announc_1_e00834
PubMedSearch : Yin_2013_Genome.Announc_1_e00834
PubMedID: 24115549
Gene_locus related to this paper: pseae-PA2927 , pseae-PA3695 , pseae-PA5080 , pseae-q9i252

Title : Cholinergic efferent synaptic transmission regulates the maturation of auditory hair cell ribbon synapses - Johnson_2013_Open.Biol_3_130163
Author(s) : Johnson SL , Wedemeyer C , Vetter DE , Adachi R , Holley MC , Elgoyhen AB , Marcotti W
Ref : Open Biol , 3 :130163 , 2013
Abstract : Spontaneous electrical activity generated by developing sensory cells and neurons is crucial for the maturation of neural circuits. The full maturation of mammalian auditory inner hair cells (IHCs) depends on patterns of spontaneous action potentials during a 'critical period' of development. The intrinsic spiking activity of IHCs can be modulated by inhibitory input from cholinergic efferent fibres descending from the brainstem, which transiently innervate immature IHCs. However, it remains unknown whether this transient efferent input to developing IHCs is required for their functional maturation. We used a mouse model that lacks the alpha9-nicotinic acetylcholine receptor subunit (alpha9nAChR) in IHCs and another lacking synaptotagmin-2 in the efferent terminals to remove or reduce efferent input to IHCs, respectively. We found that the efferent system is required for the developmental linearization of the Ca(2+)-sensitivity of vesicle fusion at IHC ribbon synapses, without affecting their general cell development. This provides the first direct evidence that the efferent system, by modulating IHC electrical activity, is required for the maturation of the IHC synaptic machinery. The central control of sensory cell development is unique among sensory systems.
ESTHER : Johnson_2013_Open.Biol_3_130163
PubMedSearch : Johnson_2013_Open.Biol_3_130163
PubMedID: 24350389

Title : Draft genome sequence for Pseudomonas aeruginosa strain PAO579, a mucoid derivative of PAO381 - Withers_2012_J.Bacteriol_194_6617
Author(s) : Withers TR , Johnson SL , Yu HD
Ref : Journal of Bacteriology , 194 :6617 , 2012
Abstract : Pseudomonas aeruginosa is an opportunistic pathogen that establishes a chronic lung infection in individuals afflicted with cystic fibrosis. Here, we announce the draft genome of P. aeruginosa strain PAO579, an alginate-overproducing derivative of strain PAO381.
ESTHER : Withers_2012_J.Bacteriol_194_6617
PubMedSearch : Withers_2012_J.Bacteriol_194_6617
PubMedID: 23144378
Gene_locus related to this paper: pseae-PA1558 , pseae-PA2927 , pseae-PA2949 , pseae-PA3695 , pseae-PA5080 , pseae-q9i252

Title : The pharmacokinetics of PF-734200, a DPP-IV inhibitor, in subjects with renal insufficiency - Dai_2011_Br.J.Clin.Pharmacol_72_85
Author(s) : Dai H , Johnson SL , Terra SG , Marbury TC , Smith WB , Alcorn H , Boyd RA , Wang R , Nguyen TT
Ref : British Journal of Clinical Pharmacology , 72 :85 , 2011
Abstract : AIMS: PF-734200 is a potent, selective inhibitor of DPP-IV. This two-part study evaluated the pharmacokinetics (PK) of oral 20mg PF-734200 in subjects with varying degrees of renal insufficiency or with end-stage renal disease (ESRD) requiring chronic haemodialysis (HD). The study also assessed the HD clearance of PF-734200 in ESRD. METHODS: Part 1 included subjects with normal renal function or renal insufficiency but not on HD. Subjects received a single dose of 20mg PF-734200 while fasting and serum and urine samples were collected. In part 2, period 1, 1h after HD, a single 20-mg dose was given to subjects with ESRD and serum samples were collected. After a 7-day washout, subjects received another dose followed by collection of serum samples (period 2), during which HD was initiated 4h after dosing. Dialysate samples were collected to quantify amount of drug removed, from which HD clearance was calculated. The fraction of drug dialysed was calculated using an AUC-based method. RESULTS: Systemic exposures of PF-734200 increased approximately 1.5-, 2.2-, 2.1- and 2.8-fold in subjects with mild, moderate, or severe renal insufficiency or ESRD, respectively, compared with subjects with normal renal function. The terminal half-life increased from 16.2h in subjects with normal renal function to 36.6h in subjects with ESRD. Approximately, 29% of PF-734200 in the body after a single-dose administration was dialysed by 4h HD. CONCLUSIONS: Systemic exposure of PF-734200 increases with decreasing renal function. The effect of HD on drug removal is modest.
ESTHER : Dai_2011_Br.J.Clin.Pharmacol_72_85
PubMedSearch : Dai_2011_Br.J.Clin.Pharmacol_72_85
PubMedID: 21366665

Title : Efficacy and safety of the dipeptidyl peptidase-4 inhibitor PF-734200 added to metformin in Type 2 diabetes - Rosenstock_2011_Diabet.Med_28_464
Author(s) : Rosenstock J , Lewin AJ , Norwood P , Somayaji V , Nguyen TT , Teeter JG , Johnson SL , Dai H , Terra SG
Ref : Diabet Med , 28 :464 , 2011
Abstract : AIMS: PF-734200 is a potent and selective oral dipeptidyl peptidase-4 (DPP-4) inhibitor. This study assessed the efficacy and safety of PF-734200 at dose rates of 20 and 30 mg/day in subjects with Type 2 diabetes mellitus inadequately controlled on metformin monotherapy. METHODS: This was a placebo-controlled, double-blind, randomized, multicentre, 12 week study. Subjects with Type 2 diabetes mellitus were eligible if screening glycosylated haemoglobin (HbA(1c) ) was 7-11% (53.0-96.7 mmol/mol) and they had been receiving metformin monotherapy for >/=2 months. Subjects receiving metformin and an insulin secretagogue or metformin and thiazolidinedione needed to have a screening HbA(1c) of 6.5-9.5% (47.5-80.3 mmol/mol), measured prior to discontinuing the insulin secretagogue or thiazolidinedione. The primary end-point of the study was a change from baseline to week 12 in HbA(1c) levels. RESULTS: Baseline characteristics for 289 subjects randomized to PF-734200 or placebo groups were similar (mean age 56.5 years, mean body mass index 32.2 kg/m(2) and mean HbA(1c) 8.2%, 66.1 mmol/mol). In the predefined per protocol data set, least-squares mean HbA(1c) at week 12 was reduced by 0.79 (8.6 mmol/mol 95% confidence interval -1.10 to -0.49, -12.0 to -5.4 mmol/mol) and 0.92% (10.1 mmol/mol; -1.23 to -0.61, -13.4 to -6.7 mmol/mol) in the 20 and 30 mg groups, respectively, compared with placebo. Differences from placebo were statistically significant (P<0.0001), but the differences between the 20 and 30 mg groups were not. The intent-to-treat analysis yielded similar findings. CONCLUSIONS: The HbA(1c) was significantly and meaningfully reduced by both doses of PF-734200, but 20 mg appears to be the more appropriate therapeutic dose for Type 2 diabetes mellitus, contingent upon confirmation by long-term controlled studies.
ESTHER : Rosenstock_2011_Diabet.Med_28_464
PubMedSearch : Rosenstock_2011_Diabet.Med_28_464
PubMedID: 21392067

Title : The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC) - Gerhard_2004_Genome.Res_14_2121
Author(s) : Gerhard DS , Wagner L , Feingold EA , Shenmen CM , Grouse LH , Schuler G , Klein SL , Old S , Rasooly R , Good P , Guyer M , Peck AM , Derge JG , Lipman D , Collins FS , Jang W , Sherry S , Feolo M , Misquitta L , Lee E , Rotmistrovsky K , Greenhut SF , Schaefer CF , Buetow K , Bonner TI , Haussler D , Kent J , Kiekhaus M , Furey T , Brent M , Prange C , Schreiber K , Shapiro N , Bhat NK , Hopkins RF , Hsie F , Driscoll T , Soares MB , Casavant TL , Scheetz TE , Brown-stein MJ , Usdin TB , Toshiyuki S , Carninci P , Piao Y , Dudekula DB , Ko MS , Kawakami K , Suzuki Y , Sugano S , Gruber CE , Smith MR , Simmons B , Moore T , Waterman R , Johnson SL , Ruan Y , Wei CL , Mathavan S , Gunaratne PH , Wu J , Garcia AM , Hulyk SW , Fuh E , Yuan Y , Sneed A , Kowis C , Hodgson A , Muzny DM , McPherson J , Gibbs RA , Fahey J , Helton E , Ketteman M , Madan A , Rodrigues S , Sanchez A , Whiting M , Madari A , Young AC , Wetherby KD , Granite SJ , Kwong PN , Brinkley CP , Pearson RL , Bouffard GG , Blakesly RW , Green ED , Dickson MC , Rodriguez AC , Grimwood J , Schmutz J , Myers RM , Butterfield YS , Griffith M , Griffith OL , Krzywinski MI , Liao N , Morin R , Palmquist D , Petrescu AS , Skalska U , Smailus DE , Stott JM , Schnerch A , Schein JE , Jones SJ , Holt RA , Baross A , Marra MA , Clifton S , Makowski KA , Bosak S , Malek J
Ref : Genome Res , 14 :2121 , 2004
Abstract : The National Institutes of Health's Mammalian Gene Collection (MGC) project was designed to generate and sequence a publicly accessible cDNA resource containing a complete open reading frame (ORF) for every human and mouse gene. The project initially used a random strategy to select clones from a large number of cDNA libraries from diverse tissues. Candidate clones were chosen based on 5'-EST sequences, and then fully sequenced to high accuracy and analyzed by algorithms developed for this project. Currently, more than 11,000 human and 10,000 mouse genes are represented in MGC by at least one clone with a full ORF. The random selection approach is now reaching a saturation point, and a transition to protocols targeted at the missing transcripts is now required to complete the mouse and human collections. Comparison of the sequence of the MGC clones to reference genome sequences reveals that most cDNA clones are of very high sequence quality, although it is likely that some cDNAs may carry missense variants as a consequence of experimental artifact, such as PCR, cloning, or reverse transcriptase errors. Recently, a rat cDNA component was added to the project, and ongoing frog (Xenopus) and zebrafish (Danio) cDNA projects were expanded to take advantage of the high-throughput MGC pipeline.
ESTHER : Gerhard_2004_Genome.Res_14_2121
PubMedSearch : Gerhard_2004_Genome.Res_14_2121
PubMedID: 15489334
Gene_locus related to this paper: human-AFMID , human-CES4A , human-CES5A , human-NOTUM , human-SERAC1 , human-SERHL2 , human-TMEM53 , mouse-acot1 , mouse-adcl4 , mouse-Ces2f , mouse-Ces4a , mouse-notum , mouse-q6wqj1 , mouse-Q9DAI6 , mouse-rbbp9 , mouse-SERHL , mouse-srac1 , mouse-tmm53 , rat-abhd6 , rat-abhda , rat-abhea , rat-abheb , rat-Ldah , rat-cd029 , rat-estd , rat-Kansl3 , rat-nceh1 , ratno-acph , ratno-CMBL , mouse-b2rwd2 , rat-b5den3 , rat-ab17c

Title : Vertebrate genome evolution and the zebrafish gene map - Postlethwait_1998_Nat.Genet_18_345
Author(s) : Postlethwait JH , Yan YL , Gates MA , Horne S , Amores A , Brownlie A , Donovan A , Egan ES , Force A , Gong Z , Goutel C , Fritz A , Kelsh R , Knapik E , Liao E , Paw B , Ransom D , Singer A , Thomson M , Abduljabbar TS , Yelick P , Beier D , Joly JS , Larhammar D , Rosa F , Westerfield M , Zon LI , Johnson SL , Talbot WS
Ref : Nat Genet , 18 :345 , 1998
Abstract : In chordate phylogeny, changes in the nervous system, jaws, and appendages transformed meek filter feeders into fearsome predators. Gene duplication is thought to promote such innovation. Vertebrate ancestors probably had single copies of genes now found in multiple copies in vertebrates and gene maps suggest that this occurred by polyploidization. It has been suggested that one genome duplication event occurred before, and one after the divergence of ray-finned and lobe-finned fishes. Holland et al., however, have argued that because various vertebrates have several HOX clusters, two rounds of duplication occurred before the origin of jawed fishes. Such gene-number data, however, do not distinguish between tandem duplications and polyploidization events, nor whether independent duplications occurred in different lineages. To investigate these matters, we mapped 144 zebrafish genes and compared the resulting map with mammalian maps. Comparison revealed large conserved chromosome segments. Because duplicated chromosome segments in zebrafish often correspond with specific chromosome segments in mammals, it is likely that two polyploidization events occurred prior to the divergence of fish and mammal lineages. This zebrafish gene map will facilitate molecular identification of mutated zebrafish genes, which can suggest functions for human genes known only by sequence.
ESTHER : Postlethwait_1998_Nat.Genet_18_345
PubMedSearch : Postlethwait_1998_Nat.Genet_18_345
PubMedID: 9537416

Title : Centromere-linkage analysis and consolidation of the zebrafish genetic map - Johnson_1996_Genetics_142_1277
Author(s) : Johnson SL , Gates MA , Johnson M , Talbot WS , Horne S , Baik K , Rude S , Wong JR , Postlethwait JH
Ref : Genetics , 142 :1277 , 1996
Abstract : The ease of isolating mutations in zebrafish will contribute to an understanding of a variety of processes common to all vertebrates. To facilitate genetic analysis of such mutations, we have identified DNA polymorphisms closely linked to each of the 25 centromeres of zebrafish, placed centromeres on the linkage map, increased the number of mapped PCR-based markers to 652, and consolidated the number of linkage groups to the number of chromosomes. This work makes possible centromere-linkage analysis, a novel, rapid method to assign mutations to a specific linkage group using half-tetrads.
ESTHER : Johnson_1996_Genetics_142_1277
PubMedSearch : Johnson_1996_Genetics_142_1277
PubMedID: 8846904

Title : A genetic linkage map for the zebrafish - Postlethwait_1994_Science_264_699
Author(s) : Postlethwait JH , Johnson SL , Midson CN , Talbot WS , Gates M , Ballinger EW , Africa D , Andrews R , Carl T , Eisen JS , Horne S , Kimmel CB , Hutchinson M , Johnson M , Rodriguez A
Ref : Science , 264 :699 , 1994
Abstract : To facilitate molecular genetic analysis of vertebrate development, haploid genetics was used to construct a recombination map for the zebrafish Danio (Brachydanio) rerio. The map consists of 401 random amplified polymorphic DNAs (RAPDs) and 13 simple sequence repeats spaced at an average interval of 5.8 centimorgans. Strategies that exploit the advantages of haploid genetics and RAPD markers were developed that quickly mapped lethal and visible mutations and that placed cloned genes on the map. This map is useful for the position-based cloning of mutant genes, the characterization of chromosome rearrangements, and the investigation of evolution in vertebrate genomes.
ESTHER : Postlethwait_1994_Science_264_699
PubMedSearch : Postlethwait_1994_Science_264_699
PubMedID: 8171321