Young S

References (25)

Title : Cardiovascular Complications of Acetylcholinesterase Inhibitors in Patients with Alzheimer's Disease: A Narrative Review - Young_2021_Ann.Geriatr.Med.Res_25_170
Author(s) : Young S , Chung E , Chen MA
Ref : Ann Geriatr Med Res , 25 :170 , 2021
Abstract : While acetylcholinesterase inhibitors are used to treat a wide range of patients with Alzheimer's disease, acetylcholinesterase inhibitor use has also been associated with a variety of cardiovascular complications, including bradycardia and syncope. Herein, we review the pathophysiology and clinical evidence for cardiovascular complications caused by acetylcholinesterase inhibitors in patients being treated for dementia and discuss options for their management.
ESTHER : Young_2021_Ann.Geriatr.Med.Res_25_170
PubMedSearch : Young_2021_Ann.Geriatr.Med.Res_25_170
PubMedID: 34610666

Title : Exploring the genomic diversity of black yeasts and relatives (Chaetothyriales, Ascomycota) - Teixeira_2017_Stud.Mycol_86_1
Author(s) : Teixeira MM , Moreno LF , Stielow BJ , Muszewska A , Hainaut M , Gonzaga L , Abouelleil A , Patane JS , Priest M , Souza R , Young S , Ferreira KS , Zeng Q , da Cunha MM , Gladki A , Barker B , Vicente VA , de Souza EM , Almeida S , Henrissat B , Vasconcelos AT , Deng S , Voglmayr H , Moussa TA , Gorbushina A , Felipe MS , Cuomo CA , de Hoog GS
Ref : Stud Mycol , 86 :1 , 2017
Abstract : The order Chaetothyriales (Pezizomycotina, Ascomycetes) harbours obligatorily melanised fungi and includes numerous etiologic agents of chromoblastomycosis, phaeohyphomycosis and other diseases of vertebrate hosts. Diseases range from mild cutaneous to fatal cerebral or disseminated infections and affect humans and cold-blooded animals globally. In addition, Chaetothyriales comprise species with aquatic, rock-inhabiting, ant-associated, and mycoparasitic life-styles, as well as species that tolerate toxic compounds, suggesting a high degree of versatile extremotolerance. To understand their biology and divergent niche occupation, we sequenced and annotated a set of 23 genomes of main the human opportunists within the Chaetothyriales as well as related environmental species. Our analyses included fungi with diverse life-styles, namely opportunistic pathogens and closely related saprobes, to identify genomic adaptations related to pathogenesis. Furthermore, ecological preferences of Chaetothyriales were analysed, in conjuncture with the order-level phylogeny based on conserved ribosomal genes. General characteristics, phylogenomic relationships, transposable elements, sex-related genes, protein family evolution, genes related to protein degradation (MEROPS), carbohydrate-active enzymes (CAZymes), melanin synthesis and secondary metabolism were investigated and compared between species. Genome assemblies varied from 25.81 Mb (Capronia coronata) to 43.03 Mb (Cladophialophora immunda). The bantiana-clade contained the highest number of predicted genes (12817 on average) as well as larger genomes. We found a low content of mobile elements, with DNA transposons from Tc1/Mariner superfamily being the most abundant across analysed species. Additionally, we identified a reduction of carbohydrate degrading enzymes, specifically many of the Glycosyl Hydrolase (GH) class, while most of the Pectin Lyase (PL) genes were lost in etiological agents of chromoblastomycosis and phaeohyphomycosis. An expansion was found in protein degrading peptidase enzyme families S12 (serine-type D-Ala-D-Ala carboxypeptidases) and M38 (isoaspartyl dipeptidases). Based on genomic information, a wide range of abilities of melanin biosynthesis was revealed; genes related to metabolically distinct DHN, DOPA and pyomelanin pathways were identified. The MAT (MAting Type) locus and other sex-related genes were recognized in all 23 black fungi. Members of the asexual genera Fonsecaea and Cladophialophora appear to be heterothallic with a single copy of either MAT-1-1 or MAT-1-2 in each individual. All Capronia species are homothallic as both MAT1-1 and MAT1-2 genes were found in each single genome. The genomic synteny of the MAT-locus flanking genes (SLA2-APN2-COX13) is not conserved in black fungi as is commonly observed in Eurotiomycetes, indicating a unique genomic context for MAT in those species. The heterokaryon (het) genes expansion associated with the low selective pressure at the MAT-locus suggests that a parasexual cycle may play an important role in generating diversity among those fungi.
ESTHER : Teixeira_2017_Stud.Mycol_86_1
PubMedSearch : Teixeira_2017_Stud.Mycol_86_1
PubMedID: 28348446
Gene_locus related to this paper: exodn-h6btr2 , exodn-h6c4y3

Title : Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts - Ma_2016_Nat.Commun_7_10740
Author(s) : Ma L , Chen Z , Huang da W , Kutty G , Ishihara M , Wang H , Abouelleil A , Bishop L , Davey E , Deng R , Deng X , Fan L , Fantoni G , FitzGerald M , Gogineni E , Goldberg JM , Handley G , Hu X , Huber C , Jiao X , Jones K , Levin JZ , Liu Y , Macdonald P , Melnikov A , Raley C , Sassi M , Sherman BT , Song X , Sykes S , Tran B , Walsh L , Xia Y , Yang J , Young S , Zeng Q , Zheng X , Stephens R , Nusbaum C , Birren BW , Azadi P , Lempicki RA , Cuomo CA , Kovacs JA
Ref : Nat Commun , 7 :10740 , 2016
Abstract : Pneumocystis jirovecii is a major cause of life-threatening pneumonia in immunosuppressed patients including transplant recipients and those with HIV/AIDS, yet surprisingly little is known about the biology of this fungal pathogen. Here we report near complete genome assemblies for three Pneumocystis species that infect humans, rats and mice. Pneumocystis genomes are highly compact relative to other fungi, with substantial reductions of ribosomal RNA genes, transporters, transcription factors and many metabolic pathways, but contain expansions of surface proteins, especially a unique and complex surface glycoprotein superfamily, as well as proteases and RNA processing proteins. Unexpectedly, the key fungal cell wall components chitin and outer chain N-mannans are absent, based on genome content and experimental validation. Our findings suggest that Pneumocystis has developed unique mechanisms of adaptation to life exclusively in mammalian hosts, including dependence on the lungs for gas and nutrients and highly efficient strategies to escape both host innate and acquired immune defenses.
ESTHER : Ma_2016_Nat.Commun_7_10740
PubMedSearch : Ma_2016_Nat.Commun_7_10740
PubMedID: 26899007
Gene_locus related to this paper: pnec8-a0a0w4zi95 , pnemu-m7nra0 , pnej8-l0pgn2 , pnemu-m7nsb0

Title : The Dynamic Genome and Transcriptome of the Human Fungal Pathogen Blastomyces and Close Relative Emmonsia - Munoz_2015_PLoS.Genet_11_e1005493
Author(s) : Munoz JF , Gauthier GM , Desjardins CA , Gallo JE , Holder J , Sullivan TD , Marty AJ , Carmen JC , Chen Z , Ding L , Gujja S , Magrini V , Misas E , Mitreva M , Priest M , Saif S , Whiston EA , Young S , Zeng Q , Goldman WE , Mardis ER , Taylor JW , McEwen JG , Clay OK , Klein BS , Cuomo CA
Ref : PLoS Genet , 11 :e1005493 , 2015
Abstract : Three closely related thermally dimorphic pathogens are causal agents of major fungal diseases affecting humans in the Americas: blastomycosis, histoplasmosis and paracoccidioidomycosis. Here we report the genome sequence and analysis of four strains of the etiological agent of blastomycosis, Blastomyces, and two species of the related genus Emmonsia, typically pathogens of small mammals. Compared to related species, Blastomyces genomes are highly expanded, with long, often sharply demarcated tracts of low GC-content sequence. These GC-poor isochore-like regions are enriched for gypsy elements, are variable in total size between isolates, and are least expanded in the avirulent B. dermatitidis strain ER-3 as compared with the virulent B. gilchristii strain SLH14081. The lack of similar regions in related species suggests these isochore-like regions originated recently in the ancestor of the Blastomyces lineage. While gene content is highly conserved between Blastomyces and related fungi, we identified changes in copy number of genes potentially involved in host interaction, including proteases and characterized antigens. In addition, we studied gene expression changes of B. dermatitidis during the interaction of the infectious yeast form with macrophages and in a mouse model. Both experiments highlight a strong antioxidant defense response in Blastomyces, and upregulation of dioxygenases in vivo suggests that dioxide produced by antioxidants may be further utilized for amino acid metabolism. We identify a number of functional categories upregulated exclusively in vivo, such as secreted proteins, zinc acquisition proteins, and cysteine and tryptophan metabolism, which may include critical virulence factors missed before in in vitro studies. Across the dimorphic fungi, loss of certain zinc acquisition genes and differences in amino acid metabolism suggest unique adaptations of Blastomyces to its host environment. These results reveal the dynamics of genome evolution and of factors contributing to virulence in Blastomyces.
ESTHER : Munoz_2015_PLoS.Genet_11_e1005493
PubMedSearch : Munoz_2015_PLoS.Genet_11_e1005493
PubMedID: 26439490
Gene_locus related to this paper: ajedr-c5gqv9 , 9euro-a0a2b7ztc4 , 9euro-a0a2b7wr51 , blags-a0a179v0z0 , 9euro-a0a0h1bel0 , blags-a0a179udh1 , ajedr-kex1 , ajedr-cbpya

Title : Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus - Perlin_2015_BMC.Genomics_16_461
Author(s) : Perlin MH , Amselem J , Fontanillas E , Toh SS , Chen Z , Goldberg J , Duplessis S , Henrissat B , Young S , Zeng Q , Aguileta G , Petit E , Badouin H , Andrews J , Razeeq D , Gabaldon T , Quesneville H , Giraud T , Hood ME , Schultz DJ , Cuomo CA
Ref : BMC Genomics , 16 :461 , 2015
Abstract : BACKGROUND: The genus Microbotryum includes plant pathogenic fungi afflicting a wide variety of hosts with anther smut disease. Microbotryum lychnidis-dioicae infects Silene latifolia and replaces host pollen with fungal spores, exhibiting biotrophy and necrosis associated with altering plant development. RESULTS: We determined the haploid genome sequence for M. lychnidis-dioicae and analyzed whole transcriptome data from plant infections and other stages of the fungal lifecycle, revealing the inventory and expression level of genes that facilitate pathogenic growth. Compared to related fungi, an expanded number of major facilitator superfamily transporters and secretory lipases were detected; lipase gene expression was found to be altered by exposure to lipid compounds, which signaled a switch to dikaryotic, pathogenic growth. In addition, while enzymes to digest cellulose, xylan, xyloglucan, and highly substituted forms of pectin were absent, along with depletion of peroxidases and superoxide dismutases that protect the fungus from oxidative stress, the repertoire of glycosyltransferases and of enzymes that could manipulate host development has expanded. A total of 14% of the genome was categorized as repetitive sequences. Transposable elements have accumulated in mating-type chromosomal regions and were also associated across the genome with gene clusters of small secreted proteins, which may mediate host interactions. CONCLUSIONS: The unique absence of enzyme classes for plant cell wall degradation and maintenance of enzymes that break down components of pollen tubes and flowers provides a striking example of biotrophic host adaptation.
ESTHER : Perlin_2015_BMC.Genomics_16_461
PubMedSearch : Perlin_2015_BMC.Genomics_16_461
PubMedID: 26076695
Gene_locus related to this paper: ustv1-u5h5e5

Title : Obituary of Theodore L. Sourkes, PhD, FRSC, OC -
Author(s) : Young S , Quik M , Almazan G , Ekker M
Ref : J Psychiatry Neurosci , 40 :214 , 2015
PubMedID: 25903035

Title : Genome Sequence of the Pathogenic Fungus Sporothrix schenckii (ATCC 58251) - Cuomo_2014_Genome.Announc_2_E00446
Author(s) : Cuomo CA , Rodriguez-Del Valle N , Perez-Sanchez L , Abouelleil A , Goldberg J , Young S , Zeng Q , Birren BW
Ref : Genome Announc , 2 :E0044614 , 2014
Abstract : Sporothrix schenckii is a pathogenic dimorphic fungus that grows as a yeast and as mycelia. This species is the causative agent of sporotrichosis, typically a skin infection. We report the genome sequence of S. schenckii, which will facilitate the study of this fungus and of the Sporothrix schenckii group.
ESTHER : Cuomo_2014_Genome.Announc_2_E00446
PubMedSearch : Cuomo_2014_Genome.Announc_2_E00446
PubMedID: 24855299
Gene_locus related to this paper: spos1-u7q5l6 , spos1-u7phh2 , spos1-u7pxz2 , spos1-u7q332 , spos1-u7pw92

Title : The genomic substrate for adaptive radiation in African cichlid fish - Brawand_2014_Nature_513_375
Author(s) : Brawand D , Wagner CE , Li YI , Malinsky M , Keller I , Fan S , Simakov O , Ng AY , Lim ZW , Bezault E , Turner-Maier J , Johnson J , Alcazar R , Noh HJ , Russell P , Aken B , Alfoldi J , Amemiya C , Azzouzi N , Baroiller JF , Barloy-Hubler F , Berlin A , Bloomquist R , Carleton KL , Conte MA , D'Cotta H , Eshel O , Gaffney L , Galibert F , Gante HF , Gnerre S , Greuter L , Guyon R , Haddad NS , Haerty W , Harris RM , Hofmann HA , Hourlier T , Hulata G , Jaffe DB , Lara M , Lee AP , MacCallum I , Mwaiko S , Nikaido M , Nishihara H , Ozouf-Costaz C , Penman DJ , Przybylski D , Rakotomanga M , Renn SC , Ribeiro FJ , Ron M , Salzburger W , Sanchez-Pulido L , Santos ME , Searle S , Sharpe T , Swofford R , Tan FJ , Williams L , Young S , Yin S , Okada N , Kocher TD , Miska EA , Lander ES , Venkatesh B , Fernald RD , Meyer A , Ponting CP , Streelman JT , Lindblad-Toh K , Seehausen O , Di Palma F
Ref : Nature , 513 :375 , 2014
Abstract : Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.
ESTHER : Brawand_2014_Nature_513_375
PubMedSearch : Brawand_2014_Nature_513_375
PubMedID: 25186727
Gene_locus related to this paper: oreni-i3j014 , oreni-i3iw22 , oreni-i3iwp5 , oreni-i3j6k7 , oreni-i3jhp1 , oreni-i3jeq5 , oreni-i3kf65 , oreni-i3j210 , oreni-i3j221 , oreni-i3k9y3 , oreni-i3k5p0 , oreni-i3jwi4 , oreni-i3jv26 , oreni-i3k9m0 , 9cich-a0a3p9d5c0 , oreni-i3knk8 , 9cich-a0a3b4hcr5 , 9cich-a0a3p9dbr8 , oreni-i3k1a6 , oreni-i3jq62 , 9cich-a0a3p9dgm2 , neobr-a0a3q4g2a1 , oreni-i3jdv9 , neobr-a0a3q4hk25 , oreni-i3jbm3 , oreni-i3jbm2 , oreni-i3jds8 , 9cich-a0a3b4hbf8 , 9cich-a0a3p9ars6 , neobr-a0a3q4ghw9 , oreni-i3kx89 , 9cich-a0a3p9d359 , oreni-i3kaa3 , 9cich-a0a3p9bvw3

Title : Genome Sequence of Fusarium oxysporum f. sp. melonis Strain NRRL 26406, a Fungus Causing Wilt Disease on Melon - Ma_2014_Genome.Announc_2_e00730
Author(s) : Ma LJ , Shea T , Young S , Zeng Q , Kistler HC
Ref : Genome Announc , 2 : , 2014
Abstract : Horizontal chromosome transfer introduces host-specific pathogenicity among members of the Fusarium oxysporum species complex and is responsible for some of the most destructive and intractable plant diseases. This paper reports the genome sequence of F. oxysporum f. sp. melonis (NRRL 26406), a causal agent of Fusarium wilt disease on melon.
ESTHER : Ma_2014_Genome.Announc_2_e00730
PubMedSearch : Ma_2014_Genome.Announc_2_e00730
PubMedID: 25081257
Gene_locus related to this paper: fusox-a0a1d3s5h0 , fusox-w9p5i8 , fusox-w9hvf0

Title : Comparative genomics of a plant-pathogenic fungus, Pyrenophora tritici-repentis, reveals transduplication and the impact of repeat elements on pathogenicity and population divergence - Manning_2013_G3.(Bethesda)_3_41
Author(s) : Manning VA , Pandelova I , Dhillon B , Wilhelm LJ , Goodwin SB , Berlin AM , Figueroa M , Freitag M , Hane JK , Henrissat B , Holman WH , Kodira CD , Martin J , Oliver RP , Robbertse B , Schackwitz W , Schwartz DC , Spatafora JW , Turgeon BG , Yandava C , Young S , Zhou S , Zeng Q , Grigoriev IV , Ma LJ , Ciuffetti LM
Ref : G3 (Bethesda) , 3 :41 , 2013
Abstract : Pyrenophora tritici-repentis is a necrotrophic fungus causal to the disease tan spot of wheat, whose contribution to crop loss has increased significantly during the last few decades. Pathogenicity by this fungus is attributed to the production of host-selective toxins (HST), which are recognized by their host in a genotype-specific manner. To better understand the mechanisms that have led to the increase in disease incidence related to this pathogen, we sequenced the genomes of three P. tritici-repentis isolates. A pathogenic isolate that produces two known HSTs was used to assemble a reference nuclear genome of approximately 40 Mb composed of 11 chromosomes that encode 12,141 predicted genes. Comparison of the reference genome with those of a pathogenic isolate that produces a third HST, and a nonpathogenic isolate, showed the nonpathogen genome to be more diverged than those of the two pathogens. Examination of gene-coding regions has provided candidate pathogen-specific proteins and revealed gene families that may play a role in a necrotrophic lifestyle. Analysis of transposable elements suggests that their presence in the genome of pathogenic isolates contributes to the creation of novel genes, effector diversification, possible horizontal gene transfer events, identified copy number variation, and the first example of transduplication by DNA transposable elements in fungi. Overall, comparative analysis of these genomes provides evidence that pathogenicity in this species arose through an influx of transposable elements, which created a genetically flexible landscape that can easily respond to environmental changes.
ESTHER : Manning_2013_G3.(Bethesda)_3_41
PubMedSearch : Manning_2013_G3.(Bethesda)_3_41
PubMedID: 23316438
Gene_locus related to this paper: pyrtr-b2vxe8 , pyrtr-b2vvm1 , pyrtr-b2vzr5 , pyrtr-b2vu22 , pyrtr-kex1

Title : Sequence-based discovery of Bradyrhizobium enterica in cord colitis syndrome - Bhatt_2013_N.Engl.J.Med_369_517
Author(s) : Bhatt AS , Freeman SS , Herrera AF , Pedamallu CS , Gevers D , Duke F , Jung J , Michaud M , Walker BJ , Young S , Earl AM , Kostic AD , Ojesina AI , Hasserjian R , Ballen KK , Chen YB , Hobbs G , Antin JH , Soiffer RJ , Baden LR , Garrett WS , Hornick JL , Marty FM , Meyerson M
Ref : N Engl J Med , 369 :517 , 2013
Abstract : BACKGROUND: Immunosuppression is associated with a variety of idiopathic clinical syndromes that may have infectious causes. It has been hypothesized that the cord colitis syndrome, a complication of umbilical-cord hematopoietic stem-cell transplantation, is infectious in origin.
METHODS: We performed shotgun DNA sequencing on four archived, paraffin-embedded endoscopic colon-biopsy specimens obtained from two patients with cord colitis. Computational subtraction of human and known microbial sequences and assembly of residual sequences into a bacterial draft genome were performed. We used polymerase-chain-reaction (PCR) assays and fluorescence in situ hybridization to determine whether the corresponding bacterium was present in additional patients and controls.
RESULTS: DNA sequencing of the biopsy specimens revealed more than 2.5 million sequencing reads that did not match known organisms. These sequences were computationally assembled into a 7.65-Mb draft genome showing a high degree of homology with genomes of bacteria in the bradyrhizobium genus. The corresponding newly discovered bacterium was provisionally named Bradyrhizobium enterica. PCR identified B. enterica nucleotide sequences in biopsy specimens from all three additional patients with cord colitis whose samples were tested, whereas B. enterica sequences were absent in samples obtained from healthy controls and patients with colon cancer or graft-versus-host disease.
CONCLUSIONS: We assembled a novel bacterial draft genome from the direct sequencing of tissue specimens from patients with cord colitis. Association of these sequences with cord colitis suggests that B. enterica may be an opportunistic human pathogen. (Funded by the National Cancer Institute and others.)
ESTHER : Bhatt_2013_N.Engl.J.Med_369_517
PubMedSearch : Bhatt_2013_N.Engl.J.Med_369_517
PubMedID: 23924002
Gene_locus related to this paper: 9brad-u1h8z5 , 9brad-u1hd63 , 9brad-u1imq3 , 9brad-u1hnp5 , 9brad-u1img6 , 9brad-u1hfx7

Title : Comparative genome analysis of Trichophyton rubrum and related dermatophytes reveals candidate genes involved in infection - Martinez_2012_MBio_3_e00259
Author(s) : Martinez DA , Oliver BG , Graser Y , Goldberg JM , Li W , Martinez-Rossi NM , Monod M , Shelest E , Barton RC , Birch E , Brakhage AA , Chen Z , Gurr SJ , Heiman D , Heitman J , Kosti I , Rossi A , Saif S , Samalova M , Saunders CW , Shea T , Summerbell RC , Xu J , Young S , Zeng Q , Birren BW , Cuomo CA , White TC
Ref : MBio , 3 :e00259 , 2012
Abstract : The major cause of athlete's foot is Trichophyton rubrum, a dermatophyte or fungal pathogen of human skin. To facilitate molecular analyses of the dermatophytes, we sequenced T. rubrum and four related species, Trichophyton tonsurans, Trichophyton equinum, Microsporum canis, and Microsporum gypseum. These species differ in host range, mating, and disease progression. The dermatophyte genomes are highly colinear yet contain gene family expansions not found in other human-associated fungi. Dermatophyte genomes are enriched for gene families containing the LysM domain, which binds chitin and potentially related carbohydrates. These LysM domains differ in sequence from those in other species in regions of the peptide that could affect substrate binding. The dermatophytes also encode novel sets of fungus-specific kinases with unknown specificity, including nonfunctional pseudokinases, which may inhibit phosphorylation by competing for kinase sites within substrates, acting as allosteric effectors, or acting as scaffolds for signaling. The dermatophytes are also enriched for a large number of enzymes that synthesize secondary metabolites, including dermatophyte-specific genes that could synthesize novel compounds. Finally, dermatophytes are enriched in several classes of proteases that are necessary for fungal growth and nutrient acquisition on keratinized tissues. Despite differences in mating ability, genes involved in mating and meiosis are conserved across species, suggesting the possibility of cryptic mating in species where it has not been previously detected. These genome analyses identify gene families that are important to our understanding of how dermatophytes cause chronic infections, how they interact with epithelial cells, and how they respond to the host immune response.
ESTHER : Martinez_2012_MBio_3_e00259
PubMedSearch : Martinez_2012_MBio_3_e00259
PubMedID: 22951933
Gene_locus related to this paper: artgp-e4uup9 , artgp-e4v450 , artgp-e5qzf5 , artgp-e5r1t8 , artoc-c5fc55 , artoc-c5fds1 , artoc-c5fig8 , artoc-c5fj58 , artoc-c5fme4 , artoc-c5fva9 , triec-f2ph15 , triec-f2plk8 , triec-f2pwm2 , trirc-f2sf42 , trirc-f2sn39 , trirc-f2srv5 , trirc-f2sy06 , triru-q5j6j0 , triru-SCPB , triru-SPCA , trit1-f2rna8 , trit1-f2s2t8 , trivh-d4dbr9 , artbc-d4avu9 , artoc-c5fsf7 , artgp-e4unv7 , artoc-c5g0v3 , triec-f2pub4 , triec-f2pi43 , artgp-e4v6t4 , trit1-f2s3n3 , artoc-c5fnl7 , artgp-e4upq1 , artgp-e4uzl7 , triec-f2pp24 , triru-a0a022u299 , 9euro-a0a059jk56 , artoc-c5fu24 , artoc-c5fic4 , artgp-e4uza8 , triec-f2pqf3 , artgp-e4uv28 , artoc-c5fiv8 , triru-a0a022w2d0 , artgp-e4uvk8 , triru-a0a178f289 , artoc-c5fyj1 , artoc-cbpya , artoc-kex1

Title : Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses - O'Connell_2012_Nat.Genet_44_1060
Author(s) : O'Connell RJ , Thon MR , Hacquard S , Amyotte SG , Kleemann J , Torres MF , Damm U , Buiate EA , Epstein L , Alkan N , Altmuller J , Alvarado-Balderrama L , Bauser CA , Becker C , Birren BW , Chen Z , Choi J , Crouch JA , Duvick JP , Farman MA , Gan P , Heiman D , Henrissat B , Howard RJ , Kabbage M , Koch C , Kracher B , Kubo Y , Law AD , Lebrun MH , Lee YH , Miyara I , Moore N , Neumann U , Nordstrom K , Panaccione DG , Panstruga R , Place M , Proctor RH , Prusky D , Rech G , Reinhardt R , Rollins JA , Rounsley S , Schardl CL , Schwartz DC , Shenoy N , Shirasu K , Sikhakolli UR , Stuber K , Sukno SA , Sweigard JA , Takano Y , Takahara H , Trail F , van der Does HC , Voll LM , Will I , Young S , Zeng Q , Zhang J , Zhou S , Dickman MB , Schulze-Lefert P , Ver Loren van Themaat E , Ma LJ , Vaillancourt LJ
Ref : Nat Genet , 44 :1060 , 2012
Abstract : Colletotrichum species are fungal pathogens that devastate crop plants worldwide. Host infection involves the differentiation of specialized cell types that are associated with penetration, growth inside living host cells (biotrophy) and tissue destruction (necrotrophy). We report here genome and transcriptome analyses of Colletotrichum higginsianum infecting Arabidopsis thaliana and Colletotrichum graminicola infecting maize. Comparative genomics showed that both fungi have large sets of pathogenicity-related genes, but families of genes encoding secreted effectors, pectin-degrading enzymes, secondary metabolism enzymes, transporters and peptidases are expanded in C. higginsianum. Genome-wide expression profiling revealed that these genes are transcribed in successive waves that are linked to pathogenic transitions: effectors and secondary metabolism enzymes are induced before penetration and during biotrophy, whereas most hydrolases and transporters are upregulated later, at the switch to necrotrophy. Our findings show that preinvasion perception of plant-derived signals substantially reprograms fungal gene expression and indicate previously unknown functions for particular fungal cell types.
ESTHER : O'Connell_2012_Nat.Genet_44_1060
PubMedSearch : O'Connell_2012_Nat.Genet_44_1060
PubMedID: 22885923
Gene_locus related to this paper: colgm-kex1 , colhi-h1vve5 , colhi-h1vkk5 , colgm-e3qtg4 , colhi-h1vbq5 , colgm-e3qyh7 , colgm-e3q7u5 , colhi-h1vs61 , colgm-e3qip4 , colgm-e3qv97 , colhi-h1v665 , colgm-e3qky4 , colhi-h1vd91 , colhi-h1uvl1 , colhi-h1v7k5 , colgm-e3qu96 , colhi-h1vhh1 , colhi-h1v638 , colhi-h1vcz3 , colgm-e3qwt6 , colgm-e3q3z6 , colhi-h1vmh6 , colgm-e3qqq8 , colhi-h1v0e8 , colgm-e3qyt9 , colgm-e3qby6 , colgm-e3qsm5 , colgm-e3q6f6 , colgm-e3qwt4 , colgm-e3qb89 , colhi-h1vh96 , colgm-e3qwz9 , colgm-e3qbd3 , colgm-e3qtz0 , colhi-h1w5n4 , colgm-e3q7y3 , colgm-e3qpz1 , colhi-h1v2e4 , colgm-e3qux5 , colgm-e3qx16 , colgm-cbpya , colgm-e3q8b3

Title : Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011 - Grad_2012_Proc.Natl.Acad.Sci.U.S.A_109_3065
Author(s) : Grad YH , Lipsitch M , Feldgarden M , Arachchi HM , Cerqueira GC , FitzGerald M , Godfrey P , Haas BJ , Murphy CI , Russ C , Sykes S , Walker BJ , Wortman JR , Young S , Zeng Q , Abouelleil A , Bochicchio J , Chauvin S , Desmet T , Gujja S , McCowan C , Montmayeur A , Steelman S , Frimodt-Moller J , Petersen AM , Struve C , Krogfelt KA , Bingen E , Weill FX , Lander ES , Nusbaum C , Birren BW , Hung DT , Hanage WP
Ref : Proc Natl Acad Sci U S A , 109 :3065 , 2012
Abstract : The degree to which molecular epidemiology reveals information about the sources and transmission patterns of an outbreak depends on the resolution of the technology used and the samples studied. Isolates of Escherichia coli O104:H4 from the outbreak centered in Germany in May-July 2011, and the much smaller outbreak in southwest France in June 2011, were indistinguishable by standard tests. We report a molecular epidemiological analysis using multiplatform whole-genome sequencing and analysis of multiple isolates from the German and French outbreaks. Isolates from the German outbreak showed remarkably little diversity, with only two single nucleotide polymorphisms (SNPs) found in isolates from four individuals. Surprisingly, we found much greater diversity (19 SNPs) in isolates from seven individuals infected in the French outbreak. The German isolates form a clade within the more diverse French outbreak strains. Moreover, five isolates derived from a single infected individual from the French outbreak had extremely limited diversity. The striking difference in diversity between the German and French outbreak samples is consistent with several hypotheses, including a bottleneck that purged diversity in the German isolates, variation in mutation rates in the two E. coli outbreak populations, or uneven distribution of diversity in the seed populations that led to each outbreak.
ESTHER : Grad_2012_Proc.Natl.Acad.Sci.U.S.A_109_3065
PubMedSearch : Grad_2012_Proc.Natl.Acad.Sci.U.S.A_109_3065
PubMedID: 22315421
Gene_locus related to this paper: ecoli-fes , ecoli-MCMK , ecoli-yaim , ecoli-ycfp , ecoli-YFBB , ecoli-yhet , ecoli-yiel , ecoli-yqia , ecoli-YfhR

Title : A high-resolution map of human evolutionary constraint using 29 mammals - Lindblad-Toh_2011_Nature_478_476
Author(s) : Lindblad-Toh K , Garber M , Zuk O , Lin MF , Parker BJ , Washietl S , Kheradpour P , Ernst J , Jordan G , Mauceli E , Ward LD , Lowe CB , Holloway AK , Clamp M , Gnerre S , Alfoldi J , Beal K , Chang J , Clawson H , Cuff J , Di Palma F , Fitzgerald S , Flicek P , Guttman M , Hubisz MJ , Jaffe DB , Jungreis I , Kent WJ , Kostka D , Lara M , Martins AL , Massingham T , Moltke I , Raney BJ , Rasmussen MD , Robinson J , Stark A , Vilella AJ , Wen J , Xie X , Zody MC , Baldwin J , Bloom T , Chin CW , Heiman D , Nicol R , Nusbaum C , Young S , Wilkinson J , Worley KC , Kovar CL , Muzny DM , Gibbs RA , Cree A , Dihn HH , Fowler G , Jhangiani S , Joshi V , Lee S , Lewis LR , Nazareth LV , Okwuonu G , Santibanez J , Warren WC , Mardis ER , Weinstock GM , Wilson RK , Delehaunty K , Dooling D , Fronik C , Fulton L , Fulton B , Graves T , Minx P , Sodergren E , Birney E , Margulies EH , Herrero J , Green ED , Haussler D , Siepel A , Goldman N , Pollard KS , Pedersen JS , Lander ES , Kellis M
Ref : Nature , 478 :476 , 2011
Abstract : The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering approximately 4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for approximately 60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease.
ESTHER : Lindblad-Toh_2011_Nature_478_476
PubMedSearch : Lindblad-Toh_2011_Nature_478_476
PubMedID: 21993624
Gene_locus related to this paper: cavpo-1plip , cavpo-2plrp , cavpo-h0v1b7 , cavpo-h0v5v8 , cavpo-h0vj36 , cavpo-lipli , rabit-1hlip , rabit-1plip , rabit-g1t6x7 , rabit-LIPH , myolu-l7n1c2 , myolu-g1pqd9 , cavpo-h0uyz6 , cavpo-h0vi56 , rabit-g1tbj4 , myolu-g1p5c0 , rabit-g1sds3 , rabit-g1sye0 , cavpo-h0v0r2 , cavpo-h0v7s5 , rabit-g1sp43 , myolu-g1p4p3 , cavpo-h0vw09 , rabit-g1ssu3 , myolu-g1pds0 , rabit-g1sic4 , cavpo-h0v2c4 , myolu-g1pg61 , myolu-g1pnb1 , myolu-g1pu06 , myolu-g1qa15 , myolu-g1qfu0 , rabit-g1sn99 , rabit-g1snq9 , rabit-g1sns7 , rabit-g1tuu8 , rabit-g1tzq7 , cavpo-h0v2i2 , cavpo-h0v2j0 , cavpo-h0vsf5 , cavpo-a0a286x8d3 , cavpo-a0a286xbr3 , cavpo-a0a286y0i8 , cavpo-a0a286y4p3 , myolu-g1q2n9 , cavpo-h0v1p4 , myolu-g1pan8 , myolu-g1paq0 , myolu-g1par4 , myolu-g1prn3 , myolu-g1q3i0 , myolu-g1q463 , myolu-g1pat6 , myolu-g1q859 , rabit-g1sul9 , rabit-g1sun0 , rabit-g1sup0 , myolu-l7n125 , myolu-g1pan2 , rabit-g1sxd0 , cavpo-h0v8j4 , rabit-d5fit0 , rabit-g1tkr5 , myolu-g1nty6 , myolu-g1p1p3 , cavpo-h0vdd5 , myolu-g1pdp2 , rabit-g1tmm5 , cavpo-h0vhq3 , myolu-g1nth4 , cavpo-h0vqx6 , rabit-g1tqr7 , myolu-g1p1e9 , cavpo-h0v8y6 , rabit-g1skt3 , myolu-g1nzg3 , cavpo-h0v5z0 , rabit-g1sgz5 , myolu-g1pkg5 , rabit-g1tmw5 , rabit-g1t134 , cavpo-a0a286x9v5 , myolu-g1qc57 , myolu-g1q061 , rabit-g1tnp4 , rabit-g1tyf7 , cavpo-h0w2w1 , rabit-g1ta36 , cavpo-h0w342 , myolu-g1q4e3 , rabit-g1sqa1 , cavpo-h0uxk7 , myolu-g1p353 , cavpo-h0vpm0 , rabit-a0a5f9cru6 , cavpo-a0a286xtc0

Title : The genome of the green anole lizard and a comparative analysis with birds and mammals - Alfoldi_2011_Nature_477_587
Author(s) : Alfoldi J , Di Palma F , Grabherr M , Williams C , Kong L , Mauceli E , Russell P , Lowe CB , Glor RE , Jaffe JD , Ray DA , Boissinot S , Shedlock AM , Botka C , Castoe TA , Colbourne JK , Fujita MK , Moreno RG , ten Hallers BF , Haussler D , Heger A , Heiman D , Janes DE , Johnson J , de Jong PJ , Koriabine MY , Lara M , Novick PA , Organ CL , Peach SE , Poe S , Pollock DD , de Queiroz K , Sanger T , Searle S , Smith JD , Smith Z , Swofford R , Turner-Maier J , Wade J , Young S , Zadissa A , Edwards SV , Glenn TC , Schneider CJ , Losos JB , Lander ES , Breen M , Ponting CP , Lindblad-Toh K
Ref : Nature , 477 :587 , 2011
Abstract : The evolution of the amniotic egg was one of the great evolutionary innovations in the history of life, freeing vertebrates from an obligatory connection to water and thus permitting the conquest of terrestrial environments. Among amniotes, genome sequences are available for mammals and birds, but not for non-avian reptiles. Here we report the genome sequence of the North American green anole lizard, Anolis carolinensis. We find that A. carolinensis microchromosomes are highly syntenic with chicken microchromosomes, yet do not exhibit the high GC and low repeat content that are characteristic of avian microchromosomes. Also, A. carolinensis mobile elements are very young and diverse-more so than in any other sequenced amniote genome. The GC content of this lizard genome is also unusual in its homogeneity, unlike the regionally variable GC content found in mammals and birds. We describe and assign sequence to the previously unknown A. carolinensis X chromosome. Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations.
ESTHER : Alfoldi_2011_Nature_477_587
PubMedSearch : Alfoldi_2011_Nature_477_587
PubMedID: 21881562
Gene_locus related to this paper: anoca-h9g670 , anoca-h9g675 , anoca-h9g680 , anoca-h9gbf2 , anoca-h9gl37 , anoca-h9gq07 , anoca-h9gqa2 , anoca-h9gqv4 , anoca-h9gr08 , anoca-h9glr3 , anoca-h9gfq0 , anoca-h9gfy1 , anoca-h9g7n4 , anoca-h9gpa2 , anoca-h9g3p8

Title : Comparative genomics yields insights into niche adaptation of plant vascular wilt pathogens - Klosterman_2011_PLoS.Pathog_7_e1002137
Author(s) : Klosterman SJ , Subbarao KV , Kang S , Veronese P , Gold SE , Thomma BP , Chen Z , Henrissat B , Lee YH , Park J , Garcia-Pedrajas MD , Barbara DJ , Anchieta A , de Jonge R , Santhanam P , Maruthachalam K , Atallah Z , Amyotte SG , Paz Z , Inderbitzin P , Hayes RJ , Heiman DI , Young S , Zeng Q , Engels R , Galagan J , Cuomo CA , Dobinson KF , Ma LJ
Ref : PLoS Pathog , 7 :e1002137 , 2011
Abstract : The vascular wilt fungi Verticillium dahliae and V. albo-atrum infect over 200 plant species, causing billions of dollars in annual crop losses. The characteristic wilt symptoms are a result of colonization and proliferation of the pathogens in the xylem vessels, which undergo fluctuations in osmolarity. To gain insights into the mechanisms that confer the organisms' pathogenicity and enable them to proliferate in the unique ecological niche of the plant vascular system, we sequenced the genomes of V. dahliae and V. albo-atrum and compared them to each other, and to the genome of Fusarium oxysporum, another fungal wilt pathogen. Our analyses identified a set of proteins that are shared among all three wilt pathogens, and present in few other fungal species. One of these is a homolog of a bacterial glucosyltransferase that synthesizes virulence-related osmoregulated periplasmic glucans in bacteria. Pathogenicity tests of the corresponding V. dahliae glucosyltransferase gene deletion mutants indicate that the gene is required for full virulence in the Australian tobacco species Nicotiana benthamiana. Compared to other fungi, the two sequenced Verticillium genomes encode more pectin-degrading enzymes and other carbohydrate-active enzymes, suggesting an extraordinary capacity to degrade plant pectin barricades. The high level of synteny between the two Verticillium assemblies highlighted four flexible genomic islands in V. dahliae that are enriched for transposable elements, and contain duplicated genes and genes that are important in signaling/transcriptional regulation and iron/lipid metabolism. Coupled with an enhanced capacity to degrade plant materials, these genomic islands may contribute to the expanded genetic diversity and virulence of V. dahliae, the primary causal agent of Verticillium wilts. Significantly, our study reveals insights into the genetic mechanisms of niche adaptation of fungal wilt pathogens, advances our understanding of the evolution and development of their pathogenesis, and sheds light on potential avenues for the development of novel disease management strategies to combat destructive wilt diseases.
ESTHER : Klosterman_2011_PLoS.Pathog_7_e1002137
PubMedSearch : Klosterman_2011_PLoS.Pathog_7_e1002137
PubMedID: 21829347
Gene_locus related to this paper: vera1-c9srn2 , vera1-c9sn46 , verdv-g2wq49 , verdv-g2xca2 , vera1-c9sea3 , verdv-g2wzn4 , vera1-c9sek2 , verdv-g2wym5 , verdv-g2x5f3 , vera1-c9sx20 , vera1-c9sw01 , verdv-g2x1l1 , verdv-g2wuv4 , verdv-g2xaw5 , verdv-g2wsb2 , verdv-g2wty6 , vera1-c9si59 , verdv-g2xdu9 , vera1-c9s818 , verdv-g2xdr1 , verdv-g2wsw7 , verdv-g2wvq8 , 9pezi-a0a0g4li73 , vera1-kex1 , verdv-g2x8m5

Title : Comparative genomic analysis of human fungal pathogens causing paracoccidioidomycosis - Desjardins_2011_PLoS.Genet_7_e1002345
Author(s) : Desjardins CA , Champion MD , Holder JW , Muszewska A , Goldberg J , Bailao AM , Brigido MM , Ferreira ME , Garcia AM , Grynberg M , Gujja S , Heiman DI , Henn MR , Kodira CD , Leon-Narvaez H , Longo LV , Ma LJ , Malavazi I , Matsuo AL , Morais FV , Pereira M , Rodriguez-Brito S , Sakthikumar S , Salem-Izacc SM , Sykes SM , Teixeira MM , Vallejo MC , Walter ME , Yandava C , Young S , Zeng Q , Zucker J , Felipe MS , Goldman GH , Haas BJ , McEwen JG , Nino-Vega G , Puccia R , San-Blas G , Soares CMF , Birren BW , Cuomo CA
Ref : PLoS Genet , 7 :e1002345 , 2011
Abstract : Paracoccidioides is a fungal pathogen and the cause of paracoccidioidomycosis, a health-threatening human systemic mycosis endemic to Latin America. Infection by Paracoccidioides, a dimorphic fungus in the order Onygenales, is coupled with a thermally regulated transition from a soil-dwelling filamentous form to a yeast-like pathogenic form. To better understand the genetic basis of growth and pathogenicity in Paracoccidioides, we sequenced the genomes of two strains of Paracoccidioides brasiliensis (Pb03 and Pb18) and one strain of Paracoccidioides lutzii (Pb01). These genomes range in size from 29.1 Mb to 32.9 Mb and encode 7,610 to 8,130 genes. To enable genetic studies, we mapped 94% of the P. brasiliensis Pb18 assembly onto five chromosomes. We characterized gene family content across Onygenales and related fungi, and within Paracoccidioides we found expansions of the fungal-specific kinase family FunK1. Additionally, the Onygenales have lost many genes involved in carbohydrate metabolism and fewer genes involved in protein metabolism, resulting in a higher ratio of proteases to carbohydrate active enzymes in the Onygenales than their relatives. To determine if gene content correlated with growth on different substrates, we screened the non-pathogenic onygenale Uncinocarpus reesii, which has orthologs for 91% of Paracoccidioides metabolic genes, for growth on 190 carbon sources. U. reesii showed growth on a limited range of carbohydrates, primarily basic plant sugars and cell wall components; this suggests that Onygenales, including dimorphic fungi, can degrade cellulosic plant material in the soil. In addition, U. reesii grew on gelatin and a wide range of dipeptides and amino acids, indicating a preference for proteinaceous growth substrates over carbohydrates, which may enable these fungi to also degrade animal biomass. These capabilities for degrading plant and animal substrates suggest a duality in lifestyle that could enable pathogenic species of Onygenales to transfer from soil to animal hosts.
ESTHER : Desjardins_2011_PLoS.Genet_7_e1002345
PubMedSearch : Desjardins_2011_PLoS.Genet_7_e1002345
PubMedID: 22046142
Gene_locus related to this paper: parbd-c1gc95 , parbp-c0s0d7 , parbp-c0s257 , parbd-c1g8z9 , parba-c1grf0 , parbp-c0s816 , parbp-c0s5g4 , parbd-c1g5f5 , parbd-c1fzf9 , parba-kex1 , parbd-kex1 , parbp-kex1 , parba-cbpya , parbp-cbpya

Title : Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium - Ma_2010_Nature_464_367
Author(s) : Ma LJ , van der Does HC , Borkovich KA , Coleman JJ , Daboussi MJ , Di Pietro A , Dufresne M , Freitag M , Grabherr M , Henrissat B , Houterman PM , Kang S , Shim WB , Woloshuk C , Xie X , Xu JR , Antoniw J , Baker SE , Bluhm BH , Breakspear A , Brown DW , Butchko RA , Chapman S , Coulson R , Coutinho PM , Danchin EG , Diener A , Gale LR , Gardiner DM , Goff S , Hammond-Kosack KE , Hilburn K , Hua-Van A , Jonkers W , Kazan K , Kodira CD , Koehrsen M , Kumar L , Lee YH , Li L , Manners JM , Miranda-Saavedra D , Mukherjee M , Park G , Park J , Park SY , Proctor RH , Regev A , Ruiz-Roldan MC , Sain D , Sakthikumar S , Sykes S , Schwartz DC , Turgeon BG , Wapinski I , Yoder O , Young S , Zeng Q , Zhou S , Galagan J , Cuomo CA , Kistler HC , Rep M
Ref : Nature , 464 :367 , 2010
Abstract : Fusarium species are among the most important phytopathogenic and toxigenic fungi. To understand the molecular underpinnings of pathogenicity in the genus Fusarium, we compared the genomes of three phenotypically diverse species: Fusarium graminearum, Fusarium verticillioides and Fusarium oxysporum f. sp. lycopersici. Our analysis revealed lineage-specific (LS) genomic regions in F. oxysporum that include four entire chromosomes and account for more than one-quarter of the genome. LS regions are rich in transposons and genes with distinct evolutionary profiles but related to pathogenicity, indicative of horizontal acquisition. Experimentally, we demonstrate the transfer of two LS chromosomes between strains of F. oxysporum, converting a non-pathogenic strain into a pathogen. Transfer of LS chromosomes between otherwise genetically isolated strains explains the polyphyletic origin of host specificity and the emergence of new pathogenic lineages in F. oxysporum. These findings put the evolution of fungal pathogenicity into a new perspective.
ESTHER : Ma_2010_Nature_464_367
PubMedSearch : Ma_2010_Nature_464_367
PubMedID: 20237561
Gene_locus related to this paper: fusox-a0a1d3s5h0 , gibf5-fus2 , fusof-f9f2k2 , fusof-f9f3l6 , fusof-f9f6t8 , fusof-f9f6v2 , fusof-f9f132 , fusof-f9f781 , fusof-f9fd72 , fusof-f9fd90 , fusof-f9fem0 , fusof-f9fhk2 , fusof-f9fj19 , fusof-f9fj20 , fusof-f9fki8 , fusof-f9fmx2 , fusof-f9fnt4 , fusof-f9fpy4 , fusof-f9fvs6 , fusof-f9fwu0 , fusof-f9fxz4 , fusof-f9fzy5 , fusof-f9g2a2 , fusof-f9g3b1 , fusof-f9g5h7 , fusof-f9g6e6 , fusof-f9g6y7 , fusof-f9g7b0 , fusof-f9g797 , fusof-f9g972 , fusof-f9ga50 , fusof-f9gck4 , fusof-f9gd15 , gibze-a8w610 , gibze-b1pdn0 , gibze-i1r9e6 , gibze-i1rda9 , gibze-i1rdk7 , gibze-i1rec8 , gibze-i1rgs0 , gibze-i1rgy0 , gibze-i1rh52 , gibze-i1rhi8 , gibze-i1rig9 , gibze-i1rip5 , gibze-i1rpg6 , gibze-i1rsg2 , gibze-i1rv36 , gibze-i1rxm5 , gibze-i1rxp8 , gibze-i1rxv5 , gibze-i1s1u3 , gibze-i1s3j9 , gibze-i1s6l7 , gibze-i1s8i8 , gibze-i1s9x4 , gibze-q4huy1 , gibze-i1rg17 , fuso4-j9mvr9 , fuso4-j9ngs6 , fuso4-j9niq8 , fuso4-j9nqm2 , gibze-i1rb76 , gibze-i1s1m7 , gibze-i1s3z6 , gibze-i1rd78 , gibze-i1rgl9 , gibze-i1rjp7 , gibze-i1s1q6 , gibze-i1ri35 , gibze-i1rf76 , gibze-i1rhp3 , fusc1-n4uj11 , fusc4-n1s9p6 , gibf5-s0dqr2 , gibm7-w7n1b5 , fusof-f9g6q0 , gibm7-w7n497 , fusox-x0bme4 , gibm7-w7mcf8 , gibm7-w7mak5 , fusox-x0a2c5 , gibm7-w7mum7 , fusox-w9iyc7 , gibm7-w7maw6 , gibm7-w7msi0 , gibm7-w7luf0 , gibm7-w7msa3 , gibm7-w7mna8 , gibm7-w7n8b7 , gibm7-w7n564 , fusox-w9jpi0 , gibm7-w7ngc3 , gibm7-w7m4v6 , gibm7-w7m4v2 , gibm7-w7lt61 , gibm7-w7mly6 , gibm7-w7ncn3 , fusox-w9ibd7 , fusof-f9fnm6 , gibm7-w7n526 , gibza-a0a016pda4 , gibza-a0a016pl96 , gibm7-w7muq1 , fusof-f9gfd3 , gibm7-w7mt52 , gibze-i1rjb5 , gibf5-s0ehu3 , fusox-w9hvf0 , gibze-i1rkc4 , gibm7-w7mv30 , gibze-a0a1c3ylb1 , fuso4-a0a0c4diy4 , gibm7-w7n4n0 , gibze-gra11 , gibze-fsl2 , gibf5-fub4 , gibf5-fub5 , gibf5-fus5 , gibm7-dlh1

Title : A catalog of reference genomes from the human microbiome - Nelson_2010_Science_328_994
Author(s) : Nelson KE , Weinstock GM , Highlander SK , Worley KC , Creasy HH , Wortman JR , Rusch DB , Mitreva M , Sodergren E , Chinwalla AT , Feldgarden M , Gevers D , Haas BJ , Madupu R , Ward DV , Birren BW , Gibbs RA , Methe B , Petrosino JF , Strausberg RL , Sutton GG , White OR , Wilson RK , Durkin S , Giglio MG , Gujja S , Howarth C , Kodira CD , Kyrpides N , Mehta T , Muzny DM , Pearson M , Pepin K , Pati A , Qin X , Yandava C , Zeng Q , Zhang L , Berlin AM , Chen L , Hepburn TA , Johnson J , McCorrison J , Miller J , Minx P , Nusbaum C , Russ C , Sykes SM , Tomlinson CM , Young S , Warren WC , Badger J , Crabtree J , Markowitz VM , Orvis J , Cree A , Ferriera S , Fulton LL , Fulton RS , Gillis M , Hemphill LD , Joshi V , Kovar C , Torralba M , Wetterstrand KA , Abouellleil A , Wollam AM , Buhay CJ , Ding Y , Dugan S , Fitzgerald MG , Holder M , Hostetler J , Clifton SW , Allen-Vercoe E , Earl AM , Farmer CN , Liolios K , Surette MG , Xu Q , Pohl C , Wilczek-Boney K , Zhu D
Ref : Science , 328 :994 , 2010
Abstract : The human microbiome refers to the community of microorganisms, including prokaryotes, viruses, and microbial eukaryotes, that populate the human body. The National Institutes of Health launched an initiative that focuses on describing the diversity of microbial species that are associated with health and disease. The first phase of this initiative includes the sequencing of hundreds of microbial reference genomes, coupled to metagenomic sequencing from multiple body sites. Here we present results from an initial reference genome sequencing of 178 microbial genomes. From 547,968 predicted polypeptides that correspond to the gene complement of these strains, previously unidentified ("novel") polypeptides that had both unmasked sequence length greater than 100 amino acids and no BLASTP match to any nonreference entry in the nonredundant subset were defined. This analysis resulted in a set of 30,867 polypeptides, of which 29,987 (approximately 97%) were unique. In addition, this set of microbial genomes allows for approximately 40% of random sequences from the microbiome of the gastrointestinal tract to be associated with organisms based on the match criteria used. Insights into pan-genome analysis suggest that we are still far from saturating microbial species genetic data sets. In addition, the associated metrics and standards used by our group for quality assurance are presented.
ESTHER : Nelson_2010_Science_328_994
PubMedSearch : Nelson_2010_Science_328_994
PubMedID: 20489017
Gene_locus related to this paper: strp2-q04l35 , strpn-AXE1 , strpn-pepx

Title : Peripheral site acetylcholinesterase inhibitors targeting both inflammation and cholinergic dysfunction - Young_2010_Bioorg.Med.Chem.Lett_20_2987
Author(s) : Young S , Fabio K , Guillon C , Mohanta P , Halton TA , Heck DE , Flowers RA, 2nd , Laskin JD , Heindel ND
Ref : Bioorganic & Medicinal Chemistry Lett , 20 :2987 , 2010
Abstract : The design and study of two classes of noncompetitive acetylcholinesterase inhibitors (AChEIs) which also function as NSAID prodrugs are reported. The most potent AChEIs disclosed contain an aromatic alkyl-aryl linker between an NSAID and a lipophilic choline mimic and they inhibit acetylcholinesterase (AChE) in the submicromolar range. These agents have the therapeutic potential to dually target inflammation by releasing an NSAID in vivo and activating the cholinergic anti-inflammatory pathway via cholinergic up-regulation.
ESTHER : Young_2010_Bioorg.Med.Chem.Lett_20_2987
PubMedSearch : Young_2010_Bioorg.Med.Chem.Lett_20_2987
PubMedID: 20347302

Title : Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control - Neafsey_2010_Genome.Res_20_938
Author(s) : Neafsey DE , Barker BM , Sharpton TJ , Stajich JE , Park DJ , Whiston E , Hung CY , McMahan C , White J , Sykes S , Heiman D , Young S , Zeng Q , Abouelleil A , Aftuck L , Bessette D , Brown A , FitzGerald M , Lui A , Macdonald JP , Priest M , Orbach MJ , Galgiani JN , Kirkland TN , Cole GT , Birren BW , Henn MR , Taylor JW , Rounsley SD
Ref : Genome Res , 20 :938 , 2010
Abstract : We have sequenced the genomes of 18 isolates of the closely related human pathogenic fungi Coccidioides immitis and Coccidioides posadasii to more clearly elucidate population genomic structure, bringing the total number of sequenced genomes for each species to 10. Our data confirm earlier microsatellite-based findings that these species are genetically differentiated, but our population genomics approach reveals that hybridization and genetic introgression have recently occurred between the two species. The directionality of introgression is primarily from C. posadasii to C. immitis, and we find more than 800 genes exhibiting strong evidence of introgression in one or more sequenced isolates. We performed PCR-based sequencing of one region exhibiting introgression in 40 C. immitis isolates to confirm and better define the extent of gene flow between the species. We find more coding sequence than expected by chance in the introgressed regions, suggesting that natural selection may play a role in the observed genetic exchange. We find notable heterogeneity in repetitive sequence composition among the sequenced genomes and present the first detailed genome-wide profile of a repeat-induced point mutation (RIP) process distinctly different from what has been observed in Neurospora. We identify promiscuous HLA-I and HLA-II epitopes in both proteomes and discuss the possible implications of introgression and population genomic data for public health and vaccine candidate prioritization. This study highlights the importance of population genomic data for detecting subtle but potentially important phenomena such as introgression.
ESTHER : Neafsey_2010_Genome.Res_20_938
PubMedSearch : Neafsey_2010_Genome.Res_20_938
PubMedID: 20516208
Gene_locus related to this paper: cocp7-c5p2u8 , cocp7-c5p5s7 , cocp7-c5pe69 , cocp7-c5pf68 , cocp7-c5pgk6 , cocim-j3ka92 , cocp7-c5phc6 , cocps-e9d3i4 , cocit-a0a0j8rde7 , cocps-e9csw0 , cocps-e9dgm8

Title : Lipoic acid as a novel treatment for Alzheimer's disease and related dementias - Holmquist_2007_Pharmacol.Ther_113_154
Author(s) : Holmquist L , Stuchbury G , Berbaum K , Muscat S , Young S , Hager K , Engel J , Munch G
Ref : Pharmacol Ther , 113 :154 , 2007
Abstract : Alzheimer's disease (AD) is a progressive neurodegenerative disorder that destroys patient memory and cognition, communication ability with the social environment and the ability to carry out daily activities. Despite extensive research into the pathogenesis of AD, a neuroprotective treatment - particularly for the early stages of disease - remains unavailable for clinical use. In this review, we advance the suggestion that lipoic acid (LA) may fulfil this therapeutic need. A naturally occurring precursor of an essential cofactor for mitochondrial enzymes, including pyruvate dehydrogenase (PDH) and alpha-ketoglutarate dehydrogenase (KGDH), LA has been shown to have a variety of properties which can interfere with pathogenic principles of AD. For example, LA increases acetylcholine (ACh) production by activation of choline acetyltransferase and increases glucose uptake, thus supplying more acetyl-CoA for the production of ACh. LA chelates redox-active transition metals, thus inhibiting the formation of hydroxyl radicals and also scavenges reactive oxygen species (ROS), thereby increasing the levels of reduced glutathione. Via the same mechanisms, downregulation redox-sensitive inflammatory processes is also achieved. Furthermore, LA can scavenge lipid peroxidation products such as hydroxynonenal and acrolein. The reduced form of LA, dihydrolipoic acid (DHLA), is the active compound responsible for most of these beneficial effects. R-alpha-LA can be applied instead of DHLA, as it is reduced by mitochondrial lipoamide dehydrogenase, a part of the PDH complex. In this review, the properties of LA are explored with particular emphasis on how this agent, particularly the R-alpha-enantiomer, may be effective to treat AD and related dementias.
ESTHER : Holmquist_2007_Pharmacol.Ther_113_154
PubMedSearch : Holmquist_2007_Pharmacol.Ther_113_154
PubMedID: 16989905

Title : Paraoxonase-2 deficiency aggravates atherosclerosis in mice despite lower apolipoprotein-B-containing lipoproteins: anti-atherogenic role for paraoxonase-2 - Ng_2006_J.Biol.Chem_281_29491
Author(s) : Ng CJ , Bourquard N , Grijalva V , Hama S , Shih DM , Navab M , Fogelman AM , Lusis AJ , Young S , Reddy ST
Ref : Journal of Biological Chemistry , 281 :29491 , 2006
Abstract : Paraoxonases (PONs) are a family of proteins that may play a significant role in providing relief from both toxic environmental chemicals as well as physiological oxidative stress. Although the physiological roles of the PON family of proteins, PON1, PON2, and PON3, remain unknown, epidemiological, biochemical, and mouse genetic studies of PON1 suggest an anti-atherogenic function for paraoxonases. To determine whether PON2 plays a role in the development of atherosclerosis in vivo, we generated PON2-deficient mice. When challenged with a high fat, high cholesterol diet for 15 weeks, serum levels of high density lipoprotein cholesterol, triglycerides, and glucose were not significantly different between wild-type and PON2-deficient mice. In contrast, serum levels of very low density lipoprotein (VLDL)/low density lipoprotein (LDL) cholesterol were significantly lower (-32%) in PON2-deficient mice compared with wild-type mice. However, despite lower levels of VLDL/LDL cholesterol, mice deficient in PON2 developed significantly larger (2.7-fold) atherosclerotic lesions compared with their wild-type counterparts. Enhanced inflammatory properties of LDL, attenuated anti-atherogenic capacity of high density lipoprotein, and a heightened state of oxidative stress coupled with an exacerbated inflammatory response from PON2-deficient macrophages appear to be the main mechanisms behind the larger atherosclerotic lesions in PON2-deficient mice. These results demonstrate that PON2 plays a protective role in atherosclerosis.
ESTHER : Ng_2006_J.Biol.Chem_281_29491
PubMedSearch : Ng_2006_J.Biol.Chem_281_29491
PubMedID: 16891303

Title : Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis - Kamper_2006_Nature_444_97
Author(s) : Kamper J , Kahmann R , Bolker M , Ma LJ , Brefort T , Saville BJ , Banuett F , Kronstad JW , Gold SE , Muller O , Perlin MH , Wosten HA , de Vries R , Ruiz-Herrera J , Reynaga-Pena CG , Snetselaar K , McCann M , Perez-Martin J , Feldbrugge M , Basse CW , Steinberg G , Ibeas JI , Holloman W , Guzman P , Farman M , Stajich JE , Sentandreu R , Gonzalez-Prieto JM , Kennell JC , Molina L , Schirawski J , Mendoza-Mendoza A , Greilinger D , Munch K , Rossel N , Scherer M , Vranes M , Ladendorf O , Vincon V , Fuchs U , Sandrock B , Meng S , Ho EC , Cahill MJ , Boyce KJ , Klose J , Klosterman SJ , Deelstra HJ , Ortiz-Castellanos L , Li W , Sanchez-Alonso P , Schreier PH , Hauser-Hahn I , Vaupel M , Koopmann E , Friedrich G , Voss H , Schluter T , Margolis J , Platt D , Swimmer C , Gnirke A , Chen F , Vysotskaia V , Mannhaupt G , Guldener U , Munsterkotter M , Haase D , Oesterheld M , Mewes HW , Mauceli EW , Decaprio D , Wade CM , Butler J , Young S , Jaffe DB , Calvo S , Nusbaum C , Galagan J , Birren BW
Ref : Nature , 444 :97 , 2006
Abstract : Ustilago maydis is a ubiquitous pathogen of maize and a well-established model organism for the study of plant-microbe interactions. This basidiomycete fungus does not use aggressive virulence strategies to kill its host. U. maydis belongs to the group of biotrophic parasites (the smuts) that depend on living tissue for proliferation and development. Here we report the genome sequence for a member of this economically important group of biotrophic fungi. The 20.5-million-base U. maydis genome assembly contains 6,902 predicted protein-encoding genes and lacks pathogenicity signatures found in the genomes of aggressive pathogenic fungi, for example a battery of cell-wall-degrading enzymes. However, we detected unexpected genomic features responsible for the pathogenicity of this organism. Specifically, we found 12 clusters of genes encoding small secreted proteins with unknown function. A significant fraction of these genes exists in small gene families. Expression analysis showed that most of the genes contained in these clusters are regulated together and induced in infected tissue. Deletion of individual clusters altered the virulence of U. maydis in five cases, ranging from a complete lack of symptoms to hypervirulence. Despite years of research into the mechanism of pathogenicity in U. maydis, no 'true' virulence factors had been previously identified. Thus, the discovery of the secreted protein gene clusters and the functional demonstration of their decisive role in the infection process illuminate previously unknown mechanisms of pathogenicity operating in biotrophic fungi. Genomic analysis is, similarly, likely to open up new avenues for the discovery of virulence determinants in other pathogens.
ESTHER : Kamper_2006_Nature_444_97
PubMedSearch : Kamper_2006_Nature_444_97
PubMedID: 17080091
Gene_locus related to this paper: ustma-q4p4j7 , ustma-q4p5d2 , ustma-q4p8h8 , ustma-q4p8x7 , ustma-q4p082 , ustma-q4p194 , ustma-q4pa07 , ustma-q4pas0 , ustma-q4pbb4 , ustma-q4pg48