Full Text Available CBRC-AGAM-07-0010 U C UNKNOWN ARCD_SHIFL 6e-83 63% ref|YP_857311.1| arginine/ornithine antiporte ... r [Aeromonas ... hydrophila subsp. hydrophila ATCC 7966] gb|ABK3938 ... 6.1| arginine/ornithine antiporter [Aeromonas ... hydrophila subsp. hydrophila ATCC 7966] 1e-135 98% ...
Full Text Available CBRC-AGAM-07-0002 U C UNKNOWN YBJE_ECOLI 1e-64 48% ref|YP_856219.1| hypothetical protein AHA_168 ... 3 [Aeromonas ... hydrophila subsp. hydrophila ATCC 7966] gb|ABK3988 ... 0.1| putative membrane protein [Aeromonas ... hydrophila subsp. hydrophila ATCC 7966] 1e-138 98% ...
Full Text Available CBRC-AGAM-07-0060 U C UNKNOWN YDAM_ECOLI 2e-11 43% ref|YP_857304.1| diguanylate cyclase/phosphod ... iesterase domain 1 [Aeromonas ... hydrophila subsp. hydrophila ATCC 7966] gb|ABK3955 ... 1| diguanylate cyclase/phosphodiesterase domain 1 [Aeromonas ... hydrophila subsp. hydrophila ATCC 7966] 0.0 98% gn ...
Full Text Available CBRC-AGAM-07-0070 U C UNKNOWN MARC_SHIFL 3e-45 43% ref|YP_854944.1| hypothetical protein AHA_041 ... 5 [Aeromonas ... hydrophila subsp. hydrophila ATCC 7966] gb|ABK3815 ... 8.1| conserved hypothetical protein [Aeromonas ... hydrophila subsp. hydrophila ATCC 7966] 1e-131 99% ...
Full Text Available CBRC-AGAM-07-0058 U C UNKNOWN NUOL_PSEAE 1e-141 70% ref|YP_856308.1| NADH-quinone oxidoreductase ... chain l [Aeromonas ... hydrophila subsp. hydrophila ATCC 7966] gb|ABK3820 ... 2.1| NADH-quinone oxidoreductase chain l [Aeromonas ... hydrophila subsp. hydrophila ATCC 7966] 0.0 98% gn ...
Full Text Available CBRC-AGAM-07-0048 Novel U C UNKNOWN KEFA_ECOLI 1e-107 53% ref|YP_857555.1| potassium efflux syst ... em KefA [Aeromonas ... hydrophila subsp. hydrophila ATCC 7966] gb|ABK3654 ... 5.1| potassium efflux system KefA [Aeromonas ... hydrophila subsp. hydrophila ATCC 7966] 0.0 90% gn ...
Full Text Available CBRC-AGAM-07-0061 U C UNKNOWN FSR_ECOLI 1e-112 63% ref|YP_854581.1| fosmidomycin resistance prot ... ein [Aeromonas ... hydrophila subsp. hydrophila ATCC 7966] gb|ABK3917 ... 4.1| fosmidomycin resistance protein [Aeromonas ... hydrophila subsp. hydrophila ATCC 7966] 0.0 98% gn ...
Full Text Available CBRC-AGAM-07-0021 U C UNKNOWN NHAA_ECOLI 3e-69 60% ref|YP_855218.1| Na+/H+ antiporter NhaA [Aeromonas ... ATCC 7966] gb|ABK38348.1| Na+/H+ antiporter NhaA [Aeromonas ... hydrophila subsp. hydrophila ATCC 7966] 1e-126 99% ...
Full Text Available CBRC-AGAM-07-0056 U C UNKNOWN POTI_ECOLI 7e-93 64% ref|YP_858557.1| putrescine ABC transporter, ... permease protein PotI [Aeromonas ... hydrophila subsp. hydrophila ATCC 7966] gb|ABK3795 ... putrescine ABC transporter, permease protein PotI [Aeromonas ... hydrophila subsp. hydrophila ATCC 7966] 1e-153 100 ...
Full Text Available CBRC-AGAM-07-0016 U C UNKNOWN MDTL_VIBPA 2e-11 32% ref|YP_855389.1| chloramphenicol resistance p ... rotein [Aeromonas ... hydrophila subsp. hydrophila ATCC 7966] gb|ABK3699 ... 6.1| chloramphenicol resistance protein [Aeromonas ... hydrophila subsp. hydrophila ATCC 7966] 1e-111 99% ...
Full Text Available CBRC-AGAM-02-0142 Novel 2R B UNKNOWN AAC2_DICDI 8e-45 49% ref|XP_001134496.1| NDT80/PhoG like DNA ... ium discoideum AX4] gb|EAS66813.1| NDT80/PhoG like DNA -binding domain-containing protein [Dictyostelium d ...
Full Text Available CBRC-AGAM-02-0035 2R C UNKNOWN COX15_BOVIN 1e-88 59% ref|XP_321341.3| AGAP001744-PA [Anopheles g ... 25BB08 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX016818 /gi=27566038 /ug=Aga.23783 ...
Full Text Available CBRC-AGAM-02-0147 2R C UNKNOWN FACR1_MOUSE 2e-62 41% ref|XP_313367.3| AGAP003607-PA [Anopheles g ... 14DB02 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX042648 /gi=27615929 /ug=Aga.27689 ...
Full Text Available CBRC-AGAM-01-0102 2L C UNKNOWN MCLN3_MOUSE 1e-114 40% ref|XP_001687855.1| AGAP007710-PA [Anophel ... 11BC06 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX006707 /gi=27555927 /ug=Aga.3139 / ...
Full Text Available CBRC-AGAM-02-0084 Novel 2R B UNKNOWN PCLO_HUMAN 5e-05 62% ref|XP_001509470.1| PREDICTED: similar ... C1AD03 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX039301 /gi=27612582 /ug=Aga.178 /l ...
Full Text Available CBRC-AGAM-04-0034 3R C UNKNOWN HM13_HUMAN 1e-123 61% ref|XP_319582.4| AGAP008838-PA [Anopheles g ... 11BF05 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX006770 /gi=27555990 /ug=Aga.44782 ...
Full Text Available CBRC-AGAM-04-0040 Novel 3R C UNKNOWN NU2M_PICCA 8e-11 28% gb|AAA29909.1| ORF 3 7e-37 25% gnl|UG| ... 24BA12 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX048820 /gi=27622101 /ug=Aga.43502 ...
Full Text Available CBRC-AGAM-07-0022 Novel U C UNKNOWN Y874_HAEIN 6e-15 23% gb|AAR27964.1| putative O-antigen ligas ... C8CA02 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX071096 /gi=27644377 /ug=Aga.3905 / ...
Full Text Available CBRC-AGAM-01-0089 Novel 2L D UNKNOWN YLLM_STAAU 0.034 23% ref|XP_001346176.1| PREDICTED: hypothe ... 17BC06 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX010794 /gi=27560014 /ug=Aga.24572 ...
Full Text Available CBRC-AGAM-02-0021 Novel 2R D UNKNOWN SRAP_STAHJ 4e-25 27% ref|XP_001078830.1| PREDICTED: hypothe ... C1AD03 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX039301 /gi=27612582 /ug=Aga.178 /l ...
Full Text Available CBRC-AGAM-02-0185 2R D UNKNOWN S17A5_HUMAN 1e-58 34% ref|XP_562148.3| AGAP004402-PA [Anopheles g ... 19DB07 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX045559 /gi=27618840 /ug=Aga.43629 ...
Full Text Available CBRC-AGAM-04-0091 Novel 3R D UNKNOWN CE290_MOUSE 0.081 24% emb|CAJ14165.1| BEL12_AG transposon p ... 16AH02 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX043529 /gi=27616810 /ug=Aga.36905 ...
Full Text Available CBRC-AGAM-01-0084 Novel 2L D UNKNOWN ZF64A_HUMAN 0.11 36% ref|XP_001623199.1| predicted protein ... 21CC07 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX014344 /gi=27563564 /ug=Aga.28177 ...
Full Text Available CBRC-AGAM-01-0060 2L C UNKNOWN S35B3_DROME 1e-122 69% ref|XP_316536.4| AGAP006509-PA [Anopheles ... 18CB11 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX044719 /gi=27618000 /ug=Aga.7445 / ...
Full Text Available CBRC-AGAM-01-0057 2L D UNKNOWN L259_DROME 1e-105 45% ref|XP_316463.3| AGAP006427-PA [Anopheles g ... 19DH04 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX012592 /gi=27561812 /ug=Aga.15248 ...
Full Text Available CBRC-AGAM-05-0034 Novel X C UNKNOWN AMPG_ECOLI 4.1 29% gb|EDP19605.1| hypothetical protein CLOBO ... 39AF01 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX058636 /gi=27631917 /ug=Aga.2369 / ...
Full Text Available CBRC-AGAM-02-0117 2R A UNKNOWN LANC3_DROME 1e-102 51% ref|XP_312838.3| AGAP003148-PA [Anopheles ... 53CB01 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX069018 /gi=27642299 /ug=Aga.19858 ...
Full Text Available CBRC-AGAM-07-0039 Novel U D UNKNOWN TROP_HUMAN 3e-09 31% ref|XP_001631278.1| predicted protein [ ... 13CB07 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX008181 /gi=27557401 /ug=Aga.44740 ...
Full Text Available CBRC-AGAM-02-0085 Novel 2R C UNKNOWN MTL1_YEAST 9e-05 28% ref|XP_001478231.1| PREDICTED: hypothe ... C6CA12 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX069732 /gi=27643013 /ug=Aga.517 /l ...
Full Text Available CBRC-AGAM-04-0072 Novel 3R C UNKNOWN HAPP_PHYPO 0.020 26% ref|XP_001073914.1| PREDICTED: hypothe ... 17BC06 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX010794 /gi=27560014 /ug=Aga.24572 ...
Full Text Available CBRC-AGAM-02-0158 Novel 2R B UNKNOWN TM16D_HUMAN 2.8 30% ref|ZP_01420534.1| conserved hypothetic ... 40BG09 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX060173 /gi=27633454 /ug=Aga.24321 ...
Full Text Available CBRC-AGAM-01-0006 Novel 2L D UNKNOWN MDC1_MACMU 1e-05 24% gb|AAC48526.1| gastric mucin [Sus scro ... 18BE05 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX011484 /gi=27560704 /ug=Aga.29568 ...
Full Text Available CBRC-AGAM-03-0082 Novel 3L D UNKNOWN WSC1_SCHPO 7e-13 34% gb|AAY29121.1| cement precursor protei ... C1AD03 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX039301 /gi=27612582 /ug=Aga.178 /l ...
Full Text Available CBRC-AGAM-03-0023 Novel 3L B UNKNOWN Y1003_TREPA 0.13 25% ref|XP_001472026.1| PREDICTED: hypothe ... C1AD03 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX039301 /gi=27612582 /ug=Aga.178 /l ...
Full Text Available CBRC-AGAM-05-0043 Novel X C UNKNOWN YCX7_YEAST 0.13 56% ref|XP_001062429.1| PREDICTED: hypotheti ... 18CE10 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX044781 /gi=27618062 /ug=Aga.43653 ...
Full Text Available CBRC-AGAM-02-0018 2R C UNKNOWN VGLX_EHV1V 1e-04 28% ref|XP_321807.3| AGAP001337-PA [Anopheles ga ... 10BG06 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX039909 /gi=27613190 /ug=Aga.33909 ...
Full Text Available CBRC-AGAM-02-0169 2R B UNKNOWN S22A5_HUMAN 4e-32 30% ref|XP_312978.3| AGAP004104-PA [Anopheles g ... 41CB05 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX027758 /gi=27601039 /ug=Aga.36025 ...
Full Text Available CBRC-AGAM-03-0021 Novel 3L C UNKNOWN CROCC_MOUSE 0.008 23% ref|XP_001074123.1| PREDICTED: hypoth ... A3BD07 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX019905 /gi=27569125 /ug=Aga.27557 ...
Full Text Available CBRC-AGAM-07-0053 Novel U C UNKNOWN NU5M_TRYBB 0.17 36% ref|XP_001070682.1| PREDICTED: hypotheti ... 12DA09 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX007656 /gi=27556876 /ug=Aga.47582 ...
Full Text Available CBRC-AGAM-07-0064 U C UNKNOWN Y1246_HAEIN 1e-119 53% ref|YP_855025.1| sulfatase [Aeromonas hydro ... A5BG05 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX033798 /gi=27607079 /ug=Aga.25122 ...
Full Text Available CBRC-AGAM-02-0087 Novel 2R D UNKNOWN CPN_DROME 4e-04 28% gb|EDP06254.1| predicted protein [Chlam ... 40BE07 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX026908 /gi=27600189 /ug=Aga.34431 ...
Full Text Available CBRC-AGAM-04-0111 3R B UNKNOWN NIPA2_BOVIN 1e-73 51% ref|XP_318951.3| AGAP009838-PA [Anopheles g ... 41BE02 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX027644 /gi=27600925 /ug=Aga.17450 ...
Full Text Available CBRC-AGAM-02-0188 2R C UNKNOWN COQ2_DROME 1e-116 70% ref|XP_313812.4| AGAP004513-PA [Anopheles g ... 24AB08 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX016012 /gi=27565232 /ug=Aga.20421 ...
Full Text Available CBRC-AGAM-02-0131 Novel 2R D UNKNOWN RHBG_BOVIN 0.012 47% ref|XP_001472026.1| PREDICTED: hypothe ... C1AF05 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX039353 /gi=27612634 /ug=Aga.3562 / ...
Full Text Available CBRC-AGAM-01-0013 2L C UNKNOWN LAMA_DROME 0.0 38% ref|XP_315098.3| AGAP004993-PA [Anopheles gamb ... 17AB08 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX010594 /gi=27559814 /ug=Aga.7207 / ...
Full Text Available CBRC-AGAM-03-0012 3L C UNKNOWN POMT1_DROME 0.0 56% ref|XP_318526.4| AGAP010784-PA [Anopheles gam ... C8CE01 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX071185 /gi=27644466 /ug=Aga.2534 / ...
Full Text Available CBRC-AGAM-01-0080 Novel 2L D UNKNOWN SMC4_HUMAN 0.67 25% emb|CAL56086.1| unnamed protein product ... 23AA05 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX015293 /gi=27564513 /ug=Aga.44552 ...
Full Text Available CBRC-AGAM-02-0016 Novel 2R C UNKNOWN CPN_DROME 5e-26 28% ref|XP_001631175.1| predicted protein [ ... 17BC06 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX010794 /gi=27560014 /ug=Aga.24572 ...
Full Text Available CBRC-AGAM-01-0095 2L C UNKNOWN YRBG_ECOLI 9e-06 22% ref|XP_308489.4| AGAP007337-PA [Anopheles ga ... 23BH02 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX048350 /gi=27621631 /ug=Aga.43521 ...
Full Text Available CBRC-AGAM-03-0079 3L D UNKNOWN SOAT1_HUMAN 8e-81 44% ref|XP_320320.4| AGAP012217-PA [Anopheles g ... 43DC10 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX029326 /gi=27602607 /ug=Aga.47603 ...
Full Text Available CBRC-AGAM-04-0042 3R D UNKNOWN HEAT1_DROME 1e-168 28% ref|XP_319753.4| AGAP009004-PA [Anopheles ... 40BC09 of strain 6-9 of Anopheles gambiae (African malaria ... mosquito) /gb=BX026866 /gi=27600147 /ug=Aga.17141 ...
Full Text Available CBRC-AGAM-07-0007 Novel U C UNKNOWN UT2_RABIT 3e-21 28% ref|YP_001197147.1| Urea ... transporter [Fl ... avobacterium johnsoniae UW101] gb|ABQ07828.1| Urea ... transporter [Flavobacterium johnsoniae UW101] 4e-6 ...
Full Text Available CBRC-AGAM-07-0067 Novel U D UNKNOWN RHAT_SHISS 1e-80 62% ref|YP_001337862.1| L-rhamnose:H+ sympo ... rter (DMT superfamily) [Klebsiella ... pneumoniae subsp. pneumoniae MGH 78578] gb|ABR7959 ... 5.1| L-rhamnose:H+ symporter (DMT superfamily) [Klebsiella ... pneumoniae subsp. pneumoniae MGH 78578] 5e-80 62% ...
Full Text Available CBRC-AGAM-04-0031 Novel 3R D UNKNOWN GTR8_MOUSE 4e-26 27% ref|XP_001662380.1| sugar ... transporter ... [Aedes aegypti] gb|EAT35545.1| sugar ... transporter [Aedes aegypti] 1e-124 72% gnl|UG|Aga# ...
Full Text Available CBRC-AGAM-04-0032 Novel 3R C UNKNOWN PLT4_ARATH 2e-25 28% ref|XP_001662380.1| sugar ... transporter ... [Aedes aegypti] gb|EAT35545.1| sugar ... transporter [Aedes aegypti] 1e-124 65% gnl|UG|Aga# ...
Wang, Ying; Zhang, Xiaomei; Liu, Zhixiong; Zhang, Dandan; Wang, Jinzi; Liu, Di; Li, Fenglan; Lu, Hai
Based on genetic and molecular analyses, the ABC model was proposed to explain the genetic control of floral development. The C-class MADS box gene AGAMOUS (AG) plays crucial roles in Arabidopsis thaliana development through regulation of the organ identity of stamens and gynoecium. The present research reports for the first time the cloning of an AG homologue (HpAG) from Hosta plantaginea Aschers. Phylogenetic analysis shows HpAG is a homologue of AG that is closely related to C-lineage AG homologues from monocot species. Semi-quantitative PCR and real-time PCR analyses show that HpAG is stamen- and gynoecium-specific in expression and has spatial and temporal expression patterns in the reproductive organs of H. plantaginea. The transcriptional activation property of HpAG is also verified by a yeast one-hybrid. Functional analysis is carried out in Arabidopsis by overexpression of HpAG. The homeotic transformations of petals into staminoid organs are observed in 35S::HpAG transgenic plants. All these results show that HpAG1 plays a crucial role in stamen specification and gynoecium development. PMID:21667245
Full Text Available CBRC-AGAM-07-0004 U C UNKNOWN CLCA_VIBPA 2e-85 59% ref|YP_857989.1| H(+)/Cl(-) exchange transpor ... ter ClcA [Aeromonas ... hydrophila subsp. hydrophila ATCC 7966] gb|ABK3753 ... 0.1| H(+)/Cl(-) exchange transporter ClcA [Aeromonas ... hydrophila subsp. hydrophila ATCC 7966] 1e-149 97% ...
Full Text Available CBRC-AGAM-07-0003 U C UNKNOWN CCMF_ECOLI 2e-67 64% ref|YP_855937.1| cytochrome c-type biogenesis ... protein CcmF [Aeromonas ... hydrophila subsp. hydrophila ATCC 7966] gb|ABK3692 ... 6.1| cytochrome c-type biogenesis protein CcmF [Aeromonas ... hydrophila subsp. hydrophila ATCC 7966] 1e-105 100 ...
Full Text Available CBRC-AGAM-07-0072 U C UNKNOWN AARD_PROST 1e-106 56% ref|YP_857531.1| ABC transporter, CydDC cyst ... ydDC-E) family, permease/ATP-binding protein CydD [Aeromonas ... hydrophila subsp. hydrophila ATCC 7966] gb|ABK3620 ... ydDC-E) family, permease/ATP-binding protein CydD [Aeromonas ... hydrophila subsp. hydrophila ATCC 7966] 1e-176 98% ...
Full Text Available CBRC-AGAM-07-0059 U C UNKNOWN PTW3C_KLEPN 8e-47 34% ref|YP_857839.1| pts system N-acetylglucosam ... e-specific eiicba component (eiicba-nag)(eii-nag) [Aeromonas ... hydrophila subsp. hydrophila ATCC 7966] gb|ABK3672 ... e-specific eiicba component (eiicba-nag)(eii-nag) [Aeromonas ... hydrophila subsp. hydrophila ATCC 7966] 0.0 99% gn ...
Full Text Available CBRC-AGAM-04-0012 Novel 3R D UNKNOWN ALS_RAT 0.25 29% ref|YP_001377972.1| DNA ... repair protein Rec ... N [Anaeromyxobacter sp. Fw109-5] gb|ABS24988.1| DNA ... repair protein RecN [Anaeromyxobacter sp. Fw109-5] ... 30% gnl|UG|Aga#S10911669 17000687446172 A.Gam.ad.cDNA .blood1 Anopheles gambiae cDNA ... clone 19600449730026 ...
Hong, R. L., Hamaguchi, L., Busch, M. A., and Weigel, D.
OAK-B135 In Arabidopsis thaliana, cis-regulatory sequences of the floral homeotic gene AGAMOUS (AG) are located in the second intron. This 3 kb intron contains binding sites for two direct activators of AG, LEAFY (LFY) and WUSCHEL (WUS), along with other putative regulatory elements. We have used phylogenetic footprinting and the related technique of phylogenetic shadowing to identify putative cis-regulatory elements in this intron. Among 29 Brassicaceae, several other motifs, but not the LFY and WUS binding sites previously identified, are largely invariant. Using reporter gene analyses, we tested six of these motifs and found that they are all functionally important for activity of AG regulatory sequences in A. thaliana. Although there is little obvious sequence similarity outside the Brassicaceae, the intron from cucumber AG has at least partial activity in A. thaliana. Our studies underscore the value of the comparative approach as a tool that complements gene-by-gene promoter dissection, but also highlight that sequence-based studies alone are insufficient for a complete identification of cis-regulatory sites.
Zhang, Bo; Liu, Zhi-Xiong; Ma, Jiang; Song, Yi; Chen, Fa-Ju
Magnolia stellata is a woody ornamental shrub with more petaloid tepals than related plants from family Magnoliaceae. Recent studies revealed that expression changes in an AGAMOUS (AG) orthologous gene could resulted in double flowers with increased numbers of petals. We isolated three transcripts encoding different isoforms of a single AG orthologous gene, MastAG, mastag_2 and mastag_3, from M. stellata. Sequence alignments and Southern blot analyses suggested that MastAG was a single-copy gene in M. stellata genomes, and that mastag_2 and mastag_3 were abnormally spliced isoforms of MastAG. An 144bp exon skipping in MastAG results in the truncated mastag_2 protein lacking the completely I domain and 18 aa of the K1 subdomain, whereas an 165bp exon skipping of MastAG produces a truncated mastag_3 protein lacking 6 aa of the K3 subdomain and the completely C terminal region. Expression analyses showed that three alternative splicing (AS) isoforms expressed only in developing stamens and carpels. Functional analyses revealed that MastAG could mimic the endogenous AG to specify carpel identity, but failed to regulate stamen development in an Arabidopsis ag-1 mutant. Moreover, the key domain or subdomain deletions represented by mastag_2 and mastag_3 resulted in loss of C-function. However, ectopic expression of mastag_2 in Arabidopsis produced flowers with sepals converted into carpeloid organs, but without petals and stamens, whereas ectopic expression of mastag_3 in Arabidopsis could mimic the flower phenotype of the ag mutant and produced double flowers with homeotic transformation of stamens into petals and carpels into another ag flower. Our results also suggest that mastag_3 holds some potential for biotechnical engineering to create multi-petal phenotypes in commercial ornamental cultivars. PMID:26706078
Liu, Juhua; Liu, Lin; Li, Yujia; Jia, Caihong; Zhang, Jianbin; Miao, Hongxia; Hu, Wei; Wang, Zhuo; Xu, Biyu; Jin, Zhiqiang
MADS-box transcription factors play important roles in organ development. In plants, most studies on MADS-box genes have mainly focused on flower development and only a few concerned fruit development and ripening. A new MADS-box gene named MaMADS7 was isolated from banana fruit by rapid amplification of cDNA ends (RACE) based on a MADS-box fragment obtained from a banana suppression subtractive hybridization (SSH) cDNA library. MaMADS7 is an AGAMOUS-like MADS-box gene that is preferentially expressed in the ovaries and fruits and in tobacco its protein product localizes to the nucleus. This study found that MaMADS7 expression can be induced by exogenous ethylene. Ectopic expression of MaMADS7 in tomato resulted in broad ripening phenotypes. The expression levels of seven ripening and quality-related genes, ACO1, ACS2, E4, E8, PG, CNR and PSY1 in MaMADS7 transgenic tomato fruits were greatly increased while the expression of the AG-like MADS-box gene TAGL1 was suppressed. Compared with the control, the contents of β-carotene, lycopene, ascorbic acid and organic acid in transformed tomato fruits were increased, while the contents of glucose and fructose were slightly decreased. MaMADS7 interacted with banana 1-aminocyclopropane-1-carboxylic acid (ACC) oxidase gene 1 (MaACO1) and tomato phytoene synthase gene (LePSY1) promoters. Our results indicated that MaMADS7 plays an important role in initiating endogenous ethylene biosynthesis and fruit ripening. PMID:25980771
Byron H. Hartman
Full Text Available Vertebrate embryogenesis gives rise to all cell types of an organism through the development of many unique lineages derived from the three primordial germ layers. The otic sensory lineage arises from the otic vesicle, a structure formed through invagination of placodal non-neural ectoderm. This developmental lineage possesses unique differentiation potential, giving rise to otic sensory cell populations including hair cells, supporting cells, and ganglion neurons of the auditory and vestibular organs. Here we present a systematic approach to identify transcriptional features that distinguish the otic sensory lineage (from early otic progenitors to otic sensory populations from other major lineages of vertebrate development. We used a microarray approach to analyze otic sensory lineage populations including microdissected otic vesicles (embryonic day 10.5 as well as isolated neonatal cochlear hair cells and supporting cells at postnatal day 3. Non-otic tissue samples including periotic tissues and whole embryos with otic regions removed were used as reference populations to evaluate otic specificity. Otic populations shared transcriptome-wide correlations in expression profiles that distinguish members of this lineage from non-otic populations. We further analyzed the microarray data using comparative and dimension reduction methods to identify individual genes that are specifically expressed in the otic sensory lineage. This analysis identified and ranked top otic sensory lineage-specific transcripts including Fbxo2, Col9a2, and Oc90, and additional novel otic lineage markers. To validate these results we performed expression analysis on select genes using immunohistochemistry and in situ hybridization. Fbxo2 showed the most striking pattern of specificity to the otic sensory lineage, including robust expression in the early otic vesicle and sustained expression in prosensory progenitors and auditory and vestibular hair cells and supporting
Full Text Available BACKGROUND: Salmonella are important human and animal pathogens. Though highly related, the Salmonella lineages may be strictly adapted to different hosts or cause different diseases, from mild local illness like gastroenteritis to fatal systemic infections like typhoid. Therefore, rapid and accurate identification of Salmonella is essential for timely and correct diagnosis of Salmonella infections. The current identification methods such as 16S rRNA sequencing and multilocus sequence typing are expensive and time consuming. Additionally, these methods often do not have sufficient distinguishing resolution among the Salmonella lineages. METHODOLOGIES/PRINCIPAL FINDINGS: We compared 27 completely sequenced Salmonella genomes to identify possible genomic features that could be used for differentiation of individual lineages. We concatenated 2372 core genes in each of the 27 genomes and constructed a neighbor-joining tree. On the tree, strains of each serotype were clustered tightly together and different serotypes were unambiguously separated with clear genetic distances, demonstrating systematic genomic divergence among the Salmonella lineages. We made detailed comparisons among the 27 genomes and identified distinct sets of genomic differences, including nucleotide variations and genomic islands (GIs, among the Salmonella lineages. Two core genes STM4261 and entF together could unambiguously distinguish all Salmonella lineages compared in this study. Additionally, strains of a lineage have a common set of GIs and closely related lineages have similar sets of GIs. CONCLUSIONS: Salmonella lineages have accumulated distinct sets of mutations and laterally acquired DNA (e.g., GIs in evolution. Two genes entF and STM4261 have diverged sufficiently among the Salmonella lineages to be used for their differentiation. Further investigation of the distinct sets of mutations and GIs will lead to novel insights into genomic evolution of Salmonella and
The conservation of gene organization in the genome with lineage-specificity is an invaluable resource to decipher their potential functionality with diverse selective constraints, especially in higher animals and plants. Gene pairs appear to be the minimal structure for such kind of gene clusters that tend to reside in their preferred locations, representing the distinctive genomic characteristics in single species or a given lineage. Despite gene families having been investigated in a widespread manner, the definition of gene pair families in various taxa still lacks adequate attention. To address this issue, we report DLGP (http://lcgbase.big.ac.cn/DLGP/) that stores the pre-calculated lineage-based gene pairs in currently available 134 animal and plant genomes and inspect them under the same analytical framework, bringing out a set of innovational features. First, the taxonomy or lineage has been classified into four levels such as Kingdom, Phylum, Class and Order. It adopts all-to-all comparison strategy to identify the possible conserved gene pairs in all species for each gene pair in certain species and reckon those that are conserved in over a significant proportion of species in a given lineage (e.g. Primates, Diptera or Poales) as the lineage-conserved gene pairs. Furthermore, it predicts the lineage-specific gene pairs by retaining the above-mentioned lineage-conserved gene pairs that are not conserved in any other lineages. Second, it carries out pairwise comparison for the gene pairs between two compared species and creates the table including all the conserved gene pairs and the image elucidating the conservation degree of gene pairs in chromosomal level. Third, it supplies gene order browser to extend gene pairs to gene clusters, allowing users to view the evolution dynamics in the gene context in an intuitive manner. This database will be able to facilitate the particular comparison between animals and plants, between vertebrates and arthropods, and
Full Text Available Abstract Background Cell-to-cell communication is a key process in multicellular organisms. In multicellular animals, scaffolding proteins belonging to the family of membrane-associated guanylate kinases (MAGUK are involved in the regulation and formation of cell junctions. These MAGUK proteins were believed to be exclusive to Metazoa. However, a MAGUK gene was recently identified in an EST survey of Capsaspora owczarzaki, an unicellular organism that branches off near the metazoan clade. To further investigate the evolutionary history of MAGUK, we have undertook a broader search for this gene family using available genomic sequences of different opisthokont taxa. Results Our survey and phylogenetic analyses show that MAGUK proteins are present not only in Metazoa, but also in the choanoflagellate Monosiga brevicollis and in the protist Capsaspora owczarzaki. However, MAGUKs are absent from fungi, amoebozoans or any other eukaryote. The repertoire of MAGUKs in Placozoa and eumetazoan taxa (Cnidaria + Bilateria is quite similar, except for one class that is missing in Trichoplax, while Porifera have a simpler MAGUK repertoire. However, Vertebrata have undergone several independent duplications and exhibit two exclusive MAGUK classes. Three different MAGUK types are found in both M. brevicollis and C. owczarzaki: DLG, MPP and MAGI. Furthermore, M. brevicollis has suffered a lineage-specific diversification. Conclusions The diversification of the MAGUK protein gene family occurred, most probably, prior to the divergence between Metazoa+choanoflagellates and the Capsaspora+Ministeria clade. A MAGI-like, a DLG-like, and a MPP-like ancestral genes were already present in the unicellular ancestor of Metazoa, and new gene members have been incorporated through metazoan evolution within two major periods, one before the sponge-eumetazoan split and another within the vertebrate lineage. Moreover, choanoflagellates have suffered an independent MAGUK
O'Halloran Damien M
Full Text Available Abstract Background Guanylyl cyclases (GCs are responsible for the production of the secondary messenger cyclic guanosine monophosphate, which plays important roles in a variety of physiological responses such as vision, olfaction, muscle contraction, homeostatic regulation, cardiovascular and nervous function. There are two types of GCs in animals, soluble (sGCs which are found ubiquitously in cell cytoplasm, and receptor (rGC forms which span cell membranes. The complete genomes of several vertebrate and invertebrate species are now available. These data provide a platform to investigate the evolution of GCs across a diverse range of animal phyla. Results In this analysis we located GC genes from a broad spectrum of vertebrate and invertebrate animals and reconstructed molecular phylogenies for both sGC and rGC proteins. The most notable features of the resulting phylogenies are the number of lineage specific rGC and sGC expansions that have occurred during metazoan evolution. Among these expansions is a large nematode specific rGC clade comprising 21 genes in C. elegans alone; a vertebrate specific expansion in the natriuretic receptors GC-A and GC-B; a vertebrate specific expansion in the guanylyl GC-C receptors, an echinoderm specific expansion in the sperm rGC genes and a nematode specific sGC clade. Our phylogenetic reconstruction also shows the existence of a basal group of nitric oxide (NO insensitive insect and nematode sGCs which are regulated by O2. This suggests that the primordial eukaryotes probably utilized sGC as an O2 sensor, with the ligand specificity of sGC later switching to NO which provides a very effective local cell-to-cell signalling system. Phylogenetic analysis of the sGC and bacterial heme nitric oxide/oxygen binding protein domain supports the hypothesis that this domain originated from a cyanobacterial source. Conclusion The most salient feature of our phylogenies is the number of lineage specific expansions
Kuert, Philipp A; Hartenstein, Volker; Bello, Bruno C; Lovick, Jennifer K; Reichert, Heinrich
The central brain of Drosophila consists of the supraesophageal ganglion (SPG) and the subesophageal ganglion (SEG), both of which are generated by neural stem cell-like neuroblasts during embryonic and postembryonic development. Considerable information has been obtained on postembryonic development of the neuroblasts and their lineages in the SPG. In contrast, very little is known about neuroblasts, neural lineages, or any other aspect of the postembryonic development in the SEG. Here we characterize the neuroanatomy of the larval SEG in terms of tracts, commissures, and other landmark features as compared to a thoracic ganglion. We then use clonal MARCM labeling to identify all adult-specific neuroblast lineages in the late larval SEG and find a surprisingly small number of neuroblast lineages, 13 paired and one unpaired. The Hox genes Dfd, Scr, and Antp are expressed in a lineage-specific manner in these lineages during postembryonic development. Hox gene loss-of-function causes lineage-specific defects in axonal targeting and reduction in neural cell numbers. Moreover, it results in the formation of novel ectopic neuroblast lineages. Apoptosis block also results in ectopic lineages suggesting that Hox genes are required for lineage-specific termination of proliferation through programmed cell death. Taken together, our findings show that postembryonic development in the SEG is mediated by a surprisingly small set of identified lineages and requires lineage-specific Hox gene action to ensure the correct formation of adult-specific neurons in the Drosophila brain. PMID:24713419
Wong, Chui E.; Singh, Mohan B.; Bhalla, Prem L.
Background The classical (C) MIKC-type MADS-box transcription factors comprise one gene family that plays diverse roles in the flowering process ranging from floral initiation to the development of floral organs. Despite their importance in regulating developmental processes that impact crop yield, they remain largely unexplored in the major legume oilseed crop, soybean. Results We identified 57 MIKCc-type transcription factors from soybean and determined the in silico gene expression profile...
The authors investigated the role of homeobox-containing genes in human hematopoiesis because homeobox genes (i) control cell fate in the Drosophila embryo, (ii) are expressed in specific patterns in human embryos, and (iii) appear to function as transcription factors that control cell phenotype in other mammalian organs. Using four homeobox probes from the HOX2 locus and a previously undescribed homeobox cDNA (PL1), they screened mRNAs from 18 human leukemic cell lines representing erythroid, myeloid, and T- and B-cell lineages. Complex patterns of lineage-restricted expression are observed. No single homeobox gene is expressed in all types of hematopoietic cells, but each cell type exhibits homeobox gene expression. They have demonstrated (i) lineage-restricted expression of five homeobox genes in erythroid and monocytic cell lines; (ii) expression of additional homeobox genes in other cell lineages (HL-60 and lymphoid cells); (iii) expression of one homeobox gene in normal marrow cells; and (iv) modulation of expression during differentiation. These data suggest that these genes play a role in human hematopoietic development and lineage commitment
Xu, Yuantao; Wu, Guizhi; Hao, Baohai; Chen, Lingling; Deng, Xiuxin; Xu, Qiang
Background With the availability of rapidly increasing number of genome and transcriptome sequences, lineage-specific genes (LSGs) can be identified and characterized. Like other conserved functional genes, LSGs play important roles in biological evolution and functions. Results Two set of citrus LSGs, 296 citrus-specific genes (CSGs) and 1039 orphan genes specific to sweet orange, were identified by comparative analysis between the sweet orange genome sequences and 41 genomes and 273 transcr...
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Zumajo-Cardona, Cecilia; Pabón-Mora, Natalia
Gene duplication is a fundamental source of functional evolutionary change and has been associated with organismal diversification and the acquisition of novel features. The APETALA2/ETHYLENE RESPONSIVE ELEMENT-BINDING FACTOR (AP2/ERF) genes are exclusive to vascular plants and have been classified into the AP2-like and ERF-like clades. The AP2-like clade includes the AINTEGUMENTA (ANT) and the euAPETALA2 (euAP2) genes, both regulated by miR172 Arabidopsis has two paralogs in the euAP2 clade, namely APETALA2 (AP2) and TARGET OF EAT3 (TOE3) that control flowering time, meristem determinacy, sepal and petal identity and fruit development. euAP2 genes are likely functionally divergent outside Brassicaceae, as they control fruit development in tomato, and regulate inflorescence meristematic activity in maize. We studied the evolution and expression patterns of euAP2/TOE3 genes to assess large scale and local duplications and evaluate protein motifs likely related with functional changes across seed plants. We sampled euAP2/TOE3 genes from vascular plants and have found three major duplications and a few taxon-specific duplications. Here, we report conserved and new motifs across euAP2/TOE3 proteins and conclude that proteins predating the Brassicaceae duplication are more similar to AP2 than TOE3. Expression data show a shift from restricted expression in leaves, carpels, and fruits in non-core eudicots and asterids to a broader expression of euAP2 genes in leaves, all floral organs and fruits in rosids. Altogether, our data show a functional trend where the canonical A-function (sepal and petal identity) is exclusive to Brassicaceae and it is likely not maintained outside of rosids. PMID:27030733
Wichmann, Ignacio A; Zavala, Kattina; Hoffmann, Federico G; Vandewege, Michael W; Corvalán, Alejandro H; Amigo, Julio D; Owen, Gareth I; Opazo, Juan C
Genes related to human diseases should be natural targets for evolutionary studies, since they could provide clues regarding the genetic bases of pathologies and potential treatments. Here we studied the evolution of the reprimo gene family, a group of tumor-suppressor genes that are implicated in p53-mediated cell cycle arrest. These genes, especially the reprimo duplicate located on human chromosome 2, have been associated with epigenetic modifications correlated with transcriptional silencing and cancer progression. We demonstrate the presence of a third reprimo lineage that, together with the reprimo and reprimo-like genes, appears to have been differentially retained during the evolutionary history of vertebrates. We present evidence that these reprimo lineages originated early in vertebrate evolution and expanded as a result of the two rounds of whole genome duplications that occurred in the last common ancestor of vertebrates. The reprimo gene has been lost in birds, and the third reprimo gene lineage has been retained in only a few distantly related species, such as coelacanth and gar. Expression analyses revealed that the reprimo paralogs are mainly expressed in the nervous system. Different vertebrate lineages have retained different reprimo paralogs, and even in species that have retained multiple copies, only one of them is heavily expressed. PMID:27432065
Full Text Available Closely related taxa living in sympatry provide good opportunities to investigate the origin of barriers to gene flow as well as the extent of reproductive isolation. The only two recognized subspecies of the Chinese rufous horseshoe bat Rhinolophus sinicus are characterized by unusual relative distributions in which R. s. septentrionalis is restricted to a small area within the much wider range of its sister taxon R. s. sinicus. To determine the history of lineage divergence and gene flow between these taxa, we applied phylogenetic, demographic and coalescent analyses to multi-locus datasets. MtDNA gene genealogies and microsatellite-based clustering together revealed three divergent lineages of sinicus, corresponding to Central China, East China and the offshore Hainan Island. However, the central lineage of sinicus showed a closer relationship with septentrionalis than with other lineages of R. s. sinicus, in contrary to morphological data. Paraphyly of sinicus could result from either past asymmetric mtDNA introgression between these two taxa, or could suggest septentrionalis evolved in situ from its more widespread sister subspecies. To test between these hypotheses, we applied coalescent-based phylogenetic reconstruction and Approximate Bayesian Computation (ABC. We found that septentrionalis is likely to be the ancestral taxon and therefore a recent origin of this subspecies can be ruled out. On the other hand, we found a clear signature of asymmetric mtDNA gene flow from septentrionalis into central populations of sinicus yet no nuclear gene flow, thus strongly pointing to historical mtDNA introgression. We suggest that the observed deeply divergent lineages within R. sinicus probably evolved in isolation in separate Pleistocene refugia, although their close phylogeographic correspondence with distinct eco-environmental zones suggests that divergent selection might also have promoted broad patterns of population genetic structure.
Guenther, Matthew G.; Lawton, Lee N.; Rozovskaia, Tatiana; Frampton, Garrett M.; Levine, Stuart S.; Thomas L Volkert; Croce, Carlo M.; Nakamura, Tatsuya; Canaani, Eli; Young, Richard A.
Mixed-lineage leukemia (MLL) fusion proteins are potent inducers of leukemia, but how these proteins generate aberrant gene expression programs is poorly understood. Here we show that the MLL-AF4 fusion protein occupies developmental regulatory genes important for hematopoietic stem cell identity and self-renewal in human leukemia cells. These MLL-AF4-bound regions have grossly altered chromatin structure, with histone modifications catalyzed by trithorax group proteins and DOT1 extending acr...
Xiuguang Mao; Guimei He; Junpeng Zhang; Rossiter, Stephen J.; Shuyi Zhang
Closely related taxa living in sympatry provide good opportunities to investigate the origin of barriers to gene flow as well as the extent of reproductive isolation. The only two recognized subspecies of the Chinese rufous horseshoe bat Rhinolophus sinicus are characterized by unusual relative distributions in which R. s. septentrionalis is restricted to a small area within the much wider range of its sister taxon R. s. sinicus. To determine the history of lineage divergence and gene flow be...
Guerzoni, Daniele; McLysaght, Aoife
De novo protein-coding gene origination is increasingly recognized as an important evolutionary mechanism. However, there remains a large amount of uncertainty regarding the frequency of these events and the mechanisms and speed of gene establishment. Here, we describe a rigorous search for cases of de novo gene origination in the great apes. We analyzed annotated proteomes as well as full genomic DNA and transcriptional and translational evidence. It is notable that results vary between database updates due to the fluctuating annotation of these genes. Nonetheless we identified 35 de novo genes: 16 human-specific; 5 human and chimpanzee specific; and 14 that originated prior to the divergence of human, chimpanzee, and gorilla and are found in all three genomes. The taxonomically restricted distribution of these genes cannot be explained by loss in other lineages. Each gene is supported by an open reading frame-creating mutation that occurred within the primate lineage, and which is not polymorphic in any species. Similarly to previous studies we find that the de novo genes identified are short and frequently located near pre-existing genes. Also, they may be associated with Alu elements and prior transcription and RNA-splicing at the locus. Additionally, we report the first case of apparent independent lineage sorting of a de novo gene. The gene is present in human and gorilla, whereas chimpanzee has the ancestral noncoding sequence. This indicates a long period of polymorphism prior to fixation and thus supports a model where de novo genes may, at least initially, have a neutral effect on fitness. PMID:27056411
Pandi, Narayanan Sathiya, E-mail: firstname.lastname@example.org; Suganya, Sivagurunathan; Rajendran, Suriliyandi
Highlights: •Identified stomach lineage specific gene set (SLSGS) was found to be under expressed in gastric tumors. •Elevated expression of SLSGS in gastric tumor is a molecular predictor of metabolic type gastric cancer. •In silico pathway scanning identified estrogen-α signaling is a putative regulator of SLSGS in gastric cancer. •Elevated expression of SLSGS in GC is associated with an overall increase in the survival of GC patients. -- Abstract: Stomach lineage specific gene products act as a protective barrier in the normal stomach and their expression maintains the normal physiological processes, cellular integrity and morphology of the gastric wall. However, the regulation of stomach lineage specific genes in gastric cancer (GC) is far less clear. In the present study, we sought to investigate the role and regulation of stomach lineage specific gene set (SLSGS) in GC. SLSGS was identified by comparing the mRNA expression profiles of normal stomach tissue with other organ tissue. The obtained SLSGS was found to be under expressed in gastric tumors. Functional annotation analysis revealed that the SLSGS was enriched for digestive function and gastric epithelial maintenance. Employing a single sample prediction method across GC mRNA expression profiles identified the under expression of SLSGS in proliferative type and invasive type gastric tumors compared to the metabolic type gastric tumors. Integrative pathway activation prediction analysis revealed a close association between estrogen-α signaling and SLSGS expression pattern in GC. Elevated expression of SLSGS in GC is associated with an overall increase in the survival of GC patients. In conclusion, our results highlight that estrogen mediated regulation of SLSGS in gastric tumor is a molecular predictor of metabolic type GC and prognostic factor in GC.
Liu, An; Yi, Zhenzhen; Lin, Xiaofeng; Hu, Xiaozhong; Al-Farraj, Saleh A.; Al-Rasheid, Khaled A. S.
Prostomates and haptorians are two basal groups of ciliates with limited morphological characteristics available for taxonomy. Morphologically, the structures used to identify prostomates and haptorians are similar or even identical, which generate heavy taxonomic and phylogenetic confusion. In present work, phylogenetic positions lineage of two rare genera, Plagiopogon and Askenasia, were investigated. Three genes including small subunit ribosomal RNA gene (hereafter SSU rDNA), internal transcribed spacer region (ITS region), and large subunit ribosomal RNA gene (LSU rDNA) were analyzed, 10 new sequences five species each. Our findings included 1) class Prostomatea and order Haptorida are multiphyletic; 2) it may not be appropriate to place order Cyclotrichiida in subclass Haptoria, and the systematic lineage of order Cyclotrichiida needs to be verified further; 3) genus Plagiopogon branches consistently within a clade covering most prostomes and is basal of clade Colepidae, implying its close lineage to Prostomatea; and 4) Askenasia is phylogenetically distant from the subclass Haptoria but close to classes Prostomatea, Plagiopylea and Oligohymenophorea. We supposed that the toxicyst of Askenasia may be close to taxa of prostomes instead of haptorians, and the dorsal brush is a more typical morphological characteristics of haptorians than toxicysts.
Full Text Available Two sets of LSGs were identified using BLAST: Caenorhabditis elegans species-specific genes (SSGs, 1423, and Caenorhabditis genus-specific genes (GSGs, 4539. The data contained in this article show SSGs and GSGs have significant differences in evolution and that most of them were formed by gene duplication and integration of transposable elements (TEs. Subsequent observation of temporal expression and protein function presents that many SSGs and GSGs are expressed and that genes involved with sex determination, specific stress, immune response, and morphogenesis are most represented. The data are related to research article “Genome-wide identification of lineage-specific genes within Caenorhabditis elegans” in Journal of Genomics .
Pollard, Daniel A.; Iyer, Venky N.; Moses, Alan M.; Eisen,Michael B.
The phylogenetic relationship of the now fully sequencedspecies Drosophila erecta and D. yakuba with respect to the D.melanogaster species complex has been a subject of controversy. All threepossible groupings of the species have been reported in the past, thoughrecent multi-gene studies suggest that D. erecta and D. yakuba are sisterspecies. Using the whole genomes of each of these species as well as thefour other fully sequenced species in the subgenus Sophophora, we set outto investigate the placement of D. erecta and D. yakuba in the D.melanogaster species group and to understand the cause of the pastincongruence. Though we find that the phylogeny grouping D. erecta and D.yakuba together is the best supported, we also find widespreadincongruence in nucleotide and amino acid substitutions, insertions anddeletions, and gene trees. The time inferred to span the two keyspeciation events is short enough that under the coalescent model, theincongruence could be the result of incomplete lineage sorting.Consistent with the lineage-sorting hypothesis, substitutions supportingthe same tree were spatially clustered. Support for the different treeswas found to be linked to recombination such that adjacent genes supportthe same tree most often in regions of low recombination andsubstitutions supporting the same tree are most enriched roughly on thesame scale as linkage disequilibrium, also consistent with lineagesorting. The incongruence was found to be statistically significant androbust to model and species choice. No systematic biases were found. Weconclude that phylogenetic incongruence in the D. melanogaster speciescomplex is the result, at least in part, of incomplete lineage sorting.Incomplete lineage sorting will likely cause phylogenetic incongruence inmany comparative genomics datasets. Methods to infer the correct speciestree, the history of every base in the genome, and comparative methodsthat control for and/or utilize this information will be
Full Text Available CBRC-AGAM-01-0043 gb|AAG22473.1|AF193045_1 unknown [Homo sapiens] gb|AAH07980.1| Transmembrane B ... sapiens] dbj|BAE93467.1| responsive to centrifugal force ... and shear stress gene 1 [Homo sapiens] gb|ABM81925 ...
Full Text Available CBRC-AGAM-04-0023 ATCCAGATAACAACTGAGAAATTTAAATCATTAAATGTTTTCAATACCaataataataataacaaaaattataataataataatggtaat...aataataataataataataatgataataataataataataataataattataataataataacaataataataataataataataataataataataataataataat...aataataataataataataataataataataataataataataataatactaataataacaataattataataataatgataataataaaaataatagtaataataat...aataataataataataaaaataaaaataatgataataataataataataataataataataataataataataataaaaat...aataaaaatacaaataataataataataataataataataataataataataataaaaataataatcataataataatTTTATT ...
Full Text Available CBRC-AGAM-01-0020 TATTATTTataataataataacaataataataacaataataataataataataataataataataataataataataatgataataat...aatgataatgataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataat...aataataataataataataataataataataataataacaataatgataataataattataataacaataataataatgataaaaattataataataataataataat...aataataataataataataataataataatactaataatcatcatcatcatcatcataataataataatagtaataataat...aataataataataataaaaacaataataataataataataataataataataataataataataataataataataataataacaataataataataataataataat
Full Text Available CBRC-AGAM-01-0092 atttaataatgataataataataataataataataataataataataataataataataataataataataataataataataataa...caataacaataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataaaattaat...aataataataataataataataataataataataataataataataataataataataataataaaattaataataataataataataataataataataataataat...aataataataataataataataataataataataataataataataataataataataataataataataataataataat...aataataataataataataataataatgatgatcataatgataataataataataacaataataataataaCTTGGTAGATATTG
Full Text Available CBRC-AGAM-05-0052 CAATCTTTATTTGTATtaataataataatagtaataataataataataataataataatgataataataataataaaaataataataat...agtaataataataaaaataataataataataataatgataataataataataataataataataataataataataataataataataataataataataataataat...aataataataaaaataataataataataatgataataataataataataataataataataataataataataataataataataataataataataataataataat...aaaataataataataataataataataatactaataataataataataataataataatgataataatattaataataat...aataataataataataataataataataataataataataataataataataataataataataataataataataataataataatattaataataataataataat
Full Text Available CBRC-AGAM-04-0022 ttaaaaaaacaataataataataatgataataataataataataataataataataatgataataataataataataataataataat...gataataataataataataataataataataataataataataataataataataataataatgataagaatagttataataataagaataataaatataataataat...aatagtaataataataataataataataatggtaaaaaaaataataataataaaaataataataataataataataataaaaaataataataataataataataataat...aataataataataataataataataataataataataataataataataataataataataataataataataataataat...aataatagtaataataataataataataataataataataataaaaataataataataataataataataataataataataataataataataataataataataataatattaatTTTATTGTATTCGACGAAATGGATATACATTGA ...
Full Text Available CBRC-AGAM-02-0086 ATGGGTGataataataataataataaaaataataatactaataaaaataataataataatagtaacaataataataataataataataat...aataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataat...aataataataataataataataataataataataataataatattattattattattaataataataataataatagtaataataacaataataataataataataat...aatattagtaataataacaataataataataataataataataataataataataataataataataataataataataat...aataataataataataataataataataataataataataataataataatagcaataataattataataataataattataataataaaaataataataataataat
Full Text Available CBRC-AGAM-04-0055 ATGTCCGTTAAAGTAAATACTCataataataataatagtaataataataataataataataataataataataataataataataataat...aataataataataataataataataataatactaatactaataataataataataataataataataataataataataataataataataataataataataataat...aataataataataataataataataataataataataataataataataataataataataataataataataatactaatactaataataataataataataataat...aataataataataataataataataataataataataataatagtaataataataataataataataataataataataa...aaataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataat
Full Text Available CBRC-AGAM-05-0020 tcctgcgagttgacgactgtacTGTTATTAAAAATTCtaataataataataaaaatagtaataataataataataataataataaaaat...actaataataataataataataataataataataataataataataataataattataataaaaataattataataaaaataaataataataataataataataataat...aataataataataataataataataataaaaataatgataataataataataataataacgataataataataatgaaaatgataataaaaataaaaataataat...catcacattaataataataatcatcataaaaataataataataaaaataataataataatcataattttaatcataattgtaat...aataataataagaattattattatcatgttaatattaacaatacttacaataataataataataataataataataataataataataataataataataataataat
Full Text Available CBRC-AGAM-05-0018 aataatgaaaatcataatgaaaataataataaaaataaaaataataataataataataataataataataataataataataataataat...aataataataataataataataataataataatcatcatcatcatattaataataatagtaataataatattaataataataataataataataataatagtaataat...aataaaaagaataataaaatcaataataataataataaaaataattataaaaataataatattaatattaataataataattataataataataatagatattat...tattattattattattattataaaaataataataataataataataataataataataattataatacttataattataat...cataataataataatTATTATTCTTCTTCTTCTTCATTGGCACAACAACCGTTGTCGGTCAAGGCCTGCCTGTACCCACTA ...
Full Text Available CBRC-AGAM-01-0000 atgataataataattataataataataataataataataataataaaaataataataaaatacaataatagtaataataataataat...gaaattaataataataaaaataataataataataataataataataataatgataataaaaataataataatattaataataataaaaatattattattaataataataat...aataataataataatcataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataat...aataataataataataaaaataataataataataataataataataataataataataataataataataataataataat...aataataataataataataataataataataataatCTTCTTCTTCTTCTTCTTTGGCTCAACAACCGATGTCGGTCAAGGCCTGCCTGTACCCACTTGTGGGCTTGGCTTTCAGTGACTAATTGA ...
Full Text Available CBRC-AGAM-04-0041 ATGACTTTACGCCAaataataaacataaaaataataaaaacaataataataataataataataataataataataataataataataat...aataataatattcctaataataataataaaaatattactaataataacaataataataataaaaataaaaataataataataataataataaaaatattactgataat...aacaataataataataataataataaaattaatattaataataataataataataataataataataataataataataataataataaaattaataattttaataat...aataataatattaataataataataatataaataattataataataattatcataataataataataataataataataat...aattataattataataataataataataataataataataataataataataaaaatattcctaataataataataataataataataataataataataataataat
Full Text Available CBRC-AGAM-05-0048 attattattaataaaaataataattataataatcataataataataataataatgataataataataataataataataataataataat...aataataataataataataataataataataataacaataataataataataataataataataataataataataataataataataataataataataataataat...aataataataataataataataataataataataataataataataacaataataataataataataataataataataataataataataatattaataataataat...aatattaatgttattattattaataaaaataataattataataatcataataataataataataatgataataataataat...aataataataatgtaacgtccggactaatatcgcccactgtgcactcaacccgaaccccgcacgcagcg ...
Full Text Available CBRC-AGAM-03-0061 ATTGAAAGGataataataataataataataataataataataataataatgataatataaataataataaaaataataataataataat...aataataataataataataataataataataataatactaataataataataataataataatactaataataataataataataataataataataataataataat...aataataataatactaataataataataataataataataataataataataataataataataatgatataaataataataataataataataataataatatcat...taataataataataataataataataataataataataataataataataataataataataataataataataataataat...aataataataataataataataataataataataataataataataataataataataataataataataataatagtaataataataataataataataataataat
Full Text Available CBRC-AGAM-04-0081 atgaaaaacaataataataataataataataataaaaattataataataataataataataacaataaaaaagataataataataataat...aataataataagaataataataataataataataataataataataataataataataataagaataagaataataataataataataataataataataataataat...aataatagtaataataataataatataaataataataataataataataataataataaaaattataataataataataataataataataataataataataataat...aatactaatagtaataataataataaaaataataataataataataataataataataataataataataatgataat...agtaataaaaataataacaataataataTTGCTTCTTCTTATATTTTGGAATCTCATTCCGAA ...
Full Text Available CBRC-AGAM-03-0020 ATGTTTATCAAACAACCGCTAGTTGTATTTTTTATAGCTTTGCTCAAAACTTTCaataataataatagtaatattcataataacaa...cacttataataataataataataataataataataataataataataataataataataataataacaataatattgataataataataataataataataataataataat...aataataataataataataataataataataataataataataataataataataataatagtaataataataataataataataataataataataataataataat...aataacactaataataataataatgtaaataataattataataataataataataataataataataataataataataat...aataataataataataataataataataataataataataataaaaataataataataataataataatgatagtaataacaataataatgatagtaataataaaaatGTTTTTTTAAGATTATAA ...
Full Text Available CBRC-AGAM-07-0015 atgacaataatcataaaaataataataaaaataataataataataataataataataataataataataataataagagtaatagtaat...cataataataataagagtaataataataataataataataataataataataataataataataataataataataataataataataataataataataataataat...aataataataaaaataataataataattataataataataataataataataataataaaaataataataataataataataataataataataataataataataat...aatgacaataatcataaaaataatcataaaaataataataaaaataataataataataataataataataataataa...gagtaataataatcataataataataataataataataataataataataataataataataataataataacaataataataataataataataataataataataataat
Full Text Available CBRC-AGAM-02-0111 ATGATTTatagtaataatattaaaacgatggtaaatgataataataataataataataataataataataataataataataataataat...aataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataat...aataatagtaataatgatgataacaattatgataataataataataataatcataataataataataataataataataataataataataataataataataataat...aataataataataataataataataataataataataataataataataataataataataataataataataataataat...aataataataataatgataataataataataataataataataataataataataataataataataataataataataataataataataataataataataaATCAAAGTTATAA ...
Full Text Available gaagaagaagaagaagaaaaagaagaataataataataataataataataataataataataataataataataataataataataataataataataataataataat...aattataataataaaaataataatactaataaaaattttaataactacacttatataaataatactaataataataataataataataataataataataataataat...aataaaaattataataataataacaataacaataataataataataataataataataaaaattataataatagtaaaaat...aataataataataataataataataataataataataataataatattttttttattcagtag ... ...CBRC-AGAM-07-0065 GCAGGCCTAGACCGACATCGGTTGTTGAGCCAaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaa
Full Text Available CBRC-AGAM-03-0052 atGTACAAGATGTTCAAGATTCAAGataataataataatagtaataataataataataataataataataataataataataataataat...aataataataataataataataataataataataataataataataataataataataataataataataataataataataatagtaataataataatattactaat...aattataataatcataatattaataatgataataataaaaatagtaataataaaaatagtaataataataatattaataataattatgataatcataataataataat...aataataatataattataataataataataataataataaaacttattataataataataattgtaataataatattcat...aaaaataataataacaataataataatattaatgagaataataataataataataataataataataataataataataataataataataataataataataataat
Full Text Available CBRC-AGAM-02-0068 tttttataataataatactaataataataatactaataataataataataataataataataataataataataataataataataat...aataataataacaataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataat...aataattataataataataataataataataataataataataataataataataataattataataataataataataataataataataataataataataataat...aataataataataataataataataataataataataataataataataataataataataataataataataataatCTAATTGCGAGAATGATTTACACTCTTCCCGCAAA ...
Full Text Available CBRC-AGAM-01-0007 ataatacaaaataaaaataataataataataataataataataataataataataataataataataataataataatgataattataat...aataattataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataatattaataat...aataattataataataatattaataattataataataataataataataataataataataataataataataataataataataataataataataataataat...agtaataataataataataataataataataataataataataatagtaataataataataataataataataataataataat...aatgacaataataaAAGTTTTTTAATAATGATTGCGGTTCATCGCTGCACACAATGTACATCGAAGCTATAA ...
Full Text Available CBRC-AGAM-07-0075 TAAAAAGaataataataataataataataataataataataataataataataataataataataataataataataataataataat...aataataataataataataataataatattaatgataataatagtaataataataataataataataataataataataataataataataataataataataataat...aaaaataaaaataataataataataataataataataataataataataataaaaataataataataataataataataataataataataataataataataataat...aataataataataataataataataataataataataataataataataataataacaataataacaataataataataataataataataataataataataataaAATCTGCATCCATTGTTGTCTAAC ...
Full Text Available CBRC-AGAM-01-0032 atgatagttataataataataataataataataataataataataatgataataataataaggattaaaatgataataataataataat...aataataataataataataataataataataataaaaataataaaaataataatcataataataataataataataataataataataataataataattataataat...aataataataataataataataataataataataataataataataataataataataataataataatcataataaaaataataataataattataataataaaaat...aataataataataataataataataataatgataataataataataataataataataataaaaataataataattataat...aataataataataataataataacaataataataataataataataataataataataataatattaataataataataataataataataataataataataataat
Full Text Available CBRC-AGAM-04-0044 taataataataataataacattaataataataacaataaaaatacgaataataatgataataataataataataataataataataat...aataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataat...aataataataataataataataataataataataataaaattaataatattaataataataaatgtaattataataaaaatattaatattaataataataataataat...aataataataataatataataataataaAATTGAAAAAAAGTATTACAATAAAGTTTCGTTTGTTTTTGGAGCGTCTTCAAGCAGCACCTGAAAATTTCGTCTAA ...
Full Text Available CBRC-AGAM-04-0046 gccgtgatgacctaattaataataataataataataataataaaaataataataataataataataataataataataataataataat...aataataataataataataataataataataataataataataataataataataataaaaataataataataataataataataataataataataataataataat...aataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataat...aataataataataataataataataataataataataataataataataataataataataatgataatgataataataat...aataatcagaagaagaataataataaCATCTGTTTGGTTTTTGATCAAATTGAATTTGTTGATCGGAAACGGTGA ...
Full Text Available CBRC-AGAM-04-0033 ATTCGTAGTTCCACAGTTTataataataataataataataataataaaaataataataataataataataataataataataaaaataa...gaataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataat...aataataataataataataataataataataataataataataataataagaaataataataataataagaaaaaataataataataataataataaaaataataat...aataataataataataataataataataataataataataataataataataataataataataataataaaaataaaaat...aataataatatttataataataaaaataataataataataataataataataataataataataataataataataatattagtaataaaaataataataaaaataat
Full Text Available CBRC-AGAM-04-0090 atgcaaatcttgtttttgttatgtttttttaatgaactgttacatcttaataaggccatacggcccgttgaagattaaATtaataataat...aataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataat...aataataataataataataataataataataataataataataataatcataataataataataataatcataataataataataatcataataataataataataat...aataataataataataataataataataataataataataataataataataataataataataataatcataataataat...aataataataataataataataatcataataataatcataataataatcataataataataatcataataataataataatcataataataataataataataataat
Full Text Available CBRC-AGAM-02-0142 ATGAAAAATAAAATCTTTTCAGAAaataataataataataataataataataataataataataataataataataataataataataat...aataataataataataataataataataataataataataataataaaaataataataaaaataataataacaataataaatataataataataaaaataaaaataat...aataataatactaacaataataataaaataataataataataattataatattaataataataataaacataataataacaataattataataataataataataat...aattccaataaaaaataataataataataataataatcagaataataatgataataataataataataataacaaaaataa...caataataataataattataataataataataataatcatactaataataatcataataataataataataatcatcataatcataataataataataataataataat
Full Text Available CBRC-AGAM-03-0018 ATGCGTCAAAAATACATAATAAGATTAaataataataataataataataataataataataataataataataataataataataataat...aataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataat...aataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataataat...aataataataataataataataataataataataataataataataataataataataataataataataataataataat...aataataataataataataataataataataataataataacagatataataataataataacaataTTATTGAAAATCAAGA
Full Text Available CBRC-AGAM-02-0106 TAaataataataataataataataataataataataataataataataataataataataataataataataataataataataataat...aataataataataataataataataataataataataataataataataataataataataataataataataataatgataatgataataataataataataataat...aataataataataataataataataataataataataataataataataataataataataataatgataatgataataataataataataataataataataataat...aataataataataataataataataatactaataataataataNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN ...
Mehta, Rohan S; Bryant, David; Rosenberg, Noah A
Monophyletic groups-groups that consist of all of the descendants of a most recent common ancestor-arise naturally as a consequence of descent processes that result in meaningful distinctions between organisms. Aspects of monophyly are therefore central to fields that examine and use genealogical descent. In particular, studies in conservation genetics, phylogeography, population genetics, species delimitation, and systematics can all make use of mathematical predictions under evolutionary models about features of monophyly. One important calculation, the probability that a set of gene lineages is monophyletic under a two-species neutral coalescent model, has been used in many studies. Here, we extend this calculation for a species tree model that contains arbitrarily many species. We study the effects of species tree topology and branch lengths on the monophyly probability. These analyses reveal new behavior, including the maintenance of nontrivial monophyly probabilities for gene lineage samples that span multiple species and even for lineages that do not derive from a monophyletic species group. We illustrate the mathematical results using an example application to data from maize and teosinte. PMID:27432988
Schreiber, A; Seibold, I; Nötzold, G; Wink, M
Partial mitochondrial cytochrome b gene sequences reveal two deeply differentiated mtDNA lineages in anoa dwarf buffaloes (Bubalus depressicornis) from the studbook herd in European zoos. Three matrilinear lineages of lowland anoas (depressicornis type) contributed three rather similar sequence haplotypes, but one remarkably distinct haplotype was observed exclusively in mountain anoas (quarlesi type) descended from one founder female. The carriers of the distinctive mtDNA haplotype were also distinguished by several chromosomal and phenotypic peculiarities too. The differentiation between the mtDNA lineages of anoa approached or even surpassed the genetic divergence between some uncontested species of wild cattle. The depth of this haplotype divergence in anoas is discussed against the background of the phylogenetic age of these paleoendemic inhabitants of a predator-free island refugium, Sulawesi, who are among the most plesiomorphic living bovines. The studbook breeding of captive anoas as a safeguard against extinction might profit from such population genetic markers. These cytochrome b gene sequences were unable to resolve the phylogeny of nine bovine taxa robustly, except the divergence of Bubalus, Synceros, Bison, and Bos (sensu lato) genera. PMID:9987926
Kim, Jin Il; Lee, Ilseob; Park, Sehee; Bae, Joon-Yong; Yoo, Kirim; Lemey, Philippe; Park, Mee Sook; Song, Jin-Won; Kee, Sun-Ho; Song, Ki-Joon; Park, Man-Seong
In addition to influenza A subtypes, two distinct lineages of influenza B virus also cause seasonal epidemics to humans. Recently, Dudas et al. have done evolutionary analyses of reassortment patterns of the virus and suggested genetic lineage relationship between PB1, PB2, and HA genes. Using genetic plasmids and reassortant viruses, we here demonstrate that a homologous lineage PB1-PB2 pair exhibits better compatibility than a heterologous one and that the lineage relationship between PB1 and HA is more important for viral replication than that between PB2 and HA. However, co-adaptation of PB1-PB2-HA genes appears to be affected by complete gene constellation. PMID:27270757
Ho, I C; Vorhees, P; Marin, N; Oakley, B K; Tsai, S F; Orkin, S H; Leiden, J. M.
In addition to its role in the recognition of foreign antigens, the T cell receptor (TCR) alpha gene serves as a model system for studies of developmentally-regulated, lineage-specific gene expression in T cells. TCR alpha gene expression is restricted to cells of the TCR alpha/beta+ lineage, and is controlled by a T cell-specific transcriptional enhancer located 4.5 kb 3' to the C alpha gene segment. The TCR alpha enhancer contains four nuclear protein binding sites called T alpha 1-T alpha ...
Full Text Available Abstract Background Hox genes are known to play a key role in shaping the body plan of metazoans. Evolutionary dynamics of these genes is therefore essential in explaining patterns of evolutionary diversity. Among extant sarcopterygians comprising both lobe-finned fishes and tetrapods, our knowledge of the Hox genes and clusters has largely been restricted in several model organisms such as frogs, birds and mammals. Some evolutionary gaps still exist, especially for those groups with derived body morphology or occupying key positions on the tree of life, hindering our understanding of how Hox gene inventory varied along the sarcopterygian lineage. Results We determined the Hox gene inventory for six sarcopterygian groups: lungfishes, caecilians, salamanders, snakes, turtles and crocodiles by comprehensive PCR survey and genome walking. Variable Hox genes in each of the six sarcopterygian group representatives, compared to the human Hox gene inventory, were further validated for their presence/absence by PCR survey in a number of related species representing a broad evolutionary coverage of the group. Turtles, crocodiles, birds and placental mammals possess the same 39 Hox genes. HoxD12 is absent in snakes, amphibians and probably lungfishes. HoxB13 is lost in frogs and caecilians. Lobe-finned fishes, amphibians and squamate reptiles possess HoxC3. HoxC1 is only present in caecilians and lobe-finned fishes. Similar to coelacanths, lungfishes also possess HoxA14, which is only found in lobe-finned fishes to date. Our Hox gene variation data favor the lungfish-tetrapod, turtle-archosaur and frog-salamander relationships and imply that the loss of HoxD12 is not directly related to digit reduction. Conclusions Our newly determined Hox inventory data provide a more complete scenario for evolutionary dynamics of Hox genes along the sarcopterygian lineage. Limbless, worm-like caecilians and snakes possess similar Hox gene inventories to animals with
OAK-B135 Results obtained during this funding period: (1) Phylogenetic footprinting of AG regulatory sequences Sequences necessary and sufficient for AGAMOUS (AG) expression in the center of Arabidopsis flowers are located in the second intron, which is about 3 kb in size. This intron contains binding sites for two transcription factors, LEAFY (LFY) and WUSCHEL (WUS), which are direct activators of AG. We used the new method of phylogenetic shadowing to identify new regulatory elements. Among 29 Brassicaceae, several other motifs, but not the LFY and WUS binding sites previously identified, are largely invariant. Using reporter gene analyses, we tested six of these motifs and found that they are all functionally important for activity of AG regulatory sequences in A. thaliana. (2) Repression of AG by MADS box genes A candidate for repressing AG in the shoot apical meristem has been the MADS box gene FUL, since it is expressed in the shoot apical meristem and since an activated version (FUL:VP16) leads to ectopic AG expression in the shoot apical meristem. However, there is no ectopic AG expression in full single mutants. We therefore started to generate VP16 fusions of several other MADS box genes expressed in the shoot apical meristem, to determine which of these might be candidates for FUL redundant genes. We found that AGL6:VP16 has a similar phenotype as FUL:VP16, suggesting that AGL6 and FUL interact. We are now testing this hypothesis. (3) Two candidate AG regulators, WOW and ULA Because the phylogenetic footprinting project has identified several new candidate regulatory motifs, of which at least one (the CCAATCA motif) has rather strong effects, we had decided to put the analysis of WOW and ULA on hold, and to focus on using the newly identified motifs as tools. We conduct ed yeast one-hybrid screen with two of the conserved motifs, and identified several classes of transcription factors that can interact with them. One of these is encoded by the PAN gene
Matson, Michael E H; Small, Ian M; Fry, William E; Judelson, Howard S
Prior work has shown that the inheritance of resistance to metalaxyl, an oomycete-specific fungicide, is complex and may involve multiple genes. Recent research indicated that a single nucleotide polymorphism (SNP) in the gene encoding RPA190, the largest subunit of RNA polymerase I, confers resistance to metalaxyl (or mefenoxam) in some isolates of the potato late blight pathogen Phytophthora infestans. Using both DNA sequencing and high resolution melt assays for distinguishing RPA190 alleles, we show here that the SNP is absent from certain resistant isolates of P. infestans from North America, Europe, and Mexico. The SNP is present in some members of the US-23 and US-24 clonal lineages, but these tend to be fairly sensitive to the fungicide based on artificial media and field test data. Diversity in the level of sensitivity, RPA190 genotype, and RPA190 copy number was observed in these lineages but were uncorrelated. Controlled laboratory crosses demonstrated that RPA190 did not cosegregate with metalaxyl resistance from a Mexican and British isolate. We conclude that while metalaxyl may be used to control many contemporary strains of P. infestans, an assay based on RPA190 will not be sufficient to diagnose the sensitivity levels of isolates. PMID:26551315
Hung Ping Shih
Full Text Available The generation of pancreas, liver, and intestine from a common pool of progenitors in the foregut endoderm requires the establishment of organ boundaries. How dorsal foregut progenitors activate pancreatic genes and evade the intestinal lineage choice remains unclear. Here, we identify Pdx1 and Sox9 as cooperative inducers of a gene regulatory network that distinguishes the pancreatic from the intestinal lineage. Genetic studies demonstrate dual and cooperative functions for Pdx1 and Sox9 in pancreatic lineage induction and repression of the intestinal lineage choice. Pdx1 and Sox9 bind to regulatory sequences near pancreatic and intestinal differentiation genes and jointly regulate their expression, revealing direct cooperative roles for Pdx1 and Sox9 in gene activation and repression. Our study identifies Pdx1 and Sox9 as important regulators of a transcription factor network that initiates pancreatic fate and sheds light on the gene regulatory circuitry that governs the development of distinct organs from multi-lineage-competent foregut progenitors.
Tran Lan T
Full Text Available Abstract Background Plant polyphenol oxidases (PPOs are enzymes that typically use molecular oxygen to oxidize ortho-diphenols to ortho-quinones. These commonly cause browning reactions following tissue damage, and may be important in plant defense. Some PPOs function as hydroxylases or in cross-linking reactions, but in most plants their physiological roles are not known. To better understand the importance of PPOs in the plant kingdom, we surveyed PPO gene families in 25 sequenced genomes from chlorophytes, bryophytes, lycophytes, and flowering plants. The PPO genes were then analyzed in silico for gene structure, phylogenetic relationships, and targeting signals. Results Many previously uncharacterized PPO genes were uncovered. The moss, Physcomitrella patens, contained 13 PPO genes and Selaginella moellendorffii (spike moss and Glycine max (soybean each had 11 genes. Populus trichocarpa (poplar contained a highly diversified gene family with 11 PPO genes, but several flowering plants had only a single PPO gene. By contrast, no PPO-like sequences were identified in several chlorophyte (green algae genomes or Arabidopsis (A. lyrata and A. thaliana. We found that many PPOs contained one or two introns often near the 3’ terminus. Furthermore, N-terminal amino acid sequence analysis using ChloroP and TargetP 1.1 predicted that several putative PPOs are synthesized via the secretory pathway, a unique finding as most PPOs are predicted to be chloroplast proteins. Phylogenetic reconstruction of these sequences revealed that large PPO gene repertoires in some species are mostly a consequence of independent bursts of gene duplication, while the lineage leading to Arabidopsis must have lost all PPO genes. Conclusion Our survey identified PPOs in gene families of varying sizes in all land plants except in the genus Arabidopsis. While we found variation in intron numbers and positions, overall PPO gene structure is congruent with the phylogenetic
Phelan, Jody E.
Background Approximately 10 % of the Mycobacterium tuberculosis genome is made up of two families of genes that are poorly characterized due to their high GC content and highly repetitive nature. The PE and PPE families are typified by their highly conserved N-terminal domains that incorporate proline-glutamate (PE) and proline-proline-glutamate (PPE) signature motifs. They are hypothesised to be important virulence factors involved with host-pathogen interactions, but their high genetic variability and complexity of analysis means they are typically disregarded in genome studies. Results To elucidate the structure of these genes, 518 genomes from a diverse international collection of clinical isolates were de novo assembled. A further 21 reference M. tuberculosis complex genomes and long read sequence data were used to validate the approach. SNP analysis revealed that variation in the majority of the 168 pe/ppe genes studied was consistent with lineage. Several recombination hotspots were identified, notably pe_pgrs3 and pe_pgrs17. Evidence of positive selection was revealed in 65 pe/ppe genes, including epitopes potentially binding to major histocompatibility complex molecules. Conclusions This, the first comprehensive study of the pe and ppe genes, provides important insight into M. tuberculosis diversity and has significant implications for vaccine development.
Eller, Franziska; Lambertini, Carla; Nielsen, Mette W; Radutoiu, Simona; Brix, Hans
It is important to investigate the molecular causes of the variation in ecologically important traits to fully understand phenotypic responses to climate change. In the Mississippi River Delta, two distinct, sympatric invasive lineages of common reed (Phragmites australis) are known to differ in several ecophysiological characteristics and are expected to become more salt resistant due to increasing atmospheric CO2 and temperature. We investigated whether different patterns of gene expression can explain their ecophysiological differences and increased vigor under future climatic conditions. We compared the transcript abundance of photosynthetic genes of the Calvin cycle (Rubisco small subunit, RbcS; Phosphoglycerate kinase, PGK; Phosphoribulokinase, PRK), genes related with salt transport (Na+/H+ antiporter, PhaNHA) and oxidative stress response genes (Manganese Superoxide dismutase, MnSOD; Glutathione peroxidase, GPX), and the total aboveground biomass production between two genotypes representing the two lineages. The two genotypes (Delta-type, Mediterranean lineage, and EU-type, Eurasian lineage) were grown under an ambient and a future climate scenario with simultaneously elevated CO2 and temperature, and under two different soil salinities (0‰ or 20‰). We found neither differences in the aboveground biomass production nor the transcript abundances of the two genotypes, but soil salinity significantly affected all the investigated parameters, often interacting with the climatic conditions. At 20‰ salinity, most genes were higher expressed in the future than in the ambient climatic conditions. Higher transcription of the genes suggests higher abundance of the protein they code for, and consequently increased photosynthate production, improved stress responses, and salt exclusion. Therefore, the higher expression of these genes most likely contributed to the significantly ameliorated salinity impact on the aboveground biomass production of both P
Full Text Available The gene order on the X chromosome of eutherians isgenerally highly conserved, although an increase in the rate ofrearrangement has been reported in the rodent lineage.Conservation of the X chromosome is thought to be caused byselection related to maintenance of dosage compensation.However, we herein reveal that the cattle (Btau4.0 lineage hasexperienced a strong increase in the rate of X-chromosomerearrangement, much stronger than that previously reported forrodents. We also show that this increase is not matched by asimilar increase on the autosomes and cannot be explained byassembly errors. Furthermore, we compared the difference intwo cattle genome assemblies: Btau4.0 and Btau6.0 (Bostaurus UMD3.1. The results showed a discrepancy betweenBtau4.0 and Btau6.0 cattle assembly version data, and webelieve that Btau6.0 cattle assembly version data are not morereliable than Btau4.0. [BMB Reports 2013; 46(6: 310-315
Park, Woncheoul; Oh, Hee-Seok; Kim, Heebal
The gene order on the X chromosome of eutherians is generally highly conserved, although an increase in the rate of rearrangement has been reported in the rodent lineage. Conservation of the X chromosome is thought to be caused by selection related to maintenance of dosage compensation. However, we herein reveal that the cattle (Btau4.0) lineage has experienced a strong increase in the rate of X-chromosome rearrangement, much stronger than that previously reported for rodents. We also show that this increase is not matched by a similar increase on the autosomes and cannot be explained by assembly errors. Furthermore, we compared the difference in two cattle genome assemblies: Btau4.0 and Btau6.0 (Bos taurus UMD3.1). The results showed a discrepancy between Btau4.0 and Btau6.0 cattle assembly version data, and we believe that Btau6.0 cattle assembly version data are not more reliable than Btau4.0. PMID:23790974
Posttranscriptional silencing of embryonic globin gene expression occurs during hemoglobin switching in chickens. Here the authors use Percoll density gradients to fractionate the red blood cells of 5-9 day embryos in order to determine the cellular source and the timing of this posttranscriptional process. By means of nuclear run-on transcription in vitro they show that it is within mature primitive cells that production of embryonic globin mRNA is terminated posttranscriptionally. In contrast, young definitive cells produce little (or no) embryonic globin mRNA because of regulation at the transcriptional level. Thus the lineage specificity of embryonic and adult globin gene expression is determined transcriptionally, and the posttranscriptional process described by Landes et al. is a property of the senescing primitive cells, not a mechanism operative in the hemoglobin switch. This conclusion is supported by [3H]leucine incorporation experiments on Percoll-fractionated cells which reveal no posttranscriptional silencing of the embryonic genes during the early stages of the switch. In the course of these studies they have noticed a strong transcriptional pause near the second exon of the globin genes which is induced by 5,6-dichloro-1-β-D-ribofuranosylbenzimidazole (DRB) and which resembles a natural pause near that position
Full Text Available The ficolins recognize carbohydrates and acetylated compounds on microorganisms and dying host cells and are able to activate the lectin pathway of the complement system. In humans, three ficolin genes have been identified: FCN1, FCN2 and FCN3, which encode ficolin-1, ficolin-2 and ficolin-3, respectively. Rodents have only two ficolins designated ficolin-A and ficolin-B that are closely related to human ficolin-1, while the rodent FCN3 orthologue is a pseudogene. Ficolin-2 and ficolin-3 have so far only been observed in humans. Thus, we performed a systematic investigation of the FCN genes in non-human primates. The exons and intron-exon boundaries of the FCN1-3 genes were sequenced in the following primate species: chimpanzee, gorilla, orangutan, rhesus macaque, cynomolgus macaque, baboon and common marmoset. We found that the exon organisation of the FCN genes was very similar between all the non-human primates and the human FCN genes. Several variations in the FCN genes were found in more than one primate specie suggesting that they were carried from one species to another including humans. The amino acid diversity of the ficolins among human and non-human primate species was estimated by calculating the Shannon entropy revealing that all three proteins are generally highly conserved. Ficolin-1 and ficolin-2 showed the highest diversity, whereas ficolin-3 was more conserved. Ficolin-2 and ficolin-3 were present in non-human primate sera with the same characteristic oligomeric structures as seen in human serum. Taken together all the FCN genes show the same characteristics in lower and higher primates. The existence of trans-species polymorphisms suggests that different FCN allelic lineages may be passed from ancestral to descendant species.
Yu, Xiao-Jing; Zheng, Hong-Kun; Wang, Jun;
Comparative genetic analysis between human and chimpanzee may detect genetic divergences responsible for human-specific characteristics. Previous studies have identified a series of genes that potentially underwent Darwinian positive selection during human evolution. However, without a closely...... related species as outgroup, it is difficult to identify human-lineage-specific changes, which is critical in delineating the biological uniqueness of humans. In this study, we conducted phylogeny-based analyses of 2633 human brain-expressed genes using rhesus macaque as the outgroup. We identified 47...... candidate genes showing strong evidence of positive selection in the human lineage. Genes with maximal expression in the brain showed a higher evolutionary rate in human than in chimpanzee. We observed that many immune-defense-related genes were under strong positive selection, and this trend was more...
Rivera-Mulia, Juan Carlos; Buckley, Quinton; Sasaki, Takayo; Zimmerman, Jared; Didier, Ruth A; Nazor, Kristopher; Loring, Jeanne F; Lian, Zheng; Weissman, Sherman; Robins, Allan J; Schulz, Thomas C; Menendez, Laura; Kulik, Michael J; Dalton, Stephen; Gabr, Haitham; Kahveci, Tamer; Gilbert, David M
Duplication of the genome in mammalian cells occurs in a defined temporal order referred to as its replication-timing (RT) program. RT changes dynamically during development, regulated in units of 400-800 kb referred to as replication domains (RDs). Changes in RT are generally coordinated with transcriptional competence and changes in subnuclear position. We generated genome-wide RT profiles for 26 distinct human cell types, including embryonic stem cell (hESC)-derived, primary cells and established cell lines representing intermediate stages of endoderm, mesoderm, ectoderm, and neural crest (NC) development. We identified clusters of RDs that replicate at unique times in each stage (RT signatures) and confirmed global consolidation of the genome into larger synchronously replicating segments during differentiation. Surprisingly, transcriptome data revealed that the well-accepted correlation between early replication and transcriptional activity was restricted to RT-constitutive genes, whereas two-thirds of the genes that switched RT during differentiation were strongly expressed when late replicating in one or more cell types. Closer inspection revealed that transcription of this class of genes was frequently restricted to the lineage in which the RT switch occurred, but was induced prior to a late-to-early RT switch and/or down-regulated after an early-to-late RT switch. Analysis of transcriptional regulatory networks showed that this class of genes contains strong regulators of genes that were only expressed when early replicating. These results provide intriguing new insight into the complex relationship between transcription and RT regulation during human development. PMID:26055160
Dröge, Jasmin; Buczek, Dorota; Suzuki, Yutaka; Makałowski, Wojciech
The Amoebozoa represent a clade of unicellular amoeboid organisms that display a wide variety of lifestyles, including free-living and parasitic species. For example, the social amoeba Dictyostelium discoideum has the ability to aggregate into a multicellular fruiting body upon starvation, while the pathogenic amoeba Entamoeba histolytica is a parasite of humans. Globins are small heme proteins that are present in almost all extant organisms. Although several genomes of amoebozoan species have been sequenced, little is known about the phyletic distribution of globin genes within this phylum. Only two flavohemoglobins (FHbs) of D. discoideum have been reported and characterized previously while the genomes of Entamoeba species are apparently devoid of globin genes. We investigated eleven amoebozoan species for the presence of globin genes by genomic and phylogenetic in silico analyses. Additional FHb genes were identified in the genomes of four social amoebas and the true slime mold Physarum polycephalum. Moreover, a single-domain globin (SDFgb) of Hartmannella vermiformis, as well as two truncated hemoglobins (trHbs) of Acanthamoeba castellanii were identified. Phylogenetic evidence suggests that these globin genes were independently acquired via horizontal gene transfer from some ancestral bacteria. Furthermore, the phylogenetic tree of amoebozoan FHbs indicates that they do not share a common ancestry and that a transfer of FHbs from bacteria to amoeba occurred multiple times. PMID:25013378
Shih, Hung Ping; Seymour, Philip A; Patel, Nisha A; Xie, Ruiyu; Wang, Allen; Liu, Patrick P; Yeo, Gene W; Magnuson, Mark A; Sander, Maike
The generation of pancreas, liver, and intestine from a common pool of progenitors in the foregut endoderm requires the establishment of organ boundaries. How dorsal foregut progenitors activate pancreatic genes and evade the intestinal lineage choice remains unclear. Here, we identify Pdx1 and Sox...
Neems, Daniel S; Garza-Gongora, Arturo G; Smith, Erica D; Kosak, Steven T
The linear distribution of genes across chromosomes and the spatial localization of genes within the nucleus are related to their transcriptional regulation. The mechanistic consequences of linear gene order, and how it may relate to the functional output of genome organization, remain to be fully resolved, however. Here we tested the relationship between linear and 3D organization of gene regulation during myogenesis. Our analysis has identified a subset of topologically associated domains (TADs) that are significantly enriched for muscle-specific genes. These lineage-enriched TADs demonstrate an expression-dependent pattern of nuclear organization that influences the positioning of adjacent nonenriched TADs. Therefore, lineage-enriched TADs inform cell-specific genome organization during myogenesis. The reduction of allelic spatial distance of one of these domains, which containsMyogenin, correlates with reduced transcriptional variability, identifying a potential role for lineage-specific nuclear topology. Using a fusion-based strategy to decouple mitosis and myotube formation, we demonstrate that the cell-specific topology of syncytial nuclei is dependent on cell division. We propose that the effects of linear and spatial organization of gene loci on gene regulation are linked through TAD architecture, and that mitosis is critical for establishing nuclear topologies during cellular differentiation. PMID:26957603
Ware Carol B
Full Text Available Abstract Background Prostate tumor heterogeneity is a major factor in disease management. Heterogeneity could be due to multiple cancer cell types with distinct gene expression. Of clinical importance is the so-called cancer stem cell type. Cell type-specific transcriptomes are used to examine lineage relationship among cancer cell types and their expression similarity to normal cell types including stem/progenitor cells. Methods Transcriptomes were determined by Affymetrix DNA array analysis for the following cell types. Putative prostate progenitor cell populations were characterized and isolated by expression of the membrane transporter ABCG2. Stem cells were represented by embryonic stem and embryonal carcinoma cells. The cancer cell types were Gleason pattern 3 (glandular histomorphology and pattern 4 (aglandular sorted from primary tumors, cultured prostate cancer cell lines originally established from metastatic lesions, xenografts LuCaP 35 (adenocarcinoma phenotype and LuCaP 49 (neuroendocrine/small cell carcinoma grown in mice. No detectable gene expression differences were detected among serial passages of the LuCaP xenografts. Results Based on transcriptomes, the different cancer cell types could be clustered into a luminal-like grouping and a non-luminal-like (also not basal-like grouping. The non-luminal-like types showed expression more similar to that of stem/progenitor cells than the luminal-like types. However, none showed expression of stem cell genes known to maintain stemness. Conclusions Non-luminal-like types are all representatives of aggressive disease, and this could be attributed to the similarity in overall gene expression to stem and progenitor cell types.
Powell, John H; Amish, Stephen J; Haynes, Gwilym D; Luikart, Gordon; Latch, Emily K
Mule deer (Odocoileus hemionus) are an excellent nonmodel species for empirically testing hypotheses in landscape and population genomics due to their large population sizes (low genetic drift), relatively continuous distribution, diversity of occupied habitats and phenotypic variation. Because few genomic resources are currently available for this species, we used exon data from a cattle (Bos taurus) reference genome to direct targeted resequencing of 5935 genes in mule deer. We sequenced approximately 3.75 Mbp at minimum 20X coverage in each of the seven mule deer, identifying 23 204 single nucleotide polymorphisms (SNPs) within, or adjacent to, 6886 exons in 3559 genes. We found 91 SNP loci (from 69 genes) with putatively fixed allele frequency differences between the two major lineages of mule deer (mule deer and black-tailed deer), and our estimate of mean genetic divergence (genome-wide FST = 0.123) between these lineages was consistent with previous findings using microsatellite loci. We detected an over-representation of gamete generation and amino acid transport genes among the genes with SNPs exhibiting potentially fixed allele frequency differences between lineages. This targeted resequencing approach using exon capture techniques has identified a suite of loci that can be used in future research to investigate the genomic basis of adaptation and differentiation between black-tailed deer and mule deer. This study also highlights techniques (and an exon capture array) that will facilitate population genomic research in other cervids and nonmodel organisms. PMID:27438092
Bidon, Tobias; Janke, Axel; Fain, Steven R; Eiken, Hans Geir; Hagen, Snorre B; Saarma, Urmas; Hallström, Björn M; Lecomte, Nicolas; Hailer, Frank
Brown and polar bears have become prominent examples in phylogeography, but previous phylogeographic studies relied largely on maternally inherited mitochondrial DNA (mtDNA) or were geographically restricted. The male-specific Y chromosome, a natural counterpart to mtDNA, has remained underexplored. Although this paternally inherited chromosome is indispensable for comprehensive analyses of phylogeographic patterns, technical difficulties and low variability have hampered its application in most mammals. We developed 13 novel Y-chromosomal sequence and microsatellite markers from the polar bear genome and screened these in a broad geographic sample of 130 brown and polar bears. We also analyzed a 390-kb-long Y-chromosomal scaffold using sequencing data from published male ursine genomes. Y chromosome evidence support the emerging understanding that brown and polar bears started to diverge no later than the Middle Pleistocene. Contrary to mtDNA patterns, we found 1) brown and polar bears to be reciprocally monophyletic sister (or rather brother) lineages, without signals of introgression, 2) male-biased gene flow across continents and on phylogeographic time scales, and 3) male dispersal that links the Alaskan ABC islands population to mainland brown bears. Due to female philopatry, mtDNA provides a highly structured estimate of population differentiation, while male-biased gene flow is a homogenizing force for nuclear genetic variation. Our findings highlight the importance of analyzing both maternally and paternally inherited loci for a comprehensive view of phylogeographic history, and that mtDNA-based phylogeographic studies of many mammals should be reevaluated. Recent advances in sequencing technology render the analysis of Y-chromosomal variation feasible, even in nonmodel organisms. PMID:24667925
Gibbs, Holly C.; Dodson, Colin R.; Bai, Yuqiang; Lekven, Arne C.; Yeh, Alvin T.
During embryogenesis, presumptive brain compartments are patterned by dynamic networks of gene expression. The spatiotemporal dynamics of these networks, however, have not been characterized with sufficient resolution for us to understand the regulatory logic resulting in morphogenetic cellular behaviors that give the brain its shape. We have developed a new, integrated approach using ultrashort pulse microscopy [a high-resolution, two-photon fluorescence (2PF)-optical coherence microscopy (OCM) platform using 10-fs pulses] and image registration to study brain patterning and morphogenesis in zebrafish embryos. As a demonstration, we used time-lapse 2PF to capture midbrain-hindbrain boundary morphogenesis and a wnt1 lineage map from embryos during brain segmentation. We then performed in situ hybridization to deposit NBT/BCIP, where wnt1 remained actively expressed, and reimaged the embryos with combined 2PF-OCM. When we merged these datasets using morphological landmark registration, we found that the mechanism of boundary formation differs along the dorsoventral axis. Dorsally, boundary sharpening is dominated by changes in gene expression, while ventrally, sharpening may be accomplished by lineage sorting. We conclude that the integrated visualization of lineage reporter and gene expression domains simultaneously with brain morphology will be useful for understanding how changes in gene expression give rise to proper brain compartmentalization and structure.
Hong Cui; Weijuan Han; Lijun Yang; Yanzhong Chang
Oligodendrocyte lineage gene-1 expressed in oligodendrocytes may trigger the repair of neuronal myelin impairment, and play a crucial role in myelin repair. Hypoxia-inducible factor 1α, a transcription factor, is of great significance in premature infants with hypoxic-ischemic brain damage. There is little evidence of direct regulatory effects of hypoxia-inducible factor 1α on oligodendrocyte lineage gene-1. In this study, brain slices of Sprague-Dawley rats were cultured and subjected to oxygen-glucose deprivation. Then, slices were transfected with hypoxia-inducible factor 1α or oligodendrocyte lineage gene-1. The expression levels of hypoxia-inducible factor 1α and oligodendrocyte lineage gene-1 were significantly up-regulated in rat brains prior to transfection, as detected by immunohistochemical staining. Eight hours after transfection of slices with hypoxia-inducible factor 1α, oligodendrocyte lineage gene-1 expression was upregulated, and reached a peak 24 hours after transfection. Oligodendrocyte lineage gene-1 transfection induced no significant differences in hypoxia-inducible factor 1α levels in rat brain tissues with oxygen-glucose deprivation. These experimental findings indicate that hypoxia-inducible factor 1α can regulate oligodendrocyte lineage gene-1 expression in hypoxic brain tissue, thus repairing the neural impairment.
O' Connor, Olivia; Bosseno, Marie-France; Barnabé, Christian; Douzery, E. J. P.; Brenière, Simone Frédérique
American trypanosomiasis or Chagas disease is endemic in Latin America and caused by the flagellate Trypanosoma cruzi, which exhibits broad genetic variation. In various areas, the transmission of Chagas disease is ensured by sylvatic vectors, mainly carrying the evolutionary lineage I of T cruzi. Despite its epidemiological importance, this lineage is poorly studied. Here, we investigated the genetic variability and the phylogenetic relationships within T cruzi I using sequences of the non-t...
Full Text Available Abstract Background The origin and prevalence of the prehispanic settlers of the Canary Islands has attracted great multidisciplinary interest. However, direct ancient DNA genetic studies on indigenous and historical 17th–18th century remains, using mitochondrial DNA as a female marker, have only recently been possible. In the present work, the analysis of Y-chromosome polymorphisms in the same samples, has shed light on the way the European colonization affected male and female Canary Island indigenous genetic pools, from the conquest to present-day times. Results Autochthonous (E-M81 and prominent (E-M78 and J-M267 Berber Y-chromosome lineages were detected in the indigenous remains, confirming a North West African origin for their ancestors which confirms previous mitochondrial DNA results. However, in contrast with their female lineages, which have survived in the present-day population since the conquest with only a moderate decline, the male indigenous lineages have dropped constantly being substituted by European lineages. Male and female sub-Saharan African genetic inputs were also detected in the Canary population, but their frequencies were higher during the 17th–18th centuries than today. Conclusion The European colonization of the Canary Islands introduced a strong sex-biased change in the indigenous population in such a way that indigenous female lineages survived in the extant population in a significantly higher proportion than their male counterparts.
Dustin A Wood
Full Text Available Accurate delineation of lineage diversity is increasingly important, as species distributions are becoming more reduced and threatened. During the last century, the subspecies category was often used to denote phenotypic variation within a species range and to provide a framework for understanding lineage differentiation, often considered incipient speciation. While this category has largely fallen into disuse, previously recognized subspecies often serve as important units for conservation policy and management when other information is lacking. In this study, we evaluated phenotypic subspecies hypotheses within shovel-nosed snakes on the basis of genetic data and considered how evolutionary processes such as gene flow influenced possible incongruence between phenotypic and genetic patterns. We used both traditional phylogenetic and Bayesian clustering analyses to infer range-wide genetic structure and spatially explicit analyses to detect possible boundary locations of lineage contact. Multilocus analyses supported three historically isolated groups with low to moderate levels of contemporary gene exchange. Genetic data did not support phenotypic subspecies as exclusive groups, and we detected patterns of discordance in areas where three subspecies are presumed to be in contact. Based on genetic and phenotypic evidence, we suggested that species-level diversity is underestimated in this group and we proposed that two species be recognized, Chionactis occipitalis and C. annulata. In addition, we recommend retention of two subspecific designations within C. annulata (C. a. annulata and C. a. klauberi that reflect regional shifts in both genetic and phenotypic variation within the species. Our results highlight the difficultly in validating taxonomic boundaries within lineages that are evolving under a time-dependent, continuous process.
Wood, Dustin A.; Fisher, Robert N.; Vandergast, Amy G.
Accurate delineation of lineage diversity is increasingly important, as species distributions are becoming more reduced and threatened. During the last century, the subspecies category was often used to denote phenotypic variation within a species range and to provide a framework for understanding lineage differentiation, often considered incipient speciation. While this category has largely fallen into disuse, previously recognized subspecies often serve as important units for conservation policy and management when other information is lacking. In this study, we evaluated phenotypic subspecies hypotheses within shovel-nosed snakes on the basis of genetic data and considered how evolutionary processes such as gene flow influenced possible incongruence between phenotypic and genetic patterns. We used both traditional phylogenetic and Bayesian clustering analyses to infer range-wide genetic structure and spatially explicit analyses to detect possible boundary locations of lineage contact. Multilocus analyses supported three historically isolated groups with low to moderate levels of contemporary gene exchange. Genetic data did not support phenotypic subspecies as exclusive groups, and we detected patterns of discordance in areas where three subspecies are presumed to be in contact. Based on genetic and phenotypic evidence, we suggested that species-level diversity is underestimated in this group and we proposed that two species be recognized, Chionactis occipitalis and C. annulata. In addition, we recommend retention of two subspecific designations within C. annulata (C. a. annulata and C. a. klauberi) that reflect regional shifts in both genetic and phenotypic variation within the species. Our results highlight the difficultly in validating taxonomic boundaries within lineages that are evolving under a time-dependent, continuous process.
Hirakawa, Satoshi; Hong, Young-Kwon; Harvey, Natasha; Schacht, Vivien; Matsuda, Kant; Libermann, Towia; Detmar, Michael
In mammals, the lymphatic vascular system develops by budding of lymphatic progenitor endothelial cells from embryonic veins to form a distinct network of draining vessels with important functions in the immune response and in cancer metastasis. However, the lineage-specific molecular characteristics of blood vascular versus lymphatic endothelium have remained poorly defined. We isolated lymphatic endothelial cells (LECs) and blood vascular endothelial cells (BVECs) by immunomagnetic isolation directly from human skin. Cultured LECs but not BVECs expressed the lymphatic markers Prox1 and LYVE-1 and formed LYVE-1-positive vascular tubes after implantation in vivo. Transcriptional profiling studies revealed increased expression of several extracellular matrix and adhesion molecules in BVECs, including versican, collagens, laminin, and N-cadherin, and of the growth factor receptors endoglin and vascular endothelial growth factor receptor-1/Flt-1. Differential immunostains of human skin confirmed the blood vessel-specific expression of these genes. During embryonic development, endoglin expression was gradually down-regulated on lymphatic endothelium whereas vascular endothelial growth factor receptor-1 was absent from lymphatics. We also identified several genes with specific expression in LECs. These results demonstrate that some lineage-specific genes are only expressed during distinct developmental stages and they identify new molecular markers for blood vascular and lymphatic endothelium with important implications for future studies of vascular development and function. PMID:12547715
Hoffmann, Federico G.; Opazho, Juan C; Hoogewijs, David; Hankeln, Thomas; Ebner, Bettina; Vinogradov, Serge N; Bailly, Xavier; Storz, Jay F.
In the Metazoa, globin proteins display an underlying unity in tertiary structure that belies an extraordinary diversity in primary structures, biochemical properties, and physiological functions. Phylogenetic reconstructions can reveal which of these functions represent novel, lineage-specific innovations, and which represent ancestral functions that are shared with homologous globin proteins in other eukaryotes and even prokaryotes. To date, our understanding of globin diversity in deuteros...
Full Text Available Gene duplication is an important mechanism for the origination of functional novelties in organisms. We performed a comparative genome analysis to systematically estimate recent lineage specific gene duplication events in Arabidopsis thaliana and further investigate whether and how these new duplicate genes (NDGs play a functional role in the evolution and adaption of A. thaliana. We accomplished this using syntenic relationship among four closely related species, A. thaliana, A. lyrata, Capsella rubella and Brassica rapa. We identified 100 NDGs, showing clear origination patterns, whose parental genes are located in syntenic regions and/or have clear orthologs in at least one of three outgroup species. All 100 NDGs were transcribed and under functional constraints, while 24% of the NDGs have differential expression patterns compared to their parental genes. We explored the underlying evolutionary forces of these paralogous pairs through conducting neutrality tests with sequence divergence and polymorphism data. Evolution of about 15% of NDGs appeared to be driven by natural selection. Moreover, we found that 3 NDGs not only altered their expression patterns when compared with parental genes, but also evolved under positive selection. We investigated the underlying mechanisms driving the differential expression of NDGs and their parents, and found a number of NDGs had different cis-elements and methylation patterns from their parental genes. Overall, we demonstrated that NDGs acquired divergent cis-elements and methylation patterns and may experience sub-functionalization or neo-functionalization influencing the evolution and adaption of A. thaliana.
Pioli, Peter D; Whiteside, Sarah K; Weis, Janis J; Weis, John H
T lymphocytes are essential contributors to the adaptive immune system and consist of multiple lineages that serve various effector and regulatory roles. As such, precise control of gene expression is essential to the proper development and function of these cells. Previously, we identified Snai2 and Snai3 as being essential regulators of immune tolerance partly due to the impaired function of CD4(+) regulatory T cells in Snai2/3 conditional double knockout mice. Here we extend those previous findings using a bone marrow transplantation model to provide an environmentally unbiased view of the molecular changes imparted onto various T lymphocyte populations once Snai2 and Snai3 are deleted. The data presented here demonstrate that Snai2 and Snai3 transcriptionally regulate the cellular fitness and functionality of not only CD4(+) regulatory T cells but effector CD8(α+) and CD4(+) conventional T cells as well. This is achieved through the modulation of gene sets unique to each cell type and includes transcriptional targets relevant to the survival and function of each T cell lineage. As such, Snai2 and Snai3 are essential regulators of T cell immunobiology. PMID:26831822
Irie, Masahito; Koga, Akihiko; Kaneko-Ishino, Tomoko; Ishino, Fumitoshi
Amongst the 11 eutherian-specific genes acquired from a sushi-ichi retrotransposon is the CCHC type zinc-finger protein-encoding gene SIRH11/ZCCHC16. Its contribution to eutherian brain evolution is implied because of its involvement in cognitive function in mice, possibly via the noradrenergic system. Although, the possibility that Sirh11/Zcchc16 functions as a non-coding RNA still remains, dN/dS ratios in pairwise comparisons between its orthologs have provided supportive evidence that it acts as a protein. It became a pseudogene in armadillos (Cingulata) and sloths (Pilosa), the only two extant orders of xenarthra, which prompted us to examine the lineage-specific variations of SIRH11/ZCCHC16 in eutherians. We examined the predicted SIRH11/ZCCHC16 open reading frame (ORF) in 95 eutherian species based on the genomic DNA information in GenBank. A large variation in the SIRH11/ZCCHC16 ORF was detected in several lineages. These include a lack of a CCHC RNA-binding domain in its C-terminus, observed in gibbons (Hylobatidae: Primates) and megabats (Megachiroptera: Chiroptera). A lack of the N-terminal half, on the other hand, was observed in New World monkeys (Platyrrhini: Primates) and species belonging to New World and African Hystricognaths (Caviomorpha and Bathyergidae: Rodents) along with Cetacea and Ruminantia (Cetartiodactyla). Among the hominoids, interestingly, three out of four genera of gibbons have lost normal SIRH11/ZCCHC16 function by deletion or the lack of the CCHC RNA-binding domain. Our extensive dN/dS analysis suggests that such truncated SIRH11/ZCCHC16 ORFs are functionally diversified even within lineages. Combined, our results show that SIRH11/ZCCHC16 may contribute to the diversification of eutherians by lineage-specific structural changes after its domestication in the common eutherian ancestor, followed by putative species-specific functional changes that enhanced fitness and occurred as a consequence of complex natural selection events
Stet, R.J.M.; Kruiswijk, C.P.; Dixon, B.
It has become increasingly clear over the course of the past decade that the immune system genes of teleosts and tetrapods are plainly derived from common ancestral genes. The last 5 years, however, have also made it abundantly clear that in the teleost genome some of these genes are organized in a
Full Text Available Trithorax proteins and long-intergenic noncoding RNAs are critical regulators of embryonic stem cell pluripotency; however, how they cooperatively regulate germ layer mesoderm specification remains elusive. We report here that HoxBlinc RNA first specifies Flk1+ mesoderm and then promotes hematopoietic differentiation through regulation of hoxb pathways. HoxBlinc binds to the hoxb genes, recruits Setd1a/MLL1 complexes, and mediates long-range chromatin interactions to activate transcription of the hoxb genes. Depletion of HoxBlinc by shRNA-mediated knockdown or CRISPR-Cas9-mediated genetic deletion inhibits expression of hoxb genes and other factors regulating cardiac/hematopoietic differentiation. Reduced hoxb expression is accompanied by decreased recruitment of Set1/MLL1 and H3K4me3 modification, as well as by reduced chromatin loop formation. Re-expression of hoxb2–b4 genes in HoxBlinc-depleted embryoid bodies rescues Flk1+ precursors that undergo hematopoietic differentiation. Thus, HoxBlinc plays an important role in controlling hoxb transcription networks that mediate specification of mesoderm-derived Flk1+ precursors and differentiation of Flk1+ cells into hematopoietic lineages.
High diversity of genetic lineages and virulence genes in nasal Staphylococcus aureus isolates from donkeys destined to food consumption in Tunisia with predominance of the ruminant associated CC133 lineage
Full Text Available Abstract Background The objective of this study was to determine the genetic lineages and the incidence of antibiotic resistance and virulence determinants of nasal Staphylococcus aureus isolates of healthy donkeys destined to food consumption in Tunisia. Results Nasal swabs of 100 donkeys obtained in a large slaughterhouse in 2010 were inoculated in specific media for S. aureus and methicillin-resistant S. aureus (MRSA recovery. S. aureus was obtained in 50% of the samples, being all of isolates methicillin-susceptible (MSSA. Genetic lineages, toxin gene profile, and antibiotic resistance mechanisms were determined in recovered isolates. Twenty-five different spa-types were detected among the 50 MSSA with 9 novel spa-types. S. aureus isolates were ascribed to agr type I (37 isolates, III (7, II (4, and IV (2. Sixteen different sequence-types (STs were revealed by MLST, with seven new ones. STs belonging to clonal clomplex CC133 were majority. The gene tst was detected in 6 isolates and the gene etb in one isolate. Different combinations of enterotoxin, leukocidin and haemolysin genes were identified among S. aureus isolates. The egc-cluster-like and an incomplete egc-cluster-like were detected. Isolates resistant to penicillin, erythromycin, fusidic acid, streptomycin, ciprofloxacin, clindamycin, tetracycline, or chloramphenicol were found and the genes blaZ, erm(A, erm(C, tet(M, fusC were identified. Conclusions The nares of donkeys frequently harbor MSSA. They could be reservoirs of the ruminant-associated CC133 lineage and of toxin genes encoding TSST-1 and other virulence traits with potential implications in public health. CC133 seems to have a broader host distribution than expected.
Eric Zinn; Simon Pacouret; Vadim Khaychuk; Heikki T. Turunen; Livia S. Carvalho; Eva Andres-Mateos; Samiksha Shah; Rajani Shelke; Anna C. Maurer; Eva Plovie; Ru Xiao; Luk H. Vandenberghe
Adeno-associated virus (AAV) vectors have emerged as a gene-delivery platform with demonstrated safety and efficacy in a handful of clinical trials for monogenic disorders. However, limitations of the current generation vectors often prevent broader application of AAV gene therapy. Efforts to engineer AAV vectors have been hampered by a limited understanding of the structure-function relationship of the complex multimeric icosahedral architecture of the particle. To develop additional reagent...
Mark de Been
Full Text Available Third-generation cephalosporins are a class of β-lactam antibiotics that are often used for the treatment of human infections caused by Gram-negative bacteria, especially Escherichia coli. Worryingly, the incidence of human infections caused by third-generation cephalosporin-resistant E. coli is increasing worldwide. Recent studies have suggested that these E. coli strains, and their antibiotic resistance genes, can spread from food-producing animals, via the food-chain, to humans. However, these studies used traditional typing methods, which may not have provided sufficient resolution to reliably assess the relatedness of these strains. We therefore used whole-genome sequencing (WGS to study the relatedness of cephalosporin-resistant E. coli from humans, chicken meat, poultry and pigs. One strain collection included pairs of human and poultry-associated strains that had previously been considered to be identical based on Multi-Locus Sequence Typing, plasmid typing and antibiotic resistance gene sequencing. The second collection included isolates from farmers and their pigs. WGS analysis revealed considerable heterogeneity between human and poultry-associated isolates. The most closely related pairs of strains from both sources carried 1263 Single-Nucleotide Polymorphisms (SNPs per Mbp core genome. In contrast, epidemiologically linked strains from humans and pigs differed by only 1.8 SNPs per Mbp core genome. WGS-based plasmid reconstructions revealed three distinct plasmid lineages (IncI1- and IncK-type that carried cephalosporin resistance genes of the Extended-Spectrum Beta-Lactamase (ESBL- and AmpC-types. The plasmid backbones within each lineage were virtually identical and were shared by genetically unrelated human and animal isolates. Plasmid reconstructions from short-read sequencing data were validated by long-read DNA sequencing for two strains. Our findings failed to demonstrate evidence for recent clonal transmission of
Zinn, Eric; Pacouret, Simon; Khaychuk, Vadim; Turunen, Heikki T; Carvalho, Livia S; Andres-Mateos, Eva; Shah, Samiksha; Shelke, Rajani; Maurer, Anna C; Plovie, Eva; Xiao, Ru; Vandenberghe, Luk H
Adeno-associated virus (AAV) vectors have emerged as a gene-delivery platform with demonstrated safety and efficacy in a handful of clinical trials for monogenic disorders. However, limitations of the current generation vectors often prevent broader application of AAV gene therapy. Efforts to engineer AAV vectors have been hampered by a limited understanding of the structure-function relationship of the complex multimeric icosahedral architecture of the particle. To develop additional reagents pertinent to further our insight into AAVs, we inferred evolutionary intermediates of the viral capsid using ancestral sequence reconstruction. In-silico-derived sequences were synthesized de novo and characterized for biological properties relevant to clinical applications. This effort led to the generation of nine functional putative ancestral AAVs and the identification of Anc80, the predicted ancestor of the widely studied AAV serotypes 1, 2, 8, and 9, as a highly potent in vivo gene therapy vector for targeting liver, muscle, and retina. PMID:26235624
Hummelshøj, Tina; Nissen, Janna; Fog, Lea Munthe; Koch, Claus; Frost Bertelsen, Mads; Garred, Peter
-human primates. The exons and intron-exon boundaries of the FCN1-3 genes were sequenced in the following primate species: chimpanzee, gorilla, orangutan, rhesus macaque, cynomolgus macaque, baboon and common marmoset. We found that the exon organisation of the FCN genes was very similar between all the non...... the Shannon entropy revealing that all three proteins are generally highly conserved. Ficolin-1 and ficolin-2 showed the highest diversity, whereas ficolin-3 was more conserved. Ficolin-2 and ficolin-3 were present in non-human primate sera with the same characteristic oligomeric structures as seen in...
Lilly, B; Galewsky, S; Firulli, A B; Schulz, R A; Olson, E N
The myocyte enhancer factor (MEF) 2 family of transcription factors has been implicated in the regulation of muscle transcription in vertebrates. We have cloned a protein from Drosophila, termed D-MEF2, that shares extensive amino acid homology with the MADS (MCM1, Agamous, Deficiens, and serum-response factor) domains of the vertebrate MEF2 proteins. D-mef2 gene expression is first detected during Drosophila embryogenesis within mesodermal precursor cells prior to specification of the somatic and visceral muscle lineages. Expression of D-mef2 is dependent on the mesodermal determinants twist and snail but independent of the homeobox-containing gene tinman, which is required for visceral muscle and heart development. D-mef2 expression precedes that of the MyoD homologue, nautilus, and, in contrast to nautilus, D-mef2 appears to be expressed in all somatic and visceral muscle cell precursors. Its temporal and spatial expression patterns suggest that D-mef2 may play an important role in commitment of mesoderm to myogenic lineages. PMID:8202544
Full Text Available Thiomicrospira were originally characterized as sulfur-oxidizing chemolithoautotrophs. Attempts to grow them on hydrogen failed for many years. Only recently we demonstrated hydrogen consumption among two of three tested Thiomicrospira and posited that hydrogen consumption may be more widespread among Thiomicrospira than previously assumed. Here, we investigate and compare the hydrogen consumption ability and the presence of group 1 [NiFe]-hydrogenase genes (enzyme catalyzes H22H+ + 2e- for sixteen different Thiomicrospira species. Seven of these Thiomicrospira species encoded group 1 [NiFe]-hydrogenase genes and five of these species could also consume hydrogen. All Thiomicrospira species exhibiting hydrogen consumption were from hydrothermal vents along the Mid-Atlantic ridge or Eastern Pacific ridges. The tested Thiomicrospira from Mediterranean and Western Pacific vents could not consume hydrogen. The [NiFe]-hydrogenase genes were categorized into two clusters: those resembling the hydrogenase from Hydrogenovibrio are in cluster I and are related to those from Alpha- and other Gammaproteobacteria. In cluster II, hydrogenases found exclusively in T. crunogena strains are combined and form a monophyletic group with those from Epsilonproteobacteria suggesting they were acquired through horizontal gene transfer. Hydrogen consumption appears to be common among some Thiomicrospira, given that five of the tested sixteen strains carried this trait. The hydrogen consumption ability expands their competitiveness within an environment.
Full Text Available Abstract Background Tenascins are a family of glycoproteins found primarily in the extracellular matrix of embryos where they help to regulate cell proliferation, adhesion and migration. In order to learn more about their origins and relationships to each other, as well as to clarify the nomenclature used to describe them, the tenascin genes of the urochordate Ciona intestinalis, the pufferfish Tetraodon nigroviridis and Takifugu rubripes and the frog Xenopus tropicalis were identified and their gene organization and predicted protein products compared with the previously characterized tenascins of amniotes. Results A single tenascin gene was identified in the genome of C. intestinalis that encodes a polypeptide with domain features common to all vertebrate tenascins. Both pufferfish genomes encode five tenascin genes: two tenascin-C paralogs, a tenascin-R with domain organization identical to mammalian and avian tenascin-R, a small tenascin-X with previously undescribed GK repeats, and a tenascin-W. Four tenascin genes corresponding to tenascin-C, tenascin-R, tenascin-X and tenascin-W were also identified in the X. tropicalis genome. Multiple sequence alignment reveals that differences in the size of tenascin-W from various vertebrate classes can be explained by duplications of specific fibronectin type III domains. The duplicated domains are encoded on single exons and contain putative integrin-binding motifs. A phylogenetic tree based on the predicted amino acid sequences of the fibrinogen-related domains demonstrates that tenascin-C and tenascin-R are the most closely related vertebrate tenascins, with the most conserved repeat and domain organization. Taking all lines of evidence together, the data show that the tenascins referred to as tenascin-Y and tenascin-N are actually members of the tenascin-X and tenascin-W gene families, respectively. Conclusion The presence of a tenascin gene in urochordates but not other invertebrate phyla
Gharsa, Haythem; Ben Slama, Karim; Gómez-Sanz, Elena; Lozano, Carmen; Klibi, Naouel; Jouini, Ahlem; Messadi, Lilia; Boudabous, Abdellatif; Torres, Carmen
Nasal swabs of 100 healthy dogs were obtained in 2011 in Tunisia and tested for Staphylococcus pseudintermedius recovery. Antimicrobial resistance profile and virulence gene content were determined. Multilocus-sequence-typing (MLST) and SmaI-pulsed-field gel electrophoresis (PFGE) were investigated. S. pseudintermedius was recovered in 55 of the 100 tested samples (55 %), and one isolate per sample was further studied. All 55 S. pseudintermedius isolates were susceptible to methicillin (MSSP) but showed resistance to the following antimicrobials (% resistant isolates/resistance gene): penicillin (56.4/blaZ), tetracycline (40/tetM), trimethoprim-sulfamethoxazole (23.7), fusidic acid (9), kanamycin (3.7/aph(3´)-Ia), erythromycin-clindamycin (1.8/erm(B)), streptomycin (1.8/ant(6)-Ia), chloramphenicol (1.8) and ciprofloxacin (1.8). The following toxin genes were identified (% of isolates): lukS/F-I (98.2), expA (5.5), se-int (98.2), sec canine (1.8), siet (100), sea (5.5), seb (3.6), sec (10.9), sed (54.5), sei (5.5), sej (29.1), sek (3.6), ser (9.1), and hlg v (38.2). Ten different sequence-types were detected among 11 representative MSSP isolates: ST20, ST44, ST69, ST70, ST78, ST100, ST108, ST160, ST161, and ST162, the last three ones revealing novel alleles or allele combinations. Eleven different PFGE-patterns were identified in these isolates. The nares of healthy dogs could be a reservoir of antimicrobial resistant and virulent MSSP, highlighting the presence of the recently described exfoliating gene expA and several enterotoxin genes. PMID:23686400
Nery, Mariana F.; Arroyo, José Ignacio; Opazo, Juan C.
Background Hair represents an evolutionary innovation that appeared early on mammalian evolutionary history, and presumably contributed significantly to the rapid radiation of the group. An interesting event in hair evolution has been its secondary loss in some mammalian groups, such as cetaceans, whose hairless phenotype appears to be an adaptive response to better meet the environmental conditions. To determine whether different repertoire of keratin genes among mammals can potentially expl...
Valenti, Maria Teresa; Giannini, Sandro; Donatelli, Luca; Zanatta, Mirko; Bertoldo, Francesco; Sella, Stefania; Vilei, Maria Teresa; Ossi, Elena; Realdi, Giuseppe; Lo Cascio, Vincenzo; Dalle Carbonare, Luca
Introduction The purpose of this study was to evaluate the effects of risedronate (Ris) in the modulation of bone formation in rats with glucocorticoid (GC)-induced osteoporosis by histomorphometric, immunohistochemical and gene expression analyses. Methods We analyzed structure, turnover and microarchitecture, cyclooxygenase 2 (COX-2) levels and osteocyte apoptosis in 40 female rats divided as follows: 1) vehicle of methylprednisolone (vGC) + vehicle of risedronate (vRis); 2) Ris 5 μg/Kg + v...
Tran Lan T; Taylor John S; Constabel C
Abstract Background Plant polyphenol oxidases (PPOs) are enzymes that typically use molecular oxygen to oxidize ortho-diphenols to ortho-quinones. These commonly cause browning reactions following tissue damage, and may be important in plant defense. Some PPOs function as hydroxylases or in cross-linking reactions, but in most plants their physiological roles are not known. To better understand the importance of PPOs in the plant kingdom, we surveyed PPO gene families in 25 sequenced genomes ...
Full Text Available Adeno-associated virus (AAV vectors have emerged as a gene-delivery platform with demonstrated safety and efficacy in a handful of clinical trials for monogenic disorders. However, limitations of the current generation vectors often prevent broader application of AAV gene therapy. Efforts to engineer AAV vectors have been hampered by a limited understanding of the structure-function relationship of the complex multimeric icosahedral architecture of the particle. To develop additional reagents pertinent to further our insight into AAVs, we inferred evolutionary intermediates of the viral capsid using ancestral sequence reconstruction. In-silico-derived sequences were synthesized de novo and characterized for biological properties relevant to clinical applications. This effort led to the generation of nine functional putative ancestral AAVs and the identification of Anc80, the predicted ancestor of the widely studied AAV serotypes 1, 2, 8, and 9, as a highly potent in vivo gene therapy vector for targeting liver, muscle, and retina.
Guerzoni, Daniele; McLysaght, Aoife
De novo protein-coding gene origination is increasingly recognized as an important evolutionary mechanism. However, there remains a large amount of uncertainty regarding the frequency of these events and the mechanisms and speed of gene establishment. Here, we describe a rigorous search for cases of de novo gene origination in the great apes. We analyzed annotated proteomes as well as full genomic DNA and transcriptional and translational evidence. It is notable that results vary between data...
Arnaud, J-F; Viard, F; Delescluse, M.; Cuguen, J
Gene flow and introgression from cultivated to wild plant populations have important evolutionary and ecological consequences and require detailed investigations for risk assessments of transgene escape into natural ecosystems. Sugar beets (Beta vulgaris ssp. vulgaris) are of particular concern because: (i) they are cross-compatible with their wild relatives (the sea beet, B. vulgaris ssp. maritima); (ii) crop-to-wild gene flow is likely to occur via weedy lineages resulting from hybridizatio...
Monier, Adam; Sudek, Sebastian; Fast, Naomi M; Worden, Alexandra Z
Inteins are rare, translated genetic parasites mainly found in bacteria and archaea, while spliceosomal introns are distinctly eukaryotic features abundant in most nuclear genomes. Using targeted metagenomics, we discovered an intein in an Atlantic population of the photosynthetic eukaryote, Bathycoccus, harbored by the essential spliceosomal protein PRP8 (processing factor 8 protein). Although previously thought exclusive to fungi, we also identified PRP8 inteins in parasitic (Capsaspora) and predatory (Salpingoeca) protists. Most new PRP8 inteins were at novel insertion sites that, surprisingly, were not in the most conserved regions of the gene. Evolutionarily, Dikarya fungal inteins at PRP8 insertion site a appeared more related to the Bathycoccus intein at a unique insertion site, than to other fungal and opisthokont inteins. Strikingly, independent analyses of Pacific and Atlantic samples revealed an intron at the same codon as the Bathycoccus PRP8 intein. The two elements are mutually exclusive and neither was found in cultured Bathycoccus or other picoprasinophyte genomes. Thus, wild Bathycoccus contain one of few non-fungal eukaryotic inteins known and a rare polymorphic intron. Our data indicate at least two Bathycoccus ecotypes exist, associated respectively with oceanic or mesotrophic environments. We hypothesize that intein propagation is facilitated by marine viruses; and, while intron gain is still poorly understood, presence of a spliceosomal intron where a locus lacks an intein raises the possibility of new, intein-primed mechanisms for intron gain. The discovery of nucleus-encoded inteins and associated sequence polymorphisms in uncultivated marine eukaryotes highlights their diversity and reveals potential sexual boundaries between populations indistinguishable by common marker genes. PMID:23635865
de Carvalho, Misael Severino Nunes; Mangolin, Claudete Aparecida; Scapim, Carlos Alberto; da Silva, Teresa Aparecida; Machado, Maria de Fátima Pires da Silva
In the present study, we analyze the genetic structure and diversity among accessions of popcorn obtained from the CIMMYT International Maize and Wheat Improvement Center that represent the diversity available for current use by breeding programs. The main objectives were to identify SSR loci that were the best indicators of genetic diversity, to measure the genetic diversity within popcorn genotypes, and to analyze the genetic structure of the promising populations destined for use in breeding programs. The mean gene diversity of all SSR loci was 0.6352. An extremely high population differentiation level was detected (F(st) = 0.3152) with F(st) for each locus ranging from 0.1125 (Umc1229) to 0.4870 (Umc1755). Analyzing the genetic structure of eight popcorn accessions was especially important for identifying both SSR loci with high levels of heterozygosity and genotypes showing high heterozygosity (BOYA462 and ARZM13 050). This analysis should be the medium and long-term selection goal for the generation of inbred lines and the future production of new cultivars. Plant accessions ARZM05 083, ARZM13 050, and URUG298 may also be useful varieties that exhibit important agronomic characteristics that can be used through crosses to broaden the genetic basis of popcorn. PMID:22467122
Ghosheh, Nidal; Olsson, Björn; Edsbagge, Josefina; Küppers-Munther, Barbara; Van Giezen, Mariska; Asplund, Annika; Andersson, Tommy B; Björquist, Petter; Carén, Helena; Simonsson, Stina; Sartipy, Peter; Synnergren, Jane
Human pluripotent stem cells- (hPSCs-) derived hepatocytes have the potential to replace many hepatic models in drug discovery and provide a cell source for regenerative medicine applications. However, the generation of fully functional hPSC-derived hepatocytes is still a challenge. Towards gaining better understanding of the differentiation and maturation process, we employed a standardized protocol to differentiate six hPSC lines into hepatocytes and investigated the synchronicity of the hPSC lines by applying RT-qPCR to assess the expression of lineage-specific genes (OCT4, NANOG, T, SOX17, CXCR4, CER1, HHEX, TBX3, PROX1, HNF6, AFP, HNF4a, KRT18, ALB, AAT, and CYP3A4) which serve as markers for different stages during liver development. The data was evaluated using correlation and clustering analysis, demonstrating that the expression of these markers is highly synchronized and correlated well across all cell lines. The analysis also revealed a distribution of the markers in groups reflecting the developmental stages of hepatocytes. Functional analysis of the differentiated cells further confirmed their hepatic phenotype. Taken together, these results demonstrate, on the molecular level, the highly synchronized differentiation pattern across multiple hPSC lines. Moreover, this study provides additional understanding for future efforts to improve the functionality of hPSC-derived hepatocytes and thereby increase the value of related models. PMID:26949401
Müller, T A; Grundler, R; Istvanffy, R; Rudelius, M; Hennighausen, L; Illert, A L; Duyster, J
Mutations that activate FMS-like tyrosine kinase 3 (FLT3) are frequent occurrences in acute myeloid leukemia. Two distinct types of mutations have been described: internal duplication of the juxtamembranous domain (ITD) and point mutations of the tyrosine kinase domain (TKD). Although both mutations lead to constitutive FLT3 signaling, only FLT3-ITD strongly activates signal transducer and activator of transcription 5 (STAT5). In a murine transplantation model, FLT3-ITD induces a myeloproliferative neoplasm, whereas FLT3-TKD leads to a lymphoid malignancy with significantly longer latency. Here we report that the presence of STAT5 is critical for the development of a myeloproliferative disease by FLT3-ITD in mice. Deletion of Stat5 in FLT3-ITD-induced leukemogenesis leads not only to a significantly longer survival (82 vs 27 days) of the diseased mice, but also to an immunophenotype switch with expansion of the lymphoid cell compartment. Interestingly, we were able to show differential STAT5 activation in FLT3-ITD(+) myeloid and lymphoid murine progenitors. STAT5 target genes such as Oncostatin M were highly expressed in FLT3-ITD(+) myeloid but not in FLT3-ITD(+) lymphoid progenitor cells. Strikingly, FLT3-TKD expression in combination with Oncostatin M is sufficient to reverse the phenotype to a myeloproliferative disease in FLT3-TKD mice. Thus, lineage-specific STAT5 activation in hematopoietic progenitor cells predicts the FLT3(+)-mediated leukemic phenotype in mice. PMID:27046463
Winther, Thilde Nordmann; Madsen, Chris D; Pedersen, Anders;
. In this study, the inter- and intra-patient genetic diversity of the lineage A hMPV F gene was investigated. Ten isolates were collected from 10 hMPV infected children. Viral RNA was isolated and amplified, and approximately 10 clones from each isolate were sequenced. Altogether 108 clones were successfully...... sequenced. The average interpatient sequence diversity was 1.68% and 1.64% at nucleotide and amino acid levels, respectively. The samples were divisible into two groups on the basis of intrapatient sequence diversity. In group 1 (4 children) the intra-patient sequence diversity was low (nt: 0.26-0.39%, aa......: 0.51-0.94%) whereas group 2 (6 children) had a higher intra-patient sequence diversity (nt: 0.85-1.98%, aa: 1.08-2.22%). Phylogenetic analyses showed that the group 1 children harboured sublineage Al only, but interestingly group 2 children harboured both sublineages Al and A2, indicating they had...
Barredo Julio C
Full Text Available Abstract Background Expression of folylpoly-γ-glutamate synthetase (FPGS gene is two- to three-fold higher in B-precursor ALL (Bp- ALL than in T-lineage ALL (T-ALL and correlates with intracellular accumulation of methotrexate (MTX polyglutamates and lymphoblast sensitivity to MTX. In this report, we investigated the molecular regulatory mechanisms directing FPGS gene expression in Bp-ALL and T-ALL cells. Methods To determine FPGS transcription rate in Bp-ALL and T-ALL we used nuclear run-on assays. 5'-RACE was used to uncover potential regulatory regions involved in the lineage differences. We developed a luciferase reporter gene assay to investigate FPGS promoter/enhancer activity. To further characterize the FPGS proximal promoter, we determined the role of the putative transcription binding sites NFY and E-box on FPGS expression using luciferase reporter gene assays with substitution mutants and EMSA. Results FPGS transcription initiation rate was 1.6-fold higher in NALM6 vs. CCRF-CEM cells indicating that differences in transcription rate led to the observed lineage differences in FPGS expression between Bp-ALL and T-ALL blasts. Two major transcripts encoding the mitochondrial/cytosolic and cytosolic isoforms were detected in Bp-ALL (NALM6 and REH whereas in T-ALL (CCRF-CEM cells only the mitochondrial/cytosolic transcript was detected. In all DNA fragments examined for promoter/enhancer activity, we measured significantly lower luciferase activity in NALM6 vs. CCRF-CEM cells, suggesting the need for additional yet unidentified regulatory elements in Bp-ALL. Finally, we determined that the putative transcription factor binding site NFY, but not E-box, plays a role in FPGS transcription in both Bp- and T-lineage. Conclusion We demonstrated that the minimal FPGS promoter region previously described in CCRF-CEM is not sufficient to effectively drive FPGS transcription in NALM6 cells, suggesting that different regulatory elements are required
Expression of folylpoly-γ-glutamate synthetase (FPGS) gene is two- to three-fold higher in B-precursor ALL (Bp- ALL) than in T-lineage ALL (T-ALL) and correlates with intracellular accumulation of methotrexate (MTX) polyglutamates and lymphoblast sensitivity to MTX. In this report, we investigated the molecular regulatory mechanisms directing FPGS gene expression in Bp-ALL and T-ALL cells. To determine FPGS transcription rate in Bp-ALL and T-ALL we used nuclear run-on assays. 5'-RACE was used to uncover potential regulatory regions involved in the lineage differences. We developed a luciferase reporter gene assay to investigate FPGS promoter/enhancer activity. To further characterize the FPGS proximal promoter, we determined the role of the putative transcription binding sites NFY and E-box on FPGS expression using luciferase reporter gene assays with substitution mutants and EMSA. FPGS transcription initiation rate was 1.6-fold higher in NALM6 vs. CCRF-CEM cells indicating that differences in transcription rate led to the observed lineage differences in FPGS expression between Bp-ALL and T-ALL blasts. Two major transcripts encoding the mitochondrial/cytosolic and cytosolic isoforms were detected in Bp-ALL (NALM6 and REH) whereas in T-ALL (CCRF-CEM) cells only the mitochondrial/cytosolic transcript was detected. In all DNA fragments examined for promoter/enhancer activity, we measured significantly lower luciferase activity in NALM6 vs. CCRF-CEM cells, suggesting the need for additional yet unidentified regulatory elements in Bp-ALL. Finally, we determined that the putative transcription factor binding site NFY, but not E-box, plays a role in FPGS transcription in both Bp- and T-lineage. We demonstrated that the minimal FPGS promoter region previously described in CCRF-CEM is not sufficient to effectively drive FPGS transcription in NALM6 cells, suggesting that different regulatory elements are required for FPGS gene expression in Bp-cells. Our data indicate
Green Eric D
Full Text Available Abstract Background The elastin gene (ELN is implicated as a factor in both supravalvular aortic stenosis (SVAS and Williams Beuren Syndrome (WBS, two diseases involving pronounced complications in mental or physical development. Although the complete spectrum of functional roles of the processed gene product remains to be established, these roles are inferred to be analogous in human and mouse. This view is supported by genomic sequence comparison, in which there are no large-scale differences in the ~1.8 Mb sequence block encompassing the common region deleted in WBS, with the exception of an overall reversed physical orientation between human and mouse. Results Conserved synteny around ELN does not translate to a high level of conservation in the gene itself. In fact, ELN orthologs in mammals show more sequence divergence than expected for a gene with a critical role in development. The pattern of divergence is non-conventional due to an unusually high ratio of gaps to substitutions. Specifically, multi-sequence alignments of eight mammalian sequences reveal numerous non-aligning regions caused by species-specific insertions and deletions, in spite of the fact that the vast majority of aligning sites appear to be conserved and undergoing purifying selection. Conclusions The pattern of lineage-specific, in-frame insertions/deletions in the coding exons of ELN orthologous genes is unusual and has led to unique features of the gene in each lineage. These differences may indicate that the gene has a slightly different functional mechanism in mammalian lineages, or that the corresponding regions are functionally inert. Identified regions that undergo purifying selection reflect a functional importance associated with evolutionary pressure to retain those features.
Espinola Emilio E
Full Text Available Abstract In recent years it was reported that the accumulation of point mutations in VP4 and VP7 genes of rotavirus strains was the main cause of the failure of the G or P-typing. Failures in the correct genotyping of G1, G2, G8, G9 and G10 rotavirus strains were reported in the most commonly used reverse transcription (RT-PCR strategies. Collecting VP7 gene sequences of G1 rotavirus strains from databases we found that 74 (61.2 % out of 121 G1 strains from lineage I showed the four specific mismatches at the 5' end of the 9T1-1 primer, previously associated with the failure of G1-typing. Thus, a great percentage of the G1 strains from lineage I worldwide reported could not have been typed if the Das's RT-PCR strategy were used. This analysis shows that the failure on the detection of the G1 strains could be due to the diversification of rotavirus strains in phylogenetic lineages. Therefore, the use of different RT-PCR strategies with different primer binding locations on the VP7 gene or new typing methodologies -like microarrays procedures- could be a better option to avoid the failure of the G-typing of rotavirus strains detected during surveillance programs.
Globalization requires areas within the national territory to compete in the free trade competitively with products from countries all over the world. Regional economic development is expected to produce superior quality products that can compete in competition, both domestically and abroad. Agam as areas that have the potential of tourism and culture has the potential to perform on the world market with superior commodity sub-sectors of the manufacturing industry. This article analyzes the e...
Hasebe, M; Wen, C K; Kato, M; Banks, J A
The MADS genes encode a family of transcription factors, some of which control the identities of floral organs in flowering plants. To understand the role of MADS genes in the evolution of floral organs, five MADS genes (CMADS1, 2, 3, 4, and 6) were cloned from the fern Ceratopteris richardii, a nonflowering plant. A gene tree of partial amino acid sequences of seed plant and fern MADS genes showed that the fern genes form three subfamilies. All members of one of the fern MADS subfamilies have additional amino-terminal amino acids, which is a synapomorphic character of the AGAMOUS subfamily of the flowering plant MADS genes. Their structural similarity indicates a sister relationship between the two subfamilies. The temporal and spatial patterns of expression of the five fern MADS genes were assessed by Northern blot analyses and in situ hybridizations. CMADS1, 2, 3, and 4 are expressed similarly in the meristematic regions and primordia of sporophyte shoots and roots, as well as in reproductive structures, including sporophylls and sporangial initials, although the amount of expression in each tissue is different in each gene. CMADS6 is expressed in gametophytic tissues but not in sporophytic tissues. The lack of organ-specific expression of MADS genes in the reproductive structures of the fern sporophyte may indicate that the restriction of MADS gene expression to specific reproductive organs and the specialization of MADS gene functions as homeotic selector genes in the flowering plant lineage were important in floral organ evolution. PMID:9600946
Yu, Xianxian; Duan, Xiaoshan; Zhang, Rui; Fu, Xuehao; Ye, Lingling; Kong, Hongzhi; Xu, Guixia; Shan, Hongyan
AP1/FUL, SEP, AGL6, and FLC subfamily genes play important roles in flower development. The phylogenetic relationships among them, however, have been controversial, which impedes our understanding of the origin and functional divergence of these genes. One possible reason for the controversy may be the problems caused by changes in the exon-intron structure of genes, which, according to recent studies, may generate non-homologous sites and hamper the homology-based sequence alignment. In this study, we first performed exon-by-exon alignments of these and three outgroup subfamilies (SOC1, AG, and STK). Phylogenetic trees reconstructed based on these matrices show improved resolution and better congruence with species phylogeny. In the context of these phylogenies, we traced evolutionary changes of exon-intron structures in each subfamily. We found that structural changes have occurred frequently following gene duplication and speciation events. Notably, exons 7 and 8 (if present) suffered more structural changes than others. With the knowledge of exon-intron structural changes, we generated more reasonable alignments containing all the focal subfamilies. The resulting trees showed that the SEP subfamily is sister to the monophyletic group formed by AP1/FUL and FLC subfamily genes and that the AGL6 subfamily forms a sister group to the three abovementioned subfamilies. Based on this topology, we inferred the evolutionary history of exon-intron structural changes among different subfamilies. Particularly, we found that the eighth exon originated before the divergence of AP1/FUL, FLC, SEP, and AGL6 subfamilies and degenerated in the ancestral FLC-like gene. These results provide new insights into the origin and evolution of the AP1/FUL, FLC, SEP, and AGL6 subfamilies. PMID:27200066
Chow, Wei Zhen; Chan, Yoke Fun; Oong, Xiang Yong; Ng, Liang Jie; Nor'E, Siti Sarah; Ng, Kim Tien; Chan, Kok Gan; Hanafi, Nik Sherina; Pang, Yong Kek; Kamarulzaman, Adeeba; Tee, Kok Keng
Human metapneumovirus (HMPV) is an important viral respiratory pathogen worldwide. Current knowledge regarding the genetic diversity, seasonality and transmission dynamics of HMPV among adults and children living in tropical climate remains limited. HMPV prevailed at 2.2% (n = 86/3,935) among individuals presented with acute respiratory tract infections in Kuala Lumpur, Malaysia between 2012 and 2014. Seasonal peaks were observed during the northeast monsoon season (November-April) and correlated with higher relative humidity and number of rainy days (P < 0.05). Phylogenetic analysis of the fusion and attachment genes identified the co-circulation of three known HMPV sub-lineages, A2b and B1 (30.2% each, 26/86) and B2 (20.9%, 18/86), with genotype shift from sub-lineage B1 to A2b observed in 2013. Interestingly, a previously unrecognized sub-lineage of A2 was identified in 18.6% (16/86) of the population. Using a custom script for network construction based on the TN93 pairwise genetic distance, we identified up to nine HMPV transmission clusters circulating as multiple sub-epidemics. Although no apparent major outbreak was observed, the increased frequency of transmission clusters (dyads) during seasonal peaks suggests the potential roles of transmission clusters in driving the spread of HMPV. Our findings provide essential information for therapeutic research, prevention strategies, and disease outbreak monitoring of HMPV. PMID:27279080
Zambetti, Noemi A; Bindels, Eric M J; Van Strien, Paulina M H; Valkhof, Marijke G; Adisty, Maria N; Hoogenboezem, Remco M; Sanders, Mathijs A; Rommens, Johanna M; Touw, Ivo P; Raaijmakers, Marc H G P
Shwachman-Diamond syndrome is a congenital bone marrow failure disorder characterized by debilitating neutropenia. The disease is associated with loss-of-function mutations in the SBDS gene, implicated in ribosome biogenesis, but the cellular and molecular events driving cell specific phenotypes in ribosomopathies remain poorly defined. Here, we established what is to our knowledge the first mammalian model of neutropenia in Shwachman-Diamond syndrome through targeted downregulation of Sbds in hematopoietic stem and progenitor cells expressing the myeloid transcription factor CCAAT/enhancer binding protein α (Cebpa). Sbds deficiency in the myeloid lineage specifically affected myelocytes and their downstream progeny while, unexpectedly, it was well tolerated by rapidly cycling hematopoietic progenitor cells. Molecular insights provided by massive parallel sequencing supported cellular observations of impaired cell cycle exit and formation of secondary granules associated with the defect of myeloid lineage progression in myelocytes. Mechanistically, Sbds deficiency activated the p53 tumor suppressor pathway and induced apoptosis in these cells. Collectively, the data reveal a previously unanticipated, selective dependency of myelocytes and downstream progeny, but not rapidly cycling progenitors, on this ubiquitous ribosome biogenesis protein, thus providing a cellular basis for the understanding of myeloid lineage biased defects in Shwachman-Diamond syndrome. PMID:26185170
María José Benítez-Galeano
Full Text Available Citrus Tristeza Virus (CTV is the most economically important virus of citrus worldwide. Genetic diversity and population structure of CTV isolates from all citrus growing areas from Uruguay were analyzed by RT-PCR and cloning of the three RNA silencing suppressor genes (p25, p20 and p23. Bayesian phylogenetic analysis revealed the circulation of three known genotypes (VT, T3, T36 in the country, and the presence of a new genetic lineage composed by isolates from around the world, mainly from South America. Nucleotide and amino acid identity values for this new genetic lineage were both higher than 97% for the three analyzed regions. Due to incongruent phylogenetic relationships, recombination analysis was performed using Genetic Algorithms for Recombination Detection (GARD and SimPlot software. Recombination events between previously described CTV isolates were detected. High intra-sample variation was found, confirming the co-existence of different genotypes into the same plant. This is the first report describing: (1 the genetic diversity of Uruguayan CTV isolates circulating in the country and (2 the circulation of a novel CTV genetic lineage, highly present in the South American region. This information may provide assistance to develop an effective cross-protection program.
Benítez-Galeano, María José; Rubio, Leticia; Bertalmío, Ana; Maeso, Diego; Rivas, Fernando; Colina, Rodney
Citrus Tristeza Virus (CTV) is the most economically important virus of citrus worldwide. Genetic diversity and population structure of CTV isolates from all citrus growing areas from Uruguay were analyzed by RT-PCR and cloning of the three RNA silencing suppressor genes (p25, p20 and p23). Bayesian phylogenetic analysis revealed the circulation of three known genotypes (VT, T3, T36) in the country, and the presence of a new genetic lineage composed by isolates from around the world, mainly from South America. Nucleotide and amino acid identity values for this new genetic lineage were both higher than 97% for the three analyzed regions. Due to incongruent phylogenetic relationships, recombination analysis was performed using Genetic Algorithms for Recombination Detection (GARD) and SimPlot software. Recombination events between previously described CTV isolates were detected. High intra-sample variation was found, confirming the co-existence of different genotypes into the same plant. This is the first report describing: (1) the genetic diversity of Uruguayan CTV isolates circulating in the country and (2) the circulation of a novel CTV genetic lineage, highly present in the South American region. This information may provide assistance to develop an effective cross-protection program. PMID:26205407
Jourda, Cyril; Cardi, Céline; Mbéguié-A-Mbéguié, Didier; Bocs, Stéphanie; Garsmeur, Olivier; D'Hont, Angélique; Yahiaoui, Nabila
Whole-genome duplications (WGDs) are widespread in plants, and three lineage-specific WGDs occurred in the banana (Musa acuminata) genome. Here, we analysed the impact of WGDs on the evolution of banana gene families involved in ethylene biosynthesis and signalling, a key pathway for banana fruit ripening. Banana ethylene pathway genes were identified using comparative genomics approaches and their duplication modes and expression profiles were analysed. Seven out of 10 banana ethylene gene families evolved through WGD and four of them (1-aminocyclopropane-1-carboxylate synthase (ACS), ethylene-insensitive 3-like (EIL), ethylene-insensitive 3-binding F-box (EBF) and ethylene response factor (ERF)) were preferentially retained. Banana orthologues of AtEIN3 and AtEIL1, two major genes for ethylene signalling in Arabidopsis, were particularly expanded. This expansion was paralleled by that of EBF genes which are responsible for control of EIL protein levels. Gene expression profiles in banana fruits suggested functional redundancy for several MaEBF and MaEIL genes derived from WGD and subfunctionalization for some of them. We propose that EIL and EBF genes were co-retained after WGD in banana to maintain balanced control of EIL protein levels and thus avoid detrimental effects of constitutive ethylene signalling. In the course of evolution, subfunctionalization was favoured to promote finer control of ethylene signalling. PMID:24716518
Zhang, Chaomei; Nietfeldt, Joe; Zhang, Min; Benson, Andrew K.
Listeria monocytogenes strains belonging to phylogenetic lineage II (serotypes 1/2a, 1/2c, and 3a) carry a lineage-specific genome segment encoding a putative sigma subunit of RNA polymerase (lmo0423, herein referred to as sigC), a gene of unknown function (lmo0422) similar to the padR family of regulators, and a gene that is similar to the rodA-ftsW family of cell wall morphology genes (lmo0421). To understand the function of this set of genes, their expression patterns and the effects of nu...
Full Text Available Abstract Background Seed plants are composed of angiosperms and gymnosperms, which diverged from each other around 300 million years ago. While much light has been shed on the mechanisms and rate of genome evolution in flowering plants, such knowledge remains conspicuously meagre for the gymnosperms. Conifers are key representatives of gymnosperms and the sheer size of their genomes represents a significant challenge for characterization, sequencing and assembling. Results To gain insight into the macro-organisation and long-term evolution of the conifer genome, we developed a genetic map involving 1,801 spruce genes. We designed a statistical approach based on kernel density estimation to analyse gene density and identified seven gene-rich isochors. Groups of co-localizing genes were also found that were transcriptionally co-regulated, indicative of functional clusters. Phylogenetic analyses of 157 gene families for which at least two duplicates were mapped on the spruce genome indicated that ancient gene duplicates shared by angiosperms and gymnosperms outnumbered conifer-specific duplicates by a ratio of eight to one. Ancient duplicates were much more translocated within and among spruce chromosomes than conifer-specific duplicates, which were mostly organised in tandem arrays. Both high synteny and collinearity were also observed between the genomes of spruce and pine, two conifers that diverged more than 100 million years ago. Conclusions Taken together, these results indicate that much genomic evolution has occurred in the seed plant lineage before the split between gymnosperms and angiosperms, and that the pace of evolution of the genome macro-structure has been much slower in the gymnosperm lineage leading to extent conifers than that seen for the same period of time in flowering plants. This trend is largely congruent with the contrasted rates of diversification and morphological evolution observed between these two groups of seed
Nozaki, Hisayoshi; Onishi, Keisuke; Morita, Eiko
Chloromonas is distinguished from Chlamydomonas primarily by the absence of pyrenoids, which are structures that are present in the chloroplasts of most algae and are composed primarily of the CO2-fixing enzyme Rubisco. In this study we compared sequences of the rbcL (Rubisco large subunit-encoding) genes of pyrenoid-less Chloromonas species with those of closely related pyrenoid-containing Chlamydomonas species in the "Chloromonas lineage" and with those of 45 other green algae. We found that the proteins encoded by the rbcL genes had a much higher level of amino acid substitution in members of the Chloromonas lineage than they did in other algae. This kind of elevated substitution rate was not observed, however, in the deduced proteins encoded by two other chloroplast genes that we analyzed: atpB and psaB. The rates of synonymous and nonsynonymous nucleotide substitutions in the rbcL genes indicate that the rapid evolution of these genes in members of the Chloromonas lineage is not due to relaxed selection (as it presumably is in parasitic land plants). A phylogenetic tree based on rbcL nucleotide sequences nested two Chlamydomonas species as a "pyrenoid-regained" clade within a monophyletic Chloromonas "pyrenoid-lost" clade. Character-state optimization with this tree suggested that the loss and the regain of pyrenoids were accompanied by eight synapomorphic amino acid replacements in the Rubisco large subunit, four of which are positioned in the region involved in its dimerization. However, both the atpB and the psaB sequence data gave robust support for a rather different set of phylogenetic relationships in which neither the "pyrenoid-lost" nor the "pyrenoid-regained" clade was resolved. The appearance of such clades in the rbcL-based tree may be an artifact of convergent evolutionary changes that have occurred in a region of the large subunit that determines whether Rubisco molecules will aggregate to form a visible pyrenoid. PMID:12355262
Full Text Available CBRC-AGAM-07-0064 ref|YP_855025.1| sulfatase [Aeromonas ... hydrophila subsp. hydrophila ATCC 7966] ... gb|ABK38012.1| sulfatase [Aeromonas ... hydrophila subsp. hydrophila ATCC 7966] YP_855025. ...
Full Text Available CBRC-AGAM-07-0002 ref|YP_001142445.1| membrane protein [Aeromonas ... salmonicida subsp. salmonicida ... A449] gb|ABO90697.1| membrane protein [Aeromonas ... salmonicida subsp. salmonicida A449] YP_001142445. ...
Full Text Available CBRC-AGAM-07-0064 ref|YP_001143407.1| sulfatase [Aeromonas ... salmonicida subsp. salmonicida A449] ... gb|ABO91659.1| sulfatase [Aeromonas ... salmonicida subsp. salmonicida A449] YP_001143407. ...
Full Text Available CBRC-AGAM-07-0070 ref|YP_001006164.1| multiple antibiotic ... resistance protein [Yersinia enterocol ... bsp. enterocolitica 8081] emb|CAL11986.1| multiple antibiotic ... resistance protein [Yersinia enterocolitica subsp. ...
Full Text Available Globalization requires areas within the national territory to compete in the free trade competitively with products from countries all over the world. Regional economic development is expected to produce superior quality products that can compete in competition, both domestically and abroad. Agam as areas that have the potential of tourism and culture has the potential to perform on the world market with superior commodity sub-sectors of the manufacturing industry. This article analyzes the election of regional commodity Agam using LQ analysis, specialization index, Shift share and SWOT analysis. The analysis finds that subsekctor processing industry has a competitive advantage and thus likely to be developed to increase the region's economy. Commodity embroidery as a creative industry is a commodity that is mapped able to compete on the sub-sectors of the processing industry because the rich local cultural values and Islamic values. A variety of programs and government policies are needed to support these commodities to appear on the international market.
Salomonsen, Jan; Chattaway, John A; Chan, Andrew C Y; Parker, Aimée; Huguet, Samuel; Marston, Denise A; Rogers, Sally L; Wu, Zhiguang; Smith, Adrian L; Staines, Karen; Butter, Colin; Riegert, Patricia; Vainio, Olli; Nielsen, Line; Kaspers, Bernd; Griffin, Darren K; Yang, Fengtang; Zoorob, Rima; Guillemot, Francois; Auffray, Charles; Beck, Stephan; Skjødt, Karsten; Kaufman, Jim
Many genes important in immunity are found as multigene families. The butyrophilin genes are members of the B7 family, playing diverse roles in co-regulation and perhaps in antigen presentation. In humans, a fixed number of butyrophilin genes are found in and around the major histocompatibility c...
夏燕; 景丹龙; 王军辉
以黄金树的花芽为材料,采用同源基因克隆技术,获得黄金树花器官特征决定的AG同源基因,将其命名为CaspAG,其开放阅读框(ORF)为738 bp,编码245个氨基酸。分子系统发生和蛋白序列比对分析表明：CaspAG是拟南芥的AG同源蛋白,被归为euAG进化分支,其MADS区有57个氨基酸, I区有32个氨基酸, K区有83个氨基酸, C区有55个氨基酸,其中C末端的转录激活区含有两个保守的基序：AGI和AGII基序。半定量RT-PCR分析表明,在花发育过程中, CaspAG基因仅在雄蕊和雌蕊中表达,而在茎、叶片、萼片和花瓣中几乎不表达。实时荧光定量PCR分析结果表明, CaspAG基因在雌雄蕊原基分化期至雌雄蕊成熟期均有表达,在雌雄蕊发育成熟期表达量达到最高；且在雄蕊的表达高峰的时间明显早于雌蕊,这与雌、雄蕊形态成熟的时间基本吻合。%A MADS-box gene CaspAG involved in lfower development was isolated from the lfower bud of Catalpa speciosa via homology cloning technique. The open reading frame (ORF) of CaspAG was 738 bp, which encoded 245 amino acid. Protein sequence alignment and molecular phylogeny analysis suggested that CaspAG was an AG homology in Arabidopsis, grouped with euAG clade. Conceptual translation revealed that the MADS domain contained 57 amino acid, the I domain contained 32 amino acid, the K domain contained 83 amino acid, the C domain contained 55 amino acid. Moreover, two highly conserved motifs speciifc to C pro-teins, AG motifs I and II, were found in the C-terminal regions of the CaspAG protein. Semi-quantitative RT-PCR analysis showed CaspAG transcriptional activity mainly concentrated on stamens and carpels while no-ex-pression in plant stem, leaves, sepals and petals during different stages of lfower development. The qRT-PCR analysis showed that the expression of CaspAG was detected at the primordium to mature stages of stamen and pistil during morphological differentiation
Mans, Ben J; de Castro, Minique H; Pienaar, Ronel; de Klerk, Daniel; Gaven, Philasande; Genu, Siyamcela; Latif, Abdalla A
Ancestral reconstruction in its fullest sense aims to describe the complete evolutionary history of a lineage. This depends on accurate phylogenies and an understanding of the key characters of each parental lineage. An attempt is made to delineate our current knowledge with regard to the ancestral reconstruction of the tick (Ixodida) lineage. Tick characters may be assigned to Core of Life, Lineages of Life or Edges of Life phenomena depending on how far back these characters may be assigned in the evolutionary Tree of Life. These include housekeeping genes, sub-cellular systems, heme processing (Core of Life), development, moulting, appendages, nervous and organ systems, homeostasis, respiration (Lineages of Life), specific adaptations to a blood-feeding lifestyle, including the complexities of salivary gland secretions and tick-host interactions (Edges of Life). The phylogenetic relationships of lineages, their origins and importance in ancestral reconstruction are discussed. Uncertainties with respect to systematic relationships, ancestral reconstruction and the challenges faced in comparative transcriptomics (next-generation sequencing approaches) are highlighted. While almost 150 years of information regarding tick biology have been assembled, progress in recent years indicates that we are in the infancy of understanding tick evolution. Even so, broad reconstructions can be made with relation to biological features associated with various lineages. Conservation of characters shared with sister and parent lineages are evident, but appreciable differences are present in the tick lineage indicating modification with descent, as expected for Darwinian evolutionary theory. Many of these differences can be related to the hematophagous lifestyle of ticks. PMID:26868413
Papenfuss, Anthony T.; Feng, Zhi-Ping; Krasnec, Katina; Deakin, Janine E; Baker, Michelle L.; Miller, Robert D.
Background Major histocompatibility complex (MHC) class I genes are found in the genomes of all jawed vertebrates. The evolution of this gene family is closely tied to the evolution of the vertebrate genome. Family members are frequently found in four paralogous regions, which were formed in two rounds of genome duplication in the early vertebrates, but in some species class Is have been subject to additional duplication or translocation, creating additional clusters. The gene family is tradi...
Full Text Available Abstract Many subtypes of acute lymphoblastic leukemia (ALL are associated with specific chromosomal rearrangements. The complex translocation t(9;14;14, a variant of the translocation (14;14(q11;q32, is a rare but recurrent chromosomal abnormality involving the immunoglobulin heavy-chain (IGH and CCAAT enhancer-binding protein (CEBPE genes in B-lineage ALL (B-ALL and may represent a new B-ALL subgroup. We report here the case of a 5-year-old girl with B-ALL, positive for CD19, CD38 and HLA-DR. A direct technique and G-banding were used for chromosomal analysis and fluorescentin situ hybridization (FISH with BAC probes was used to investigate a possible rearrangement of the IGH andCEBPE genes. The karyotype exhibit the chromosomal aberration 46,XX,del(9(p21,t(14;14(q11;q32. FISH with dual-color break-apartIGH-specific and CEPBE-specific bacterial artificial chromosome (BAC probes showed a complex t(9;14;14 associated with a deletion of cyclin-dependent kinase inhibitor 2A (CDKN2A and paired box gene 5 (PAX5 at 9p21-13 and duplication of the fusion gene IGH-CEBPE.
Full Text Available Abstract Background Uncoupling proteins (UCP are evolutionary conserved mitochondrial carriers that control energy metabolism and therefore play important roles in several physiological processes such as thermogenesis, regulation of reactive oxygen species (ROS, growth control, lipid metabolism and regulation of insulin secretion. Despite their importance in various physiological processes, their molecular function remains controversial. The evolution and phylogenetic distribution may assist to identify their general biological function and structure-function relationships. The exact number of uncoupling protein genes in the fish genome and their evolution is unresolved. Results Here we report the first characterisation of UCP gene family members in sea bass, Dicentrarchus labrax, and then retrace the evolution of the protein family in vertebrates. Four UCP genes that are shared by five other fish species were identified in sea bass genome. Phylogenetic reconstitution among vertebrate species and synteny analysis revealed that UCP1, UCP2 and UCP3 evolved from duplication events that occurred in the common ancestor of vertebrates, whereas the novel fourth UCP originated specifically in the teleost lineage. Functional divergence analysis among teleost species revealed specific amino acid positions that have been subjected to altered functional constraints after duplications. Conclusions This work provides the first unambiguous evidence for the presence of a fourth UCP gene in teleost fish genome and brings new insights into the evolutionary history of the gene family. Our results suggest functional divergence among paralogues which might result from long-term and differential selective pressures, and therefore, provide the indication that UCP genes may have diverse physiological functions in teleost fishes. Further experimental analysis of the critical amino acids identified here may provide valuable information on the physiological functions of
Fungi that have the enzymes cyanase and carbonic anhydrase show a limited capacity to detoxify cyanate, a fungicide employed by both plants and humans. Here, we describe a novel two-gene cluster that comprises duplicated cyanase and carbonic anhydrase copies, which we name the CCA gene cluster, trac...
Full Text Available TEEQEDRRNNNRHSPGRIGRDELEAIKTNLLNTNEVTFSTVLDTDLGPPGSPPGRGGNYGKNLSMAQLKVPGVGGEPADDGGGNGGGDGTRRIRLISELSEADSILSSYHEGGYKKKPPKIPDGG...YGWVIVFSSFMISLIMDGVSFSFGLIYTELLDYFGESKSKTAWIGSLFIAVPLLSGPIMSNLVDRYGCRKMTMLGGFIGGMGFVLASICQSVEQLYFTFGILSGVGL...GFGYVTVVVCVAFWFDKRRTFATGIGASGTGIGTFVYAPLTQWLINNFGWRGTTLILAGTLFNMV...ASIGDGSRTEKCRSFRGNSLDVVYENEIFNPNVDTNVTLVVPKQTKWLHQRAVAPRGGGLKKQTSLGRQHSMRYSNFYKDMRLHRNSIHYRGALLNTHRYRLKASSCPNIYRNSMTTIAKEQDEVSLRAR ... ...AMGALMRDPEWMIEESRLESRAQSIQTFSNSSVYLDEIKKLIETGIPKEHVLDTLVTNVNTEANQAIPPEDPAMTKKYSSEVALPTFFSEQEQHGAGGGGPRAGGGNL
Full Text Available HPLHNNPPPPSYAVSVQAKLNKAASGYATPPPPSPSALGHEGGGAGRHVGAAASAAAGGPGSGVPKQPLRAKPSLPGLQNVLPSNVPVQTVGGGGGGGVGGG...VIRSFDVNKPGCEVNDLKGGVAGGSILRGVLKVGQEIEVRPGLVSKDAEGRLTCKPIFSKIVSLYTEQNELQFAVPGGLIGVGTKIEPT...EIKTTCVLKVITLPSAETTPATFTRAVKEFYDIRADDLVLEVNVHGLPKPTISWQKDGEDIVLGDKLLINREPNGVYQLCIHKPAPADCGVYECRAVNSAGTAKVSHEVSFTSKDKLI...LLAIAAVTEVEFKEAETVKEFIKDPSKFAAATATTASAAAPAAKAEEKKLHVGNLQRHEQAGKAFRWVVLPVRYHALGRQDTRRIENGGFFLPHEPLENWLHSDTARGFVVADLIAGITVGLTVLPQGL...QQQQQLNHQHHQQQQQQQQHDAKQRGIASTAASGGVRSSLMKSVRFPGTGGNTNNSGPAPAYTNGGGGLDHGTPSGSSTAESSPATTPTSASGGRTSSGGGGGGAEAGSSVASGVGNASTSGASSSGGG
Full Text Available DSDVDTILEEFEFATQDYDEIYQETQERNELLDGSDYIEEGETSTEEYSTTEKGFQEATTTDNEAMGSSISLSSAEDLIDNGTVAAAAPLQISDAIANLIASELDKFLE...PLVVARVDAQLLQGEQPLKGTLGQLQQLARLEPQLAERGQPAKAVPRQLALEQDQLAARNVQPGRALGPLQVQPGQQTQPSSGTVVAGVFCPR...RHNLSLQDNSRYIPLQNLNMDANRQFDGEAAAVPAEPRNVPIELTHAPAPASDARNATKIFLNGGGSTMEGTSGGLNPVATVEGMSVPAHRQLGEEQRA...KRRNNVMELQQQAQHQSSEKLTNHVASFVSLAGPSGRVPAGPKERQQMELKAELEQKRRELERIEKMTQSIKKNTELSRSAATEGVGAHEPTTSAHDPKPAGPSSVVSSSVESCSGGAGSHHRGTPSTHTT...MGGMQQQQQQQPQTHGGMNGGPSSTNGNIPPGGGGNNGNNINNNWQSEEVADEHLEQTESRHPGGTVLRHLLQPFARHLPILPEPIVDRVRCADNVAEPR
Full Text Available cds=p(1,3606) /gb=AJ535205 /gi=27227575 /ug=Aga.35084 /len=3606 9e-51 24% MSSASTPEPSTTPGTTRTTPTRPTSTESTDTTMSSASTSEPS...TTPGTTRTTPTRPTSTESTDTTMSSASTPEPSTTPGTTRTTPTRPTPTDTTMSSASTPEPSTTPGTTRTTPTRPTPTDSTMSSSMSSESTPEPS...TTPGTTRTTPTRPTPTDSTMSSSYSMSSASTPEPSTTPGTTRTTPTRPTPTDTTMSSPSMSSASTPEPPSTPGTTRTTPTRPTLSTDTTMSSASTPEPSTTPGTTRTTPTRPTPTDSTMSSSMSSE...TTPGTTRTTPTRPTPTDTTMSSASTPEPSTTPGTTRTTPTRPTSTETPDTTRTTPKTNTYRYHNVVSLYSGTIHDTCMSSESTPEPS...TTPGTTRTTPTRPTSTESTDTTMSSASTPEPSTTPGTTRTTPTRPTSTESTDTTMSSASTPEPSTTSGTTRTTPTRPTPTDTTMSSASTPEPS
Full Text Available 6 /ug=Aga.48379 /len=797 0.006 80% MKYFKRIHRVSFFFFFFFFFFFFFFFXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
Full Text Available CPQVFDPRKLVLVEHRSCTKYNLCVLGLMLTVSCPNDLRFNNERCECDFKEKVHCEGEDPATTTVDYASSTDATTVYDSTTEDSTTEESTTELATSESTTEDSTTEESTTEVTVSES...TTEDSTTEESTTEGTVSESTTEDSTTEESTTEVATSESTTEESTTEESTTEVTVSESTTEDSTTKESTTEVTVSESTTEDSTTEESTTEVATSES...TTEDSTTEESTTEVTVSESTTEDSTTEESTTEAATSESTTEDSTTEEATTEVTVSESTTEDSTTEESTTEVVTSESTTEDSTTEESTTEVVTSES...TTEDSTTEESTTEVATSESTTEDSTTEESTTEVTVSESTTEDSTTEESTTEAATSESTTEDSTTEEATTEVTVSESTTEDSTTEESTTEVAVSESTTEDSTTEESTTEVATSES...TTEESTTEESTTEVTVSEPTTEDSTTEESTTEVTTSESTTEESTTEESTTEVTVSESTTEDSTTEESTTEVTTSES
Full Text Available f a full-length cDNA clone made from Anopheles gambiae total adult females. 5-PRIME end of clone FK0AAA17BC06 of strai...27560014 /ug=Aga.24572 /len=986 7e-09 22% MVANTFAIVAKRSAIVAKRSAIIANTFTIVANYSAVVAKSSAIDPKSSAIVGKTFAIVAKTFAIVAKTFAIVANYSAVVANYSAI...VAKSSAIVAKSSAIVANTFAIFANTFAIVANTFAIIAKTFAIVAKTFAIVAKTFAIVAKSSAIVAKSSAIVAKSSAIVANTFAIVAKSSAIVAKSSAI...ITNTFTIVANYSAVVAKSSAIVPKNSAIVGKTFAIVAKTFAIVAKTFAIVANTFAIVANYSAVVANYSAIVAKSSAIVAKSSAIVAKTFAI...FANTFAIVANTFAIVANYSAIVAKSSAIVAKSFEIIVKTFAIFAKTFAIVANYSAIVAKTFAIVAINSEIVAKSSATVANTFAIVANTFAIVANTFAIVAKTFAIVANYSAIVA ...
Morrish, D W; Dakour, J; Li, H
Differential techniques have revealed several novel genes and peptides involved in trophoblast development including PL74/gdf15/MIC-1, a TGFbeta family cytokine that controls apoptosis and differentiation, PL48, a new serine-threonine protein kinase, serum and glucocorticoid-induced kinase, PBK-1, a tunicamycin-responsive gene, a cathepsin D-like gene (DAP-1) and hypoxia- regulated genes HRF-1,2,6,8 and HIF-1alpha, HIF-1beta, and hEPAS-1. Syncytin, a cell fusion- inducing gene, has been cloned from placenta where it regulates cell fusion. ERV-3 has also been demonstrated to promote cell fusion. These two genes represent the first demonstrated functions of endogenous retroviral sequences in human tissues. Endoglin, PlGF, TGFbeta3, IGF-II, IGFBP-1, and a placental IGFBP protease have found new roles in regulating cytotrophoblast proliferation and invasiveness. A specific placental p105 rasGAP protein has been identified. The homeobox genes DLX4, HB24, MSX2 and MOX2 also likely play a role in development at the epithelial-mesenchymal boundary. Transcription factors such as TEF-5, Hand1, HEB, HASH-2 and two genes represented by ESTs may have regulatory roles in placental development. Evidence suggests that the placenta has an unusual two-cell system for apoptosis regulation in which the cytotrophoblast may direct later apoptotic events in the syncytium, and with syncytialization possibly triggered by the "phosphatidylserine flip". Thus, the placenta is both a rich source of new growth-regulatory substances, and a model system for originating new paradigms of developmental biology. PMID:12369935
Messina, Monica; Chiaretti, Sabina; Wang, Jiguang; Fedullo, Anna Lucia; Peragine, Nadia; Gianfelici, Valentina; Piciocchi, Alfonso; Brugnoletti, Fulvia; Di Giacomo, Filomena; Pauselli, Simona; Holmes, Antony B; Puzzolo, Maria Cristina; Ceglie, Giulia; Apicella, Valerio; Mancini, Marco; Te Kronnie, Geertruy; Testi, Anna Maria; Vitale, Antonella; Vignetti, Marco; Guarini, Anna; Rabadan, Raul; Foà, Robin
To shed light into the molecular bases of B-lineage acute lymphoblastic leukemia lacking known fusion transcripts, i.e. BCR-ABL1, ETV6-RUNX1, E2A-PBX1, and MLL rearrangements (B-NEG ALL) and the differences between children, adolescents/young adults (AYA) and adults, we analyzed 168 B-NEG ALLs by genome-wide technologies. This approach showed that B-NEG cases carry 10.5 mutations and 9.1 copy-number aberrations/sample. The most frequently mutated druggable pathways were those pertaining to RAS/RTK (26.8%) and JAK/STAT (12.5%) signaling. In particular, FLT3 and JAK/STAT mutations were detected mainly in AYA and adults, while KRAS and NRAS mutations were more frequent in children. RAS/RTK mutations negatively affected the outcome of AYA and adults, but not that of children. Furthermore, adult B-NEG ALL carrying JAK/STAT mutations had a shorter survival. In vitro experiments showed that FLT3 inhibitors reduced significantly the proliferation of FLT3-mutated primary B-NEG ALL cells. Likewise, PI3K/mTOR inhibitors reduced the proliferation of primary cells harboring RAS and IL7R mutations. These results refine the genetic landscape of B-NEG ALL and suggest that the different distribution of lesions and their prognostic impact might sustain the diverse outcome between children, adults and partly AYA - whose genomic scenario is similar to adults - and open the way to targeted therapeutic strategies. PMID:26883104
Hummelshøj, Tina; Nissen, Janna; Munthe-Fog, Lea; Koch, Claus; Bertelsen, Mads Frost; Garred, Peter
-human primates. The exons and intron-exon boundaries of the FCN1-3 genes were sequenced in the following primate species: chimpanzee, gorilla, orangutan, rhesus macaque, cynomolgus macaque, baboon and common marmoset. We found that the exon organisation of the FCN genes was very similar between all the non...... the Shannon entropy revealing that all three proteins are generally highly conserved. Ficolin-1 and ficolin-2 showed the highest diversity, whereas ficolin-3 was more conserved. Ficolin-2 and ficolin-3 were present in non-human primate sera with the same characteristic oligomeric structures as seen in...
Mayasich, Sally A; Clarke, Benjamin L
The sea lamprey (Petromyzon marinus) is a jawless vertebrate at an evolutionary nexus between invertebrates and jawed vertebrates. Lampreys are known to possess the arginine vasotocin (AVT) hormone utilized by all non-mammalian vertebrates. We postulated that the lamprey would possess AVT receptor orthologs of predecessors to the arginine vasopressin (AVP)/oxytocin (OXT) family of G protein-coupled receptors found in mammals, providing insights into the origins of the mammalian V1A, V1B, V2 and OXT receptors. Among the earliest animals to diverge from the vertebrate lineage in which these receptors are characterized is the jawed, cartilaginous elephant shark, which has genes orthologous to all four mammalian receptor types. Therefore, our work was aimed at helping resolve the critical gap concerning the outcomes of hypothesized large-scale (whole-genome) duplication events. We sequenced one partial and four full-length putative lamprey AVT receptor genes and determined their mRNA expression patterns in 15 distinct tissues. Phylogenetically, three of the full-coding genes possess structural characteristics of the V1 clade containing the V1A, V1B and OXT receptors. Another full-length coding gene and the partial sequence are part of the V2 clade and appear to be most closely related to the newly established V2B and V2C receptor subtypes. Our synteny analysis also utilizing the Japanese lamprey (Lethenteron japonicum) genome supports the recent proposal that jawless and jawed vertebrates shared one-round (1R) of WGD as the most likely scenario. PMID:26764211
Zeidán-Chuliá, Fares; de Oliveira, Ben-Hur Neves; Casanova, Manuel F; Casanova, Emily L; Noda, Mami; Salmina, Alla B; Verkhratsky, Alexei
Autism is a neurodevelopmental disorder manifested by impaired social interaction, deficits in communication skills, restricted interests, and repetitive behaviors. In neurodevelopmental, neurodegenerative, and psychiatric disorders, glial cells undergo morphological, biochemical, and functional rearrangements, which are critical for neuronal development, neurotransmission, and synaptic connectivity. Cerebellar function is not limited to motor coordination but also contributes to cognition and may be affected in autism. Oligodendrocytes and specifically oligodendroglial precursors are highly susceptible to oxidative stress and excitotoxic insult. In the present study, we searched for evidence for developmental oligodendropathy in the context of autism by performing a network analysis of gene expression of cerebellar tissue. We created an in silico network model (OLIGO) showing the landscape of interactions between oligodendrocyte markers and demonstrated that more than 50 % (16 out of 30) of the genes within this model displayed significant changes of expression (corrected p value disorders (ASD). PMID:26189831
Kaftanovskaya, Elena M; Huang, Zaohua; Lopez, Carolina; Conrad, Kirk; Agoulnik, Alexander I
Relaxin hormone secreted into the circulation during pregnancy was discovered through its effects on pubic symphysis relaxation and parturition. Genetic inactivation of the relaxin gene or its cognate relaxin family peptide receptor 1 (RXFP1) in mice caused failure of parturition and mammary nipple enlargement, as well as increased collagen fiber density in the cervix and vagina. However, the relaxin effect on discrete cells and tissues has yet to be determined. Using transgenic mice with a knockin LacZ reporter in the Rxfp1 allele, we showed strong expression of this gene in vaginal and cervical stromal cells, as well as pubic ligament cells. We produced a floxed Rxfp1 allele that was used in combination with the Tagln-cre transgene to generate mice with a smooth muscle-specific gene knockout. In pregnant females, the ROSA26 reporter activated by Tagln-cre was detected in smooth muscle cells of the cervix, vagina, uterine artery, and in cells of the pubic symphysis. In late pregnant females with conditional gene ablation, the length of pubic symphysis was significantly reduced compared with wild-type or heterozygous Rxfp1(+/-) females. Denser collagen content was revealed by Masson trichrome staining in reproductive tract organs, uterine artery, and pubic symphysis. The cervical and vaginal epithelium was less developed than in heterozygous or wild-type females, although nipple size was normal and the dams were able to nurse their pups. In summary, our data indicate that relaxin/RXFP1 signaling in smooth muscle cells is important for normal collagen turnover and relaxation of the pubic symphysis during pregnancy. PMID:25715795
Rijpkema, Anneke S; Royaert, Stefan; Zethof, Jan; van der Weerden, Gerard; Gerats, Tom; Vandenbussche, Michiel
Antirrhinum majus DEFICIENS (DEF) and Arabidopsis thaliana APETALA3 (AP3) MADS box proteins are required to specify petal and stamen identity. Sampling of DEF/AP3 homologs revealed two types of DEF/AP3 proteins, euAP3 and TOMATO MADS BOX GENE6 (TM6), within core eudicots, and we show functional divergence in Petunia hybrida euAP3 and TM6 proteins. Petunia DEF (also known as GREEN PETALS [GP]) is expressed mainly in whorls 2 and 3, and its expression pattern remains unchanged in a blind (bl) mutant background, in which the cadastral C-repression function in the perianth is impaired. Petunia TM6 functions as a B-class organ identity protein only in the determination of stamen identity. Atypically, Petunia TM6 is regulated like a C-class rather than a B-class gene, is expressed mainly in whorls 3 and 4, and is repressed by BL in the perianth, thereby preventing involvement in petal development. A promoter comparison between DEF and TM6 indicates an important change in regulatory elements during or after the duplication that resulted in euAP3- and TM6-type genes. Surprisingly, although TM6 normally is not involved in petal development, 35S-driven TM6 expression can restore petal development in a def (gp) mutant background. Finally, we isolated both euAP3 and TM6 genes from seven solanaceous species, suggesting that a dual euAP3/TM6 B-function system might be the rule in the Solanaceae. PMID:16844905
Full Text Available F-box proteins (FBPs represent one of the largest and fastest evolving gene/protein families in the plant kingdom. The FBP superfamily can be divided in several subfamilies characterized by different C-terminal protein-protein interaction domains that recruit targets for proteasomal degradation. Hence, a clear picture of their phylogeny and molecular evolution is of special interest for the general understanding of evolutionary histories of multi-domain and/or large protein families in plants. In an effort to further understand the molecular evolution of F-box family proteins, we asked whether the largest subfamily in Arabidopsis thaliana, which carries a C-terminal F-box associated domain (FBA proteins shares evolutionary patterns and signatures of selection with other FBPs. To address this question, we applied phylogenetic and molecular evolution analyses in combination with the evaluation of transcriptional profiles. Based on the 2219 FBA proteins we de novo identified in 34 completely sequenced plant genomes, we compared their evolutionary patterns to a previously analyzed large subfamily carrying C-terminal kelch repeats. We found that these two large FBP subfamilies generally tend to evolve by massive waves of duplication, followed by sequence conservation of the F-box domain and sequence diversification of the target recruiting domain. We conclude that the earlier in evolutionary time a major wave of expansion occurred, the more pronounced these selection signatures are. As a consequence, when performing cross species comparisons among FBP subfamilies, significant differences will be observed in the selective signatures of protein-protein interaction domains. Depending on the species, the investigated subfamilies comprise up to 45% of the complete superfamily, indicating that other subfamilies possibly follow similar modes of evolution.
The Zygomycete lineages mark the major transition from zoosporic life histories of the common ancestors of Fungi and the earliest diverging chytrid lineages (Chytridiomycota and Blastocladiomycota). Genome comparisons from these lineages may reveal gene content changes that reflect the transition to...
Full Text Available Abstract Background Nasopharyngeal carcinoma (NPC is commonly found in Southern China and South East Asia. Epstein-Barr virus (EBV infection is well associated with NPC and has been implicated in its pathogenesis. Moreover, various chromosome rearrangements were reported in NPC. However, the underlying mechanism of chromosome rearrangement remains unclear. Furthermore, the relationship between EBV and chromosome rearrangement with respect to the pathogenesis of NPC has not been established. We hypothesize that during virus- or stress-induced apoptosis, chromosomes are initially cleaved at the base of the chromatin loop domain structure. Upon DNA repair, cell may survive with rearranged chromosomes. Methods In this study, cells were seeded at various densities to induce apoptosis. Genomic DNA extracted was processed for Southern hybridization. In order to investigate the role of EBV, especially the latent membrane protein 1 (LMP1, LMP1 gene was overexpressed in NPC cells and chromosome breaks were analyzed by inverse polymerase chain (IPCR reaction. Results Southern analysis revealed that high cell density resulted in cleavage of the mixed lineage leukemia (MLL gene within the breakpoint cluster region (bcr. This high cell density-induced cleavage was significantly reduced by caspase inhibitor, Z-DEVD-FMK. Similarly, IPCR analysis showed that LMP1 expression enhanced cleavage of the MLL bcr. Breakpoint analysis revealed that these breaks occurred within the matrix attachment region/scaffold attachment region (MAR/SAR. Conclusions Since MLL locates at 11q23, a common deletion site in NPC, our results suggest a possibility of stress- or virus-induced apoptosis in the initiation of chromosome rearrangements at 11q23. The breakpoint analysis results also support the role of chromatin structure in defining the site of chromosome rearrangement.
Sieburth, L E; Meyerowitz, E M
AGAMOUS (AG) is an Arabidopsis MADS box gene required for the normal development of the internal two whorls of the flower. AG RNA accumulates in distinct patterns early and late in flower development, and several genes have been identified as regulators of AG gene expression based on altered AG RNA accumulation in mutants. To understand AG regulatory circuits, we are now identifying cis regulatory domains by characterizing AG::beta-glucuronidase (GUS) gene fusions. These studies show that a normal AG::GUS staining pattern is conferred by a 9.8-kb region encompassing 6 kb of upstream sequences and 3.8 kb of intragenic sequences. Constructs lacking the 3.8-kb intragenic sequences confer a GUS staining pattern that deviates both spatially and temporally from normal AG expression. The GUS staining patterns in the mutants for the three negative regulators of AG, apetala2, leunig, and curly leaf, showed the predicted change of expression for the construct containing the intragenic sequences, but no significant change was observed for the constructs lacking this intragenic region. These results suggest that intragenic sequences are essential for AG regulation and that these intragenic sequences contain the ultimate target sites for at least some of the known regulatory molecules. PMID:9090880
Full Text Available r membrane component [Herpetosiphon aurantiacus ATCC 23779] ZP_01426475.1 0.33 20% ... ...nt [Herpetosiphon aurantiacus ATCC 23779] gb|EAU16751.1| binding-protein-dependent transport systems inne...CBRC-AGAM-01-0042 ref|ZP_01426475.1| binding-protein-dependent transport systems inner membrane compone
Full Text Available r membrane component [Herpetosiphon aurantiacus ATCC 23779] ZP_01426474.1 1e-59 45% ... ...nt [Herpetosiphon aurantiacus ATCC 23779] gb|EAU16750.1| binding-protein-dependent transport systems inne...CBRC-AGAM-07-0030 ref|ZP_01426474.1| binding-protein-dependent transport systems inner membrane compone
Full Text Available CBRC-AGAM-02-0012 ref|YP_304864.1| hypothetical protein Mbar_A1321 [Methanosarcina barkeri str. Fusar...o] gb|AAZ70284.1| hypothetical protein Mbar_A1321 [Methanosarcina barkeri str. Fusaro] YP_304864.1 0.39 34% ...
Full Text Available CBRC-AGAM-04-0028 ref|YP_305972.1| hypothetical protein Mbar_A2479 [Methanosarcina barkeri str. Fusar...o] gb|AAZ71392.1| hypothetical protein Mbar_A2479 [Methanosarcina barkeri str. Fusaro] YP_305972.1 9e-19 35% ...
Full Text Available CBRC-AGAM-02-0188 ref|NP_649789.1| CG9613-PA [Drosophila melanogaster] sp|Q9VHS7|COQ2_DROME Para ... e--polyprenyltransferase, mitochondrial precursor (PHB :polyprenyltransferase) gb|AAF54222.1| CG9613-PA [D ...
Full Text Available CBRC-AGAM-01-0070 ref|NP_476722.1| shotgun CG3722-PA [Drosophila melanogaster] sp|Q...24298|CADE_DROME DE-cadherin precursor (Protein shotgun) gb|AAF46659.1| CG3722-PA [Drosophila melanogaster] NP_476722.1 0.0 42% ...
Full Text Available CBRC-AGAM-02-0165 ref|NP_524393.2| Fsh-Tsh -like receptor CG7665-PA, isoform A [Drosophila melano ... gaster] ref|NP_732265.1| Fsh-Tsh -like receptor CG7665-PB, isoform B [Drosophila mel ...
Full Text Available CBRC-AGAM-07-0003 ref|YP_855937.1| cytochrome c-type biogenesis protein CcmF [Aeromonas ... hydrophi ... 6926.1| cytochrome c-type biogenesis protein CcmF [Aeromonas ... hydrophila subsp. hydrophila ATCC 7966] YP_855937. ...
Full Text Available CBRC-AGAM-07-0060 ref|YP_001142002.1| GGDEF domain protein [Aeromonas ... salmonicida subsp. salmoni ... cida A449] gb|ABO90254.1| GGDEF domain protein [Aeromonas ... salmonicida subsp. salmonicida A449] YP_001142002. ...
Full Text Available CBRC-AGAM-07-0010 ref|YP_001141362.1| amino acid permease [Aeromonas ... salmonicida subsp. salmonic ... ida A449] gb|ABO89614.1| amino acid permease [Aeromonas ... salmonicida subsp. salmonicida A449] YP_001141362. ...
Full Text Available CBRC-AGAM-01-0054 ref|YP_001142086.1| transporter, NadC family [Aeromonas ... salmonicida subsp. sal ... ida A449] gb|ABO90338.1| transporter, NadC family [Aeromonas ... salmonicida subsp. salmonicida A449] YP_001142086. ...
Full Text Available CBRC-AGAM-07-0002 ref|YP_856219.1| hypothetical protein AHA_1683 [Aeromonas ... hydrophila subsp. hy ... CC 7966] gb|ABK39880.1| putative membrane protein [Aeromonas ... hydrophila subsp. hydrophila ATCC 7966] YP_856219. ...
Full Text Available CBRC-AGAM-07-0060 ref|YP_001141367.1| GGDEF domain protein [Aeromonas ... salmonicida subsp. salmoni ... cida A449] gb|ABO89619.1| GGDEF domain protein [Aeromonas ... salmonicida subsp. salmonicida A449] YP_001141367. ...
Full Text Available CBRC-AGAM-03-0010 ref|ZP_00373744.1| SD27140p [Wolbachia endosymbiont of Drosophila... ananassae] gb|EAL58741.1| SD27140p [Wolbachia endosymbiont of Drosophila ananassae] ZP_00373744.1 0.0 39% ...
Full Text Available CBRC-AGAM-05-0053 ref|ZP_00373744.1| SD27140p [Wolbachia endosymbiont of Drosophila... ananassae] gb|EAL58741.1| SD27140p [Wolbachia endosymbiont of Drosophila ananassae] ZP_00373744.1 0.0 39% ...
Full Text Available CBRC-AGAM-02-0094 ref|ZP_00373744.1| SD27140p [Wolbachia endosymbiont of Drosophila... ananassae] gb|EAL58741.1| SD27140p [Wolbachia endosymbiont of Drosophila ananassae] ZP_00373744.1 0.0 39% ...
Full Text Available CBRC-AGAM-03-0057 ref|ZP_00373744.1| SD27140p [Wolbachia endosymbiont of Drosophila... ananassae] gb|EAL58741.1| SD27140p [Wolbachia endosymbiont of Drosophila ananassae] ZP_00373744.1 0.0 37% ...
Full Text Available CBRC-AGAM-02-0155 ref|ZP_00373744.1| SD27140p [Wolbachia endosymbiont of Drosophila... ananassae] gb|EAL58741.1| SD27140p [Wolbachia endosymbiont of Drosophila ananassae] ZP_00373744.1 0.0 39% ...
Full Text Available CBRC-AGAM-04-0091 ref|ZP_00373744.1| SD27140p [Wolbachia endosymbiont of Drosophila... ananassae] gb|EAL58741.1| SD27140p [Wolbachia endosymbiont of Drosophila ananassae] ZP_00373744.1 1e-163 38% ...
Full Text Available CBRC-AGAM-04-0093 ref|ZP_00373744.1| SD27140p [Wolbachia endosymbiont of Drosophila... ananassae] gb|EAL58741.1| SD27140p [Wolbachia endosymbiont of Drosophila ananassae] ZP_00373744.1 0.0 40% ...