Sequence Alignment

Publication Title: 
International Journal of Molecular Sciences

Thapsia laciniata Rouy (Apiaceae) produces irregular and regular sesquiterpenoids with thapsane and guaiene carbon skeletons, as found in other Apiaceae species. A transcriptomic analysis utilizing Illumina next-generation sequencing enabled the identification of novel genes involved in the biosynthesis of terpenoids in Thapsia. From 66.78 million HQ paired-end reads obtained from T. laciniata roots, 64.58 million were assembled into 76,565 contigs (N50: 1261 bp). Seventeen contigs were annotated as terpene synthases and five of these were predicted to be sesquiterpene synthases.

Drew, Damian Paul
Dueholm, Bjørn
Weitzel, Corinna
Zhang, Ye
Sensen, Christoph W.
Simonsen, Henrik Toft
Publication Title: 
The American Journal of Tropical Medicine and Hygiene

A 35-year-old Japanese man had an intermittent fever and mild headache for eight weeks after he returned to Japan from working in Mozambique. He had taken antimalarial prophylaxis (doxycycline) for 25 weeks, and stopped taking this drug two weeks after his return. Microscopic examination of a peripheral blood smear showed a mixed infection with Plasmodium vivax, P. falciparum, and P. ovale. In addition, a nested polymerase chain reaction and subsequent sequencing detected specific DNA sequences of four species of Plasmodium, including P. malariae.

Oki, Masayuki
Asai, Satomi
Saito-Nakano, Yumiko
Nakayama, Taira
Tanaka, Yumiko
Tachibana, Hiroshi
Ohmae, Hiroshi
Nozaki, Tomoyoshi
Miyachi, Hayato
Publication Title: 
Antimicrobial Agents and Chemotherapy

Polymorphism in the ortholog gene of the Plasmodium falciparum K13 gene was investigated in Plasmodium vivax isolates collected in Cambodia. All of them were Sal-1 wild-type alleles except two (2/284, 0.7%), and P. vivax K12 polymorphism was reduced compared to that of the P. falciparum K13 gene. Both mutant allele isolates had the same nonsynonymous mutation at codon 552 (V552I) and were from Ratanak Kiri province. These preliminary data should encourage additional studies for associating artemisinin or chloroquine resistance and K12 polymorphism.

Popovici, Jean
Kao, Sokheng
Eal, Leanghor
Bin, Sophalai
Kim, Saorin
Ménard, Didier
Publication Title: 

The inducible IkappaB kinase (IKKi/IKKepsilon) is a recently described serine-threonine kinase that activates the transcription factors NFkappaB, interferon regulatory factor-3 (IRF3) and CCAAA/enhancer-binding protein (C/EBPdelta). Several inflammatory agents have been shown to induce the expression of the IKKi gene in macrophages and other cell types but the mechanism is unknown.

Wang, Naizhen
Ahmed, Salahuddin
Haqqi, Tariq M.
Publication Title: 
Proceedings of the National Academy of Sciences of the United States of America

One of the hallmarks of the Gram-negative bacterium Pseudomonas aeruginosa is its ability to thrive in diverse environments that includes humans with a variety of debilitating diseases or immune deficiencies. Here we report the complete sequence and comparative analysis of the genomes of two representative P. aeruginosa strains isolated from cystic fibrosis (CF) patients whose genetic disorder predisposes them to infections by this pathogen. The comparison of the genomes of the two CF strains with those of other P.

Mathee, Kalai
Narasimhan, Giri
Valdes, Camilo
Qiu, Xiaoyun
Matewish, Jody M.
Koehrsen, Michael
Rokas, Antonis
Yandava, Chandri N.
Engels, Reinhard
Zeng, Erliang
Olavarietta, Raquel
Doud, Melissa
Smith, Roger S.
Montgomery, Philip
White, Jared R.
Godfrey, Paul A.
Kodira, Chinnappa
Birren, Bruce
Galagan, James E.
Lory, Stephen
Publication Title: 
The Journal of Neuroscience: The Official Journal of the Society for Neuroscience

MicroRNA has emerged as a critical regulator of neuronal functions. This study aimed to test whether let-7 microRNAs can regulate the mu opioid receptor (MOR) and opioid tolerance. Employing bioinformatics, we identified a let-7 binding site in the 3'-untranslated region (UTR) of MOR mRNA, which was experimentally confirmed as a direct target of let-7. The repressive regulation of MOR by let-7 was revealed using a LNA-let-7 inhibitor to knockdown let-7 in SH-SY5Y cells.

He, Ying
Yang, Cheng
Kirkmire, Chelsea M.
Wang, Zaijie Jim
Publication Title: 
Microbial Cell Factories

BACKGROUND: Lactobacillus reuteri harbors the genes responsible for glycerol utilization and vitamin B12 synthesis within a genetic island phylogenetically related to gamma-Proteobacteria. Within this island, resides a gene (lreu_1750) that based on its genomic context has been suggested to encode the regulatory protein PocR and presumably control the expression of the neighboring loci. However, this functional assignment is not fully supported by sequence homology, and hitherto, completely lacks experimental confirmation.

Santos, Filipe
Spinler, Jennifer K.
Saulnier, Delphine M. A.
Molenaar, Douwe
Teusink, Bas
de Vos, Willem M.
Versalovic, James
Hugenholtz, Jeroen
Publication Title: 
The American Journal of Tropical Medicine and Hygiene

Cryptosporidium is a major cause of diarrhea in children in developing countries. However, there is no vaccine available and little is known about immune responses to protective antigens. We investigated antibody responses to p23, a putative vaccine candidate, in children in Bangladesh with cryptosporidiosis and diarrhea (cases) and uninfected children with diarrhea (controls), and p23 gene polymorphisms in infecting species. Serum IgM, IgG, and IgA responses to p23 were significantly greater in cases than controls after three weeks of follow-up.

Borad, Anoli J.
Allison, Geneve M.
Wang, David
Ahmed, Sabeena
Karim, Mohammad M.
Kane, Anne V.
Moy, Joy
Hibberd, Patricia L.
Ajjampur, Sitara Swarna Rao
Kang, Gagandeep
Calderwood, Stephen B.
Ryan, Edward T.
Naumova, Elena
Khan, Wasif A.
Ward, Honorine D.
Publication Title: 
BMC bioinformatics

BACKGROUND: Novel proteins entering the food chain, for example by genetic modification of plants, have to be tested for allergenicity. Allermatch is a webtool for the efficient and standardized prediction of potential allergenicity of proteins and peptides according to the current recommendations of the FAO/WHO Expert Consultation, as outlined in the Codex alimentarius. DESCRIPTION: A query amino acid sequence is compared with all known allergenic proteins retrieved from the protein databases using a sliding window approach.

Fiers, Mark W. E. J.
Kleter, Gijs A.
Nijland, Herman
Peijnenburg, Ad A. C. M.
Nap, Jan Peter
van Ham, Roeland C. H. J.
Publication Title: 
Plant Biotechnology Journal

Three natural somatic mutations at codon 304 of the phytoene desaturase gene (pds) of Hydrilla verticillata (L. f. Royle) have been reported to provide resistance to the herbicide fluridone. We substituted the arginine 304 present in the wild-type H. verticillata phytoene desaturase (PDS) with all 19 other natural amino acids and tested PDS against fluridone. In in vitro assays, the threonine (Thr), cysteine (Cys), alanine (Ala) and glutamine (Gln) mutations imparted the highest resistance to fluridone.

Arias, Renée S.
Dayan, Franck E.
Michel, Albrecht
Howell, J'Lynn
Scheffler, Brian E.


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