Alan L Kwan's research while affiliated with Washington University in St. Louis and other places

Publications (22)

Article
Full-text available
Cilia are microtubule based organelles that project from cells. Cilia are found on almost every cell type of the human body and numerous diseases, collectively termed ciliopathies, are associated with defects in cilia including respiratory infections, male infertility, situs inversus, polycystic kidney disease, retinal degeneration, and Bardet-Bied...
Article
Full-text available
Whole-genome sequencing (WGS) provides a new platform for the identification of mutations that produce a mutant phenotype. We used Illumina sequencing to identify the mutational profile of three Chlamydomonas reinhardtii mutant strains. The three strains have more than 38,000 changes from the reference genome. NG6 is aflagellate and maps to 269 kb...
Article
Cilia are evolutionarily conserved, complex, microtubule-based structures that protrude from many eukaryotic cells. In humans, cilia can be found on almost all cell types. The effect of abnormal or absent cilia has been established as the common underlying cause of a recently emerging class of genetic diseases collectively referred to as ciliopathi...
Data
The nic15-1 mutant strain has a missense mutation in aspartate oxidase (ASO). Protein sequence alignment of ASO from various organisms was performed by ClustalW [83] and the result is shown using Colorfy. Colorfy groups the twenty amino acids into eight separate conservation groups ({G, A}, {V, L, I}, {F, Y, W}, {C, M}, {K, R, H}, {D, E, N, Q}, {S,...
Data
The nic1-1 mutant strain contains a premature stop codon in nicotinamide/nicotinate mononucleotide adenylyltransferase (NMNAT). Protein sequence alignment of NMNAT from various organisms was performed by ClustalW and the result is shown by Colorfy. Partial nucleotide and the corresponding protein sequences for wild-type and nic1-1 are indicated in...
Data
Sequence alignment of nicotinamide phosphoribosyltransferase (NAMPT) from various organisms. Protein sequence alignment of NAMPT was performed by ClustalW and the result is shown by Colorfy. (1.93 MB TIF)
Data
The nic7-1 mutant strain has a missense mutation in quinolinate synthetase (QS). Protein sequence alignment of QS from various organisms was performed by ClustalW and the result is shown by Colorfy. The nucleotide sequences and the corresponding protein sequences around the mutation point for wild-type and nic7-1 are shown in the box. The mutated n...
Data
Sequence alignment of SIRT/Sir2 from various organisms. Protein sequence alignment was performed by ClustalW and the result is shown by Colorfy. (1.77 MB TIF)
Data
The nic13-1 mutant has a missense mutation in NAD+ synthase (NS). Protein sequence alignment of NS from various organisms was performed by ClustalW and the result is shown by Colorfy. Partial nucleotide and the corresponding protein sequences for wild-type and nic13-1 are indicated in the box. The mutated nucleotides are underlined and the mutated...
Data
The nic2-1 mutant strain has a deletion of a single nucleotide in quinolinate phosphoribosyltransferase (QPT). Protein sequence alignment of QPT from various organisms was performed by ClustalW and the result is shown by Colorfy. The conserved quinolinate-binding sites are indicated by blue reverse triangles. Partial nucleotide and the correspondin...
Article
Full-text available
The essential coenzyme nicotinamide adenine dinucleotide (NAD+) plays important roles in metabolic reactions and cell regulation in all organisms. Bacteria, fungi, plants, and animals use different pathways to synthesize NAD+. Our molecular and genetic data demonstrate that in the unicellular green alga Chlamydomonas NAD+ is synthesized from aspart...
Conference Paper
Full-text available
Sequence similarity based protein clustering methods organize proteins into families of similar sequences, a task that continues to be critical for automated protein characterization. However, many protein families cannot be automatically characterized further because little is known about the function of any protein in a family of similar sequence...
Article
Full-text available
The availability of whole-genome sequences allows for the identification of the entire set of protein coding genes as well as their regulatory regions. This can be accomplished using multiple complementary methods that include ESTs, homology searches and ab initio gene predictions. Previously, the Genie gene-finding algorithm was trained on a small...
Data
Tabulated List of NCBI Protein ID codes for gb140. A table listing the NCBI Protein ID codes that comprise the set gb140.
Data
List of Primers: FGC07 Exclusive Genes. A table of primers used to test five FGC07 gene models that have no overlapping model in gg2v3.
Data
List of Primers: gg2v3 Predictions with partially overlapping exons. A table of primers used to test five pairs of partially overlapping gene models between gg2v3 and FGC07 with alternative exon termini.
Data
List of Primers: 13 Novel PASA Assemblies. A table of primers used to test 13 randomly chosen, single-exon PASA EST assembled gene models.
Data
List of Primers: gg2v3 Predictions with novel exons. A table of primers used to test eight gg2v3 gene models with extra exons when compared to FGC07.
Data
List of Primers: gg2v3 Exclusive Genes. A table of primers used to test five gg2v3 gene models that have no overlapping model in FGC07.
Data
Histogram of exon overlap gg2v3 models with partial overlaps in FGC07. A histogram detailing the different classes of exons that are overlapping between gg2v3 and FGC07 gene models.

Citations

... Consistent with this observation, it has been found that genes encoding flagellar proteins are upregulated during flagellar regrowth Lefebvre 1980;Baker 1984;Lefebvre 1986). This fact has been exploited to identify flagella-related genes based on their upregulation during flagellar assembly (Stolc 2005;Pazour 2005;Chamberlain 2008;Albee 2013;Lin 2015;Zones 2015). These studies have shown that for most flagellar genes, mRNA levels increase over a time-scale of approximately 30 minutes, and then decrease back to baseline over the next hour, creating a pulse of gene expression that coincides with the growth of the flagella. ...
... This analysis has identified numerous structural components, but components that regulate cilia assembly or function such as those which preassemble dynein components in the cytoplasm were not identified (Mitchison et al. 2012). Genomic comparisons have also added to the list of ciliary components (Avidor-Reiss et al. 2004;Li et al. 2004;Merchant et al. 2007;Kwan et al. 2010;Hodges et al. 2011). These methods are complementary to proteomic methods, but they also generate an incomplete list because genes with conserved motifs such as kinases are discarded as a result of being in a nonciliated species. ...
... No reuse allowed without permission. All subunits of the core IFT machinery, including IFT81, IFT74 and RabL2 are conserved between Chlamydomonas and human (van Dam et al., 2013), which is quite astonishing given the more than 1B years of evolution separating the two species (Dutcher et al., 2012). CrRabL2 and HsRabL2 share 49% identity on the amino acid level. ...
... Nicotinic acid is used in metabolism for the synthesis of nicotinamide adenine dinucleotide (NAD + ). NAD + is essential for glycolysis and the citric acid cycle as well as for the regeneration of ATP [33,56,57]. NAD + can be synthesised either de novo from the amino acids aspartate or tryptophan or from the vitamin nicotinic acid [56][57][58]. ...
... After 8 rounds, GRAbB assembled reads into a 1,121-bp in silico cDNA, encoding a 333-amino acid protein that includes the 6 transmembrane domains and the RING domain. The position of the STOP codon is supported by PASA-assembled expressed sequence tags (103); the gene model should therefore not include the 3′ end encoding the C-terminal low-complexity region. ...