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author:("pages, Jan")
1.  Intraspecific sequence comparisons reveal similar rates of non-collinear gene insertion in the B and D genomes of bread wheat 
BMC Plant Biology  2012;12:155.
Background
Polyploidization is considered one of the main mechanisms of plant genome evolution. The presence of multiple copies of the same gene reduces selection pressure and permits sub-functionalization and neo-functionalization leading to plant diversification, adaptation and speciation. In bread wheat, polyploidization and the prevalence of transposable elements resulted in massive gene duplication and movement. As a result, the number of genes which are non-collinear to genomes of related species seems markedly increased in wheat.
Results
We used new-generation sequencing (NGS) to generate sequence of a Mb-sized region from wheat chromosome arm 3DS. Sequence assembly of 24 BAC clones resulted in two scaffolds of 1,264,820 and 333,768 bases. The sequence was annotated and compared to the homoeologous region on wheat chromosome 3B and orthologous loci of Brachypodium distachyon and rice. Among 39 coding sequences in the 3DS scaffolds, 32 have a homoeolog on chromosome 3B. In contrast, only fifteen and fourteen orthologs were identified in the corresponding regions in rice and Brachypodium, respectively. Interestingly, five pseudogenes were identified among the non-collinear coding sequences at the 3B locus, while none was found at the 3DS locus.
Conclusion
Direct comparison of two Mb-sized regions of the B and D genomes of bread wheat revealed similar rates of non-collinear gene insertion in both genomes with a majority of gene duplications occurring before their divergence. Relatively low proportion of pseudogenes was identified among non-collinear coding sequences. Our data suggest that the pseudogenes did not originate from insertion of non-functional copies, but were formed later during the evolution of hexaploid wheat. Some evidence was found for gene erosion along the B genome locus.
doi:10.1186/1471-2229-12-155
PMCID: PMC3445842  PMID: 22935214
Wheat; BAC sequencing; Homoeologous genomes; Gene duplication; Non-collinear genes; Allopolyploidy
2.  Retroposition of processed pseudogenes: the impact of RNA stability and translational control 
Trends in genetics : TIG  2005;22(2):69-73.
Summary
Human processed pseudogenes are copies of cellular RNAs reverse transcribed and inserted into the nuclear genome by the enzymatic machinery of L1/LINE1 non-LTR retrotransposons. While it is generally accepted that germline expression is crucial for heritable retroposition of cellular mRNAs, almost nothing is known about the influences of RNA stability, mRNA quality control, and compartmentalization of translation on retroposition of processed pseudogenes. Here we found that frequently retroposed human mRNAs are derived from stable transcripts with translation-competent functional reading frames resistant to nonsense-mediated RNA decay. They are preferentially translated on free cytoplasmic ribosomes and encode soluble proteins. Our results indicate that interactions between mRNAs and L1 proteins seem to occur at free cytoplasmic ribosomes.
doi:10.1016/j.tig.2005.11.005
PMCID: PMC1379630  PMID: 16356584
mRNA surveillance; NMD; retropseudogene; retrotransposition; soluble proteins; membrane proteins
3.  WAViS server for handling, visualization and presentation of multiple alignments of nucleotide or amino acids sequences 
Nucleic Acids Research  2004;32(Web Server issue):W48-W49.
Web Alignment Visualization Server contains a set of web-tools designed for quick generation of publication-quality color figures of multiple alignments of nucleotide or amino acids sequences. It can be used for identification of conserved regions and gaps within many sequences using only common web browsers. The server is accessible at http://wavis.img.cas.cz.
doi:10.1093/nar/gkh358
PMCID: PMC441496  PMID: 15215348
4.  LIME 
The Journal of Experimental Medicine  2003;198(10):1453-1462.
Lymphocyte membrane rafts contain molecules critical for immunoreceptor signaling. Here, we report identification of a new raft-associated adaptor protein LIME (Lck-interacting molecule) expressed predominantly in T lymphocytes. LIME becomes tyrosine phosphorylated after cross-linking of the CD4 or CD8 coreceptors. Phospho-LIME associates with the Src family kinase Lck and its negative regulator, Csk. Ectopic expression of LIME in Jurkat T cells results in an increase of Csk in lipid rafts, increased phosphorylation of Lck and higher Ca2+ response to CD3 stimulation. Thus, LIME appears to be involved in regulation of T cell activation by coreceptors.
doi:10.1084/jem.20031484
PMCID: PMC2194115  PMID: 14610046
membrane microdomains; Lck; Csk; signal transduction; phosphorylation
5.  HERVd: the Human Endogenous RetroViruses Database: update 
Nucleic Acids Research  2004;32(Database issue):D50.
An elaboration of HERVd (http://herv.img.cas.cz) is being carried out in two directions. One of them is the integration and better classification of families that diverge considerably from typical retroviral genomes. This leads to a more precise identification of members with individual families. The second improvement is better accessibility of the database and connection with human genome annotation.
doi:10.1093/nar/gkh075
PMCID: PMC308809  PMID: 14681356
6.  HERVd: database of human endogenous retroviruses 
Nucleic Acids Research  2002;30(1):205-206.
The human endogenous retroviruses database (HERVd) is maintained at the Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, and is accessible via the World Wide Web at http://herv.img.cas.cz. The HERVd provides complex information on and analysis of retroviral elements found in the human genome. It can be used for searches of individual HERV families, identification of HERV parts, graphical output of HERV structures, comparison of HERVs and identification of retrovirus integration sites.
PMCID: PMC99133  PMID: 11752294

Results 1-6 (6)