Common genetic variation in the <em>HLA</em> region is associated with late-onset sporadic Parkinson's disease

Parkinson’s diseas

Feasibiity analysis of MBMS deployment with the introduction of LTE

Multimedia Broadcast Multicast service (MBMS) proposed by 3GPP for efficient use of network resources in broadcast and multicast services, provides the operator a delivery mechanism to simultaneously send to multiple recipients at high speed. Although MBMS was introduced in 3GPP Release 6 at the time of 3G networks, the MBMS feature did not find much attention from the 3G network operators. This thesis studies the technical and market feasibility for a successful MBMS deployment today at the time of commercial LTE deployment. UE and RAN advancements that make MBMS technologically feasible are studied together with the market feasibility factors such as user demand on media streaming and the impending data explosion. The thesis concludes that today at the time of LTE, it is more feasible from both technology and market perspectives to deploy MBMS in comparison to the time of 3G. As a future work, the thesis provides some suggestions that the operators should take care of before deploying MBMS

Isolation of the Syntenic Genomic Regions Containing the <i>ASPM</i> Gene from Human, Chimpanzee, Gorilla, Orangutan, and Rhesus Macaque by TAR Cloning

<p>The method exploits a high level of recombination between homologous DNA sequences during transformation in the yeast Saccharomyces cerevisiae. For isolation, genomic DNA is transformed into yeast spheroplasts along with a TAR vector that contains targeting hooks homologous to the genomic DNA sequence. <i>CEN</i> corresponds to the yeast Chromosome VI centromere; <i>HIS3</i> is a yeast selectable marker. Recombination between the vector and the genomic DNA fragment results in cloning of the gene/region of interest as YAC. Chromosomal regions with sizes up to 250 kb can be isolated by TAR cloning. For cloning purposes, TAR vector was designed containing a 5′ hook specific to exon 1 and a 3′ hook specific to the 3′ end of the human <i>ASPM</i>. Transformation experiments were carried out with freshly prepared spheroplasts for each species. To identify <i>ASPM</i>-containing clones, the transformants were combined into pools and examined by PCR for the presence of the unique <i>ASPM</i> sequences not present in the vector. The yield of <i>ASPM</i>-positive clones from primate species was the same as that from the human DNA (3%). Because the TAR procedure produces multiple gene isolates, six independent TAR isolates for each species were checked. The detectable size of the cloned material corresponded to that predicted if the entire <i>ASPM</i> gene had been cloned, i.e., all gene-positive clones contained circular YACs with approximately 65-kb DNA inserts. <i>Alu</i> profiles for each species were determined and found to be identical for each species, suggesting that the isolated YACs contained nonrearranged genomic segments. Finally the YACs were retrofitted into BACs, and their restriction patterns were examined by three restriction endonuclease digestions. No differences between <i>ASPM</i> clones for each species were found.</p

Phylogenetic Trees and ω ratio for Complete <i>ASPM</i> and Three Selected Segments

<div><p>Trees and ω (Ka/Ka) ratios were computed using the ML method for codons implemented in PAML. Branch lengths represent ML distances for codons, i.e., using both synonymous and nonsynonymous nucleotide sites, and in all branches the ω ratio was set free to vary. All trees are drawn to the same scale. Branch labels mark the ω ratios for corresponding branches. Values in square brackets show ω for additional cDNA sequences whenever available. Default values and branch lengths were calculated from genomic copies. Selected tested hypotheses are listed. ω_H stands for the ω rate in the human lineage, ω_C in the chimpanzee lineage, ω_CH in the common human–chimpanzee ancestral lineage after the gorilla divergence, ω_G in the gorilla lineage, and ω₀ in all other branches. Single asterisks indicate <i>p</i> < 0.05, χ²₁ = 3.84; double asterisks indicate <i>p</i> < 0.01, χ²₁ = 6.63.</p> <p>(A) Phylogeny for the complete <i>ASPM</i> CDS. In addition to testing different ω values in the human lineage, we also tested the hypothesis that the complete gorilla–chimpanzee–human clade evolved at a constant rate, different from the rest of the tree (compared to the one-ratio model, boxed).</p> <p>(B) The <i>ASPM</i> phylogeny derived from a conserved segment from exon 5 to the beginning of the IQ domain (amino acids 676–1,266). The branch connecting the human and chimpanzee common ancestor with the gorilla–chimpanzee–human common ancestor had no substitutions, therefore the ω ratio could not be calculated.</p> <p>(C) IQ domain (amino acids 1,267–3,225). We also tested the hypothesis that the gorilla and human lineages evolved at the same ω rate, different from the rest of the tree (compared to the one-ratio model, boxed).</p> <p>(D) Phylogeny of eight primate sequences from a 1,215-amino-acid-long segment of exon 18 (amino acids 1,640–2,855). We also tested the hypothesis that the gorilla and human lineages evolved at the same ω rate, different from the rest of the tree (compared to the one-ratio model, boxed).</p></div

Structure and Evolution of the <i>ASPM</i> Gene in Primates

<div><p>The scale of all plots corresponds to the consensus sequence obtained based on a multiple alignment of five <i>ASPM</i> genes.</p> <p>(A) Schematic representation of the alignment. Promoter regions, exons, and introns are marked in gray, red, and blue, respectively. White segments correspond to gaps.</p> <p>(B) Positions of long (50 bp or longer) insertions/deletions. “O” denotes orangutan, “M” macaque, “OGCH” the orangutan–gorilla–chimpanzee–human clade, and “GCH” the gorilla–chimpanzee–human clade.</p> <p>(C) Positions of polymorphic bases derived from the GenBank single nucleotide polymorphism (SNP) database.</p> <p>(D) Positions of the CpG island. The approximately 800-bp-long CpG island includes promoter, 5′ UTR, first exon, and a small portion of the first intron.</p> <p>(E) Location of an approximately 3-kb-long segmental duplication.</p> <p>(F) Positions of selected motifs associated with genomic rearrangements in the human sequence. Numbers in parentheses reflect number of allowed differences from the consensus motif (zero for short or two ambiguous motifs, two for longer sites).</p> <p>(G) Distribution of repetitive elements. The individual <i>ASPM</i> genes share the same repeats except of indels marked in (B).</p> <p>(H) DNA identity and GC content. Both plots were made using a 1-kb-long sliding window with 100-bp overlaps. The GC profile corresponds to the consensus sequence; the individual sequences have nearly identical profiles.</p></div

Structure of <i>ASPM</i> CDSs and Evolution in Primates

<div><p>The scale of all plots corresponds to the 3,480-amino-acid-long protein alignment; positions in the CDS were scaled accordingly.</p> <p>(A) Structure of the human <i>ASPM</i> CDS and protein. The first scheme shows positions of major domains in the ASPM protein (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020126#pbio-0020126-Bond1" target="_blank">Bond et al. 2002</a>). The putative microtubule-binding domain is in gray, the calponin-homology domain in orange, IQ repeats in blue, and the terminal domain in black. Positions of exons in the CDS are drawn in the second block. To separate individual exons, odd numbered exons are colored in black and even numbered ones in white.</p> <p>(B) Positions of insertions/deletions in the protein sequences. Coordinates correspond to the human protein sequence. “O” denotes orangutan, “G” gorilla, “M” macaque, “Gm” African green monkey, and “OGCH” the orangutan–gorilla–chimpanzee–human clade.</p> <p>(C) Substitutions in hominoid CDSs relative to the common ancestor. The expected ancestor CDS was derived using ML codon reconstruction implemented in PAML. African green monkey and rhesus macaque were outgroups. Nonsynonymous/synonymous (ω = Ka/Ks) ratios were free to vary in all branches. Positions marked in green correspond to synonymous changes relative to the ancestral sequence; the red bars indicate nonsynonymous changes.</p> <p>(D) Synonymous (red) and nonsynonymous (green) changes in ancestral lineages leading to human. aOGCH–aGCH is the ancestral lineage from the orangutan divergence to the gorilla divergence; aGCH–aCH represents the lineage from the gorilla divergence to the chimpanzee common ancestor. aCH–human corresponds to the human lineage after the chimpanzee divergence. There are seven synonymous and 19 nonsynonymous human-specific substitutions. Methods and description are the same as in (C).</p> <p>(E) Positions of polymorphic bases for different CDSs of African green monkey, gorilla, chimpanzee, and human. Positions marked in green correspond to synonymous polymorphisms, and the red bars indicate nonsynonymous sites. Numbers of compared sequences are in parentheses; in the case of human we show nine polymorphic positions (four synonymous and five nonsynomous) from the GenBank SNP database. <i>ASPM</i> mutations detected in MCPH patients are shown separately in (F).</p> <p>(F) Positions of 19 mutations reported for MCPH patients (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020126#pbio-0020126-Bond1" target="_blank">Bond et al. 2002</a>; <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020126#pbio-0020126-Bond2" target="_blank">Bond et al. 2003</a>). All the reported mutations introduce premature stop codons. Mutation sites located within CpG dinucleotides are highlighted in red.</p> <p>(G) Positions of CpG dinucleotides in the human CDS.</p> <p>(H) Comparison of Ka and Ks rates with codon adaptation index (CAI). Ka and Ks values are for all branches (fixed ω ratio); CAI is an average for all five primates (note that CAI differences are very small between the five species). The window was set to 300 bp (100 amino acids) with a 30-bp (10-amino-acid) step.</p> <p>(I) Conservation at the nucleotide and protein level in primates. Y-axis corresponds to proportions of conserved (identical) positions in the CDS and the protein alignment. The plot was obtained using 100-amino-acid-long, overlapping windows, and the step was set to 10 amino acids. In the case of CDS conservation, the window was 300 bp and step 30 bp.</p></div