Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution

Arising from either retrotransposition or genomic duplication of functional genes, pseudogenes are “genomic fossils” valuable for exploring the dynamics and evolution of genes and genomes. Pseudogene identification is an important problem in computational genomics, and is also critical for obtaining an accurate picture of a genome’s structure and function. However, no consensus computational scheme for defining and detecting pseudogenes has been developed thus far. As part of the ENCyclopedia Of DNA Elements (ENCODE) project, we have compared several distinct pseudogene annotation strategies and found that different approaches and parameters often resulted in rather distinct sets of pseudogenes. We subsequently developed a consensus approach for annotating pseudogenes (derived from protein coding genes) in the ENCODE regions, resulting in 201 pseudogenes, two-thirds of which originated from retrotransposition. A survey of orthologs for these pseudogenes in 28 vertebrate genomes showed that a significant fraction (∼80%) of the processed pseudogenes are primate-specific sequences, highlighting the increasing retrotransposition activity in primates. Analysis of sequence conservation and variation also demonstrated that most pseudogenes evolve neutrally, and processed pseudogenes appear to have lost their coding potential immediately or soon after their emergence. In order to explore the functional implication of pseudogene prevalence, we have extensively examined the transcriptional activity of the ENCODE pseudogenes. We performed systematic series of pseudogene-specific RACE analyses. These, together with complementary evidence derived from tiling microarrays and high throughput sequencing, demonstrated that at least a fifth of the 201 pseudogenes are transcribed in one or more cell lines or tissues.

Prominent use of distal 5’ transcription start sites and discovery of a large number of additional exons in ENCODE regions

This report presents systematic empirical annotation of transcript products from 399 annotated protein-coding loci across the 1% of the human genome targeted by the Encyclopedia of DNA elements (ENCODE) pilot project using a combination of 5' rapid amplification of cDNA ends (RACE) and high-density resolution tiling arrays. We identified previously unannotated and often tissue- or cell-line-specific transcribed fragments (RACEfrags), both 5' distal to the annotated 5' terminus and internal to the annotated gene bounds for the vast majority (81.5%) of the tested genes. Half of the distal RACEfrags span large segments of genomic sequences away from the main portion of the coding transcript and often overlap with the upstream-annotated gene(s). Notably, at least 20% of the resultant novel transcripts have changes in their open reading frames (ORFs), most of them fusing ORFs of adjacent transcripts. A significant fraction of distal RACEfrags show expression levels comparable to those of known exons of the same locus, suggesting that they are not part of very minority splice forms. These results have significant implications concerning (1) our current understanding of the architecture of protein-coding genes; (2) our views on locations of regulatory regions in the genome; and (3) the interpretation of sequence polymorphisms mapping to regions hitherto considered to be "noncoding," ultimately relating to the identification of disease-related sequence alterations.

Welcoming New Iowans; A Guide for Christians and Churches, 2002

Immigrant and refugee newcomers have an important role in Iowa. These newcomers have revitalized many Iowa communities, workplaces and faith-based institutions. The arrival of immigrants and refugees poses challenges as well as rewards; understanding and addressing these issues is vital to welcoming and accommodating new Iowans and assuring their part in the long-term economic and social health of our state. This handbook represents a unique collaboration between the University of Northern Iowa (UNI) and Ecumenical Ministries of Iowa (EMI). The goal of this collaboration is to create a guidebook for Iowans to learn more about Iowa’s growing immigrant and refugee population and discover ways to welcome these newcomers and accommodate them in our communities and churches. The unique nature of this joint publication between a public university and Christian churches acknowledges that both institutions have a stake in accommodating immigrants in Iowa. UNI and all institutions of higher education need to support population growth to assure future enrollments. Churches and many other community institutions need immigrants and other newcomers to help maintain their viability. Universities and churches also need healthy local economies. Newcomers can provide much needed skills and labor to make this happen. In short, His collaboration recognizes that making immigration in Iowa work has important long-term implications for us all. This book was written and compiled by two university faculty members, but it is not an official university endorsement of Christianity as the only religion practiced and accepted by Iowans, and no university funds were used to print or distribute this handbook. This handbook is written for Iowa’s Christian community and is based on the Biblical mandate to welcome newcomers, but we acknowledge Iowa’s other religious groups and their role in accommodating newcomers as well. We readily acknowledge that other faith-based organizations also welcome newcomers and have a stake in making immigration a positive experience. In order to accommodate the perspectives and needs of these groups, the UNI New Iowans Program is planning to develop similar handbooks for Iowa’s Jewish and Muslim communities. This handbook includes a number of resource lists for individuals, newcomers, churches and others. Of course, as soon as these lists are printed, they may become out-of-date. In order to obtain the most up-to-date information, please visit the UNI New Iowans Web site: www.bcs.uni.edu/idm/newiowans/ The UNI New Iowans website also makes this handbook available in a PDF format.

Incorporating features of distribution and progression for automatic Makam classification

Automatic classification of makams from symbolic data is a rarely studied topic. In this paper, first a review of an n-gram based approach is presented using various representations of the symbolic data. While a high degree of precision can be obtained, confusion happens mainly for makams using (almost) the same scale and pitch hierarchy but differ in overall melodic progression, seyir. To further improve the system, first n-gram based classification is tested for various sections of the piece to take into account a feature of the seyir that melodic progression starts in a certain region of the scale. In a second test, a hierarchical classification structure is designed which uses n-grams and seyir features in different levels to further improve the system.

(Re-) Shaping hatred: Anti-Semitic attitudes in Germany, 1890-2006

In this paper, we assess the determinants of long-run persistence of localculture, and examine the success of policy interventions designed to change attitudes.We analyze anti-Semitic attitudes drawing on individual-level survey results fromGermany s social value survey in 1996 and 2006. On average, we find that historicalvoting patterns for anti-Semitic parties between 1890 and 1933 are powerfulpredictors of anti-Jewish attitudes today. There is evidence that transmission takesplace both vertically (parent to child) and horizontally (among peers). Policy modifiedGerman views on Jews in important ways: The cohort that grew up under the Naziregime shows significantly higher levels of anti-Semitism. After 1945, the victoriousAllies implemented denazification programs in their zones of occupation. We usedifferences in these policies between the occupying powers as a source of identifyingvariation. The US and French zones today still show high anti-Semitism, reflecting anambitious botched attempt at denazification. In contrast, the British and Soviet zones,register much lower levels of Jew-hatred.

Persecution perpetuated: The medieval origins of anti-semitic violence in Nazi Germany

How persistent are cultural traits? This paper uses data on anti-Semitism in Germany and finds continuity at the local level over more than half a millennium. When the Black Death hit Europe in 1348-50, killing between one third and one half of the population, its cause was unknown. Many contemporaries blamed the Jews. Cities all over Germany witnessed mass killings of their Jewish population. At the same time, numerous Jewish communities were spared these horrors. We use plague pogroms as an indicator for medieval anti-Semitism. Pogroms during the Black Death are a strong and robust predictor of violence against Jews in the 1920s, and of votes for the Nazi Party. In addition, cities that saw medieval anti-Semitic violence also had higher deportation rates for Jews after 1933, were more likely to see synagogues damaged or destroyed in the Night of Broken Glass in 1938, and their inhabitants wrote more anti-Jewish letters to the editor of the Nazi newspaper Der Stürmer.