Hominoid fission of chromosome 14/15 and the role of segmental duplications.

Ape chromosomes homologous to human chromosomes 14 and 15 were generated by a fission event of an ancestral submetacentric chromosome, where the two chromosomes were joined head-to-tail. The hominoid ancestral chromosome most closely resembles the macaque chromosome 7. In this work, we provide insights into the evolution of human chromosomes 14 and 15, performing a comparative study between macaque boundary region 14/15 and the orthologous human regions. We construct a 1.6-Mb contig of macaque BAC clones in the region orthologous to the ancestral hominoid fission site and use it to define the structural changes that occurred on human 14q pericentromeric and 15q subtelomeric regions. We characterize the novel euchromatin-heterochromatin transition region (∼20 Mb) acquired during the neocentromere establishment on chromosome 14, and find it was mainly derived through pericentromeric duplications from ancestral hominoid chromosomes homologous to human 2q14-qter and 10. Further, we show a relationship between evolutionary hotspots and low-copy repeat loci for chromosome 15, revealing a possible role of segmental duplications not only in mediating but also in "stitching" together rearrangement breakpoints.

Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21

The goals of the human genome project did not include sequencing of the heterochromatic regions. We describe here an initial sequence of 1.1 Mb of the short arm of human chromosome 21 (HSA21p), estimated to be 10% of 21p. This region contains extensive euchromatic-like sequence and includes on average one transcript every 100 kb. These transcripts show multiple inter- and intrachromosomal copies, and extensive copy number and sequence variability. The sequencing of the "heterochromatic" regions of the human genome is likely to reveal many additional functional elements and provide important evolutionary information.

Notas sobre a bionomia de Trichotrigona extranea Camargo & Moure (Hymenoptera, Apidae, Meliponini)

Três ninhos de T. extranea, encontrados nas matas de igapó, na localidade de Samaúma, foz do rio Daraã (64°45'35" W, 0°27'7" S), AM, Brasil, são descritos e ilustrados. Este é o único lugar onde esta espécie é conhecida. Todos os ninhos estavam em ocos de ramos secos de "Tanimbuca" - Buchenavia suaveolens Eichler (Combretaceae). Dois deles compartilhavam o oco com ninhos de Frieseomelitta sp. e um era solitário. Um ninho continha 46 células de cria, 43 operárias adultas e uma rainha fisogástrica; o segundo, 240 células, 117 operárias, 25 machos e uma rainha fisogástrica; o terceiro, 260 células, 163 operárias, uma rainha fisogástrica e uma pupa de rainha. As células são construídas na forma de cacho, como em Friseomelitta, e as células de rainha são do mesmo tamanho e forma que as de operária. Não há potes de alimento - este é o único Meliponini que se conhece que não armazena alimento. Supostamente, esta espécie tem hábitos cleptobióticos. Rainhas e machos são também descritos.

Death and resurrection of the human IRGM gene

Immunity-related GTPases (IRG) play an important role in defense against intracellular pathogens. One member of this gene family in humans, IRGM, has been recently implicated as a risk factor for Crohn's disease. We analyzed the detailed structure of this gene family among primates and showed that most of the IRG gene cluster was deleted early in primate evolution, after the divergence of the anthropoids from prosimians ( about 50 million years ago). Comparative sequence analysis of New World and Old World monkey species shows that the single-copy IRGM gene became pseudogenized as a result of an Alu retrotransposition event in the anthropoid common ancestor that disrupted the open reading frame (ORF). We find that the ORF was reestablished as a part of a polymorphic stop codon in the common ancestor of humans and great apes. Expression analysis suggests that this change occurred in conjunction with the insertion of an endogenous retrovirus, which altered the transcription initiation, splicing, and expression profile of IRGM. These data argue that the gene became pseudogenized and was then resurrected through a series of complex structural events and suggest remarkable functional plasticity where alleles experience diverse evolutionary pressures over time. Such dynamism in structure and evolution may be critical for a gene family locked in an arms race with an ever-changing repertoire of intracellular parasites.

A burst of segmental duplications in the genome of the African great ape ancestor

It is generally accepted that the extent of phenotypic change between human and great apes is dissonant with the rate of molecular change. Between these two groups, proteins are virtually identical, cytogenetically there are few rearrangements that distinguish ape-human chromosomes, and rates of single-base-pair change and retrotransposon activity have slowed particularly within hominid lineages when compared to rodents or monkeys. Studies of gene family evolution indicate that gene loss and gain are enriched within the primate lineage. Here, we perform a systematic analysis of duplication content of four primate genomes (macaque, orang-utan, chimpanzee and human) in an effort to understand the pattern and rates of genomic duplication during hominid evolution. We find that the ancestral branch leading to human and African great apes shows the most significant increase in duplication activity both in terms of base pairs and in terms of events. This duplication acceleration within the ancestral species is significant when compared to lineage-specific rate estimates even after accounting for copy-number polymorphism and homoplasy. We discover striking examples of recurrent and independent gene-containing duplications within the gorilla and chimpanzee that are absent in the human lineage. Our results suggest that the evolutionary properties of copy-number mutation differ significantly from other forms of genetic mutation and, in contrast to the hominid slowdown of single-base-pair mutations, there has been a genomic burst of duplication activity at this period during human evolution.

Sequencing primate genomes: what have we learned?

We summarize the progress in whole-genome sequencing and analyses of primate genomes. These emerging genome datasets have broadened our understanding of primate genome evolution revealing unexpected and complex patterns of evolutionary change. This includes the characterization of genome structural variation, episodic changes in the repeat landscape, differences in gene expression, new models regarding speciation, and the ephemeral nature of the recombination landscape. The functional characterization of genomic differences important in primate speciation and adaptation remains a significant challenge. Limited access to biological materials, the lack of detailed phenotypic data and the endangered status of many critical primate species have significantly attenuated research into the genetic basis of primate evolution. Next-generation sequencing technologies promise to greatly expand the number of available primate genome sequences; however, such draft genome sequences will likely miss critical genetic differences within complex genomic regions unless dedicated efforts are put forward to understand the full spectrum of genetic variation.

The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild

BACKGROUND: The only known albino gorilla, named Snowflake, was a male wild born individual from Equatorial Guinea who lived at the Barcelona Zoo for almost 40 years. He was diagnosed with non-syndromic oculocutaneous albinism, i.e. white hair, light eyes, pink skin, photophobia and reduced visual acuity. Despite previous efforts to explain the genetic cause, this is still unknown. Here, we study the genetic cause of his albinism and making use of whole genome sequencing data we find a higher inbreeding coefficient compared to other gorillas.RESULTS: We successfully identified the causal genetic variant for Snowflake's albinism, a non-synonymous single nucleotide variant located in a transmembrane region of SLC45A2. This transporter is known to be involved in oculocutaneous albinism type 4 (OCA4) in humans. We provide experimental evidence that shows that this amino acid replacement alters the membrane spanning capability of this transmembrane region. Finally, we provide a comprehensive study of genome-wide patterns of autozygogosity revealing that Snowflake's parents were related, being this the first report of inbreeding in a wild born Western lowland gorilla.CONCLUSIONS: In this study we demonstrate how the use of whole genome sequencing can be extended to link genotype and phenotype in non-model organisms and it can be a powerful tool in conservation genetics (e.g., inbreeding and genetic diversity) with the expected decrease in sequencing cost.

PRECISION V: Randomisierte Phase II-Studie mit Drug Eluting Beads (DEB) zur Behandlung des hepatozelluläre Karzinoms (HCC) mittels transarterieller Chemoemblisation [PRECISION V: Randomized Phase II-Study with Drug Eluting Beads (DEB) for the Treatment of Hepatocellular cancer (HCC) using transarterial Chemoemblisation.]

Zielsetzung: Vergleich von Drug Eluting Bead (DEB)-TACE mit konventioneller TACE bei der Behandlung von ,,intermediate stage-HCC bei Patienten mit Zirrhose. Material und Methodik: 212 Patienten (185 ♂, 27 ♀; mittleres Alter, 67 Jahre) mit Child-Pugh A oder B Leberzirrhose und großem und/oder multinodulärem, irresektablen HCC wurden randomisiert, um das Therapieansprechen nach der Behandlung mit DEB (DC Bead; Biocompatibles, UK) beladen mit Doxorubicin oder konventioneller TACE mit Doxorubicin zu vergleichen. Die Randomisierung wurde nach Child-Pugh Status (A oder B), Performance Status (ECOG 0 oder 1), bilobärer Erkrankung (ja/nein) und frühere kurative Behandlung (ja/nein) stratifiziert. Der primäre Studienendpunkt war das 6-Monats-Tumoransprechen. Eine unabhängige verblindete MRT-Studie wurde durchgeführt, um das Tumoransprechen nach den RECIST Kriterien zu beurteilen. Ergebnisse: DEB-TACE mit Doxorubicin zeigte eine höhere Rate an komplettem Tumoransprechen, objektivem Ansprechen und Tumorkontrolle im Vergleich zur konventionellen TACE (27% vs 22%; 52% vs 44%; and 63% vs 52%; P>0.05). Patienten mit Child-Pugh B Zirrhose, ECOG 1 Performance Status, bilobärer Erkrankung und Rezidiven nach kurativer Behandlung zeigte einen signifikanten Anstieg des objektiven Ansprechens (p = 0.038) im Vergleich zur Kontrollgruppe. Bei Patienten, die mit DEB-TACE behandelt wurden, konnte eine deutliche Reduktion der gravierenden Lebertoxizität erreicht werden. Die Doxorubicin-Nebenwirkungsrate war in der DEB-TACE Gruppe deutlich geringer (p = 0.0001) als in der konventionellen TACEGruppe. Schlussfolgerung: DEB-TACE mit Doxorubicin ist sicher und effektiv in der Behandlung von ,,intermediate-stage HCC und bietet einen signifikanten Vorteil bei Patienten mit fortgeschrittener Erkrankung.

Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21.

The goals of the human genome project did not include sequencing of the heterochromatic regions. We describe here an initial sequence of 1.1 Mb of the short arm of human chromosome 21 (HSA21p), estimated to be 10% of 21p. This region contains extensive euchromatic-like sequence and includes on average one transcript every 100 kb. These transcripts show multiple inter- and intrachromosomal copies, and extensive copy number and sequence variability. The sequencing of the "heterochromatic" regions of the human genome is likely to reveal many additional functional elements and provide important evolutionary information.

Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee

Structural variation has played an important role in the evolutionary restructuring of human and great ape genomes. Recent analyses have suggested that the genomes of chimpanzee and human have been particularly enriched for this form of genetic variation. Here, we set out to assess the extent of structural variation in the gorilla lineage by generating 10-fold genomic sequence coverage from a western lowland gorilla and integrating these data into a physical and cytogenetic framework of structural variation. We discovered and validated over 7665 structural changes within the gorilla lineage, including sequence resolution of inversions, deletions, duplications, and mobile element insertions. A comparison with human and other ape genomes shows that the gorilla genome has been subjected to the highest rate of segmental duplication. We show that both the gorilla and chimpanzee genomes have experienced independent yet convergent patterns of structural mutation that have not occurred in humans, including the formation of subtelomeric heterochromatic caps, the hyperexpansion of segmental duplications, and bursts of retroviral integrations. Our analysis suggests that the chimpanzee and gorilla genomes are structurally more derived than either orangutan or human genomes.

Sequencing human-gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sites

The gibbon genome exhibits extensive karyotypic diversity with an increased rate of chromosomal rearrangements during evolution. In an effort to understand the mechanistic origin and implications of these rearrangement events, we sequenced 24 synteny breakpoint regions in the white-cheeked gibbon (Nomascus leucogenys, NLE) in the form of high-quality BAC insert sequences (4.2 Mbp). While there is a significant deficit of breakpoints in genes, we identified seven human gene structures involved in signaling pathways (DEPDC4, GNG10), phospholipid metabolism (ENPP5, PLSCR2), beta-oxidation (ECH1), cellular structure and transport (HEATR4), and transcription (ZNF461), that have been disrupted in the NLE gibbon lineage. Notably, only three of these genes show the expected evolutionary signatures of pseudogenization. Sequence analysis of the breakpoints suggested both nonclassical nonhomologous end-joining (NHEJ) and replication-based mechanisms of rearrangement. A substantial number (11/24) of human-NLE gibbon breakpoints showed new insertions of gibbon-specific repeats and mosaic structures formed from disparate sequences including segmental duplications, LINE, SINE, and LTR elements. Analysis of these sites provides a model for a replication-dependent repair mechanism for double-strand breaks (DSBs) at rearrangement sites and insights into the structure and formation of primate segmental duplications at sites of genomic rearrangements during evolution.

The origins and impact of primate segmental duplications

Duplicated sequences are substrates for the emergence of new genes and are an important source of genetic instability associated with rare and common diseases. Analyses of primate genomes have shown an increase in the proportion of interspersed segmental duplications (SDs) within the genomes of humans and great apes. This contrasts with other mammalian genomes that seem to have their recently duplicated sequences organized in a tandem configuration. In this review, we focus on the mechanistic origin and impact of this difference with respect to evolution, genetic diversity and primate phenotype. Although many genomes will be sequenced in the future, resolution of this aspect of genomic architecture still requires high quality sequences and detailed analyses.

Programme national VIH/sida 1999-2003 : état et dynamique de la mise en oeuvre à fin 2001

Cette étude a été menée par l'Unité d'évaluation de programmes de prévention de l'Institut de médecine sociale et préventive (IUMSP) de Lausanne. Elle s'inscrit dans le cadre de l'évaluation globale de la stratégie de prévention du VIH/sida pour laquelle l'IUMSP a reçu mandat de l'Office fédéral de la santé publique. Le programme national "VIH et sida : Programme national de 1999 à 2003" a été préparé en 1998 par l'OFSP en collaboration avec des experts et publié en février 1999. Il fait suite au manuel "Prévention du VIH en Suisse : buts, stratégies, mesures" publié en 1993 et couvre la période de 1999 à 2003. Les 14 objectifs qu'il définit, avec leurs jalons, sont répartis dans cinq grands domaines à savoir: promotion de la santé, prévention, thérapie et diagnostic, conseil et soutien, savoir et transfert des compétences. Afin d'en planifier la mise en oeuvre, l'OFSP a organisé 14 plates-formes régionales en août et septembre 1999 qui ont fait l'objet d'un rapport publié en janvier 2000. Les plates-formes ont été suivies d'une "Conférence intercantonale VIH/sida" le 8 septembre 2000 à Berne, organisée conjointement par l'Office fédéral de la santé publique (OFSP)/Section Sida et l'Aide Suisse contre le Sida (ASS), dont le thème général était "Transfert dans la lutte contre le VIH/sida". Faisant suite à la première phase d'évaluation qui, elle, a porté sur l'état des activités de lutte contre le VIH/sida dans les cantons, la deuxième phase de l'évaluation fait le point sur la mise en oeuvre du programme national 1999-2003 au niveau national et dans les cinq cantons pour la période 2000-2001 et porte sur l'implantation du programme national. Y sont analysés le développement des activités dans tous les domaines, la pertinence des objectifs et jalons, les éléments garantissant la pérennité et la qualité des interventions, et le développement des collaborations à différents niveaux.

Management of Pharyngeal Fistulas After Anterior Cervical Spine Surgery: A Treatment Algorithm for Severe Complications.

STUDY DESIGN:: Retrospective database- query to identify all anterior spinal approaches. OBJECTIVES:: To assess all patients with pharyngo-cutaneous fistulas after anterior cervical spine surgery. SUMMARY OF BACKGROUND DATA:: Patients treated in University of Heidelberg Spine Medical Center, Spinal Cord Injury Unit and Department of Otolaryngology (Germany), between 2005 and 2011 with the diagnosis of pharyngo-cutaneous fistulas. METHODS:: We conducted a retrospective study on 5 patients between 2005 and 2011 with PCF after ACSS, their therapy management and outcome according to radiologic data and patient charts. RESULTS:: Upon presentation 4 patients were paraplegic. 2 had PCF arising from one piriform sinus, two patients from the posterior pharyngeal wall and piriform sinus combined and one patient only from the posterior pharyngeal wall. 2 had previous unsuccessful surgical repair elsewhere and 1 had prior radiation therapy. In 3 patients speech and swallowing could be completely restored, 2 patients died. Both were paraplegic. The patients needed an average of 2-3 procedures for complete functional recovery consisting of primary closure with various vascularised regional flaps and refining laser procedures supplemented with negative pressure wound therapy where needed. CONCLUSION:: Based on our experience we are able to provide a treatment algorithm that indicates that chronic as opposed to acute fistulas require a primary surgical closure combined with a vascularised flap that should be accompanied by the immediate application of a negative pressure wound therapy. We also conclude that particularly in paraplegic patients suffering this complication the risk for a fatal outcome is substantial.