Alu retrotransposition-mediated deletion

Alu repeats contribute to genomic instability in primates via insertional and recombinational mutagenesis. Here, we report an analysis of Alu element-induced genomic instability through a novel mechanism termed retrotransposition-mediated deletion, and assess its impact on the integrity of primate genomes. For human and chimpanzee genomes, we find evidence of 33 retrotransposition-mediated deletion events that have eliminated approximately 9000 nucleotides of genomic DNA. Our data suggest that, during the course of primate evolution, Alu retrotransposition may have contributed to over 3000 deletion events, eliminating approximately 900 kb of DNA in the process. Potential mechanisms for the creation of Alu retrotransposition-mediated deletions include L1 endonuclease-dependent retrotransposition, L1 endonuclease-independent retrotransposition, internal priming on DNA breaks, and promiscuous target primed reverse transcription. A comprehensive analysis of the collateral effects by Alu mobilization on all primate genomes will require sequenced genomes from representatives of the entire order. © 2005 Elsevier Ltd. All rights reserved

Patterns in reduction or cessation of drinking in Australia (2001-2013) and motivation for change

Aims: This paper examines: 1) change over time (2001-2013) in recently reducing or ceasing drinking in the Australian population, and 2) the reasons given for reducing or ceasing drinking in the most recent survey (2013); stratified by sex and age group. Methods: Data are from five waves of the National Drug Strategy Household Survey (N=119,397). Logistic regression models with interaction terms were used to identify a shift in sex or age over time in predicting reduction or cessation of drinking, and to predict motivations for reducing or ceasing drinking by sex and age. Results: Reports of recently reducing the quantity or frequency of drinking increased from 2001 to 2007, and remained stable between 2007 and 2013. There was a steady increase in the number of Australians reporting recently ceasing drinking from 2001 to 2013, with a significant effect for age (younger groups more likely than older groups to cease drinking in the past two waves). Reasons for reducing or ceasing drinking varied by age, with older people more likely to report health reasons, and younger people more likely to report lifestyle reasons or enjoyment. Conclusion: Increases over time in reports of reduction or cessation of drinking due to health, lifestyle, social and enjoyment reasons, suggests that the social position of alcohol in Australia may be shifting, particularly among young people

Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages

Long INterspersed Elements (LINE-1s or L1s) are abundant non-LTR retrotransposons in mammalian genomes that are capable of insertional mutagenesis. They have been associated with target site deletions upon insertion in cell culture studies of retrotransposition. Here, we report 50 deletion events in the human and chimpanzee genomes directly linked to the insertion of L1 elements, resulting in the loss of ∼18 kb of sequence from the human genome and ∼15 kb from the chimpanzee genome. Our data suggest that during the primate radiation, L1 insertions may have deleted up to 7.5 Mb of target genomic sequences. While the results of our in vivo analysis differ from those of previous cell culture assays of L1 insertion-mediated deletions in terms of the size and rate of sequence deletion, evolutionary factors can reconcile the differences. We report a pattern of genomic deletion sizes similar to those created during the retrotransposition of Alu elements. Our study provides support for the existence of different mechanisms for small and large L1-mediated deletions, and we present a model for the correlation of L1 element size and the corresponding deletion size. In addition, we show that internal rearrangements can modify L1 structure during retrotransposition events associated with large deletions

Emergence of Epizootic Ulcerative Syndrome in Native Fish of the Murray-Darling River System, Australia: Hosts, Distribution and Possible Vectors

Epizootic ulcerative syndrome (EUS) is a fish disease of international significance and reportable to the Office International des Epizootics. In June 2010, bony herring Nematalosa erebi, golden perch Macquaria ambigua, Murray cod Maccullochella peelii and spangled perch Leiopotherapon unicolor with severe ulcers were sampled from the Murray-Darling River System (MDRS) between Bourke and Brewarrina, New South Wales Australia. Histopathology and polymerase chain reaction identified the fungus-like oomycete Aphanomyces invadans, the causative agent of EUS. Apart from one previous record in N. erebi, EUS has been recorded in the wild only from coastal drainages in Australia. This study is the first published account of A. invadans in the wild fish populations of the MDRS, and is the first confirmed record of EUS in M. ambigua, M. peelii and L. unicolor. Ulcerated carp Cyprinus carpio collected at the time of the same epizootic were not found to be infected by EUS, supporting previous accounts of resistance against the disease by this species. The lack of previous clinical evidence, the large number of new hosts (n = 3), the geographic extent (200 km) of this epizootic, the severity of ulceration and apparent high pathogenicity suggest a relatively recent invasion by A. invadans. The epizootic and associated environmental factors are documented and discussed within the context of possible vectors for its entry into the MDRS and recommendations regarding continued surveillance, research and biosecurity are made

Human genomic deletions mediated by recombination between Alu elements

Recombination between Alu elements results in genomic deletions associated with many human genetic disorders. Here, we compare the reference human and chimpanzee genomes to determine the magnitude of this recombination process in the human lineage since the human-chimpanzee divergence ∼6 million years ago. Combining computational data mining and wet-bench experimental verification, we identified 492 human-specific deletions (for a total of ∼400 kb) attributable to this process, a significant component of the insertion/deletion spectrum of the human genome. The majority of the deletions (295 of 492) coincide with known or predicted genes (including 3 that deleted functional exons, as compared with orthologous chimpanzee genes), which implicates this process in creating a substantial portion of the genomic differences between humans and chimpanzees. Overall, we found that Alu recombination-mediated genomic deletion has had a much higher impact than was inferred from previously identified isolated events and that it continues to contribute to the dynamic nature of the human genome. © 2006 by The American Society of Human Genetics. All rights reserved

Where do high‐risk drinking occasions occur more often? A cross‐sectional, cross‐country study

Introduction The current paper examines the proportion of drinking occasions and total alcohol consumed that takes place at off-premise locations. Comparisons are made between high-income countries: Australia, New Zealand, England and Scotland, and across drinker-types: high-risk and lower-risk. Methods Data were taken from the International Alcohol Control study in Australia (N = 1789), New Zealand (N = 1979), England (N = 2844) and Scotland (N = 1864). The cross-national survey measures location and beverage-specific alcohol consumption. The number of drinking occasions and mean consumption across on- and off-premise locations and the proportion of drinking occasions that high- and lower-risk drinkers had at on- and off-premise locations was estimated for each country. Results The majority of drinking occasions among high-risk drinkers occurred at off-premise locations across all four countries; Australia 80.1%, New Zealand 72.0%, England 61.7% and Scotland 60.7%. High-risk drinkers in Australia had significantly larger proportions of drinking occasions occurring at off-premise locations compared to England and Scotland. Across all countries, high-risk drinkers and lower-risk drinkers consumed significantly larger quantities of alcohol per occasion at off-premise locations compared to on-premises locations. Finally, the majority of total alcohol consumed occurred at off-premise locations across all countries for high- and lower-risk drinkers. Discussion and Conclusions As the accessibility to alcohol outside of licensed premises continues to increase, particularly with the expansion of home delivery services, it is important to be mindful of the high proportion of heavy drinking occasions that occur off-premise

Evaluasi Penerapan Petunjuk Budidaya yang Baik (Better Management Practices, Bmp) pada Tambak Udang Tradisional di Kabupaten Pangkajene Kepulauan

Kegiatan penelitian ini bertujuan untuk menilai peningkatan produktivitas dan dampak dari pelaksanaan budidaya udang tradisional yang menerapkan BMP. Lokasi penelitian di Desa Gentung, Labakkang Kecamatan, Pangkajene Kepulauan Kabupaten. Empat tambak udang yang dipilih untuk wilayah uji coba, dua kolam yang menerapkan BMP dan dua kontrol lainnya. Pelaksanaan kegiatan yang dilakukan di 3 siklus tanaman, seperti review penelitian yang berlaku atau penelitian tindakan, maka pada setiap siklus membuat sejumlah perbaikan. Data yang dikumpulkan meliputi: produktivitas pertanian (produksi biomassa dan tingkat kelangsungan hidup) dan tingkat partisipasi masyarakat. Selanjutnya, data dianalisis dengan statistik deskriptif dan SPSS-16 Uji T Indepenedent terus. Berdasarkan hasil membuktikan bahwa penerapan kegiatan BMP di tambak udang tradisional telah mampu meningkatkan produktivitas tambak dengan rata-rata produksi udang di BMP tambak 185,18 kg ha-1 dan kontrol 61,53 kg ha-1, sedangkan rata-rata tingkat kelangsungan hidup yang 38,60% untuk BMP kolam dan 12,99% untuk kontrol. Hasil uji Independent T yang diperoleh menunjukkan bahwa secara signifikan BMP kolam dan kontrol berbeda. Sementara dampak dari implementasi BMP mulai muncul dalam siklus panen kedua dengan 7 peternakan yang mengikuti BMP (kategori dasar BMP), dan yang ketiga tanaman siklus peningkatan menjadi 13 pengikut BMP kolam. Hal ini membuktikan bahwa petani mulai antusias untuk mengadopsi dan menerapkan prinsip-prinsip BMP. Tapi masih perlu beberapa perbaikan untuk mendapatkan hasil yang maksimal, selain mendapatkan dampak yang lebih luas pada daerah, teknik perbaikan yang diperlukan terintegrasi dalam pola cluster atau overlay. Kata kunci: Biosekuriti, WSSV gratis, implementasi BMP, kualitas lingkungan.This research activity aims to assess the improvement of productivity and impact of the implementation of traditional shrimp aquaculture that applying BMP. The research location in the Village of Gentung, Labakkang Sub-District, Pangkajene Kepulauan District. Four shrimp ponds selected for the trial area, two ponds that applying BMP and the other two controls. Implementation of the activities carried out in 3 cycles of crop, as is the review of applicable research or action research, then in each cycle made a number of improvements. Data collected included: farm productivity (biomass production and survival rate) and the level of community participation. Furthermore, the data were analyzed with descriptive statistics and SPSS-16 Test T Indepenedent continued. Based on the results proved that the application of BMP activity in traditional shrimp farms have been able to increase the productivity of ponds with an average production of shrimp in BMP ponds 185.18 kg ha-1 and the control of 61.53 kg ha-1, while the average of survival rate are 38.60% for BMP pond and 12.99% for controls. The results of Independent T test that be obtained showing that significantly BMP pond and control is different. While the impact of BMP implementation began to emerge in the second crop cycle with 7 farms that follow BMPs (category of basis BMP), and the third crop cycle increase become 13 follower BMP pond. It is proving that farmers began enthusiastically to adopt and implement the principles of BMP. But it still needs some improvement to get the maximum results, in addition to getting a wider impact on a region, the necessary repair techniques integrated in a cluster pattern or overlay.Keywords : Biosecurity, free WSSV, BMP implementation, environmental quality

Comprehensive analysis of Alu-associated diversity on the human sex chromosomes

A comprehensive analysis of the human sex chromosomes was undertaken to assess Alu-associated human genomic diversity and to identify novel Alu insertion polymorphisms for the study of human evolution. Three hundred forty-five recently integrated Alu elements from eight different Alu subfamilies were identified on the X and Y chromosomes, 225 of which were selected and analyzed by polymerase chain reaction (PCR). From a total of 225 elements analyzed, 16 were found to be polymorphic on the X chromosome and one on the Y chromosome. In line with previous research using other classes of genetic markers, our results indicate reduced Alu-associated insertion polymorphism on the human sex chromosomes, presumably reflective of the reduced recombination rates and lower effective population sizes on the sex chromosomes. The Alu insertion polymorphisms identified in this study should prove useful for the study of human population genetics. © 2003 Elsevier B.V. All rights reserved

DNA Methylation Signatures within the Human Brain

DNA methylation is a heritable modification of genomic DNA central to development, imprinting, transcriptional regulation, chromatin structure, and overall genomic stability. Aberrant DNA methylation of individual genes is a hallmark of cancer and has been shown to play an important role in neurological disorders such as Rett syndrome. Here, we asked whether normal DNA methylation might distinguish individual brain regions. We determined the quantitative DNA methylation levels of 1,505 CpG sites representing 807 genes with diverse functions, including proliferation and differentiation, previously shown to be implicated in human cancer. We initially analyzed 76 brain samples representing cerebral cortex (n=35), cerebellum (n=34), and pons (n=7), along with liver samples (n=3) from 43 individuals. Unsupervised hierarchical analysis showed clustering of 33 of 35 cerebra distinct from the clustering of 33 of 34 cerebella, 7 of 7 pons, and all 3 livers. By use of comparative marker selection and permutation testing, 156 loci representing 118 genes showed statistically significant differences—a ⩾17% absolute change in DNA methylation (P<.004)—among brain regions. These results were validated for all six genes tested in a replicate set of 57 samples. Our data suggest that DNA methylation signatures distinguish brain regions and may help account for region-specific functional specialization