CLUSTER MODEL FOR EXTENSIVE GIANT TIGER SHRIMP (Penaeus monodon Fab.) TO PREVENT TRANSMISSION OF WHITE SPOT SYNDROME VIRUS

White spot syndrome virus (WSSV) has become epidemic in Indonesia and affecting shrimp aquaculture interm of its production. White spot syndrome virus is transmitted from one to other ponds, through crustacean, included planktonic copepode as carrier for WSSV and through water from affected shrimp pond. A cluster model, consist of shrimp grow out ponds surrounded by non-shrimp pond as a role of biosecurity has been developed. The model aimed to prevent white spot virus transmission in extensive giant tiger shrimp pond. The study was conducted in two sites at Demak District, Central Java Province. As the treatment, a cluster consist of three shrimp ponds in site I, and two shrimp ponds in site II, each was surrounded by buffer ponds rearing only finfish. As the control, five extensive shrimp grow out ponds in site I and three shrimp grow out ponds in site II, with shrimp pond has neither applied biosecurity nor surrounded by non-shrimp pond as biosecurity as well considered as control ponds. The results found that treatment of cluster shrimp ponds surrounded by non-shrimp ponds could hold shrimp at duration of culture in the grow out pond (DOC) 105.6±4.5 days significantly much longer than that of control that harvested at 60.9±16.0 days due to WSSV outbreak. Survival rate in trial ponds was 77.6±3.6%, significantly higher than that of control at 22.6±15.8%. Shrimp production in treatment ponds has total production of 425.1±146.6 kg/ha significantly higher than that of control that could only produced 54.5±47.6 kg/ha. Implementation of Better Management Practices (BMP) by arranging shrimp ponds in cluster and surrounding by non-shrimp ponds proven effectively prevent WSSV transmission from traditional shrimp ponds in surrounding area

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

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

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

CLUSTER MODEL FOR EXTENSIVE GIANT TIGER SHRIMP (Penaeus monodon Fab.) TO PREVENT TRANSMISSION OF WHITE SPOT SYNDROME VIRUS

White spot syndrome virus (WSSV) has become epidemic in Indonesia and affecting shrimp aquaculture interm of its production. White spot syndrome virus is transmitted from one to other ponds, through crustacean, included planktonic copepode as carrier for WSSV and through water from affected shrimp pond. A cluster model, consist of shrimp grow out ponds surrounded by non-shrimp pond as a role of biosecurity has been developed. The model aimed to prevent white spot virus transmission in extensive giant tiger shrimp pond. The study was conducted in two sites at Demak District, Central Java Province. As the treatment, a cluster consist of three shrimp ponds in site I, and two shrimp ponds in site II, each was surrounded by buffer ponds rearing only finfish. As the control, five extensive shrimp grow out ponds in site I and three shrimp grow out ponds in site II, with shrimp pond has neither applied biosecurity nor surrounded by non-shrimp pond as biosecurity as well considered as control ponds. The results found that treatment of cluster shrimp ponds surrounded by non-shrimp ponds could hold shrimp at duration of culture in the grow out pond (DOC) 105.6±4.5 days significantly much longer than that of control that harvested at 60.9±16.0 days due to WSSV outbreak. Survival rate in trial ponds was 77.6±3.6%, significantly higher than that of control at 22.6±15.8%. Shrimp production in treatment ponds has total production of 425.1±146.6 kg/ha significantly higher than that of control that could only produced 54.5±47.6 kg/ha. Implementation of Better Management Practices (BMP) by arranging shrimp ponds in cluster and surrounding by non-shrimp ponds proven effectively prevent WSSV transmission from traditional shrimp ponds in surrounding area

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

Establishing the baseline level of repetitive element expression in the human cortex

Background: Although nearly half of the human genome is comprised of repetitive sequences, the expression profile of these elements remains largely uncharacterized. Recently developed high throughput sequencing technologies provide us with a powerful new set of tools to study repeat elements. Hence, we performed whole transcriptome sequencing to investigate the expression of repetitive elements in human frontal cortex using postmortem tissue obtained from the Stanley Medical Research Institute. Results: We found a significant amount of reads from the human frontal cortex originate from repeat elements. We also noticed that Alu elements were expressed at levels higher than expected by random or background transcription. In contrast, L1 elements were expressed at lower than expected amounts. Conclusions: Repetitive elements are expressed abundantly in the human brain. This expression pattern appears to be element specific and can not be explained by random or background transcription. These results demonstrate that our knowledge about repetitive elements is far from complete. Further characterization is required to determine the mechanism, the control, and the effects of repeat element expression