Fosmid library end sequencing reveals a rarely known genome structure of marine shrimp Penaeus monodon

<p>Abstract</p> <p>Background</p> <p>The black tiger shrimp (<it>Penaeus monodon</it>) is one of the most important aquaculture species in the world, representing the crustacean lineage which possesses the greatest species diversity among marine invertebrates. Yet, we barely know anything about their genomic structure. To understand the organization and evolution of the <it>P. monodon </it>genome, a fosmid library consisting of 288,000 colonies and was constructed, equivalent to 5.3-fold coverage of the 2.17 Gb genome. Approximately 11.1 Mb of fosmid end sequences (FESs) from 20,926 non-redundant reads representing 0.45% of the <it>P. monodon </it>genome were obtained for repetitive and protein-coding sequence analyses.</p> <p>Results</p> <p>We found that microsatellite sequences were highly abundant in the <it>P. monodon </it>genome, comprising 8.3% of the total length. The density and the average length of microsatellites were evidently higher in comparison to those of other taxa. AT-rich microsatellite motifs, especially poly (AT) and poly (AAT), were the most abundant. High abundance of microsatellite sequences were also found in the transcribed regions. Furthermore, <it>via </it>self-BlastN analysis we identified 103 novel repetitive element families which were categorized into four groups, <it>i.e</it>., 33 WSSV-like repeats, 14 retrotransposons, 5 gene-like repeats, and 51 unannotated repeats. Overall, various types of repeats comprise 51.18% of the <it>P. monodon </it>genome in length. Approximately 7.4% of the FESs contained protein-coding sequences, and the Inhibitor of Apoptosis Protein (IAP) gene and the Innexin 3 gene homologues appear to be present in high abundance in the <it>P. monodon </it>genome.</p> <p>Conclusions</p> <p>The redundancy of various repeat types in the <it>P. monodon </it>genome illustrates its highly repetitive nature. In particular, long and dense microsatellite sequences as well as abundant WSSV-like sequences highlight the uniqueness of genome organization of penaeid shrimp from those of other taxa. These results provide substantial improvement to our current knowledge not only for shrimp but also for marine crustaceans of large genome size.</p

Joint analysis of three genome-wide association studies of esophageal squamous cell carcinoma in Chinese populations

We conducted a joint (pooled) analysis of three genome-wide association studies (GWAS) 1-3 of esophageal squamous cell carcinoma (ESCC) in ethnic Chinese (5,337 ESCC cases and 5,787 controls) with 9,654 ESCC cases and 10,058 controls for follow-up. In a logistic regression model adjusted for age, sex, study, and two eigenvectors, two new loci achieved genome-wide significance, marked by rs7447927 at 5q31.2 (per-allele odds ratio (OR) = 0.85, 95% CI 0.82-0.88; P=7.72x10−20) and rs1642764 at 17p13.1 (per-allele OR= 0.88, 95% CI 0.85-0.91; P=3.10x10−13). rs7447927 is a synonymous single nucleotide polymorphism (SNP) in TMEM173 and rs1642764 is an intronic SNP in ATP1B2, near TP53. Furthermore, a locus in the HLA class II region at 6p21.32 (rs35597309) achieved genome-wide significance in the two populations at highest risk for ESSC (OR=1.33, 95% CI 1.22-1.46; P=1.99x10−10). Our joint analysis identified new ESCC susceptibility loci overall as well as a new locus unique to the ESCC high risk Taihang Mountain region

Potential of Core-Collapse Supernova Neutrino Detection at JUNO

JUNO is an underground neutrino observatory under construction in Jiangmen, China. It uses 20kton liquid scintillator as target, which enables it to detect supernova burst neutrinos of a large statistics for the next galactic core-collapse supernova (CCSN) and also pre-supernova neutrinos from the nearby CCSN progenitors. All flavors of supernova burst neutrinos can be detected by JUNO via several interaction channels, including inverse beta decay, elastic scattering on electron and proton, interactions on C12 nuclei, etc. This retains the possibility for JUNO to reconstruct the energy spectra of supernova burst neutrinos of all flavors. The real time monitoring systems based on FPGA and DAQ are under development in JUNO, which allow prompt alert and trigger-less data acquisition of CCSN events. The alert performances of both monitoring systems have been thoroughly studied using simulations. Moreover, once a CCSN is tagged, the system can give fast characterizations, such as directionality and light curve

Detection of the Diffuse Supernova Neutrino Background with JUNO

As an underground multi-purpose neutrino detector with 20 kton liquid scintillator, Jiangmen Underground Neutrino Observatory (JUNO) is competitive with and complementary to the water-Cherenkov detectors on the search for the diffuse supernova neutrino background (DSNB). Typical supernova models predict 2-4 events per year within the optimal observation window in the JUNO detector. The dominant background is from the neutral-current (NC) interaction of atmospheric neutrinos with 12C nuclei, which surpasses the DSNB by more than one order of magnitude. We evaluated the systematic uncertainty of NC background from the spread of a variety of data-driven models and further developed a method to determine NC background within 15\% with {\it{in}} {\it{situ}} measurements after ten years of running. Besides, the NC-like backgrounds can be effectively suppressed by the intrinsic pulse-shape discrimination (PSD) capabilities of liquid scintillators. In this talk, I will present in detail the improvements on NC background uncertainty evaluation, PSD discriminator development, and finally, the potential of DSNB sensitivity in JUNO

Real-time Monitoring for the Next Core-Collapse Supernova in JUNO

Core-collapse supernova (CCSN) is one of the most energetic astrophysical events in the Universe. The early and prompt detection of neutrinos before (pre-SN) and during the SN burst is a unique opportunity to realize the multi-messenger observation of the CCSN events. In this work, we describe the monitoring concept and present the sensitivity of the system to the pre-SN and SN neutrinos at the Jiangmen Underground Neutrino Observatory (JUNO), which is a 20 kton liquid scintillator detector under construction in South China. The real-time monitoring system is designed with both the prompt monitors on the electronic board and online monitors at the data acquisition stage, in order to ensure both the alert speed and alert coverage of progenitor stars. By assuming a false alert rate of 1 per year, this monitoring system can be sensitive to the pre-SN neutrinos up to the distance of about 1.6 (0.9) kpc and SN neutrinos up to about 370 (360) kpc for a progenitor mass of 30$M_{\odot}$ for the case of normal (inverted) mass ordering. The pointing ability of the CCSN is evaluated by using the accumulated event anisotropy of the inverse beta decay interactions from pre-SN or SN neutrinos, which, along with the early alert, can play important roles for the followup multi-messenger observations of the next Galactic or nearby extragalactic CCSN.Comment: 24 pages, 9 figure

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Genetic analysis of tiger shrimp genome: stock identification and construction of genetic linkage map

草蝦(Penaeus monodon)是全球養殖產業中最重要的海產物種之一，也是具有生物多樣性研究價值的海洋生物。因此，本研究利用分子遺傳標記去研究草蝦基因組的特性，包括兩個大主題: (1)草蝦地理族群的遺傳多樣性與種源分析。(2)草蝦遺傳圖譜的建構。論文共分為四章，第一章包括研究主題之文獻回顧，與研究方法的論述，並論文的研究方向。論文的第二章，為利用分子遺傳標記進行野生草蝦族群遺傳多樣性的研究成果，此部分已發表於Animal Genetics期刊中。論文的第三章則為草蝦遺傳圖譜建構之研究成果。論文的第四章則為本研究的總結論與未來的展望。文的第一個主題-草蝦地理族群遺傳與種源分析的研究(論文第二章)，是使用來自於8個不同地理區域，一共355隻野生草蝦作為實驗樣本，以自行開發的10個微隨體標記及粒線體控制區(mtCR)序列，來分析草蝦族群與個體的遺傳分化情形。結果顯示，不論是使用微隨體標記或粒線體控制區(mtCR)序列進行地理親緣關係分析，均得到相同的結論，即西印度洋(馬達加斯加及肯亞)與西太平洋(台灣、越南、菲律賓、澳洲及泰國東岸泰國灣)的草蝦族群在遺傳上已有明顯分隔。此項研究結果對於草蝦養殖產業的種源鑑定應大有助益。文的第二個主題-草蝦遺傳圖譜的建構(論文第三章)，是利用多型性微隨體標記，輔以多型性AFLP標記，以一個isofemale F1家族(內含280個子代個體)為樣本，共使用148個草蝦微隨體標記以及134個AFLP標記，進行基因型分析及連鎖分析，建構出草蝦雌性及雄性遺傳圖譜。雌性遺傳圖譜含128個微隨體標記及55個AFLP標記，並組成了46個連鎖群，而連鎖群的總遺傳長度是2248.9 cM；雄性遺傳圖譜含126個微隨體標記及79個AFLP標記，並組成了43個連鎖群，而連鎖群的總遺傳長度是2286.8 cM。這兩個遺傳圖譜共同擁有106個標記，並座落於36個同源連鎖群(homologous linkage group)。此遺傳圖譜將能應用於數量性狀基因座(quantitative trait loci; QTL]的定位與分子育種選殖。The black tiger shrimp (Penaeus monodon) is an ecologically and economically important marine crustacean and is widely distributed in the Indo-Pacific region. Here I investigated the genome of P. monodon in two aspects, i.e., (1) the genetic diversity of wild populations, (2) the construction of a genetic linkage map. here are 4 chapters in this thesis. Chapter 1 contained the paper review of the research topics, the research methods, and the research aspects. In chapter 2 the genetic diversity and the stock identification of wild P. monodon populations in Indo-Pacific region was revealed, and this part of work has been published in Animal Genetics. In chapter 3 the constructed linkage maps of the tiger shrimp based on microsatellites and AFLP markers were presented. Chapter 4, the final chapter, was concerned with the research summary and future perspectives. n order to investigate the genetic diversity of wild P. monodon populations, tiger shrimps (n = 355) from eight geographical regions were genotyped using of 10 microsatellite markers. A high level of genetic variability (average HO: 0.638-0.743) and significant genetic differentiation (Pairwise FST and RST values) among the populations were revealed. The non-metric multidimensional scaling analysis indicated the presence of three geographic groups in the Indo-Pacific region, i.e., the African populations, a population from western Thailand, and the remaining populations as a whole. In addition, the phylogenetic analysis using the sequences from the mitochondrial control region (mtCR) revealed that the West Indian Ocean populations were genetically differentiated from the West Pacific populations, consistent with the result obtained from the microsatellite data. n order to acquire more genetic information of tiger shrimp genome, the linkage maps of male and female tiger shrimp (P. monodon) were constructed based on microsatellite and amplified fragment length polymorphism (AFLP) markers. 621 microsatellite and 1151 AFLP markers were tested for polymorphism. Consequently, 372 (167 microsatellite and 203 AFLP markers) were used for genotyping an isofemale F1 family comprising two parents and 280 progeny. From the linkage analysis (LOD score= 4.5), a male and a female linkage map consisting of 43 and 46 linkage groups were constructed, respectively. The male map consisted of 126 microsatellite markers and 79 AFLP markers, whereas the female map consisted of 128 microsatellite markers and 55 AFLP markers. These two maps shared 36 homologous linkage groups.目 錄文口試委員審定書………………………………………i謝…………………………………………………………ii文摘要……………………………………………………iii 文摘要……………………………………………………iv一章 文獻回顧、研究原理與方法………………………1.1 DNA遺傳標記在養殖業上的應用………………………1.1.1 DNA遺傳標記記………………………………………1.1.2 DNA遺傳標記在養殖業上的應用……………………3.2以DNA遺傳標記建立草蝦遺傳圖譜之方法論……………5.2.1 STR基因型分析………………………………………5.2.1.1標記多型性測試……………………………………5.2.1.2 標記分離率偏離測試………………………………7.2.2 AFLP基因型分析………………………………………7.2.2.1 AFLP基因型判讀方式.……………………………7.2.2.2 標記分離率偏離測試.……………………………7.2.3 AFLP基因型屬於相似長度卻無關聯的問題與改進…8 1.2.4 草蝦遺傳連鎖圖譜的建立………9.2.4.1 草蝦遺傳圖譜的建立所需的F1樣本數……………9 1.2.4.2 標記連鎖及關聯性分析方法……………13.2.4.3 雙基因座分析………………………………………13.2.4.4 連鎖標記之分群……………………………………14.2.4.5 各連鎖群內基因座排列順序分析…………………14.2.4.6 Mapping function的使用…………………………15.2.4.7 JoinMap&reg; 4軟體的使用……………………………15.2.5 計算遺傳圖譜的總長度及包含範圍…………………16 .2.6 草蝦遺傳圖譜的重組研究……………………………16.3 研究方向…………………………………………………16.4 論文結構…………………………………………………19二章 印度洋及太平洋地區草蝦族群的遺傳分化………21三章 草蝦之遺傳圖譜……………………………………33四章 研究總結與未來展望………………………………54考文獻………………………………………………………55錄一、草蝦遺傳圖譜中部分STR基因型原始資料…………63錄二、草蝦遺傳圖譜中部分AFLP基因型原始資料………64一、AFLP實驗流程圖。……………………………………2二、在不同的樣本數及預期分離率的條件下，挑選多型性基因座所獲得的統計power……………………………………………6 圖三、重組率與所需F1子代樣本數的關係圖 A1A2B1B2 X A1A2B1B2)……………………………………11四、重組率與所需F1子代樣本數的關係圖 (A1A2B1B2 X A3A4B3B4)……………………………12一、比較幾種製備DNA遺傳標記的DNA遺傳技術…………2二、本實驗中AFLP應用於建立遺傳圖譜的基因型組合…8三、設親代雙方在此兩基因座的基因型為AaBb X AaBb， 則F1子代的基因型、出現頻率的觀察值及期望值之列表 …………………………………………………………10四、過去草蝦遺傳圖譜研究的成果………………………1

Foldable-circuit-enabled miniaturized multifunctional sensor for smart digital dust

Smart dust, which refers to miniaturized, multifunctional sensor motes, would open up data acquisition opportunities for Internet of Things (IoT) and Environmental protection applications. However, critical obstacles remain challenging in the integration of high-density sensors, further miniaturization of device platforms, and reduction of cost. Here, we demonstrate the concept of smart digital dust to address these problems, the results of which combine the benefit of (i) maturity of complementary metal-oxide semiconductor (CMOS) processing approaches and (ii) unique form factors of emerging flexible electronics. As a prototype for smart digital dust, we present a millimeter-scale multifunctional optoelectronic sensor platform consisting of high-performance optoelectronic sensor cores and commercially available integrated-circuit components. The smart material-assisted optoelectronic sensing mechanism enables real-time, high-sensitivity hydrogen, temperature, and relative humidity (RH) sensing based on a single chip with ultralow power consumption. Such a microsystem presented here introduces a viable solution to the multifunctional sensing need of IoT and could serve as a building block for the rapidly evolving future framework of smart dust