Sequencing, annotation and comparative analysis of nine BACs of giant panda (Ailuropoda melanoleuca)

A 10-fold BAC library for giant panda was constructed and nine BACs were selected to generate finish sequences. These BACs could be used as a validation resource for the de novo assembly accuracy of the whole genome shotgun sequencing reads of giant panda newly generated by the Illumina GA sequencing technology. Complete sanger sequencing, assembly, annotation and comparative analysis were carried out on the selected BACs of a joint length 878 kb. Homologue search and de novo prediction methods were used to annotate genes and repeats. Twelve protein coding genes were predicted, seven of which could be functionally annotated. The seven genes have an average gene size of about 41 kb, an average coding size of about 1.2 kb and an average exon number of 6 per gene. Besides, seven tRNA genes were found. About 27 percent of the BAC sequence is composed of repeats. A phylogenetic tree was constructed using neighbor-join algorithm across five species, including giant panda, human, dog, cat and mouse, which reconfirms dog as the most related species to giant panda. Our results provide detailed sequence and structure information for new genes and repeats of giant panda, which will be helpful for further studies on the giant panda.

The sequence and de novo assembly of the giant panda genome

Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes.

Impacts of the Wenchuan Earthquake on the Giant Panda Nature Reserves in China

Ministry of Science and Technology of China [2008BAK47B02, 2008BAC44B04, 2008BAK50B06, 2008BAC43B01, 2006BAC08B06]

cDNA cloning and overexpression of acidic ribosomal phosphoprotein P1 gene (RPLP1) from the Giant Panda

RPLP1 is one of acidic ribosomal phosphoproteins encoded by RPLP1 gene, which plays an important role in the elongation step of protein synthesis. The cDNA of RPLP1 was cloned successfully for the first time from the Giant Panda (Ailuropoda melanoleuca) using RT-PCR technology, which was also sequenced, analyzed preliminarily and expressed in E. coli. The cDNA fragment cloned is 449bp in size, containing an open reading frame of 344bp encoding 114 amino acids. Alignment analysis indicated that the nucleotide sequence and the deduced amino acid sequence are highly conserved to other five species studied, including Homo sapiens, Mus musculus, Rattus norvegicus, Bos Taurus and Sus scrofa. The homologies for nucleotide sequences of Giant Panda PPLP1 to that of these species are 92.4%, 89.8%, 89.0%, 91.3% and 87.5%, while the homologies for amino acid sequences are 96.5%, 94.7%, 95.6%, 96.5% and 88.6%. Topology prediction showed there are three Casein kinase II phosphorylation sites and two N-myristoylation sites in the RPLP1 protein of the Giant Panda (Ailuropoda melanoleuca). The RPLP1 gene was overexpressed in E. coli and the result indicated that RPLP1 fusion with the N-terminally His-tagged form gave rise to the accumulation of an expected 18kDa polypeptide, which was in accordance with the predicted protein and could also be used to purify the protein and study its function.

图像图形文字混合处理系统PANDA的设计与实现

本文描述了图像、图形、文字混合处理系统PANDA的设计与实现技术。详细讨论了PANDA系统的数据结构组织方法,其中包括多文件、多窗口处理的结构设计以及动态的数据结构设计,同时给出了PANDA系统在其实现过程中所使用的一些关键处理技术。

Schooner Ranger document

A page of entries detailing the financial history of the Schooner Ranger, a Great Lakes cargo ship, from 1810-1815. The ship sustained damage in 1811 on its journey from Detroit to Black Rock, in which 3 people drowned. The ship was subsequently “destroyed by the enemy in January 1813”. In August 1815, the ship’s account was settled. The settlement acknowledged that the ship was “taken by the U.S. Navy Officers for the use of the Government”, and is signed by Porter, Barton & Co., and George Kibbe.

Schooner Ranger document, 1810-1815

Partial transcription: Buffalo, August 15, 1815 This day settled all accounts between… respecting the purchase and sailing of the Schooner Ranger until she was laid up in the fare of 1811. For the value of the…of the said Schooner destroyed by the enemy in January 1813 and the rigging & c taken by the U.S. Navy Officers for the use of the Government a [Joint][appreciation] is to be made... Government for our mutual benefit. Porter & Barton for [the firm] of Porter Barton & Co. George Kibbe

Shipping form for 2 bundles placed aboard the schooner the Britannia to be delivered to Henry Nelles

Shipping form for 2 bundles placed aboard the schooner the Britannia to be delivered to Henry Nelles. This form has a note written on the second page to Mr. Henry Nelles from Mr. Henderson. This item is badly stained and torn but most of the text is legible, June 6, 1828.

Panda.

El pequeño panda está teniendo un día ajetreado en el bosque: juega, come y corre a través de los árboles. Cuando el día termina, es hora de que vaya hasta su madre para dormir. Las imágenes son brillantes, con unas pocas frases rítmicas en cada página, adecuado para primeros lectores.

Feasibility study of performing high precision gamma spectroscopy of lambda lambda hypernuclei in the PANDA experiment

Hypernuclear physics is currently attracting renewed interest, due tornthe important role of hypernuclei spectroscopy rn(hyperon-hyperon and hyperon-nucleon interactions) rnas a unique toolrnto describe the baryon-baryon interactions in a unified way and to rnunderstand the origin of their short-range.rnrnHypernuclear research will be one of the main topics addressed by the {sc PANDA} experimentrnat the planned Facility for Antiproton and Ion Research {sc FAIR}.rnThanks to the use of stored $overline{p}$ beams, copiousrnproduction of double $Lambda$ hypernuclei is expected at thern{sc PANDA} experiment, which will enable high precision $gamma$rnspectroscopy of such nuclei for the first time.rnAt {sc PANDA} excited states of $Xi^-$ hypernuclei will be usedrnas a basis for the formation of double $Lambda$ hypernuclei.rnFor their detection, a devoted hypernuclear detector setup is planned. This setup consists ofrna primary nuclear target for the production of $Xi^{-}+overline{Xi}$ pairs, a secondary active targetrnfor the hypernuclei formation and the identification of associated decay products and a germanium array detector to perform $gamma$ spectroscopy.rnrnIn the present work, the feasibility of performing high precision $gamma$rnspectroscopy of double $Lambda$ hypernuclei at the {sc PANDA} experiment has been studiedrnby means of a Monte Carlo simulation. For this issue, the designing and simulation of the devoted detector setup as well as of the mechanism to produce double $Lambda$ hypernuclei have been optimizedrntogether with the performance of the whole system. rnIn addition, the production yields of double hypernuclei in excitedrnparticle stable states have been evaluated within a statistical decay model.rnrnA strategy for the unique assignment of various newly observed $gamma$-transitions rnto specific double hypernuclei has been successfully implemented by combining the predicted energy spectra rnof each target with the measurement of two pion momenta from the subsequent weak decays of a double hypernucleus.rn% Indeed, based on these Monte Carlo simulation, the analysis of the statistical decay of $^{13}_{Lambda{}Lambda}$B has been performed. rn% As result, three $gamma$-transitions associated to the double hypernuclei $^{11}_{Lambda{}Lambda}$Bern% and to the single hyperfragments $^{4}_{Lambda}$H and $^{9}_{Lambda}$Be, have been well identified.rnrnFor the background handling a method based on time measurement has also been implemented.rnHowever, the percentage of tagged events related to the production of $Xi^{-}+overline{Xi}$ pairs, variesrnbetween 20% and 30% of the total number of produced events of this type. As a consequence, further considerations have to be made to increase the tagging efficiency by a factor of 2.rnrnThe contribution of the background reactions to the radiation damage on the germanium detectorsrnhas also been studied within the simulation. Additionally, a test to check the degradation of the energyrnresolution of the germanium detectors in the presence of a magnetic field has also been performed.rnNo significant degradation of the energy resolution or in the electronics was observed. A correlationrnbetween rise time and the pulse shape has been used to correct the measured energy. rnrnBased on the present results, one can say that the performance of $gamma$ spectroscopy of double $Lambda$ hypernuclei at the {sc PANDA} experiment seems feasible.rnA further improvement of the statistics is needed for the background rejection studies. Moreover, a more realistic layout of the hypernuclear detectors has been suggested using the results of these studies to accomplish a better balance between the physical and the technical requirements.rn

Feasibility studies of the pp pi 0 e + e - electromagnetic channel at PANDA

Among all possible realizations of quark and antiquark assembly, the nucleon (the proton and the neutron) is the most stable of all hadrons and consequently has been the subject of intensive studies. Mass, shape, radius and more complex representations of its internal structure are measured since several decades using different probes. The proton (spin 1/2) is described by the electric GE and magnetic GM form factors which characterise its internal structure. The simplest way to measure the proton form factors consists in measuring the angular distribution of the electron-proton elastic scattering accessing the so-called Space-Like region where q2 < 0. Using the crossed channel antiproton proton <--> e+e-, one accesses another kinematical region, the so-called Time-Like region where q2 > 0. However, due to the antiproton proton <--> e+e- threshold q2th, only the kinematical domain q2 > q2th > 0 is available. To access the unphysical region, one may use the antiproton proton --> pi0 e+ e- reaction where the pi0 takes away a part of the system energy allowing q2 to be varied between q2th and almost 0. This thesis aims to show the feasibility of such measurements with the PANDA detector which will be installed on the new high intensity antiproton ring at the FAIR facility at Darmstadt. To describe the antiproton proton --> pi0 e+ e- reaction, a Lagrangian based approach is developed. The 5-fold differential cross section is determined and related to linear combinations of hadronic tensors. Under the assumption of one nucleon exchange, the hadronic tensors are expressed in terms of the 2 complex proton electromagnetic form factors. An extraction method which provides an access to the proton electromagnetic form factor ratio R = |GE|/|GM| and for the first time in an unpolarized experiment to the cosine of the phase difference is developed. Such measurements have never been performed in the unphysical region up to now. Extended simulations were performed to show how the ratio R and the cosine can be extracted from the positron angular distribution. Furthermore, a model is developed for the antiproton proton --> pi0 pi+ pi- background reaction considered as the most dangerous one. The background to signal cross section ratio was estimated under different cut combinations of the particle identification information from the different detectors and of the kinematic fits. The background contribution can be reduced to the percent level or even less. The corresponding signal efficiency ranges from a few % to 30%. The precision on the determination of the ratio R and of the cosine is determined using the expected counting rates via Monte Carlo method. A part of this thesis is also dedicated to more technical work with the study of the prototype of the electromagnetic calorimeter and the determination of its resolution.

Feasibility studies for accessing nucleon structure observables with the PANDA experiment at the future FAIR facility

The availability of a high-intensity antiproton beam with momentum up to 15,GeV/c at the future FAIR will open a unique opportunity to investigate wide areas of nuclear physics with the $overline{P}$ANDA (anti{$overline{P}$}roton ANnihilations at DArmstadt) detector. Part of these investigations concern the Electromagnetic Form Factors of the proton in the time-like region and the study of the Transition Distribution Amplitudes, for which feasibility studies have been performed in this Thesis. rnMoreover, simulations to study the efficiency and the energy resolution of the backward endcap of the electromagnetic calorimeter of $overline{P}$ANDA are presented. This detector is crucial especially for the reconstruction of processes like $bar pprightarrow e^+ e^- pi^0$, investigated in this work. Different arrangements of dead material were studied. The results show that both, the efficiency and the energy resolution of the backward endcap of the electromagnetic calorimeter fullfill the requirements for the detection of backward particles, and that this detector is necessary for the reconstruction of the channels of interest. rnrnThe study of the annihilation channel $bar pprightarrow e^+ e^-$ will improve the knowledge of the Electromagnetic Form Factors in the time-like region, and will help to understand their connection with the Electromagnetic Form Factors in the space-like region. In this Thesis the feasibility of a measurement of the $bar pprightarrow e^+ e^-$ cross section with $overline{P}$ANDA is studied using Monte-Carlo simulations. The major background channel $bar pprightarrow pi^+ pi^-$ is taken into account. The results show a $10^9$ background suppression factor, which assure a sufficiently clean signal with less than 0.1% background contamination. The signal can be measured with an efficiency greater than 30% up to $s=14$,(GeV/c)$^2$. The Electromagnetic Form Factors are extracted from the reconstructed signal and corrected angular distribution. Above this $s$ limit, the low cross section will not allow the direct extraction of the Electromagnetic Form Factors. However, the total cross section can still be measured and an extraction of the Electromagnetic Form Factors is possible considering certain assumptions on the ratio between the electric and magnetic contributions.rnrnThe Transition Distribution Amplitudes are new non-perturbative objects describing the transition between a baryon and a meson. They are accessible in hard exclusive processes like $bar pprightarrow e^+ e^- pi^0$. The study of this process with $overline{P}$ANDA will test the Transition Distribution Amplitudes approach. This work includes a feasibility study for measuring this channel with $overline{P}$ANDA. The main background reaction is here $bar pprightarrow pi^+ pi^- pi^0$. A background suppression factor of $10^8$ has been achieved while keeping a signal efficiency above 20%.rnrnrnPart of this work has been published in the European Physics Journal A 44, 373-384 (2010).rn