Ancient human genome sequence of an extinct Palaeo-Eskimo.

We report here the genome sequence of an ancient human. Obtained from approximately 4,000-year-old permafrost-preserved hair, the genome represents a male individual from the first known culture to settle in Greenland. Sequenced to an average depth of 20x, we recover 79% of the diploid genome, an amount close to the practical limit of current sequencing technologies.

Bis(N'-benzoyl-pyridine-4-carbohydrazide)(1,10-phenanthroline)copper(II) dinitrate.

In the title complex, [Cu(C(13)H(11)N(3)O(2))(2)(C(12)H(8)N(2))](NO(3))(2), the Cu(II )atom (site symmetry 2) is coordinated by four N atoms from one 1,10-phenanthroline and two hydrazine ligands, respectively. The hydrazine ligands coordinate to the Cu(II)atom by a pyridine N atom. These four atoms form a slightly distorted square-planar N(4) donor set.

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.

Building the sequence map of the human pan-genome.

Here we integrate the de novo assembly of an Asian and an African genome with the NCBI reference human genome, as a step toward constructing the human pan-genome. We identified approximately 5 Mb of novel sequences not present in the reference genome in each of these assemblies. Most novel sequences are individual or population specific, as revealed by their comparison to all available human DNA sequence and by PCR validation using the human genome diversity cell line panel.

3D genome tuner: compare multiple circular genomes in a 3D context.

Circular genomes, being the largest proportion of sequenced genomes, play an important role in genome analysis. However, traditional 2D circular map only provides an overview and annotations of genome but does not offer feature-based comparison. For remedying these shortcomings, we developed 3D Genome Tuner, a hybrid of circular map and comparative map tools.

The genome of the cucumber, Cucumis sativus L.

Cucumber is an economically important crop as well as a model system for sex determination studies and plant vascular biology. Here we report the draft genome sequence of Cucumis sativus var. sativus L.

Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx).

A single-base pair resolution silkworm genetic variation map was constructed from 40 domesticated and wild silkworms, each sequenced to approximately threefold coverage, representing 99.88% of the genome. We identified ~16 million single-nucleotide polymorphisms, many indels, and structural variations.

DNA copy number aberrations in breast cancer by array comparative genomic hybridization.

Array comparative genomic hybridization (CGH) has been popularly used for analyzing DNA copy number variations in diseases like cancer. In this study, we investigated 82 sporadic samples from 49 breast cancer patients using 1-Mb resolution bacterial artificial chromosome CGH arrays. A number of highly frequent genomic aberrations were discovered, which may act as "drivers" of tumor progression.

Preparing a re-sequencing DNA library of 2 cancer candidate genes using the ligation-by-amplification protocol by two PCR reactions.

To meet the needs of large-scale genomic/genetic studies, the next-generation massively parallelized sequencing technologies provide high throughput, low cost and low labor-intensive sequencing service, with subsequent bioinformatic software and laboratory methods developed to expand their applications in various types of research. PCR-based genomic/genetic studies, which have significant usage in association studies like cancer research, haven't benefited much from those next-generation sequencing technologies, because the shortgun re-sequencing strategy used by such sequencing machines as the Illumina/Solexa Genome Analyzer may not be applied to direct re-sequencing of short-length target regions like those in PCR-based genomic/genetic studies. Although several methods have been proposed to solve this problem, including microarray-based genomic selections and selector-based technologies, they require advanced equipment and procedures which limit their applications in many laboratories.

An improved method for genome wide DNA methylation profiling correlated to transcription and genomic instability in two breast cancer cell lines.

Background: DNA methylation is a widely studied epigenetic mechanism known to correlate with gene repression and genomic stability. Development of sensitive methods for global detection of DNA methylation events is of particular importance.

Results: We here describe a technique, called modified methylation-specific digital karyotyping (MMSDK) based on methylation-specific digital karyotyping (MSDK) with a novel sequencing approach.

Alterations of NR2B and PSD-95 expression in hippocampus of kainic acid-exposed rats with behavioural deficits.

Temporal lobe epilepsy (TLE), characterized by spontaneous recurrent seizure (SRS), is associated with behavioural problems, but the underlying molecular mechanisms have not been clearly identified. In the present study, kainic acid (KA) was administered systemically in adult male Wistar rats to induce SRS. Behavioural performance analyses at 2, 4, and 6 weeks post-status epilepticus (post-SE) showed spatial learning memory deficit, anxiety and increased locomotor activity in rats with long-term SRS compared with rats without SRS after normal saline (NS) or KA-valproate (KA-VPA) treatment.

Elevated NaCl concentration improves cryotolerance and developmental competence of porcine oocytes.

High hydrostatic pressure has been reported to improve the fertilizing or developmental ability of mammalian spermatozoa, oocytes and embryos. This study investigated the effect of another stress, temporarily increased NaCl concentration, on cryotolerance and developmental competence of porcine oocytes. In Experiment 1, survival rates were compared after 1 h exposure to seven elevated NaCl concentrations and 1 h recovery time.

Osmotic stress induced by sodium chloride, sucrose or trehalose improves cryotolerance and developmental competence of porcine oocytes.

Exposure of porcine oocytes to increased concentrations of NaCl prior to manipulation has been reported not only to increase cryotolerance after vitrification, but also to improve developmental competence after somatic cell nuclear transfer (SCNT). In the present study we compared the effects of NaCl with those of concentrated solutions of two non-permeable osmotic agents, namely sucrose and trehalose, on the cryotolerance and developmental competence of porcine oocytes. In Experiment 1, porcine in vitro-matured cumulus-oocyte complexes (COCs; n = 1200) were exposed to 588 mOsmol NaCl, sucrose or trehalose solutions for 1 h, allowed to recover for a further 1 h, vitrified, warmed and subjected to parthenogenetic activation.

Effects of shear and charge on the microphase formation of P123 polymer in the SBA-15 synthesis investigated by mesoscale simulations.

Mesoscale simulation was performed to investigate the dynamical structural behavior of the pluronic P123 block copolymer in the synthesis of mesoporous SBA-15. Shear is introduced to represent stirring in the actual experiment, and a weak charge is included to simulate the acidic conditions in the synthesis. Under shear, with the increase in weak charge in the PEO [poly(ethylene oxide)] block, the template forms more ordered hexagonal phases, and the pore sizes of the cylindrical hydrophobic PPO [poly(propylene oxide)] blocks decrease.

Consistent deregulation of gene expression between human and murine MLL rearrangement leukemias.

Important biological and pathologic properties are often conserved across species. Although several mouse leukemia models have been well established, the genes deregulated in both human and murine leukemia cells have not been studied systematically. We performed a serial analysis of gene expression in both human and murine MLL-ELL or MLL-ENL leukemia cells and identified 88 genes that seemed to be significantly deregulated in both types of leukemia cells, including 57 genes not reported previously as being deregulated in MLL-associated leukemias.

Hexaaqua-cobalt(II) 5,5'-(propane-1,3-diyldithio)bis-(1H-tetra-zole-1-acetate).

The asymmetric unit of the title complex, [Co(H(2)O)(6)](C(9)H(10)N(8)O(4)S(2)), contains one-half of a [Co(H(2)O)(6)](2+) cation and one-half of a 5,5'-(propane-1,3-diyldithio)bis-(1H-tetra-zole-1-acetate) (battp(2-)) anion. The Co(II) center is coordinated by six H(2)O mol-ecules in a distorted octa-hedral coordination environment. In the crystal structure, intra- and inter-molecular O-H⋯O and O-H⋯N hydrogen bonds link the cations and anions into a three-dimensional network.

{N,N-Dimethyl-N'-[phen-yl(2-pyrid-yl)methyl-ene]ethane-1,2-diamine-κN,N',N''}dithio-cyanato-κN,κS-copper(II).

In the title complex, [Cu(NCS)(2)(C(16)H(19)N(3))], the Cu(II) atom is coordinated by a total of four N atoms; three from one tridentate Schiff base ligand and one from one of the NCS(-) ions. The S atom from the other NCS(-) ion completes the distorted square-pyramidal coordination.

Aqua[N-(2,5-dihydroxybenzyl)imino-diacetato]copper(II).

The title complex, [Cu(C(11)H(11)NO(6))(H(2)O)], contains a Cu(II) atom in a distorted square-pyramidal geometry. The metal centre is coordinated in the basal sites by one water mol-ecule and two carboxyl-ate O atoms and one N atom of the tetra-dentate ligand [Cu-O range, 1.9376 (11)-1.

Polymorphisms of DNA repair genes: ADPRT, XRCC1, and XPD and cancer risk in genetic epidemiology.

Many studies have suggested that adenosine diphosphate ribosyl transferase (ADPRT), X-ray repair cross-complementing 1 (XRCC1), and xeroderma pigmentosum complementary group D (XPD) are three major DNA base excision repair (BER) genes and that they act interactively in stimulating and executing BER processes. Polymorphisms of these genes may influence the rate of gene transcription, the stability of the messenger RNA, or the quantity and activity of the resulting protein. Thus, the susceptibility or severity of several disorders is influenced by possession of specific alleles of polymorphic genes.

The YH database: the first Asian diploid genome database.

The YH database is a server that allows the user to easily browse and download data from the first Asian diploid genome. The aim of this platform is to facilitate the study of this Asian genome and to enable improved organization and presentation large-scale personal genome data. Powered by GBrowse, we illustrate here the genome sequences, SNPs, and sequencing reads in the MapView.

The novel antimicrobial peptides from skin of Chinese broad-folded frog, Hylarana latouchii (Anura:Ranidae).

Broad-folded frogs (Hylarana latouchii), one member of 12 species of the genus Hylarana in the Chinese frog fauna, are widely distributed in the South of China. In this study, we purified and characterized three antimicrobial peptides from the skin secretion of H. latouchii.

Omics-based profiling of carcinoma of the breast and matched regional lymph node metastasis.

Axillary lymph node (ALN) status is currently used as an important clinical indicator of breast cancer prognosis. However, the molecular mechanisms underlying lymph node metastasis are poorly understood and the relationship between ALN metastasis and the primary tumor remains unclear. In an effort to reveal structural changes in the genome and related protein responses that may drive regional metastatic progression we have analyzed matched pairs of primary breast tumors and ALN metastases both at the genomic and proteomic levels using comparative genomic hybridization (CGH) array, quantitative high-resolution 2-D PAGE in combination with MS, and immunohistochemistry (IHC).

The diploid genome sequence of an Asian individual.

Here we present the first diploid genome sequence of an Asian individual. The genome was sequenced to 36-fold average coverage using massively parallel sequencing technology. We aligned the short reads onto the NCBI human reference genome to 99.

Linkage disequilibrium mapping of a breast cancer susceptibility locus near RAI/PPP1R13L/iASPP.

Background: Previous results have suggested an association of the region of 19q13.3 with several forms of cancer. In the present study, we investigated 27 public markers within a previously identified 69 kb stretch of chromosome 19q for association with breast cancer by using linkage disequilibrium mapping.

High hydrostatic pressure treatment of porcine oocytes before handmade cloning improves developmental competence and cryosurvival.

An innovative technique, called the high hydrostatic pressure (HHP) treatment, has been recently reported to improve the cryosurvival of gametes or embryos in certain mammalian species. The aim of the present study was to investigate the in vitro and in vivo developmental competence and cryotolerance of embryos produced by handmade cloning (HMC) after pressure treatment of recipient oocytes. In vitro-matured porcine oocytes were treated with a sublethal hydrostatic pressure of 20 MPa (200 times greater than atmospheric pressure) and recovered for either 1 or 2 h (HHP1 and HHP2 groups, respectively) before they were used for HMC.