The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

/pdf/initial-sequencing-and-analysis-of-the-human-genome-5dapk1rsx1.pdf

Initial sequencing and analysis of the human genome.

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

http://science.sciencemag.org/content/sci/291/5507/1304.full.pdf

The sequence of the human genome.

Probability Distributions.- Linear Models for Regression.- Linear Models for Classification.- Neural Networks.- Kernel Methods.- Sparse Kernel Machines.- Graphical Models.- Mixture Models and EM.- Approximate Inference.- Sampling Methods.- Continuous Latent Variables.- Sequential Data.- Combining Models.

Pattern Recognition and Machine Learning

As vertebrate genome sequences near completion and research refocuses to their analysis, the issue of effective genome annotation display becomes critical. A mature web tool for rapid and reliable display of any requested portion of the genome at any scale, together with several dozen aligned annotation tracks, is provided at http://genome.ucsc.edu. This browser displays assembly contigs and gaps, mRNA and expressed sequence tag alignments, multiple gene predictions, cross-species homologies, single nucleotide polymorphisms, sequence-tagged sites, radiation hybrid data, transposon repeats, and more as a stack of coregistered tracks. Text and sequence-based searches provide quick and precise access to any region of specific interest. Secondary links from individual features lead to sequence details and supplementary off-site databases. One-half of the annotation tracks are computed at the University of California, Santa Cruz from publicly available sequence data; collaborators worldwide provide the rest. Users can stably add their own custom tracks to the browser for educational or research purposes. The conceptual and technical framework of the browser, its underlying MYSQL database, and overall use are described. The web site currently serves over 50,000 pages per day to over 3000 different users.

/pdf/the-human-genome-browser-at-ucsc-4zclgthyly.pdf

The Human Genome Browser at UCSC

Disclosed are T7 RNA polymerase variants with enhanced transcriptional activity. T7 RNA polymerase variants are known which have the ability to incorporate modified ribonucleotides into growing RNA molecules. However, these variants have relatively low levels of transcriptional activity. Presented herein are mutations that increase the transcriptional activity of the variants with broad substrate range.

T7 rna polymerase variants with expanded substrate range and enhanced transcriptional yield

(2006) Developing RNA Tools for Engineered Regulatory Systems Biotechnology and Genetic Engineering Reviews: Vol 22, No 1, pp 21-44

Developing RNA Tools for Engineered Regulatory Systems

/pdf/www-guide-shopping-for-biotechnology-products-on-the-web-a-5fa7oq1bvu.pdf

WWW Guide: Shopping for Biotechnology Products on the Web: A User's Guide

Proc Amer Assoc Cancer Res, Volume 46, 2005

6183 

PSMA is a transmembrane receptor whose expression increases on prostatic tumor cells during disease progression This protein is also expressed on the endotheluim of tumor vasculature but not normal vasculature Aptamers are small nucleic acids selected to bind proteins such as cell-surface tumor antigens with high affinity and specificity Aptamers have the potential to serve as replacements for cell-targeting antibodies or other cell-targeting ligands We utilized a modified RNA aptamer (designated PSMAA) known to bind the external domain of PSMA with high affinity (previously reported Ki = 2 nM) The 22 kDa PSMAA molecule was conjugated to recombinant gelonin(rGel) toxin using the heterobifunctional cross-linking agent SPDP The PSMAA/rGel conjugate was then purified by ion exchange and gel permeation chromatography The final product was uncontaminated by free aptamer or free rGel and migrated as a single species (∼50 kDa) by SDS-PAGE Analysis of the construct demonstrated that the rGel component was enzymatically active compared to free rGel In addition, the conjugate was found to bind specifically to PSMA-expressing LNCAP cells Cytotoxicity studies of the PSMAA/rGel conjugate demonstrated an IC50 of 32 nM on antigen-positive LNCAP cells compared to an IC50 of 350,000 nM on PC3 cells, which contain much less antigen; a targeting index of approximately 10,000 fold Internalization studies should reveal the details of toxin conjugate entry, and animal model studies are ongoing These data suggest that aptamers can be used to successfully deliver protein molecules such as toxins to tumor cells and may provide a novel approach to development of targeted therapeutic agents The fact that aptamers can be chemically synthesized and thereby site-specifically conjugated makes them especially interesting as targeting ligands The PSMAA-rGel construct may prove useful to target PSMA on prostate cells and on tumor vasculature Research conducted, in part, by the Clayton Foundation for Research

Targeting PSMA on tumor cells using novel aptamer-gelonin conjugates

Embodiments of the disclosure concern methods and compositions related to generation and/or use of proofreading reverse transcriptases, including those that are thermophilic or hyperthermophilic The disclosure encompasses specific recombinant polymerases and their use In some embodiments, the polymerases are utilized for RNA sequencing in the absence of generation of a cDNA intermediate

Andrew D. Ellington

Papers

T7 rna polymerase variants with expanded substrate range and enhanced transcriptional yield

Developing RNA Tools for Engineered Regulatory Systems

WWW Guide: Shopping for Biotechnology Products on the Web: A User's Guide

Targeting PSMA on tumor cells using novel aptamer-gelonin conjugates

Thermostable reverse transcriptase