Category Archives: Genome

The genome of the cell line, which originated from a deadly cervical tumor taken from a patient named Henrietta Lacks, is riddled with errors, raising questions about its continued use in research

Flickr/GE Healthcare

The research worlds most famous human cell has had its genome decoded, and its a mess. German researchers this week report the genome sequence of the HeLa cell line, which originates from a deadly cervical tumor taken from a patient named Henrietta Lacks.

Established after Lacks died in 1951, HeLa cells were the first human cells to grow well in the laboratory. The cells have contributed to more than 60,000 research papers, the development of a polio vaccine in the 1950s and, most recently, an international effort to characterize the genome, known as ENCODE.

Previous work showed that HeLa cells, like many tumors, have bizarre, error-filled genomes, with one or more extra copies of many chromosomes. To get a closer look at these alterations, a team led by Lars Steinmetz, a geneticist at the European Molecular Biology Laboratory in Heidelberg, Germany, sequenced the popular 'Kyoto' version of the cell line and compared the sequence with that of a reference human genome. The team's results are published in G3.

Steinmetzs team confirmed that HeLa cells contain one extra version of most chromosomes, with up to five copies of some. Many genes were duplicated even more extensively, with four, five or six copies sometimes present, instead of the usual two. Furthermore, large segments of chromosome 11 and several other chromosomes were reshuffled like a deck of cards, drastically altering the arrangement of the genes.

Without the genome sequence of Lacks healthy cells or that of her original tumor, it is difficult to trace the origin of these alterations. Steinmetz points out that other cervical tumors have massive rearrangements on chromosome 11, so the changes in the HeLa cell may have contributed to Lacks tumor.

Potential uses Having been replicating in labs around the world for six decades, HeLa cells have also accrued errors not present in the original tumor DNA. Moreover, not all HeLa cells are identical, and Steinmetz says that it would be interesting to chart the cells evolution.

Whatever their origin, the genetic changes raise questions over the widespread use of HeLa cells as models for human cell biology, Steinmetz says. For instance, his team found that around 2000 genes are expressed at levels higher than those of normal human tissues because of the duplications. Alternative cell lines, such as induced pluripotent stem cells generated from patient skin cells, offer a more accurate window on human biology, he says.

Mathew Garnett, a cancer biologist at the Wellcome Trust Sanger Institute near Cambridge, UK, says that HeLa cells could prove useful for studying aspects of the biology of cervical tumors, such as their response to cancer drugs. In recent years, the genomes of many cervical tumors have been sequenced, and so it should be possible to see how these compare with the HeLa genome.

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Famous "HeLa" Human Cell Line Gets Its DNA Sequenced

Craig Venter, who managed to make science both lucrative and glamorous with his pioneering approach to gene sequencing and synthetic biology, is taking on a new venture: aging.

He has joined forces with the founder of the X Prize and an expert in cell therapy to launch on Tuesday a new company called Human Longevity Inc. The man who once took off on his personal yacht to sample all the microscopic life in the seas plans to leverage some of the most fashionable new scientific approaches to figure out what makes us sick and old.

The San Diego-based company will tackle aging using gene sequencing; stem cell approaches; the collection of bacteria and other life forms that live in and on us called the microbiome; and the metabolome, which includes the byproducts of life called metabolites.

Theyll start out with what they are calling the largest human sequencing operation in the world.

We are building a lab to a scale never attempted (before), Venter told NBC News.

Venter first shot to fame when he raced with government scientists to finish the first map of all human DNA, called the human genome. Venter, himself a former government scientist, annoyed his former colleagues with a brash new approach to gene sequencing that was much faster but far less accurate, in their opinion.

We are building a lab to a scale never attempted (before).

The two teams joined forces, the partnership worked, and they finished their first draft in 2001.

Venter later parted ways with the company he founded to sequence genes and went on to tackle other challenges, including a venture that included weeks on his personal yacht sequencing the DNA of microbial life in the ocean.

He also took a crack at creating artificial life, making a synthetic bacterium of sorts, and making more controversy with that.

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Genome Pioneer, X Prize Founder Tackle Aging

Validating, improving and applying genome assemblies using NGS
4th International Workshop on Next Generation Genomics and Integrated Breeding for Crop Improvement February 19-21, 2014 Title: Validating, improving and app...

By: KSIconnect

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Validating, improving and applying genome assemblies using NGS - Video

Cheng Qin

Zunla-1 peppers grow in a cultivated field.

Scientists have sequenced the genome of the pepper plant, revealing the genes responsible for pepper's spiciness.

The new genome, detailed Monday in the Proceedings of the National Academy of Sciences, could pave the way for even more mouth-numbingly hot peppers.

"The findings will provide foundation for further developing molecular makers and [incite] research on related pepper agronomy traits, and help breeders accelerate the research of new breeds by molecular biology techniques," said study co-author Cheng Qin, a researcher at Sichuan Agricultural University in China.

Peppers were first domesticated in South America as far back as 8,000 years ago. The pepper, which is part of a family that includes the tomato and the potato, spread from the New World after Columbus arrived in the Americas.

Chili peppers now come in a dizzying array of colors and flavors. In recent years, pepper aficionados have used old-fashioned breeding to amp up the heat-producing compound, called capsaicin, and create ever more insanely hot peppers. [Tip of the Tongue: The 7 (Other) Flavors We Can Taste]

Qin and his colleagues sequenced the genome of a pepper cultivated at their institution, known as Zunla-1, along with its wild counterpart. They found that the pepper diverged from tomatoes and potatoes about 36 million years ago.

Researchers also scanned the genomes of 18 cultivated peppers to compare differences between wild and cultivated varieties. They identified genes associated with how long the seeds stay dormant, resistance to pests and longer shelf life. They also found that a key gene can be duplicated a different number of times to produce more or less capsaicin.

Qin said the findings suggest that spicier peppers can be created either by identifying peppers with the right genes and cross-breeding them, or by genetically engineering the peppers to express more copies of the heat-producing genes.

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That's Hot! Genome Could Lead to Even Spicier Peppers

Genome GPS 2.0
Genome GPS is the comprehensive secondary analysis pipeline for next-generation sequencing data at Mayo Clinic. Secondary analysis entails three steps: align...

By: Mayo Bioinformatics

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Genome GPS 2.0 - Video

Ganam Patri to Genome Patri by Anu Acharya, CEO, mapmygenome.in
In this video, Anu Acharya talks about #39;Research as a service #39;.

By: yourstorytv

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Ensembl: Intro to genome browsing
This video provides a basic introduction to genome browsers, with a focus on data and analysis available in Ensembl. A brief overview of genome sequencing, i...

By: EBImedia

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Ensembl: Intro to genome browsing - Video

Genome sequence and QTL identification for major agronomic traits of mungbean (Vigna radiata)
4th International Workshop on Next Generation Genomics and Integrated Breeding for Crop Improvement February 19-21, 2014 Title: Genome sequence and QTL ident...

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Genome sequence and QTL identification for major agronomic traits of mungbean (Vigna radiata) - Video

1217) Pandora Radio Station - Genome Music Project
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1217) Pandora Radio Station - Genome Music Project - Video

Detection of the Genome and Transcripts of a Persistent DNA Virus in Neuronal Tissues by Fluores...
To watch this video on jove.com, click here: http://www.jove.com/video/51091?utm_source=youtube We established a fluorescent in situ hybridization protocol f...

By: JoVEJournalVideo

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Detection of the Genome and Transcripts of a Persistent DNA Virus in Neuronal Tissues by Fluores... - Video