To Seq, or Not to Seq

Seq—shorthand for “sequence”— has become a more recognizable term thanks to a novel and provocative genomics initiative called the BabySeq Project. The project, officially launched in May 2015, was designed to explore the impact of whole-exome sequencing (WES) on newborn infants and their families. A randomized, controlled trial to sequence healthy and sick infants and then provide sequencing information, it is the first of its kind. Those infants randomized to receive WES undergo genetic sequencing of all protein-coding genes and analysis of about 1,700 genes implicated in childhood health, along with 18 years of follow up genetic counseling.29813751-nov-2-blog-post-nicole-600x470-web

The project is directed by Robert C. Green, geneticist and physician at Brigham and Women’s Hospital, Harvard Medical School and the Broad Institute, and Alan H. Beggs of Boston Children’s Hospital and Harvard Medical School. Funding, totaling $25 million, comes from the National Institute of Child Health and Development and the National Human Genome Research Institute. Continue reading

Christensenellaceae—A Natural Way to Stay Thin?

microbiome studies show how bacterial colonists influence healthA study published in the Nov 6 issue of Cell outlined results suggesting that an obscure family of bacteria colonizing the human gut may be inherited and may also have a direct influence on body weight. The paper is the first to identify such an association and to link a particular microbial colonist with lower BMI. Continue reading

Learning About the $1,000 Genome

Personalized MedicineAt the recent International Symposium on Human Identification, Kevin Davies, the keynote speaker and author of The $1,000 Genome, entertained attendees with a history of human genome sequencing efforts and discussed ways in which the resulting information has infiltrated our everyday lives. Obviously, there is enough material on the subject to fill a book, but I will describe just a few of the high points of his talk here.

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Thermometers in Wine, the Edge of the Solar System and Redefining Junk DNA: Science News of the Week

Science keeps on producing new discoveries every week. It can be difficult to keep up with the latest news even when it is part of your job. There were a few science stories that caught my attention this week so I thought I would share them.

Galilean Thermometer Not So Galilean” was a surprising news item. I love my Galileo thermometer received as a Christmas gift several years ago. However, as Peter Loyson’s commentary in the Journal of Chemical Education points out, Galileo Galilei invented a thermometer but it was based on air. The one attributed to him was created by a Florentine group of academics and technicians founded by the Grand Duke Ferdinand II and his brother Leopoldo. And those first thermometers? Used wine to float the little glass balls.

Voyager 1, which just turned 35 on September 5, and Voyager 2 are pushing at the boundaries of our solar system as well as our understanding of space. In fact, NASA is saying that Voyager 1 was expected to pass through the heliopause, the edge that defines the end of the influence of our sun and the beginning of true interstellar space, but recent data indicated that this edge is further than we imagined. In fact, it could lie seven years beyond Voyager 1’s current position, and the battery in each Voyager estimated to deplete between 2020 and 2025. Still, these two small satellites have boldly gone beyond their initial mission to explore the far reaches of space and are still sending data back to our humble Earth.

Sequencing the human genome was an accomplishment but just this week, the scientists involved in the Encyclopedia of DNA Elements (ENCODE) project published 30 papers in Nature and other journals (summarized here). With the complete human sequence in hand, most scientists thought the items of interest in the genome were the genes, the coding regions. But as researchers started to dig into the data and use it for their experiments, it became evident understanding the genome was more complex than the sequence. The ENCODE project is a consortium of scientists that wanted to understand the entire genome and ended up finding that the 2% that encodes proteins is controlled by those sequences between genes nicknamed “junk DNA”. It is an incredible effort that has implications across aging and cancer, and ENCODE claims it can assign functions to 80% of the genome.

Sequencing the Black Death is a Window to the Past

After writing my review of the Proceedings of the National Academy of Sciences USA article “Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death”, I vaguely wondered if the authors could have sequenced more than a single 10kb plasmid. If the single-copy chromosomal DNA was too scarce, maybe one of the other Yersina pestis plasmids that may exist at a higher copy number (e.g., pMT1) might be sequenced. Continue reading

Giant Panda Genome: Answers About the Carnivore that Eats Plants

They are the cuddly, roly-poly giants that are the face of the wildlife conservation movement. Unfortunately, giant pandas have earned the honor. They are one of the most endangered species on earth. They are also something of an enigma. They are carnivores who subsist almost entirely on a diet of plants. They have opposable thumb-like appendages on their front paws. They look like a bear that wants to be a raccoon (or a raccoon that wants to be a bear?). Their unique characteristics kept scientists debating their classification for years. Did they belong with the bears (Ursidae), raccoons (Procyonidae) or did they belong in a family of their own?

Molecular studies seem to have resolved the classification debate; giant pandas (Ailuropoda melanoleuca) are most closely related to bears. Their ancestors split from the ursid lineage just before the radiation that led to modern bears, and thus have their own subfamily Ailuropodinae. But what of the other puzzling characteristics? Why on earth do they eat bamboo?

In a paper published in the January 21, 2010 issue of Nature, we begin to find answers. The authors have generated and assembled a draft sequence of the giant panda genome (Li, R. et al.;1). Continue reading