An Unproven Theorem

Custom gene editing rewrites zebrafish DNA Artificial-enzyme method could make model organisms more useful in study of diseases. Nicky Guttridge 23 September 2012 Article tools print email rights & permissions share/bookmark The zebrafish is a major player in the study of vertebrate biology and human disease. Its transparent, externally fertilized eggs, short reproductive cycle and fast growth mean that its embryonic development can be studied closely while the animal is alive, and the fish is a useful model for studying gene behaviour and function. Now, researchers led by Stephen Ekker, a molecular biologist at the Mayo Clinic in Rochester, Minnesota, have for the first time made custom changes to parts of the zebrafish ( Danio rerio ) genome, using artificial enzymes to cut portions of DNA out of targeted positions in a gene sequence, and replace them with synthetic DNA. The work is published today in Nature 1 . Zebrafish are common model organ...

In massive genome analysis ENCODE data suggests 'gene' redefinition Most   people understand genes to  be   specific  segments of DNA that determine traits or diseases that  are inherited. Textbooks suggest that gene are copied (“transcribed”) into RNA molecules, which are then used as templates for making protein – the highly diverse set of molecules that act as building  blocks and engines of our cells.  The truth, it now appears, is not so simple. As part of a huge collaborative effort called ENCODE (Encyclopedia of DNA Elements),  a research team led by Cold Spring Harbor Laboratory (CSHL) Professor Thomas Gingeras, Ph.D.,  today publishes a genome-wide analysis of RNA messages, called transcripts, produced within human  cells. Their analysis – one component of a massive release of research results by ENCODE teams from 32  institutes in 5 countries, with 30 p...

Junk DNA? What Junk DNA? New data reveals that at least 80% of the human genome encodes elements that have some sort of biological function Far from containing vast amounts of junk DNA between its protein-coding genes, at least 80% of the human genome encodes elements that have some sort of biological function, according to newly released data from the Encyclopedia of DNA Elements (Encode) project, a five-year initiative that aims to delineate all functional elements within human DNA. The massive international project, data from which are published in 30 different papers in  Nature ,  Genome Research ,  Genome Biology , the  Journal of Biological Chemistry ,  Science , and  Cell,  has identified four million gene switches, effectively regulatory regions in the genome where proteins interact with the DNA to control gene expression. Overall, the Encode data define tens of thousands of genes and hundreds of thousands of regu...

Drawing Out Cancer With Biomarkers Zachary Russ There is seemingly no shortage of markers for cancer cells in vitro. Every week brings a new antigen, genotype, morphology, or molecule for identifying some particular cancer cell line or behavior. The tools available for identifying additional markers are also improving. High-throughput assays such as next-generation sequencing, cDNA and protein microarrays, and ELISA/purification-assisted mass spectrometry provide a better look into the molecular world of cancer biology. At the same time, computing resources permit analysis across more data sets (different cell lines) and data types (proteins, mRNA, epigenetic modifications, and genomes), generating even more hits. Cancer Then and Now While the equipment and procedures for identifying these hits was improving, so too did the understanding of cancer behavior. The immense complexity and diversity of cancer was highlighted as more genotypes and phenotypes were found in patient cell...

Ancient Plants May Be Source of New Medicines John Sterling The recent report that a group of Russian researchers was able to regrow a plant that had not seen the light of day for 32,000 years drew great, and well deserved, interest from around the globe. Previously, the oldest similar achievement was the growth of a date palm from a 2,000-year-old seed found in Israel. Working with an arctic flower named Silene stenophylla, the Russians extracted cells from the placenta, an organ found in the fruit that makes plant seeds, and cultured the antediluvian materials until they became entire plants. The plant fruits and seeds had been buried more than 100 feet under the banks of a river in Siberia. The researchers were able to carry out their project because the seeds and fruits had been protected by permafrost. While this scientific advance is immensely noteworthy in its own right, the Russian team’s huge botanical success portends other potential opportunities. For instance, inves...

Click Chemistry for Peptide Synthesis Jyothi Thundimadathil, Ph.D. Click chemistry is a term introduced by Professors Valery V. Fokin and Nobel laureate K.B. Sharpless to describe chemistry tailored to generate substances quickly and reliably by joining small units together similar to the modular strategy adopted by Mother Nature. The term “click chemistry” implies that the reactions are highly efficient, wide in scope, product isolation is easy, stereospecific, simple to perform using inexpensive reagents, and can be conducted in benign solvents such as water. The copper-catalyzed variant of Huisgen azide-alkyne cycloaddition (CuAAC) fits the concept well and is one of the most popular prototype click reactions to date. Click chemistry is finding a number of applications in the areas of drug discovery, bioconjugation, and material science. It has been successfully utilized in the synthesis of peptides, particularly in peptide cyclization and modifi...

Curing Cancer in the Cell Culture Flask Nicholas Miliaras, Ph.D. When President Richard Nixon signed into law the National Cancer Act of 1971, declaring the “War on Cancer,” he began what is now a 40-plus year-long effort to eliminate cancer as a major cause of death. At the time, curing cancer probably seemed a realistic goal for a nation that had just put a man on the moon. Much progress has been made since then in controlling some of the lifestyle and environmental causes of cancer and advances in medical imaging allow for earlier detection of breast and prostate tumors. Thanks to increases in funding for basic cancer research, we also know more about the molecular biology of the cell now than ever before. Despite these advances, cancer mortality has not decreased significantly in the past few decades. In fact, cancer is soon predicted to overtake cardiovascular disease as the number one killer in developed countries (1). So how can we find a path to victory? It may be clos...