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DNA repeats identify novel virulence genes in Haemophilus influenzae.
The whole genome sequence (1.83 Mbp) of Haemophilus influenzae strain Rd was searched to identify tandem oligonucleotide repeat sequences. Loss or gain of one or more nucleotide repeats through a recombination-independent slippage mechanism is known to mediate phase variation of surface molecules of pathogenic bacteria, including H. influenzae. This facilitates evasion of host defenses and adaptation to the varying microenvironments of the host. We reasoned that iterative nucleotides could...
Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.
Arabidopsis thaliana (Arabidopsis) is unique among plant model organisms in having a small genome (130-140 Mb), excellent physical and genetic maps, and little repetitive DNA. Here we report the sequence of chromosome 2 from the Columbia ecotype in two gap-free assemblies (contigs) of 3.6 and 16 megabases (Mb). The latter represents the longest published stretch of uninterrupted DNA sequence assembled from any organism to date. Chromosome 2 represents 15% of the genome and encodes 4,037...
Scientists Decipher Genetic Code of Malaria Parasite
October 2, 2002 Rockville, MD - In a landmark contribution to the age-old battle against malaria, a consortium of scientists including The Institute for Genomic Research (TIGR) announced today that they have deciphered the complex genetic code of the parasite that causes the deadliest form of the disease. Malaria is one of the world's most devastating infectious diseases, killing more than a million people a year in developing nations. The scientific paper analyzing the genome of that...
Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains.
Virulence and immunity are poorly understood in Mycobacterium tuberculosis. We sequenced the complete genome of the M. tuberculosis clinical strain CDC1551 and performed a whole-genome comparison with the laboratory strain H37Rv in order to identify polymorphic sequences with potential relevance to disease pathogenesis, immunity, and evolution. We found large-sequence and single-nucleotide polymorphisms in numerous genes. Polymorphic loci included a phospholipase C, a membrane lipoprotein,...
Scientist Spotlight: Lauren Oldfield
Since high school, Lauren Oldfield, PhD found that science was her calling. It started with a love of reading encouraged by her mom and grandmother, both avid readers, and weekly trips to the public library. Books by Michael Crichton and Richard Preston were staples in her grandmother’s collection. After devouring “The Hot Zone,” a fictionalized account of an almost outbreak of Ebola in the United States, microbiology and the study of infectious diseases became her passion....
Genome Solver Annotation Workshops
The Human Microbiome Project (HMP) has created a wealth of new questions for scientists. However, the current rate of microbial DNA sequencing far outpaces the ability of experts to analyze the genomes and metagenomes that have resulted from the HMP, creating a need for additional hands and minds to deal with the myriad of questions. This need in turn creates an opportunity for undergraduates to get involved in research on the HMP. Through the National Science Foundation (NSF) TUES...
Sequencing and analysis of globally obtained human parainfluenza viruses 1 and 3 genomes.
Human Parainfluenza viruses (HPIV) type 1 and 3 are important causes of respiratory tract infections in young children globally. HPIV infections do not confer complete protective immunity so reinfections occur throughout life. Since no effective vaccine is available for the two virus subtypes, comprehensive understanding of HPIV-1 and HPIV-3 genetic and epidemic features is important for diagnosis, prevention, and treatment of HPIV-1 and HPIV-3 infections. Relatively few whole genome...
Back To Sampling In The Black Sea and Rough Rough Weather
September 9th 2010 Hello everyone! I know it has been a long time since the last post from Sorcerer II. Let me take the time to explain…………..in early August we sailed to Greece. As I have mentioned in the past we have permits with each country to collect samples, these permits have certain time windows and other country specific stipulations. Once stipulation on the Greek permit was that for each Greek sample collected we must have a Greek collaborator onboard Sorcerer II. One...
10 Days of Italian Sampling Coming to a Close
Tuesday July 20th On July 16th we finished our Straits of Messina sampling and headed into the Ionian and Adriatic Seas. We sailed overnight and collected our Ionian Sea sample, we continued northeast and on July 18th we collected our Adriatic Sea sample. After we collected the Adriatic Sea sample we turned around and headed back to the Straits of Messina to resample the south entrance on July 19th. We proceeded through the straits...
Research Schooner Tara in San Diego Calls for Innovative Citizen Science and Oceanography 2.0
Sampling of ocean life is hindered by the extreme cost, limited logistical flexibility, and high carbon footprint of classical oceanographic research vessels. The Global Ocean Sampling (GOS) expedition aboard the Sorcerer II yacht (2004-2010) paved the way for a new brand of oceanography based on the use of sailing boats to obtain samples suitable for DNA sequencing analyses of plankton. The Tara Oceans Expedition (2009-2013) extended this concept and sampled eco-morpho-genetic data from...