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Assembly of large, high G+C bacterial DNA fragments in yeast.
The ability to assemble large pieces of prokaryotic DNA by yeast recombination has great application in synthetic biology, but cloning large pieces of high G+C prokaryotic DNA in yeast can be challenging. Additional considerations in cloning large pieces of high G+C DNA in yeast may be related to toxic genes, to the size of the DNA, or to the absence of yeast origins of replication within the sequence. As an example of our ability to clone high G+C DNA in yeast, we chose to work with...
Scientists map how iron, a critical mineral for survival, is processed by algae, a cornerstone of the ocean food web
(La Jolla, California)—March 18, 2021—Scientists from the J. Craig Venter Institute (JCVI), Harvard University, and Scripps Institution of Oceanography (SIO) have made significant strides in understanding how iron is processed beneath the cell surface in Phaeodactylum tricornutum, a model marine diatom, publishing their results today in the journal eLife. Diatoms are among the most abundant type of algae found in oceans worldwide contributing up to 40 percent of the 45 to 50 billion...
Environmental genome shotgun sequencing of the Sargasso Sea.
We have applied "whole-genome shotgun sequencing" to microbial populations collected en masse on tangential flow and impact filters from seawater samples collected from the Sargasso Sea near Bermuda. A total of 1.045 billion base pairs of nonredundant sequence was generated, annotated, and analyzed to elucidate the gene content, diversity, and relative abundance of the organisms within these environmental samples. These data are estimated to derive from at least 1800 genomic species based...
Genes necessary for cell division in modern bacterial cells identified
(La Jolla, California)—March 29, 2021—Scientists from the J. Craig Venter Institute (JCVI), Massachusetts Institute of Technology (MIT), and National Institute of Standards and Technology (NIST) have identified 5 genes of previously unknown function which are used in cell division by nearly all modern bacterial species. Identifying these genes is an extension of decades of synthetic biology advances at JCVI, expanding on our understanding of the first principles of life. JCVI...
Direct transfer of a Mycoplasma mycoides genome to yeast is enhanced by removal of the mycoides glycerol uptake factor gene glpF.
We previously discovered that intact bacterial chromosomes can be directly transferred to yeast host cell where they can propagate as centromeric plasmids by fusing bacterial cells with Saccharomyces cerevisiae spheroplasts. Inside the host any desired number of genetic changes can be introduced into the yeast centromeric plasmid to produce designer genomes that can be brought to life using a genome transplantation protocol. Earlier research demonstrated that the removal of...
Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima.
The 1,860,725-base-pair genome of Thermotoga maritima MSB8 contains 1,877 predicted coding regions, 1,014 (54%) of which have functional assignments and 863 (46%) of which are of unknown function. Genome analysis reveals numerous pathways involved in degradation of sugars and plant polysaccharides, and 108 genes that have orthologues only in the genomes of other thermophilic Eubacteria and Archaea. Of the Eubacteria sequenced to date, T. maritima has the highest percentage (24%) of genes...
Profound Perturbation of the Metabolome in Obesity Is Associated with Health Risk.
Obesity is a heterogeneous phenotype that is crudely measured by body mass index (BMI). There is a need for a more precise yet portable method of phenotyping and categorizing risk in large numbers of people with obesity to advance clinical care and drug development. Here, we used non-targeted metabolomics and whole-genome sequencing to identify metabolic and genetic signatures of obesity. We find that obesity results in profound perturbation of the metabolome; nearly a third of the assayed...
Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14.
The mosquito-borne malaria parasite Plasmodium falciparum kills an estimated 0.7-2.7 million people every year, primarily children in sub-Saharan Africa. Without effective interventions, a variety of factors-including the spread of parasites resistant to antimalarial drugs and the increasing insecticide resistance of mosquitoes-may cause the number of malaria cases to double over the next two decades. To stimulate basic research and facilitate the development of new drugs and vaccines, the...
A robust ambient temperature collection and stabilization strategy: Enabling worldwide functional studies of the human microbiome.
As reports on possible associations between microbes and the host increase in number, more meaningful interpretations of this information require an ability to compare data sets across studies. This is dependent upon standardization of workflows to ensure comparability both within and between studies. Here we propose the standard use of an alternate collection and stabilization method that would facilitate such comparisons. The DNA Genotek OMNIgene∙Gut Stool Microbiome Kit was compared to...
Interplay between the human gut microbiome and host metabolism.
The human gut is inhabited by a complex and metabolically active microbial ecosystem. While many studies focused on the effect of individual microbial taxa on human health, their overall metabolic potential has been under-explored. Using whole-metagenome shotgun sequencing data in 1,004 twins, we first observed that unrelated subjects share, on average, almost double the number of metabolic pathways (82%) than species (43%). Then, using 673 blood and 713 faecal metabolites, we found...