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Scientists develop method to efficiently construct single-copy human artificial chromosomes (HACs)
Philadelphia, PA—March 21, 2024—Scientists from the University of Pennsylvania (Penn), J. Craig Venter Institute (JCVI), and the University of Edinburgh have developed a method to efficiently construct single-copy human artificial chromosomes (HACs). The ability to control the construction of HACs gives synthetic biologists a powerful tool for delivering DNA directly to the nucleus of a human cell. In the near term, synthetic biologists, spanning disciplines, will use HACs to advance...
Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1.
The complete genome sequence of the radiation-resistant bacterium Deinococcus radiodurans R1 is composed of two chromosomes (2,648,638 and 412,348 base pairs), a megaplasmid (177,466 base pairs), and a small plasmid (45,704 base pairs), yielding a total genome of 3,284, 156 base pairs. Multiple components distributed on the chromosomes and megaplasmid that contribute to the ability of D. radiodurans to survive under conditions of starvation, oxidative stress, and high amounts of DNA damage...
Frequency and distribution of DNA uptake signal sequences in the Haemophilus influenzae Rd genome.
The naturally transformable, Gram-negative bacterium Haemophilus influenzae Rd preferentially takes up DNA of its own species by recognizing a 9-base pair sequence, 5'-AAGTGCGGT, carried in multiple copies in its chromosome. With the availability of the complete genome sequence, 1465 copies of the 9-base pair uptake site have been identified. Alignment of these sites unexpectedly reveals an extended consensus region of 29 base pairs containing the core 9-base pair region and two downstream...
Fast and accurate HLA typing from short-read next-generation sequence data with xHLA.
The HLA gene complex on human chromosome 6 is one of the most polymorphic regions in the human genome and contributes in large part to the diversity of the immune system. Accurate typing of HLA genes with short-read sequencing data has historically been difficult due to the sequence similarity between the polymorphic alleles. Here, we introduce an algorithm, xHLA, that iteratively refines the mapping results at the amino acid level to achieve 99-100% four-digit typing accuracy for both...
A whole-genome assembly of Drosophila.
We report on the quality of a whole-genome assembly of Drosophila melanogaster and the nature of the computer algorithms that accomplished it. Three independent external data sources essentially agree with and support the assembly's sequence and ordering of contigs across the euchromatic portion of the genome. In addition, there are isolated contigs that we believe represent nonrepetitive pockets within the heterochromatin of the centromeres. Comparison with a previously sequenced 2.9-...
Functional characterization of 3D protein structures informed by human genetic diversity.
Sequence variation data of the human proteome can be used to analyze 3D protein structures to derive functional insights. We used genetic variant data from nearly 140,000 individuals to analyze 3D positional conservation in 4,715 proteins and 3,951 homology models using 860,292 missense and 465,886 synonymous variants. Sixty percent of protein structures harbor at least one intolerant 3D site as defined by significant depletion of observed over expected missense variation. Structural...
One step engineering of the small-subunit ribosomal RNA using CRISPR/Cas9.
Bacteria are indispensable for the study of fundamental molecular biology processes due to their relatively simple gene and genome architecture. The ability to engineer bacterial chromosomes is quintessential for understanding gene functions. Here we demonstrate the engineering of the small-ribosomal subunit (16S) RNA of Mycoplasma mycoides, by combining the CRISPR/Cas9 system and the yeast recombination machinery. We cloned the entire genome of M. mycoides in yeast and used constitutively...
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...