MOTIVATION A review of the available single nucleotide polymorphism (SNP) calling procedures for Illumina high-throughput sequencing (HTS) platform data reveals that most rely mainly on base-calling and mapping qualities as sources of error when calling SNPs. Thus, errors not involved in base-calling or alignment, such as those in genomic sample preparation, are not accounted for. RESULTS A n...

For species with potential as new crops, rapid improvement may be facilitated by new genomic methods. Apios (Apios americana Medik.), once a staple food source of Native American Indians, produces protein-rich tubers, tolerates a wide range of soils, and symbiotically fixes nitrogen. We report the first high-quality de novo transcriptome assembly, an expression atlas, and a set of 58,154 SNP an...

This paper studies markets plagued with asymmetric information on the quality of traded goods. In Akerlof's setting, sellers are better informed than buyers. contrast, we examine cases where buyers sellers. creates an inverse adverse selection problem: market tends to disappear from bottom rather top. contrast traditional model, it is high-value goods (gems) that market, low-value (lemons). We ...

Our aim in this note is to present four remarkable facts about quotient sets. These observations seem to have been overlooked by the MONTHLY, despite its intense coverage of quotient sets over the years. Introduction If A is a subset of the natural numbers N = {1, 2, . . .}, then we let R(A) = {a/a : a, a ∈ A} denote the corresponding quotient set (sometimes called a ratio set). Our aim in this...

As we mentioned in the last lecture, one of the core components of our algorithm for distinct elements problem is a space-efficient construction of 2-wise independent functions. Formally, a k-wise independent hash function f : [m]→ [T ] is a randomized function that provides the guarantee that, for any k distinct elements j1, . . . , jk ∈ [m] and any k possible values t1, . . . , tk ∈ [T ], the...

Recent research into the commercial exploitation of genetically engineered micro-organisms (GEMs) in the environment, for bioremediation and improvement of plant growth and protection, has raised concerns regarding associated potential risks. This in turn has led to legislation regarding environmental release of GEMs such that detailed information on their ecology and environmental impact must ...

The nuclear SMN complex localizes to specific structures called Gems. The loss of Gems is a cellular marker for several neurodegenerative diseases. Here, we identified the U1 snRNP specific protein U1-70K localized to nuclear Gems and showed that U1-70K is necessary for Gem integrity. Further we showed the interaction between U1-70K and the SMN complex is RNA independent and mapped the SMN comp...

In the past few decades, increased awareness of environmental pollution has led to the exploitation of microbial metabolic potential in the construction of several genetically engineered microorganisms (GEMs) for bioremediation purposes. At the same time, environmental concerns and regulatory constraints have limited the in situ application of GEMs, the ultimate objective behind their developme...

The human gut microbiome plays an influential role in maintaining human health, and it is a potential target for prevention and treatment of disease. Genome-scale metabolic models (GEMs) can provide an increased understanding of the mechanisms behind the effects of diet, the genotype-phenotype relationship and microbial robustness. Here we reconstructed GEMs for three key species, (Bacteroides ...

The linker molecule LAT is a critical substrate of the tyrosine kinases activated upon TCR engagement. Phosphorylated LAT binds Grb2, PLC-gamma1, and other signaling molecules. We demonstrate that human LAT is palmitoylated and that palmitoylated LAT predominantly localizes into glycolipid-enriched microdomains (GEMs). Although the LAT transmembrane domain is sufficient for membrane localizatio...