Impact of DNA-binding position variants on yeast gene expression

Transcription factors (TFs) regulate gene expression by binding to specific binding sites (TFBSs) in gene promoters. TFBS motifs may contain one or more variable positions. Although the prevailing assumption is that nucleotide variants at such positions are functionally equivalent, there is increasing evidence that such variants play a role in regulation of gene expression. In this article, we propose a method for studying the relationship between the expression of target genes and nucleotide variants in TFBS motifs at a genome-wide scale in Saccharomyces cerevisiae, especially the combinatorial effects of variants at two positions. Our analysis shows that nucleotide variations in more than one-third of variable positions and in 20% of dependent position pairs are highly correlated to gene expression. We define such positions as ‘functional’. However, some positions are only functional as dependent pairs, but not individually. In addition, a significant proportion of the functional positions have been well conserved across all yeast-related species studied. We also find that some positions require the presence of co-occurring TFs, while others maintain their functionality in the absence of a co-occurring TF. Our analysis supports the importance of nucleotide variants at variable positions of TFBSs in gene regulation

Consistency of in vitro drug sensitivities within pharmacological classes

Multiple comparative analyses between the common drugs and cell lines of the Genomics of Drug Sensitivity in Cancer (GDSC) and the Cancer Therapeutics Response Portal (CTRP) have previously shown low consistency between the in vitro phenotypic measures of a drug in one study with the other. While several potential sources of inconsistency have been tested, the similar targets of tested compounds has yet to be tested as a contributing factor of discrepancy. This analysis includes two methods of reclassifying drugs into classes based on their targets to identify the truer set of consistent cell lines, showing an increased correlation between the two pharmacogenomic studies

An opportunistic survey reveals an unexpected coronavirus diversity hotspot in North America

In summer 2020, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was detected on mink farms in Utah. An interagency One Health response was initiated to assess the extent of the outbreak and included sampling animals from on or near affected mink farms and testing them for SARS-CoV-2 and non-SARS coronaviruses. Among the 365 animals sampled, including domestic cats, mink, rodents, raccoons, and skunks, 261 (72%) of the animals harbored at least one coronavirus. Among the samples that could be further characterized, 127 alphacoronaviruses and 88 betacoronaviruses (including 74 detections of SARS-CoV-2 in mink) were identified. Moreover, at least 10% (n = 27) of the coronavirus-positive animals were found to be co-infected with more than one coronavirus. Our findings indicate an unexpectedly high prevalence of coronavirus among the domestic and wild free-roaming animals tested on mink farms. These results raise the possibility that mink farms could be potential hot spots for future trans-species viral spillover and the emergence of new pandemic coronaviruses

Why rare targets are slow: Evidence that the target probability effect has an attentional locus

10.3758/s13414-013-0434-0Attention, Perception, and Psychophysics753388-39

The TESS-HERMES survey Data Release 1: high-resolution spectroscopy of the TESS southern continuous viewing zone

The Transiting Exoplanet Survey Satellite (TESS) will provide high precisiontime-series photometry for millions of stars with at least a half-hour cadence.Of particular interest are the circular regions of 12-degree radius centeredaround the ecliptic poles that will be observed continuously for a full year.Spectroscopic stellar parameters are desirable to characterize and selectsuitable targets for TESS, whether they are focused on exploring exoplanets,stellar astrophysics, or Galactic archaeology. Here, we present spectroscopicstellar parameters ($T_{\rm eff}$, $\log g$, [Fe/H], $v \sin i$, v_{\rmmicro}) for about 16,000 dwarf and subgiant stars in TESS' southern continuousviewing zone. For almost all the stars, we also present Bayesian estimates ofstellar properties including distance, extinction, mass, radius, and age usingtheoretical isochrones. Stellar surface gravity and radius are made availablefor an additional set of roughly 8,500 red giants. All our target stars are inthe range $10<V<13.1$. Among them, we identify and list 227 stars belonging tothe Large Magellanic Cloud. The data were taken using the the High Efficiencyand Resolution Multi-Element Spectrograph (HERMES, R $\sim 28,000$) at theAnglo-Australian Telescope as part of the TESS-HERMES survey. Comparing ourresults with the TESS Input Catalog (TIC) shows that the TIC is generallyefficient in separating dwarfs and giants, but it has flagged more than hundredcool dwarfs ($T_{\rm eff}< 4800$ K) as giants, which ought to be high-prioritytargets for the exoplanet search. The catalog can be accessed viahttp://www.physics.usyd.edu.au/tess-hermes/