A direct RT-qPCR approach to test large numbers of individuals for SARS-CoV-2

SARS-CoV-2 causes substantial morbidity and mortality in elderly and immunocompromised individuals, particularly in retirement homes, where transmission from asymptomatic staff and visitors may introduce the infection. Here we present a cheap and fast approach to detect SARSCoV-2 in single or pooled gargle lavages (“mouthwashes”). With this approach, we test all staff at a nursing home daily over a period of three weeks in order to reduce the risk that the infection penetrates the facility. This or similar approaches could be implemented to protect hospitals, nursing homes and other institutions in this and future viral epidemics

A Comparison of Brain Gene Expression Levels in Domesticated and Wild Animals

Domestication has led to similar changes in morphology and behavior in several animal species, raising the questionwhether similarities between different domestication events also exist at the molecular level. We used mRNA sequencing toanalyze genome-wide gene expression patterns in brain frontal cortex in three pairs of domesticated and wild species (dogsand wolves, pigs and wild boars, and domesticated and wild rabbits). We compared the expression differences with thosebetween domesticated guinea pigs and a distant wild relative (Cavia aperea) as well as between two lines of rats selectedfor tameness or aggression towards humans. There were few gene expression differences between domesticated and wilddogs, pigs, and rabbits (30–75 genes (less than 1%) of expressed genes were differentially expressed), while guinea pigs andC. aperea differed more strongly. Almost no overlap was found between the genes with differential expression in thedifferent domestication events. In addition, joint analyses of all domesticated and wild samples provided only suggestiveevidence for the existence of a small group of genes that changed their expression in a similar fashion in differentdomesticated species. The most extreme of these shared expression changes include up-regulation in domesticates of SOX6and PROM1, two modulators of brain development. There was almost no overlap between gene expression in domesticatedanimals and the tame and aggressive rats. However, two of the genes with the strongest expression differences betweenthe rats (DLL3 and DHDH) were located in a genomic region associated with tameness and aggression, suggesting a role ininfluencing tameness. In summary, the majority of brain gene expression changes in domesticated animals are specific tothe given domestication event, suggesting that the causative variants of behavioral domestication traits may likewise bedifferent.funding agencies|Max Planck Society||European Research Council|233297|German Science Foundation (DFG)|AL 1525/1-1|CAS young scientists fellowship|2009Y2BS12|National Science Foundation of China research grant|31010022||SFRH/BPD/65464/2009|</p

Ancient DNA Methods Improve Forensic DNA Profiling of Korean War and World War II Unknowns

The integration of massively parallel sequencing (MPS) technology into forensic casework has been of particular benefit to the identification of unknown military service members. However, highly degraded or chemically treated skeletal remains often fail to provide usable DNA profiles, even with sensitive mitochondrial (mt) DNA capture and MPS methods. In parallel, the ancient DNA field has developed workflows specifically for degraded DNA, resulting in the successful recovery of nuclear DNA and mtDNA from skeletal remains as well as sediment over 100,000 years old. In this study we use a set of disinterred skeletal remains from the Korean War and World War II to test if ancient DNA extraction and library preparation methods improve forensic DNA profiling. We identified an ancient DNA extraction protocol that resulted in the recovery of significantly more human mtDNA fragments than protocols previously used in casework. In addition, utilizing single-stranded rather than double-stranded library preparation resulted in increased attainment of reportable mtDNA profiles. This study emphasizes that the combination of ancient DNA extraction and library preparation methods evaluated here increases the success rate of DNA profiling, and likelihood of identifying historical remains

Pairwise differential expression.

1<p>variance explained by domestication/species, mean across expressed genes.</p>2<p>absolute fold change, mean across expressed genes.</p>3<p>Fraction of all possible permutations of the domestication factor where the respective statistic is matched or exceeded.</p

Expression differences between domesticated and wild animals.

<p>A. Pairwise expression differences. Plotted for each comparison is in black on the left the mean variance explained by domestication, along with 95% confidence intervals (box whiskers) based on 10,000 bootstraps across genes. On the right in light blue is the null distribution of mean variance explained by domestication based on permutations of the domestication factor (box whiskers comprise 95% of the distribution, central horizontal bar is the median). B. For each comparison, the mean variance explained by domestication across genes is plotted as a function of sequence divergence expressed as the median fraction of nucleotides that differ between any two domesticated and wild animals in that comparison.</p

Pairwise overlap of DE genes among domestication events.

<p>Above diagonal: number of genes that are DE in both species, with Fisher's exact test p-values.</p><p>Below diagonal: Odds ratios of FET testing if DE genes in the one species predict expression direction in the other species, with Fisher's exact test p-values. Only the more significant direction is shown (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002962#s4" target="_blank">Materials and Methods</a> for details).</p

Gene expression across domesticated species.

<p>A and B) For each of three models, the figure shows the number of genes that match or exceed the p-value for the domestication factor and that are expressed in the same direction in domesticated animals. The thick black line shows the real data. Each grey line shows the result from one of the possible extreme permutations (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002962#pgen.1002962.s013" target="_blank">Note S1</a> for details). p = 1 is included to show the effect of only requiring genes to be expressed in the same direction, irrespective of significance. vsd: variance stabilized data. A) joint analyses of dogs, pigs and rabbits. B) As in A, but including guinea pigs.</p

Expression levels of four genes with common expression in domesticated dogs, pigs, rabbits, and guinea pigs.

<p>Blue: domesticated animals, red: wild animals. Shown are the four genes with the lowest p-values for the domestication factor across dogs, pigs and rabbits, and with expression change in the same direction in these three species as well as guinea pigs. Expression levels are from variance stabilized data, separately normalized to the median in each species pair.</p