Did Charles Darwin’s thirst for skulls contribute to the near-extinction of the Aboriginal Tasmanian people? If you believe certain creationists, Darwin sought examples of Tasmanian skulls in order to prove that this unfortunate race was a ‘missing link’ between humans and apes. However, according to John van Wyhe in a new paper called Darwin’s body-snatchers?, …
We examined RNA-Seq data on 211 biological samples from 24 different Arabidopsis experiments carried out by different labs. We grouped the samples according to tissue types, and in each of the groups, we identified genes that are stably expressed across biological samples, treatment conditions, and experiments. We fit a Poisson log-linear mixed-effect model to the read counts for each gene and decomposed the total variance into between-sample, between-treatment and between-experiment variance components. Identifying stably expressed genes is useful for count normalization and differential expression analysis. The variance component analysis that we explore here is a first step towards understanding the sources and nature of the RNA-Seq count variation. When using a numerical measure to identify stably expressed genes, the outcome depends on multiple factors: the background sample set and the reference gene set used for count normalization, the technology used for measuring gene expression, and the specific numerical stability measure used. Since differential expression (DE) is measured by relative frequencies, we argue that DE is a relative concept. We advocate using an explicit reference gene set for count normalization to improve interpretability of DE results, and recommend using a common reference gene set when analyzing multiple RNA-Seq experiments to avoid potential inconsistent conclusions.
Despite the central place held by bioinformatics in modern life sciences and related areas, it has only recently been integrated to a limited extent into high-school teaching and learning programs. Here we describe the assessment of a learning environment entitled ‘Bioinformatics in the Service of Biotechnology’.... Analysis of students’ affective outcomes revealed positive attitudes toward bioinformatics and the learning environment, as well as their perception of the teacher’s role. Insights from this analysis yielded implications and recommendations for curriculum design, classroom enactment, teacher education and research. For example, we recommend teaching bioinformatics in an integrative and comprehensive manner, through an inquiry process, and linking it to the wider science curriculum.
Source: A Necessary Retelling of the Smallpox Vaccine Story A curious confluence of events unfolded Tuesday night. Just hours before President Obama uttered the powerful “science and reason matter” in his farewell address, Robert F. Kennedy Jr. announced that the incoming president had tapped him to head a committee on vaccine safety. RFK Jr. is not a pediatric immunologist nor an epidemiologist, but a vocal “vaccine skeptic.” Although the PEOTUS dialed back on the purported appointment shortly after social media erupted, a tweet from March 28, 2014 makes his analysis of the history and science of vaccines clear: Healthy young child goes to doctor, gets pumped with massive shot of many vaccines, doesnt feel good and changes – AUTISM. Many such cases! As a child I devoured books on the history of medicine. One of my favorite stories was how Edward Jenner developed the first vaccine, testing an approach that had been used for centuries. Knowing his story made me understand why my little
By Michelle Ziegler Smallpox is one of those diseases long believed to have an ancient pedigree, the suspected culprit of legendary epidemics. Yet, so far, smallpox hasn't made a big impression in ancient DNA surveys. If it was truly endemic throughout the Old World before 1492, so much so that it pops up in the…
Studies on the epidemiology of viral diseases in aquaculture have for a long time depended on isolation of viruses from infected aquatic organisms. The role of aquatic environments in the epidemiology of viral diseases in aquaculture has not been extensivel
In cells, DNA is transcribed into RNAs that provide the molecular recipe for cells to make proteins. Most of the genome is transcribed into RNA, but only a small proportion of RNAs are actually from the protein-coding regions of the genome.
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