Commentary

A revolution in DNA sequencing technology has enabled new insights from thousands of genomes sequenced across taxa.

Much of our knowledge about biological systems has been obtained by examining ensembles of molecules. However, this has begun to change because of the unprecedented precision and clarity afforded by single-molecule measurements. The last decade has seen amazing advances in the resolution and complexity of these methods, making it possible to ask and answer entirely new types of biological questions.

The optogenetic revolution is transforming neuroscience. The dramatic recent progress in using light to both control and read out neural activity has highlighted the need for better probes, improved light delivery and more careful interpretation of results, which will all be required for optogenetics to fully realize its remarkable potential.

We argue that standard thermodynamic considerations and scaling laws show that a single cell cannot substantially raise its temperature by endogenous thermogenesis. This statement seriously questions the interpretations of recent work reporting temperature heterogeneities measured in single living cells.

'Irreproducibility' is symptomatic of a broader challenge in measurement in biomedical research. From the US National Institute of Standards and Technology (NIST) perspective of rigorous metrology, reproducibility is only one aspect of establishing confidence in measurements. Appropriate controls, reference materials, statistics and informatics are required for a robust measurement process. Research is required to establish these tools for biological measurements, which will lead to greater confidence in research results.

Authors discuss how synthetic biology approaches could be applied to assemble synthetic quasibiological systems able to replicate and evolve, illuminating universal properties of life and the search for its origins.

Single-molecule super-resolution techniques emerged only several years ago but have revolutionized fluorescence microscopy of cellular structures. We discuss some key principles of these techniques, point out pitfalls, highlight recent developments and identify opportunities for the future.

Individual cells of the same phenotype are commonly viewed as identical functional units of a tissue or organ. However, the deep sequencing of DNA and RNA from single cells suggests a more complex ecology of heterogeneous cell states that together produce emergent system-level function. Continuing development of high-content, real-time, multimodal single-cell measurement technologies will lead to the ultimate goal of understanding the function of an individual cell in the context of its microenvironment.

Emerging technologies are bringing single-cell genome sequencing into the mainstream; this field has already yielded insights into the genetic architecture and variability between cells that highlight the dynamic nature of the genome.

Recent technical advances have enabled RNA sequencing (RNA-seq) in single cells. Exploratory studies have already led to insights into the dynamics of differentiation, cellular responses to stimulation and the stochastic nature of transcription. We are entering an era of single-cell transcriptomics that holds promise to substantially impact biology and medicine.

Two surveys of over 1,700 publications whose authors use quantitative real-time PCR (qPCR) reveal a lack of transparent and comprehensive reporting of essential technical information. Reporting standards are significantly improved in publications that cite the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines, although such publications are still vastly outnumbered by those that do not.

Optimism about biomedicine is challenged by the increasingly complex ethical, legal and social issues it raises. Reporting of scientific methods is no longer sufficient to address the complex relationship between science and society. To promote 'ethical reproducibility', we call for transparent reporting of research ethics methods used in biomedical research.

We present a summary of the scientific deliberations and major conclusions that arose from a workshop on the BRAIN Initiative.

Much of what is known about mammalian cell regulation has been achieved with the aid of transiently transfected cells. However, overexpression can violate balanced gene dosage, affecting protein folding, complex assembly and downstream regulation. To avoid these problems, genome engineering technologies now enable the generation of stable cell lines expressing modified proteins at (almost) native levels.

New methods for mapping synaptic connections and recording neural signals generate rich and complex data on the structure and dynamics of brain networks. Making sense of these data will require a concerted effort directed at data analysis and reduction as well as computational modeling.

Opinions diverge on whether mapping the synaptic connectivity of the brain is a good idea. Here we argue that albeit their limitations, such maps will reveal essential characteristics of neural circuits that would otherwise be inaccessible.

By delivering precise, reproducible quantification of proteins of interest in biological samples, targeted proteomics approaches are allowing researchers to apply the scientific method using mass spectrometry.

Physical modeling is increasingly important for generating insights into intracellular processes. We describe situations in which combined spatial and stochastic aspects of chemical reactions are needed to capture the relevant dynamics of biochemical systems.

Widely used behavioral assays need re-evaluation and validation against their intended use. We focus here on measures of chronic anxiety in mouse models and posit that widely used assays such as the open-field test are performed at the wrong time, for inadequate durations and using inappropriate mouse strains. We propose that behavioral assays be screened for usefulness on the basis of their replicability across laboratories.

Many scholars claim there is a consensus on broad consent for biobanking. We analyzed the literature in PubMed and found no evidence for consensus. Public perception studies report mixed findings on consent, but many biobanks adopt broad consent. A belief in consensus may stem from knowledge of biobank consent practices.