Studying genomic processes at the single-molecule level: introducing the tools and applications

To understand genomic processes such as transcription, translation or splicing, we need to be able to study their spatial and temporal organization at the molecular level. Single-molecule approaches provide this opportunity, allowing researchers to monitor molecular conformations, interactions or diffusion quantitatively and in real time in purified systems and in the context of the living cell. This Review introduces the types of application of single-molecule approaches that can enhance our understanding of genome function.

David Dulin, et al.
Nature Reviews Genetics 14, 9-22 (January 2013) |doi:10.1038/nrg3316

New South Pole Telescope shows Omaga = 1.006 +- 0.004

The South Pole Telescope published the new results.
Omega_K=-0.003+0.014-0.018. Using the SPT+WMAP7 data, the spectral index of scalar fluctuations tis ns=0.9623+/-0.0097 in the LCDM model, a 3.9sigma preference for a scale-dependent spectrum with ns<1.

Dark Matter Filament Studied in 3-D for the First Time

Astronomers using the NASA/ESA Hubble Space Telescope have studied a giant filament of dark matter in 3D for the first time. Extending 60 million light-years from one of the most massive galaxy clusters known, the filament is part of the cosmic web that constitutes the large-scale structure of the Universe, and is a leftover of the very first moments after the Big Bang. If the high mass measured for the filament is representative of the rest of the Universe, then these structures may contain more than half of all the mass in the Universe.
Science Daily, Oct 16 2012
Nature 487, 202–204 (12 July 2012) doi:10.1038/nature11224

Newborn cortical neurons: only for neonates?

Despite a century of debate over the existence of adult cortical neurogenesis, a consensus has not yet been reached. Here, we review evidence of the existence, origin, migration, and integration of neurons into the adult and neonatal cerebral cortex. We find that the lack of consensus likely stems from the low rate of postnatal cortical neurogenesis that has been observed, the fact that neurogenesis may be limited to subtypes of interneurons, and variability in other conditions, both physiological and environmental. We emphasize that neurogenesis occurs in the neonatal cortex and that neural stem cells are present into adulthood; it is possible that these progenitors are dormant, but they may be reactivated, for example, following injury.

David M. Feliciano, Angélique Bordey

Trends in Neurosciences, Volume 36, Issue 1, 51-61, 12 October 2012
10.1016/j.tins.2012.09.004

Optimization of a GCaMP Calcium Indicator for Neural Activity Imaging

Genetically encoded calcium indicators (GECIs) are powerful tools for systems neuroscience. Recent efforts in protein engineering have significantly increased the performance of GECIs. The state-of-the art single-wavelength GECI, GCaMP3, has been deployed in a number of model organisms and can reliably detect three or more action potentials in short bursts in several systems in vivo.
Akerboom J et al.

J Neurosci. 2012 Oct 3;32(40):13819-40. doi: 10.1523/JNEUROSCI.2601-12.2012.

Tian L et al.
Imaging neural activity in worms, flies and mice with improved GCaMP calcium indicators.
Nat Methods. 2009 Dec;6(12):875-81. doi: 10.1038/nmeth.1398. Epub 2009 Nov 8.

Genetically encoded optical indicators for the analysis of neuronal circuits

In a departure from previous top-down or bottom-up strategies used to understand neuronal circuits, many forward-looking research programs now place the circuit itself at their centre. This has led to an emphasis on the dissection and elucidation of neuronal circuit elements and mechanisms, and on studies that ask how these circuits generate behavioural outputs. This movement towards circuit-centric strategies is progressing rapidly as a result of technological advances that combine genetic manipulation with light-based methods. The core tools of these new approaches are genetically encoded optical indicators and actuators that enable non-destructive interrogation and manipulation of neuronal circuits in behaving animals with cellular-level precision. This Review examines genetically encoded reporters of neuronal function and assesses their value for circuit-oriented neuroscientific investigations.

Thomas Knöpfel
Nature Reviews Neuroscience 13, 687-700 (October 2012) | doi:10.1038/nrn3293

In vivo genome editing using a high-efficiency TALEN system

Improvements in artificial transcription activator-like effector nucleases (TALENs) provide a powerful new approach for targeted zebrafish genome editing and functional genomic applications1–5. Using the Goldy TALEN modified scaffold and zebrafish delivery system, it was shown that this enhanced TALEN toolkit has a high efficiency in inducing locus-specific DNA breaks in somatic and germline tissues. 
Science 21 December 2012
Nature (2013) Sept 23 

ENCODE Project Writes Eulogy For Junk DNA

SCIENCE VOL 337 7 SEPTEMBER 2012

30 research papers, including six in Nature and additional papers published by Science, sound the death knell for the idea that our DNA is mostly littered with useless bases. A decadelong project, the Encyclopedia of DNA Elements (ENCODE), has found that 80% of the human genome serves some purpose, biochemically speaking.

Axion search by Liquid Xenon

Arisaka's group has studied a possibility of searching for axion and axion-like particles by liquid Xenon detectors such as XENON100 and XENON1T.

The paper has been submitted to Astroparticle Physcis Journal, and available at

http://arxiv.org/abs/1209.3810

Disorder of Neuronal Circuits in Autism Is Reversible, New Study Suggests

People with autism suffer from a pervasive developmental disorder of the brain that becomes evident in early childhood. Peter Scheiffele and Kaspar Vogt, Professors at the Biozentrum of the University of Basel, have identified a specific dysfunction in neuronal circuits that is caused by autism. In the journal Science, the scientists also report about their success in reversing these neuronal changes. These findings are an important step in drug development for the treatment for autism.Science

Daily Sept 22, 2012
Stéphane J. Baudouin, et al.

Shared Synaptic Pathophysiology in Syndromic and Nonsyndromic Rodent Models of Autism. Science, 13 September 2012 DOI: 10.1126/science.1224159