The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

I have developed "tennis elbow" from lugging this book around the past four weeks, but it is worth the pain, the effort, and the aspirin. It is also worth the (relatively speaking) bargain price. Including appendixes, this book contains 894 pages of text. The entire panorama of the neural sciences is surveyed and examined, and it is comprehensive in its scope, from genomes to social behaviors. The editors explicitly state that the book is designed as "an introductory text for students of biology, behavior, and medicine," but it is hard to imagine any audience, interested in any fragment of neuroscience at any level of sophistication, that would not enjoy this book. The editors have done a masterful job of weaving together the biologic, the behavioral, and the clinical sciences into a single tapestry in which everyone from the molecular biologist to the practicing psychiatrist can find and appreciate his or

Principles of Neural Science

Neurons in the brain communicate by short electrical pulses, the so-called action potentials or spikes. How can we understand the process of spike generation? How can we understand information transmission by neurons? What happens if thousands of neurons are coupled together in a seemingly random network? How does the network connectivity determine the activity patterns? And, vice versa, how does the spike activity influence the connectivity pattern? These questions are addressed in this 2002 introduction to spiking neurons aimed at those taking courses in computational neuroscience, theoretical biology, biophysics, or neural networks. The approach will suit students of physics, mathematics, or computer science; it will also be useful for biologists who are interested in mathematical modelling. The text is enhanced by many worked examples and illustrations. There are no mathematical prerequisites beyond what the audience would meet as undergraduates: more advanced techniques are introduced in an elementary, concrete fashion when needed.

/pdf/spiking-neuron-models-single-neurons-populations-plasticity-58gzrd6ih6.pdf

Spiking Neuron Models: Single Neurons, Populations, Plasticity

中枢神経系疾患の治療は正常細胞（ニューロン）の機能維持を目的とするが，脳血管障害のように機能障害の原因が細胞の死滅に基づくことは多い．一方，脳腫瘍の治療においては薬物療法や放射線療法といった腫瘍細胞の死滅を目標とするものが大きな位置を占める．いずれの場合にも，細胞死の機序を理解することは各種病態や治療法の理解のうえで重要である．現在のところ最も研究の進んでいる細胞死の型はアポトーシスである．そのなかで重要な位置を占めるミトコンドリアにおける反応および抗アポトーシス因子について概要を紹介する．

Neuroscience 細胞死：最近の知見

Hebbian models of development and learning require both activity-dependent synaptic plasticity and a mechanism that induces competition between different synapses. One form of experimentally observed long-term synaptic plasticity, which we call spike-timing-dependent plasticity (STDP), depends on the relative timing of pre- and postsynaptic action potentials. In modeling studies, we find that this form of synaptic modification can automatically balance synaptic strengths to make postsynaptic firing irregular but more sensitive to presynaptic spike timing. It has been argued that neurons in vivo operate in such a balanced regime. Synapses modifiable by STDP compete for control of the timing of postsynaptic action potentials. Inputs that fire the postsynaptic neuron with short latency or that act in correlated groups are able to compete most successfully and develop strong synapses, while synapses of longer-latency or less-effective inputs are weakened.

/pdf/competitive-hebbian-learning-through-spike-timing-dependent-17innjp0ag.pdf

Competitive Hebbian learning through spike-timing-dependent synaptic plasticity

Data for: Development of ear asymmetry in the American barn owl (Tyto furcata pratincola)

The geometry of the barn owl wing, i.e., the planform, the camber line, and the thickness distribution, differs significantly from the wing geometry of other bird species of comparable weight and size. To investigate the flow field of this special geometry with its distinct nose region and large thickness in context with a small chordwise position of the maximum thickness, technical wing models based on the barn owl wing were designed. The influence on the flow field of one of the owl-specific adaptations, namely the velvet-like surface structure on the suction side of the wing, was analyzed via high-speed particle-image velocimetry (PIV). Measurements were performed in a Reynolds number range of 40,000 ≤ Rec ≤ 120,000 and angels of attack of 0° ≤ α ≤ 6°. The first artificial surface structure, referred to as velvet 1, was selected to imitate the hair length, density and thus, the softness of the natural surface. Velvet 2, the second artificial surface, possesses longer, softer filaments and a preferred hair direction. A strong influence of the surface structures on the flow field was found for both velvet structures. The velvets seem to force the laminar to turbulent transition in the free shear layer at higher Reynolds numbers and thus, enable the flow to reattach earlier. This leads to a reduction of the separation bubble on the suction side of the wing.

High-speed PIV measurements of the influence of artificial surface structures on the near-wall flow field of 3D wing models based on an owl geometry

It is a challenge to understand how the brain represents temporal events. One of the most intriguing questions is how sub-millisecond representations can be achieved despite the large temporal variations at all levels of processing. For example, the neurophonic potential, a frequency-following potential occurring in the network formed by nucleus magnocellularis and nucleus laminaris in the brainstem of the bird, has a temporal precision below 100 μs.

/pdf/signal-to-noise-ratio-of-the-neurophonic-potential-in-the-y7j8hkhzhj.pdf

Signal-to-noise ratio of the neurophonic potential in the laminar nucleus of the barn owl

Abstract In this personal view article, the impact of an auditory specialist, the barn owl, to our understanding of sensory processing, especially auditory processing, is discussed from the perspective of a long-lasting career. In times when research on model systems such as the mouse or the fruit fly, both generalists for most of the behaviors examined, celebrates big successes, one may ask what the work on animals occupying specialized niches, “specialists”, can contribute to advance our knowledge about sensory systems. A specialist in this context is an animal that occupies a certain ecological niche and shows corresponding adaptations in anatomy and physiology. This article presents a personal view on the impact of the work on such a specialist. In my article I shall focus on audition in the barn owl, a specialist for hunting by listening. I started my scientific career in 1979, working with houseflies, and have worked with barn owls since my time as a postdoc at the California Institute of Technology (“Caltech”, Pasadena, CA, USA) in 1985. My interest in specialists derived from my work as an ornithologist when I realized that adaptations like the long and curved bill of the curlew help animals to occupy certain ecological niches. I wanted to understand in a formal sense, and in comparison to engineering, how evolution shapes such specializations.

Hermann Wagner

Papers

Data for: Development of ear asymmetry in the American barn owl (Tyto furcata pratincola)

High-speed PIV measurements of the influence of artificial surface structures on the near-wall flow field of 3D wing models based on an owl geometry

Signal-to-noise ratio of the neurophonic potential in the laminar nucleus of the barn owl

Personal View: The barn owl — a specialist for studying sensory systems

Data for: EvoDevo in owl ear asymmetry – the little owl (Athene noctua)