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

Barn owls, like primates, have frontally oriented eyes, which allow for a large binocular overlap. While owls have similar binocular vision and visual-search strategies as primates, it is less clear whether reflexive visual behavior also resembles that of primates or is more similar to that of closer related, but lateral-eyed bird species. Test cases are visual responses driven by wide-field movement: the optokinetic, optocollic, and optomotor responses, mediated by eye, head and body movements, respectively. Adult primates have a so-called symmetric horizontal response: they show the same following behavior, if the stimulus, presented to one eye only, moves in the nasal-to-temporal direction or in the temporal-to-nasal direction. By contrast, lateral-eyed birds have an asymmetric response, responding better to temporal-to-nasal movement than to nasal-to-temporal movement. We show here that the horizontal optocollic response of adult barn owls is less asymmetric than that in the chicken for all velocities tested. Moreover, the response is symmetric for low velocities (  40 deg/s) is not possible.

/pdf/optocollic-responses-in-adult-barn-owls-tyto-furcata-2mz7lpxy3l.pdf

Optocollic responses in adult barn owls (Tyto furcata)

For prey capture in the dark, the barn owl Tyto alba has evolved into an auditory specialist with an exquisite capability of sound localization. Adaptations include asymmetrical ears, enlarged auditory processing centers, the utilization of minute interaural time differences, and phase locking along the entire hearing range up to 10 kHz. Adaptations on the molecular level have not yet been investigated. Here, we tested the hypothesis that divergence in the amino acid sequence of the voltage-gated K(+) channel Kv3.1 contributes to the accuracy and high firing rates of auditory neurons in the barn owl. We therefore cloned both splice variants of Kcnc1, the gene encoding Kv3.1. Both splice variants, Kcnc1a and Kcnc1b, encode amino acids identical to those of the chicken, an auditory generalist. Expression analyses confirmed neural-restricted expression of the channel. In summary, our data reveal strong evolutionary conservation of Kcnc1 in the barn owl and point to other genes involved in auditory specializations of this animal. The data also demonstrate the feasibility to address neuroethological questions in organisms with no reference genome by molecular approaches. This will open new avenues for neuroethologists working in these organisms.

Evolutionary Conservation of Kv3.1 in the Barn Owl Tyto alba

Characteristic delay and characteristic phase are shape parameters of interaural time difference tuning curves. The standard procedure for the estimation of these parameters is based on the measurement of delay curves measured for tonal stimuli with varying frequencies. Common to all procedures is the detection of a linear behavior of the phase spectrum. Hence a reliable estimate can only be expected if sufficiently many relevant frequencies are tested. Thus, the estimation precision depends on the given bandwidth. Based on a linear model, we develop and implement methods for the estimation of characteristic phase and delay from a single broadband tuning curve. We present two different estimation algorithms, one based on a Fourier-analytic interpretation of characteristic delay and phase, and the other based on mean square error minimization. Estimation precision and robustness of the algorithms are tested on artificially generated data with predetermined characteristic delay and phase values, and on sample data from electrophysiological measurements in birds and in mammals. Increasing the signal-to-noise ratio or the bandwidth increases the estimation accuracy of the algorithms. Frequency band location and strong rectification also affect the estimation accuracy. For realistic bandwidths and signal-to-noise ratios, the minimization algorithm reliably and robustly estimates characteristic delay and phase and is superior to the Fourier-analytic method. Bandwidth-dependent significance thresholds allow to assess whether the estimated characteristic delay and phase values are meaningful shape parameters of a measured tuning curve. These thresholds also indicate the sampling rates needed to obtain reliable estimates from interaural time difference tuning curves.

Estimating characteristic phase and delay from broadband interaural time difference tuning curves

![Figure][1] 

Laura Hausmann, Martin Singheiser and Hermann Wagner discuss Roger Payne's 1971 paper entitled: Acoustic Location of Prey by Barn Owls ( Tyto alba ).

A copy of the paper can be obtained from 



In 1971, Roger Payne

Hermann Wagner

Papers

Optocollic responses in adult barn owls (Tyto furcata)

Evolutionary Conservation of Kv3.1 in the Barn Owl Tyto alba

Estimating characteristic phase and delay from broadband interaural time difference tuning curves

Why are barn owls a model system for sound localization

Representation of spatial and spectro-temporal cues in the midbrain and forebrain of North American barn owls (Tyto furcata pratincola)