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 have neurons sensitive to acoustic motion-direction in the midbrain. We report here that acoustic motion-direction sensitive neurons with receptive-field centres in frontal auditory space are not randomly distributed. In the inferior colliculus and optic tectum in the left (right) brain, the responses of about two-thirds of the motion-direction sensitive neurons were sensitive to clockwise (counter-clockwise) motion. The midbrain contains maps of auditory space that represent about 15° of ipsilateral and all of contralateral space. Since a similar bias in motion-direction sensitivity was observed for neurons with receptive-field centres in ipsilateral as well as for neurons with receptive fields centres in contralateral auditory space, the brain side at which a motion-direction sensitive neuron was recorded was a more important predictor for the preferred direction of a cell than the spatial direction of the centre of the receptive field. Within one dorso-ventral electrode pass motion-direction sensitivity typically stayed constant suggesting a clustered or even a columnar-like organization. We hypothesize from these distributions that the right brain is important for orientating movements to the left hemisphere and vice versa.

Distribution of auditory motion-direction sensitive neurons in the barn owl's midbrain

Avian uropygial glands have received increasing attention in recent years, but little is known about micro-organisms in uropygial glands. In this study, we isolated a strain of Gram-stain-positive, non-motile, non-spore-forming cocci, designated 442T, from the uropygial gland of an American barn owl (Tyto furcata) and characterized it using a polyphasic approach. 16S rRNA gene sequence analysis placed the isolate in the genus 
Kocuria
. The G+C content was 70.8 mol%, the major menaquinone was MK-7(H2) and the predominant cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C15 : 0. Phylogenetic analyses based on the 16S rRNA gene identified 
Kocuria rhizophila
DSM 11926T (99.6 % similarity), 
Kocuria salsicia
DSM 24776T (98.7 %), 
Kocuria varians
DSM 20033T (98.3 %) and 
Kocuria marina
DSM 16420T (98.3 %) as the most closely related species. However, average nucleotide identity values below 86 % indicated that the isolate differed from all species hitherto described. Chemotaxonomic analyses and whole-cell protein profiles corroborated these findings. Accordingly, the isolate is considered to be a member of a novel species, for which the name 
Kocuria
tytonis sp. nov. is proposed. The type strain is 442T (=DSM 104130T=LMG 29944T).

Kocuria tytonis sp. nov., isolated from the uropygial gland of an American barn owl (Tyto furcata).

Here, we studied neural correlates of orientation-contrast-based saliency in the optic tectum (OT) of barn owls. Neural responses in the intermediate/deep layers of the OT were recorded from lightly anesthetized owls confronted with arrays of bars in which one bar (the target) was orthogonal to the remaining bars (the distractors). Responses to target bars were compared with responses to distractor bars in the receptive field (RF). Initially, no orientation-contrast sensitivity was observed. However, if the position of the target bar in the array was randomly shuffled across trials so that it occasionally appeared in the RF, then such sensitivity emerged. The effect started to become significant after three or four positional changes of the target bar and strengthened with additional trials. Our data further suggest that this effect arises due to specific adaptation to the stimulus in the RF combined with suppression from the surround. By jittering the position of the bar inside the RF across trials, we demonstrate that the adaptation has two components, one position specific and one orientation specific. The findings give rise to the hypothesis that barn owls, by active scanning of the scene, can induce adaptation of the tectal circuitry to the common orientation and thus achieve a “pop-out” of rare orientations. Such a model is consistent with several behavioral observations in owls and may be relevant to other visual features and species. SIGNIFICANCE STATEMENT Natural scenes are often characterized by a dominant orientation, such as the scenery of a pine forest or the sand dunes in a windy desert. Therefore, orientation that contrasts the regularity of the scene is perceived salient for many animals as a means to break camouflage. By actively moving the scene between each trial, we show here that neurons in the retinotopic map of the barn owl9s optic tectum specifically adapt to the common orientation, giving rise to preferential representation of odd orientations. Based on this, we suggest a new mechanism for orientation-based camouflage breaking that links active scanning of scenes with neural adaptation. This mechanism may be relevant to pop-out in other species and visual features.

https://www.jneurosci.org/content/jneuro/36/17/4876.full.pdf

Responses to Pop-Out Stimuli in the Barn Owl's Optic Tectum Can Emerge through Stimulus-Specific Adaptation

We demonstrate and characterize response adaptation in neurons of the auditory space map in the barn owl’s midbrain with acoustic double-stimulation paradigms. An increase of the second level by 5 ...

Hermann Wagner

Papers

Distribution of auditory motion-direction sensitive neurons in the barn owl's midbrain

Kocuria tytonis sp. nov., isolated from the uropygial gland of an American barn owl (Tyto furcata).

Responses to Pop-Out Stimuli in the Barn Owl's Optic Tectum Can Emerge through Stimulus-Specific Adaptation

Response adaptation in the barn owl’s auditory space map

Development of ear asymmetry in the American barn owl (Tyto furcata pratincola).