神经元信息编码的代谢消耗：动作电位与能量效率

人脑是一个高效、可靠的信息处理系统,它主导着个体的认知、情感、意识与行为,这些功能的实现需要不断地消耗代谢能量.大脑的能量需求主要被神经元信息编码所消耗,相应的亚细胞过程包括产生和传导动作电位、维持静息电位以及突触传递.神经元编码信息的主要载体是动作电位序列,它的产生与传导贡献了大脑的大部分代谢消耗.动作电位的能量消耗受离子通道的生物物理特性控制.生物物理特性的细胞特异性和空间异质性使得动作电位对代谢能量的利用效率呈现高度可变性,它为理解神经元代谢消耗的规律、起因与结果带来了挑战.本文首先介绍参与神经元编码的亚细胞过程及它们在大脑和小脑皮层中的代谢消耗,然后详细梳理近年来关于动作电位代谢消耗的研究成果,重点讨论影响其能量效率的生物物理因素和放电形状特性,并归纳总结放电消耗的特点,最后对未来神经元编码的代谢消耗研究进行展望.     

基于PAE编码系统构建的半自然条件下长江江豚行为谱

识别和编制动物行为谱是深入研究动物行为及其与环境复杂关系的基础和前提。本研究于2013年8月至2014年4月以栖息在铜陵淡水豚国家级自然保护区半自然水域的8头长江江豚为研究对象,采用焦点动物取样法和随机动物取样法观察记录了动物行为发生的过程、内容和环境,并以"姿势—动作—环境"(posture-act-environment,PAE)为轴心,以行为的功能为依据,构建了长江江豚的PAE行为谱。共分辨记录了半自然水域长江江豚的8种姿势、33种动作和46种行为,并定性描述了不同行为出现频率与年龄组、性别的关系。该行为谱综合了姿势和环境信息,有助于进一步研究长江江豚的生态与行为、促进长江江豚的保护。     

《自然》：研究阐明控制平顺讲话的神经编码

试着念一下”黑化肥发灰会挥发,灰化肥挥发会发黑”：就在这一瞬间,你身体的许多部位一嘴唇、舌头、下巴与喉咙一刚刚表演了一场复杂的舞蹈。然而,很少有人知道大脑如何协调这些声道运动,从而帮助哪怕是最笨的人也不会被自己的舌头所”绊倒”。     

《自然-遗传学》：转移性乳腺癌中雌激素受体编码基因或变异

据《自然一遗传学》上的两项独立研究显示,在某些转移性乳腺癌病例中,负责编码雌激素受体的基因会发生变异。这意味着雌激素受体对抗药物或对某些转移性乳腺癌病例具有疗效。Sarat Chandarlapaty等人选取了36个对激素疗法产生抗性的转移性乳腺癌肿瘤,对其中的230种基因进行测序,在9个肿瘤中发现ESRl基因突变。他们分析了44个转移性乳腺癌肿瘤中的ESRl基因,发现其中5个肿瘤存在基因突变。     

《自然-方法学》：基因编码“温度计”可潜入细胞测温度

据物理学家组织网10月16日报道,日本京都大学科学家最近将绿色荧光蛋白和沙门氏菌体内感受热量的一种蛋白融合在一起。制造出一种能检测细胞内部不同细胞器温度波动的基因编码”温度计”,并将细胞器温度变化与细胞内部功能联系在一起。有助于人们进一步理解细胞行为。相关论文发表在最近的《自然-方法学》杂志上。     

《自然-结构和分子生物学》：首次获得膜蛋白形成瞬间图像

据美国物理学家组织网近日报道,在两项最新的研究中,研究人员首次详细地描述了生产蛋白质的核糖体如何将刚形成的蛋白质嵌入到细胞膜内。并首次获得蛋白质进入膜的图片。     

《自然》：长链非编码RNA推动癌细胞生长机制阐明

一个研究小组确定了侵袭性前列腺癌背后的一个关键机制。发表在8月14日《自然》（Nature）杂志上的这项新研究。证实了两个长链非编码RNAs：PRNCRl和PCGEM1通过激活雄激素受体。逃避了雄激素剥夺治疗（androgen—deprivation therapy）。     

纯林自然稀疏研究综述

自然稀疏是林分内的个体由于部分有限的资源而引起的一部分个体死亡的现象。评述40a来世界上有关纯林自然稀疏的研究内容,包括了自然稀疏法则,异速生长模型、平均个体重与密度的时间轨线,种的自然稀疏线和自然稀疏动力线的关系,自然稀疏线的斜率与生物量的生物量的关系,自然稀疏的机理。     

大兴安岭小尺度草甸火燃烧效率研究

燃烧效率是进行生物质燃烧温室气体释放量计算的关键因子,以大兴安岭典型草甸区为研究区域,通过样地调查和采样,应用GIS和地统计学的方法对燃烧格局和燃烧效率进行计算。结果表明:研究区域内草甸可燃物的平均载量为37.3t/hm²,草本层、枯落物层和腐殖层载量平均所占比例分别为18.50%,28.95%和52.55%。样地的块金系数分别在80.84%-97.88%之间变化,过火迹地的燃烧深度具有弱的空间相关性。研究区域内平均燃烧效率为64.51%,根据不同的火烧强度,研究区域的燃烧效率在44.35%-90.6%之间变化。     

DNA存储中的编码技术

脱氧核糖核酸(Deoxyribonucleic Acid, DNA)是一种天然的信息存储介质,具有存储密度高、存储时间长、损耗率低等特点。在传统存储方式不能满足信息增长的需求时,DNA数据存储技术逐渐成为研究热点。DNA编码是用尽可能少的碱基序列无错的存储数据信息,包括压缩(尽可能少的占用空间)、纠错(无错存储)和转换(数字信息转为碱基序列)3部分。DNA编码是DNA存储中的关键技术,它的结果直接影响存储性能的优劣和数据读写的完整。本文首先介绍DNA存储的发展历史,然后介绍DNA存储的框架,其中重点介绍DNA编码技术,最后对DNA存储中的编解码技术的未来发展方向进行讨论。     

多重二元响应Probit模型的渐近有效估计

针对多重二元响应Probit模型提出了两步估计方法,第一步由边际似然得到参数√n相合的估计,第二步通过一步迭代得到渐近有效估计,由于只需一步迭代,因此在利用模拟方法计算信息阵时,可以增加模拟的次数,从而减少模拟所产生的扰动对估计的影响．     

Neural coding of categories: information efficiency and optimal population codes

This paper deals with the analytical study of coding a discrete set of categories by a large assembly of neurons. We consider population coding schemes, which can also be seen as instances of exemplar models proposed in the literature to account for phenomena in the psychophysics of categorization. We quantify the coding efficiency by the mutual information between the set of categories and the neural code, and we characterize the properties of the most efficient codes, considering different regimes corresponding essentially to different signal-to-noise ratio. One main outcome is to find that, in a high signal-to-noise ratio limit, the Fisher information at the population level should be the greatest between categories, which is achieved by having many cells with the stimulus-discriminating parts (steepest slope) of their tuning curves placed in the transition regions between categories in stimulus space. We show that these properties are in good agreement with both psychophysical data and with the neurophysiology of the inferotemporal cortex in the monkey, a cortex area known to be specifically involved in classification tasks.     

The state of gustatory neural coding

Debates on gustatory neural coding have been dominated by asmall number of fundamental issues since the inception of thefield in 1941. Three of these are discussed in this review:(1) are there basic tastes? (2) are there gustatory neuron types?(3) is the code for a taste read simultaneously across all participatingneurons (across-fiber patterning), or is it confined to a selectivechannel composed of cells of one type (labeled-line or channeling)?No conclusions are drawn regarding (1), primarily because auniversal definition of ‘basic tastes’ is lacking.It is concluded that gustatory neuron types are likely to existafter reviewing the issue from multiple perspectives and discoveringrecurring indications of neuron types from several. A firm conclusion,however, also awaits a widely accepted definition of what constitutesa neuron type. Issue (3) cannot yet be resolved for lack ofdefinitive data, specifically whether the discharges of inhibited,unresponsive, or weakly responsive cells add to (signal) ordetract from (noise) the neural code for a tastant.     

Efficiency of coding in macaque vocal communication

A key characteristic of human language efficiency is that more frequently used words tend to be shorter in length—the ‘law of brevity’. To date, no test of this relationship between frequency of use and length has been carried out on non-human animal vocal communication. We show here that the vocal repertoire of the Formosan macaque (Macaca cyclopis) conforms to the pattern predicted by the law of brevity, with an inverse relationship found between call duration and rate of utterance. This finding provides evidence for coding efficiency in the vocal communication system of this species, and indicates commonality in the basic structure of the coding system between human language and vocal communication in this non-human primate.     

非编码RNA在骨骼肌发育中的功能

近几年的研究表明,非编码RNA的功能几乎涉及生命活动的各个方面。非编码RNA在骨骼肌发育中的功能研究揭示了骨骼肌发育调控的复杂性。该文总结了骨骼肌发育中非编码RNA的系统发现与鉴定以及非编码RNA在骨骼肌发育和再生中的功能研究。     

High-precision coding in visual cortex

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Neural dynamics of envelope coding

We consider the processing of narrowband signals that modulate carrier waveforms in sensory systems. The tuning of sensory neurons to the carrier frequency results in a high sensitivity to the amplitude modulations of the carrier. Recent work has revealed how specialized circuitry can extract the lower-frequency modulation associated with the slow envelope of a narrowband signal, and send it to higher brain along with the full signal. This paper first summarizes the experimental evidence for this processing in the context of electroreception, where the narrowband signals arise in the context of social communication between the animals. It then examines the mechanism of this extraction by single neurons and neural populations, using intracellular recordings and new modeling results contrasting envelope extraction and stochastic resonance. Low noise and peri-threshold stimulation are necessary to obtain a firing pattern that shows high coherence with the envelope of the input. Further, the output must be fed through a slow synapse. Averaging networks are then considered for their ability to detect, using additional noise, signals with power in the envelope bandwidth. The circuitry that does support envelope extraction beyond the primary receptors is available in many areas of the brain including cortex. The mechanism of envelope extraction and its gating by noise and bias currents is thus accessible to non-carrier-based coding as well, as long as the input to the circuit is a narrowband signal. Novel results are also presented on a more biophysical model of the receptor population, showing that it can encode a narrowband signal, but not its envelope, as observed experimentally. The model is modified from previous models by stimulus reducing contrast in order to make it sufficiently linear to agree with the experimental data.     

Degenerate coding in neural systems

When the dimensionality of a neural circuit is substantially larger than the dimensionality of the variable it encodes, many different degenerate network states can produce the same output. In this review I will discuss three different neural systems that are linked by this theme. The pyloric network of the lobster, the song control system of the zebra finch, and the odor encoding system of the locust, while different in design, all contain degeneracies between their internal parameters and the outputs they encode. Indeed, although the dynamics of song generation and odor identification are quite different, computationally, odor recognition can be thought of as running the song generation circuitry backwards. In both of these systems, degeneracy plays a vital role in mapping a sparse neural representation devoid of correlations onto external stimuli (odors or song structure) that are strongly correlated. I argue that degeneracy between input and output states is an inherent feature of many neural systems, which can be exploited as a fault-tolerant method of reliably learning, generating, and discriminating closely related patterns.     

Olfactory coding in the insect brain: molecular receptive ranges, spatial and temporal coding

Odor information is coded in the insect brain in a sequence of steps, ranging from the receptor cells, via the neural network in the antennal lobe, to higher order brain centers, among which the mushroom bodies and the lateral horn are the most prominent. Across all of these processing steps, coding logic is combinatorial, in the sense that information is represented as patterns of activity across a population of neurons, rather than in individual neurons. Because different neurons are located in different places, such a coding logic is often termed spatial, and can be visualized with optical imaging techniques. We employ in vivo calcium imaging in order to record odor‐evoked activity patterns in olfactory receptor neurons, different populations of local neurons in the antennal lobes, projection neurons linking antennal lobes to the mushroom bodies, and the intrinsic cells of the mushroom bodies themselves, the Kenyon cells. These studies confirm the combinatorial nature of coding at all of these stages. However, the transmission of odor‐evoked activity patterns from projection neuron dendrites via their axon terminals onto Kenyon cells is accompanied by a progressive sparsening of the population code. Activity patterns also show characteristic temporal properties. While a part of the temporal response properties reflect the physical sequence of odor filaments, another part is generated by local neuron networks. In honeybees, γ‐aminobutyric acid (GABA)‐ergic and histaminergic neurons both contribute inhibitory networks to the antennal lobe. Interestingly, temporal properties differ markedly in different brain areas. In particular, in the antennal lobe odor‐evoked activity develops over slow time courses, while responses in Kenyon cells are phasic and transient. The termination of an odor stimulus is reflected by a decrease in activity within most glomeruli of the antennal lobe and an off‐response in some glomeruli, while in the mushroom bodies about half of the odor‐activated Kenyon cells also exhibit off‐responses.     

Models of coding sequence evolution

Probabilistic models of sequence evolution are in widespreaduse in phylogenetics and molecular sequence evolution. Thesemodels have become increasingly sophisticated and combined withstatistical model comparison techniques have helped to shedlight on how genes and proteins evolve. Models of codon evolutionhave been particularly useful, because, in addition to providinga significant improvement in model realism for protein-codingsequences, codon models can also be designed to test hypothesesabout the selective pressures that shape the evolution of thesequences. Such models typically assume a phylogeny and canbe used to identify sites or lineages that have evolved adaptively.Recently some of the key assumptions that underlie phylogenetictests of selection have been questioned, such as the assumptionthat the rate of synonymous changes is constant across sitesor that a single phylogenetic tree can be assumed at all sitesfor recombining sequences. While some of these issues have beenaddressed through the development of novel methods, others remainas caveats that need to be considered on a case-by-case basis.Here, we outline the theory of codon models and their applicationto the detection of positive selection. We review some of themore recent developments that have improved their power andutility, laying a foundation for further advances in the modelingof coding sequence evolution.