Use of overall dynamic body acceleration for estimating energy expenditure in cormorants: Does locomotion in different media affect relationships?

The way in which animals use and acquire energy is fundamental to their fitness. Overall dynamic body acceleration (ODBA) has recently been suggested as a new method for the determination of energy expenditure in wild animals. Although the relationship between ODBA and energy expenditure has been calibrated using gas-respirometry, it has only been validated for animals moving in a single medium. In this work we examined whether the relationship between ODBA and energy expenditure varies between activity types and in particular, how locomotion in different media affects the regressions using the Imperial Cormorant Phalacrocorax atriceps as a model species. Regressing mean ODBA values for resting, diving and walking periods on a single graph against mean power values, the mass-specific power (W kg⁻¹) was related to ODBA via; Power = 12.09 + 41.31 ODBA (r² = 0.93). Although values for resting, walking and swimming all fell close to a single linear fit, values for flight deviated substantially from this. The different relationships found between locomotory types are discussed in terms of the muscle groups involved in each kind of behavior.     

Repeatable measures of take-off flight performance in auklets

Rapid acceleration is the key to a successful escape manoeuvre and has attracted considerable research attention in a wide array of taxa. I recorded take-offs of least auklets Aethia pusilla and crested auklets Aethia cristatella with digital video (60 frames per second). To smooth time–location data derived from video, I used predicted mean square error quintic splines, which have been shown to be good predictors of true acceleration. Repeated recordings of the same individual bird allowed me to measure repeatability of take-off acceleration and velocity to find the most robust and biologically meaningful measure. The most repeatable take-off parameters were power at time t =0.17 s after take-off ( r =75%) and acceleration at t =0.17 s ( r =72%). The horizontal component of velocity at t =0.32 s was least affected by the slope of the take-off trajectory. The mean acceleration of both species is close to expected values based on body mass, even though all previously studied species had considerably lower body mass. Within least auklets, however, I did not find a significant relationship of velocity or acceleration with mass. This would be expected if the observed drop in mass after hatching was an adaptation to reduce the risk of predation. I conclude that acceleration and exerted power at a certain time after take-off is repeatable and the most suitable measure of performance for both inter- and intra-specific comparisons.     

Performance improvements for iterative electron tomography reconstruction using graphics processing units (GPUs)

Iterative reconstruction algorithms are becoming increasingly important in electron tomography of biological samples. These algorithms, however, impose major computational demands. Parallelization must be employed to maintain acceptable running times. Graphics Processing Units (GPUs) have been demonstrated to be highly cost-effective for carrying out these computations with a high degree of parallelism. In a recent paper by Xu et al. (2010), a GPU implementation strategy was presented that obtains a speedup of an order of magnitude over a previously proposed GPU-based electron tomography implementation. In this technical note, we demonstrate that by making alternative design decisions in the GPU implementation, an additional speedup can be obtained, again of an order of magnitude. By carefully considering memory access locality when dividing the workload among blocks of threads, the GPU’s cache is used more efficiently, making more effective use of the available memory bandwidth.     

Development of hematological respiratory variables in late chicken embryos: the relative importance of incubation time and embryo mass

Oxygen demand increases during embryonic development, requiring an increase in red blood cells (RBCs) containing hemoglobin (Hb) to transport O(2) between the respiratory organ and systemic tissues. A thorough ontogenetic understanding of the onset and maturation of the complex regulatory processes for RBC concentration ([RBC]), Hb concentration ([Hb]), hematocrit (Hct), mean corpuscular indices (mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH) and mean corpuscular hemoglobin concentration ([MCHb])) is currently lacking. We hypothesize that during the last half of incubation when the respiratory organ (the chorioallantoic membrane) envelops most of the egg contents, mean corpuscular indices will stabilize. Accordingly, Hct, [RBC] and [Hb] must also all change proportionally across development. Further, we hypothesize that the hematological respiratory variables develop and mature as a function of incubation duration, independently of embryonic growth. As predicted, a similar increase in Hct (from 18.7±0.6% on day 10 (d10) to 34.1±0.5% on d19 of incubation), [RBC] (1.13±0.03×10(6)/μL to 2.50±0.03×10(6)/μL) and [Hb] (6.1±0.2 g% to 11.2±0.1 g%) occurred during d10-19. Both [RBC] and [Hb] demonstrated high linear correlation with Hct, resulting in constant [MCHb] (~33 g% from d10 to d19). The decrease in MCV (from ~165 μ(3) on d10 to ~140 μ(3) on d13) and MCH (~55 pg to ~45 pg) during d10-13, may be attributed to a changeover from larger primary to smaller secondary and adult-type erythrocytes with MCV and MCH remaining constant (~140 μ(3) and ~45 pg respectively) for the rest of the incubation period (d13-19). Hematological respiratory values on a given incubation day were identical between embryos of different masses using either natural mass variation or experimental growth acceleration, indicating that the hematological variables develop as a function of incubation time, irrespective of embryo growth.     

动物离心机中大鼠行为状态无线视频采集装置的研制

目的:研制一种在正加速度作用下能实时观测大鼠行为状态的实验视频采集装置,为研究正加速度导致脑损伤的病理生理机制和防治措施提供新的方法。方法:依据正加速度对大鼠体位的要求和离心机特殊的环境,通过特制的大鼠座舱和无线视频采集单元来实现对动物离心机中正加速度作用下大鼠行为状态的实时观测;固定大鼠的座舱主要由胸部固定圈、身长调节圈、头部运动限制框构成;无线视频采集单元由2.4 G无线摄像头、无线信号接收器、信号放大器、计算机以及视频采集软件组成。结果:座舱特殊的大鼠固定方式,既满足了正加速度对体位的要求,又不影响对大鼠行为状态的观测,2.4 G无线视频采集技术保证视频信号在离心机高速旋转环境下的实时传输和观测,视频画面清晰流畅,并且能保存视频供回放分析。结论:动物离心机无线视频采集装置可用于正加速度作用下大鼠行为状态的实时观测与研究。     

Understanding How H‐NOX (Heme Nitric Oxide/Oxygen) Domain Works Needs First Clarifying How Diatomic Gases Are Relocated Inside This Sensing Protein. A Molecular‐Mechanics Approach

H‐NOX (Heme Nitric Oxide/Oxygen) domain has widespread occurrence, either standalone or associated with functional proteins, sending signals for functions that span from modulating vasodilation and neurotransmission with humans to competition and symbiosis with bacteria. Understanding how H‐NOX works, and possibly intervening on degeneration for health purposes, needs first clarifying how diatomic gases are relocated through this protein in relation to the deeply buried heme. To this end, a biased form of molecular dynamics, i.e., Random Accelaration Molecular Dynamics (RAMD), is used by applying a randomly oriented tiny force to heme‐dissociated CO of Nostoc sp. H‐NOX, while changing randomly the direction of the force, if CO travels less than specified for the evaluated block. The result is that a large area of the protein, comprising amino acids from serine 44 to leucine 67 along two adjacent helices, offers a broad portal to CO from the surrounding medium to the deeply buried heme. Most traffic is concentrated through a channel lined by tyrosine 49, valine 52, and leucine 67. This modifies the picture drawn from mapping Xe cavities on pressurizing Nostoc sp. H‐NOX with Xe gas. What is the main pathway with Xe‐cavity mapping becomes a minor pathway with RAMD, and vice versa. The reason is that the fluctuating protein under MD creates clefts for CO slipping through, as it is expected to occur in nature.     

Electron transfer and proton pumping under excitation of dark-adapted chloroplasts with flashes of light

Proton release inside thylakoids, which is linked to the action of the water-oxidizing enzyme system, was investigated spectrophotometrically with the dye neutral red under conditions when the external phase was buffered. Under excitation of dark-adapted chloroplasts with four short laser flashes in series, the pattern of proton release as a function of the flash number was recorded and interpreted in the light of the generally accepted scheme for consecutive transitions of the water-oxidizing enzyme system: S₀ → S₁, S₁ → S₂, S₂ → S₃, S₃ → S₄, S₀. It was found that the proton yield after the first flash varied in a reproducible manner, being dependent upon the dark pretreatment given. In terms of the proton-electron reaction during these transitions, the pattern was as follows. In strictly dark-adapted chloroplasts (frozen chloroplasts thawed in darkness and kept for at least 7 min in the dark after dilution), it was fitted well by a stoichiometry of 1:0:1:2. In a less stringently dark-adapted preparation (as above but thawed under light), it was fitted by 0:1:1:2. Mechanistically this is not yet understood. However, it is a first step towards resolving controversy over this pattern among different laboratories. Under conditions where the 1:0:1:2 stoichiometry was observed, proton release was time resolved. Components with half-rise times of 500 and 1000 μs could be correlated with the S₂ → S₃ and S₃ → S₄ transitions, respectively. Proton release during the S₀ → S₁ transition is more rapid, but is less well attributable to the transitions due to error proliferation. A distinct component with a half-rise time of only 100 μs was observed after the second flash. Since it did not fit into the expected kinetics (based on literature data) for the S_i → S_i+1 transitions, we propose that it reflects proton release from a site which is closer to the reaction center of Photosystem (PS) II than the water-splitting enzyme system. This is supported by the observation of rapid proton release under conditions where water oxidation is blocked. Related experiments on the pattern of proton uptake at the reducing side of PS II indicated that protons act as specific counterions for semiquinone anions without binding to them.     

全基因组基因-基因相互作用研究现状

复杂疾病目前正在全球范围流行, 极大地影响人类的健康。研究发现, 复杂疾病的性状受到多个位点的相互作用影响。目前的全基因组关联分析(Genome-wide association study, GWAS)仅仅解析单个SNP位点对疾病易感性的贡献, 单纯依靠这一种策略并不能在寻找复杂疾病的病因上得到根本性的突破。基因-基因相互作用可能是复杂疾病致病的主要因素之一。针对这一点, 科学家已经提出了一些检验基因相互作用的算法, 包括惩罚logistic回归模型、多因子降维(Multifactor dimensional reduction)、集合关联法(Set-association approach)、贝叶斯网络(Bayesian networks)、随机森林法等。文章首先对目前这些方法做了综述, 并指出了其中的不足, 包括计算复杂度太高、假设驱动、数据会过度拟合、对低维数据不敏感等, 进而简述了一种由笔者所在实验室开发的基于GPU的研究基因相互作用的算法, 该算法复杂度低, 不需要任何假设, 没有边际效应, 有很好的稳定性, 速度快, 适用于进行全基因组范围内的基因-基因相互作用计算。