Changes in size and age at maturity of the northern stock of Tilefish (Lopholatilus chamaeleonticeps) after a period of overfishing

The modern fishery for Tilefish (Lopholatilus chamaeleonticeps) developed during the 1970s, offshore of southern New England, in the western North Atlantic Ocean. The population quickly became over exploited, with documented declines in catch rates and changes in demographic traits. In an earlier study, median size at maturity (L50) of males declined from 62.6 to 38.6 cm fork length (FL) and median age at maturity (A50) of males declined from 7.1 to 4.6 years between 1978 and 1982. As part of a cooperative research effort to improve the data-limited Tilefish assessment, we updated maturity parameter estimates through the use of an otolith aging method and macroscopic and microscopic evaluations of gonads. The vital rates for this species have continued to change, particularly for males. By 2008, male L50 and A50 had largely rebounded, to 54.1 cm FL and 5.9 years. Changes in female reproductive schedules were less variable among years, but the smallest L50 and youngest A50 were recorded in 2008. Tilefish are dimorphic, where the largest fish are male, and male spawning success is postulated to be socially mediated. These traits may explain the initial rapid decline and the subsequent rebound in male L50 and A50 and less dramatic effects on females. Other factors that likely contribute to the dynamics of maturity parameter estimates are the relatively short period of overfishing and the amount of time since efforts to rebuild this fishery began, as measured in numbers of generations. This study also confirms the gonochoristic sexual pattern of the northern stock, and it reveals evidence of age truncation and relatively high proportions of immature Tilefish in the recent catch.

新生代孢粉分析与古气候定量重建的研究

定量重建地球生态系统的气候参数是当前国际古气候研究的目标之一. 自20世纪70年代以来, 尤其是在海洋学研究领域, 新技术的不断应用使得定量的古气候研究蓬勃发展. 相比之下陆地古气候参数的重建要困难得多, 陆地植物作为对环境的良好记录，一直备受重视. 近数十年来, 国际上广泛开展了利用植物材料定量研究气候的探索, 大量新的方法层出不穷. 德国科学家Mosbrugger和Utescher在1997年倡导的共存分析法(The Coexistence Approach)就是其中之一, 它依据现存最近亲缘类群原理以及植物分布与气候的关系原理, 找到化石植物群中各类群的现存最近亲缘类群对各气候参数的耐受范围; 并将各亲缘类群对同一气候参数的耐受范围叠加一起, 获得对该气候参数的共存区间, 用该区间作为对古气候参数的精确估测. 本文首先阐述在原文位于展开讨论的共存分析的理论基础——探讨植物分布与气候之间关系的耐受性理论. 并以此为指导, 对在该方法中气候台站的选用方法作了改进, 气象台站的选择应以植物的标本记录点为基础: 即使在某一特定的植物分布区内部也应该查看气象台站所在县级行政区域是否有该植物的标本采集信息, 并以此为依据来决定是否选用该气象台站的记录; 选用的气象台站的数量多寡应该以植物分布点的多少来决定. 以此为基础, 我们采用中国的植物分布与气象记录数据, 利用孢粉学的研究结果，定量重建了我国新生代三个地点的古气候参数, 结果如下: 1.内蒙古呼伦湖地区全新世初期气候 MAT: 4.4~10.2℃; MWMT: 22.9~24.1℃; MCMT: -18~-9.1℃; DT: 33.5~40.9℃; MAP: 354.3~686.7mm; MMaP: 103.8~191.9mm; MMiP: 2.7~7.3mm. 我们以扎赉诺尔地区的孢粉学研究为基础, 依据孢粉和盘星藻(Pediastrum Meyen)提供的环境信息并结合前人工作, 恢复了全新世初升温期的植被变化; 定量重建了10.4~10.2kaB.P.时的气候, 为全面理解呼伦湖地区的气候变化以及东亚的夏季风变化提供新的依据. 2.云南洱源上新世气候 MAT: 13.3~18.6℃; MWMT: 24.6~27.5℃; MCMT: 1.9~12.1℃; DT: 14.2~16.6℃; MAP: 619.9~1484.3mm; MMaP: 143.8~245.6mm; MMiP: 12.7~16.4mm. 该结果与羊邑、龙陵上新世古气候及三地的现代气候分析对比表明, 在上新世, 三地年均温符合纬向变化, 而降水量则基本一致. 在现代，洱源与羊邑在气候与植被上很相近, 且与上新世相差不大; 而龙陵地区则发生了显著的变化, 年均温比上新世低, 而降水量则大幅增加. 该变化指示了上新世以来作为青藏高原东部边缘的龙陵地区可能出现了地形的抬升. 3.吉林珲春始新世和中新世气候 始新世: MAT: 14.3~14.9℃; MWMT: 25~26.3℃; MCMT: 1.9~3.7℃; DT: 21.7~23℃; MAP: 797.5~1344mm; MMaP: 185.3~209.8mm; MMiP: 14.2~16.4mm. 中新世: MAT: 14.3~14.9℃; MWMT: 24.3~25.4℃; MCMT: 2.1~3.7℃; DT: 21.7~22.7℃; MAP: 658.7~817.7mm; MMaP: 158.9~174.6mm; MMiP: 7.4~7.6mm. 通过对两个时段的气候参数对比, 始新世时, 吉林珲春地区的气候属于北亚热带气候; 中新世时气候发生了改变, 归属于暖温带南部的气候, 改变了前人关于中新世也归属于被亚热带的认识, 这反映了我国东北部地区与全球新生代降温总趋势具有一定的同步性.

On-line learning of mutually orthogonal subspaces for face recognition by image sets.

We address the problem of face recognition by matching image sets. Each set of face images is represented by a subspace (or linear manifold) and recognition is carried out by subspace-to-subspace matching. In this paper, 1) a new discriminative method that maximises orthogonality between subspaces is proposed. The method improves the discrimination power of the subspace angle based face recognition method by maximizing the angles between different classes. 2) We propose a method for on-line updating the discriminative subspaces as a mechanism for continuously improving recognition accuracy. 3) A further enhancement called locally orthogonal subspace method is presented to maximise the orthogonality between competing classes. Experiments using 700 face image sets have shown that the proposed method outperforms relevant prior art and effectively boosts its accuracy by online learning. It is shown that the method for online learning delivers the same solution as the batch computation at far lower computational cost and the locally orthogonal method exhibits improved accuracy. We also demonstrate the merit of the proposed face recognition method on portal scenarios of multiple biometric grand challenge.

Fundamental limits on the suppression of molecular fluctuations.

Negative feedback is common in biological processes and can increase a system's stability to internal and external perturbations. But at the molecular level, control loops always involve signalling steps with finite rates for random births and deaths of individual molecules. Here we show, by developing mathematical tools that merge control and information theory with physical chemistry, that seemingly mild constraints on these rates place severe limits on the ability to suppress molecular fluctuations. Specifically, the minimum standard deviation in abundances decreases with the quartic root of the number of signalling events, making it extremely expensive to increase accuracy. Our results are formulated in terms of experimental observables, and existing data show that cells use brute force when noise suppression is essential; for example, regulatory genes are transcribed tens of thousands of times per cell cycle. The theory challenges conventional beliefs about biochemical accuracy and presents an approach to the rigorous analysis of poorly characterized biological systems.

蔷薇类的分子系统学研究—兼论系统发育基因组学的原理和方法(以SET基因超家族为例)

分子系统发育分析的主要任务包括：（1）帮助建立生命之树（tree of life）;（2）追踪基因和基因家族（gene family）的起源和进化, 以获知基因在进化过程中的功能分化和伴随发生的重要分子事件（key molecular events）和形态性状的关键创新（key innovation）。这两个方面在本研究中都有所涉及。对于前者，选用植物线粒体matR基因重建被子植物蔷薇类群的系统发育关系;对于后者，则以SET基因超家族为例，探讨其在真核生物中的进化分类以及与功能多样性的关系。 I 蔷薇类的分子系统学 蔷薇类（rosids）是基于分子数据建立的被子植物的主要分支之一，包含13个目，大约三分之一的被子植物物种。两个主要蔷薇类内部分支是豆类fabids（包含7个目）和锦葵类malvids（包含3个目）。然而，这两个分支内部，以及这两个分支与蔷薇类基部类群，包括牻牛儿苗目（Geraniales）、桃金娘目（Myrtales）和流苏子目（Crossosomatales）之间的关系大多是不清楚的。本研究中，我们选取174个物种来代表72个蔷薇类（rosids）的科，利用两个数据集，即线粒体matR单基因数据集和包括线粒体matR基因、两个质体基因(rbcL、 atpB)和一个核基因(18S rDNA) 的4基因数据集，重建蔷薇类在科以上分类阶元水平的系统发育关系。同时，还对线粒体matR基因的进化特征和用于大尺度系统发育分析的适合度和潜力进行了评价。 线粒体matR单基因数据支持malvids和大多数蔷薇类目的单系性质，然而，豆类（fabids）成员没有形成一个分支，其COM亚支，包括卫矛目（Celastrales）、酢浆草目（Oxalidales）、金虎尾目（Malpighiales）和蒜树科（Huaceae），分辨为锦葵类（malvids）的姐妹群。这个关系在最近根据花结构特征曾被提出过，但从未在之前的分子系统发育分析中得到分辨。4基因数据集支持首先是牻牛儿苗目（Geraniales），接着是桃金娘目（Myrtales）作为蔷薇类（rosids）的最基部的分支;流苏子目（Crossosomatales）是锦葵类（malvids）姐妹群，以及蔷薇类（rosids）的核心部分包括豆类（fabids），锦葵类（malvids）和流苏子目（Crossosomatales）。线粒体matR基因的进化特征分析显示，与两个叶绿体基因(rbcL 和atpB)比较，同义替代速率约是它们的1/4，而非同义替代速率接近于自身的同义替代速率，表明matR 基因具有松弛的选择压力。线粒体matR基因相对慢速的进化使非同源相似（homoplasious）突变减少，提高了系统发育信息的质量，同时，松弛的选择压力使非同义替代数量增加，弥补了慢速进化导致的系统发育信息数量不足的缺陷，这两个方面的结合使线粒体matR基因非常适用于被子植物在科以上水平的系统发育研究。 II SET基因超家族的系统发育基因组学分析 SET基因超家族基因编码含有SET结构域的蛋白，在真核生物中，SET-domain蛋白一般是多结构域（multi-domain）的。SET-domain蛋白具有对组蛋白H3和H4的N末端尾部进行赖氨酸残基甲基化修饰的酶活性;从异染色质形成到基因转录，甲基化的组蛋白广泛影响染色质水平的基因调控。依据SET结构域一级序列的相似性和结构域组织（domain architecture）特征，目前，SET-domain基因超家族被划分为4-7个家族。由于这些划分或者使用动物或者使用植物SET基因，只有少数其它类群的物种加入分析，因此这样的划分可能是不完整的。本研究采用系统发育基 因组学方法（phylogenomic approach），在真核生物范围内广泛取样，期望获得相对完整的SET-domain基因家族的 进化分类方案，在此基础上加深理解SET-domain基因的进化机制和功能多样性。 在提取了17个物种，代表5个真核超群的SET蛋白序列基础上，系统发育分析结合“结构域组织特征”鉴别了9个SET基因家族，其中一个是新的SET基因家族。以前的SET8和Class VI家族,及SMYD和SUV4-20家族分别合并为一个家族。大部分家族在进化过程中发生了2次以上的基因重复事件，通过获得不同的结构域产生具有不同功能的新基因。一个SET基因家族在进化过程中推测发生了从脊椎动物祖先向盘基网柄菌（Dictyostelium discoideum）的水平基因转移。

Electroosmotic flow analysis of a branched U-turn nanofluidic device.

In this paper, we present the analysis of electroosmotic flow in a branched -turn nanofluidic device, which we developed for detection and sorting of single molecules. The device, where the channel depth is only 150 nm, is designed to optically detect fluorescence from a volume as small as 270 attolitres (al) with a common wide-field fluorescent setup. We use distilled water as the liquid, in which we dilute 110 nm fluorescent beads employed as tracer-particles. Quantitative imaging is used to characterize the pathlines and velocity distribution of the electroosmotic flow in the device. Due to the device's complex geometry, the electroosmotic flow cannot be solved analytically. Therefore we use numerical flow simulation to model our device. Our results show that the deviation between measured and simulated data can be explained by the measured Brownian motion of the tracer-particles, which was not incorporated in the simulation.