基于不同标度伪氨基酸组成预测脂肪酶的类型

从序列出发预测某蛋白质是否为脂肪酶以及属于哪种脂肪酶具有重要的理论和应用价值.提出了基于Z标度和T标度的伪氨基酸组成方法提取序列特征值,采用了k-近邻算法回答上述问题.经参数选择后,三种方法在各自最优运行参数下,其1倍交叉验证的结果为:对脂肪酶和非脂肪酶预测精度分别为92.8%、91.4%和91.3%;对脂肪酶类型预测的精度分别为92.3%、90.3%和89.7%.其中基于Z标度伪氨基酸组成效果最佳.基于T标度的次之,但均明显优于其他6种常见的特征值提取方法,并对其可能的原因进行了探讨.     

基于氨基酸组成分布的嗜热和嗜冷蛋白随机森林分类模型

文献报道采用氨基酸组成分布提取特征值能有效提高预测分类精度, 本文采用该方法提取特征值, 使用一种新的组合分类器——随机森林, 从蛋白质一级结构对嗜热和嗜冷蛋白进行分类。通过10倍交叉验证和独立样本测试两种方法检测, 结果表明：当分段数量为1时, 其精度最优, 分别为92.9％和90.2％, 暗示使用基于氨基酸组成分布提取特征值在该算法中并不能有效提高识别精度, 这与报道结果不符, 而该提取方法在SVM中却能适当提高识别精度; 当引入6个新变量后, 其精度分别提高到93.2%和92.2%, ROC曲线下面积分别为0.9771和0.9696, 优于其它组合分类器。     

基于氨基酸组成分布的嗜热和嗜冷蛋白随机森林分类模型

文献报道采用氨基酸组成分布提取特征值能有效提高预测分类精度, 本文采用该方法提取特征值, 使用一种新的组合分类器——随机森林, 从蛋白质一级结构对嗜热和嗜冷蛋白进行分类。通过10倍交叉验证和独立样本测试两种方法检测, 结果表明：当分段数量为1时, 其精度最优, 分别为92.9％和90.2％, 暗示使用基于氨基酸组成分布提取特征值在该算法中并不能有效提高识别精度, 这与报道结果不符, 而该提取方法在SVM中却能适当提高识别精度; 当引入6个新变量后, 其精度分别提高到93.2%和92.2%, ROC曲线下面积分别为0.9771和0.9696, 优于其它组合分类器。     

基于分段伪氨基酸组成成分特征提取方法预测蛋白质亚细胞定位

蛋白质的亚细胞定位与蛋白质的功能密切相关,其定位预测有助于人们了解蛋白质功能.文章提出一种分段伪氨基酸组成成分特征提取方法,采用支持向量机算法对Chou构建的两个蛋白质亚细胞定位数据集(C2129,CS2423)进行了分类研究,并采用总分类精度Q3、内容平衡精度指数Q9等参数评估预测分类系统性能.预测结果表明,基于分段伪氨基酸组成成分特征提取方法的预测性能,优于基于完整蛋白质序列的伪氨基酸组成成分特征提取方法.例如,基于分段矩描述子伪氨基酸组成成分特征提取方法,数据集C2129的Q3和Q9分别为84.7%和60.8%,比基于完整蛋白质序列的矩描述子伪氨基酸组成成分特征提取方法分别提高1.8和2.2个百分点,且Q3比现有Xiao等人的方法提高了9.1个百分点.基于分段伪氨基酸组成成分特征提取方法构成的特征向量不仅包含残基之间的位置信息,而且还包含蛋白质子序列之问的耦合信息,另外蛋白质分段子序列可能和蛋白质的功能域有一定的联系,从而使这一方法能够有效地预测蛋白质亚细胞定位.     

基于氨基酸和二肽组成的蛋白质四级结构分类研究

基于最近邻居算法,从蛋白质一级序列出发,利用蛋白质序列氨基酸组成、二肤组成以及混合组成方法对蛋白质单聚体、二聚体、三聚体、四聚体、五聚体、六聚体和八聚体进行分类研究。结果表明:采用二肽组成编码方法的预洲效果最好,Jackknife检验和独立测试集检验的总体预测精度分别达到90.83%和95.48%,比相同数据集上基于伪氨基酸组成和组分耦合预测的方法提高了12和15个百分点;特别是对于五聚体蛋白,预测精度分别提高了90和50个百分点;说明二肽组成对于蛋白质四级结构分类研究是一种非常有效的特征提取方法。     

支持向量机及组合预测在蛋白质四级结构分类中的应用

目的:基于支持向量机建立一个自动化识别新肽链四级结构的方法,提高现有方法的识别精度.方法:改进4种已有的蛋白质一级序列特征值提取方法,采用线性和非线性组合预测方法建立一个有效的组合预测模型.结果:以同源二聚体及非同源二聚体为例.对4种特征值提取方法进行改进后其分类精度均提升了2～3%;进一步实施线性与非线性组合预测后,其分类精度再次提高了2～3%,使独立测试集的分类精度达到了90%以上.结论:4种特征值提取方法均较好地反应出蛋白质一级序列包含四级结构信息,组合预测方法能有效地集多种特征值提取方法优势于一体.     

集成改进KNN算法预测蛋白质亚细胞定位

基于Adaboost算法对多个相似性比对K最近邻(K-nearest neighbor,KNN)分类器集成实现蛋白质的亚细胞定位预测。相似性比对KNN算法分别以氨基酸组成、二肽、伪氨基酸组成为蛋白序列特征,在KNN的决策阶段使用Blast比对决定蛋白质的亚细胞定位。在Jackknife检验下,Adaboost集成分类算法提取3种蛋白序列特征,3种特征在数据集CH317和Gram1253的最高预测成功率分别为92.4%和93.1%。结果表明Adaboost集成改进KNN分类预测方法是一种有效的蛋白质亚细胞定位预测方法。     

随机森林方法预测膜蛋白类型

膜蛋白的类型与其功能是密切相关的,因此膜蛋白类型的预测是研究其功能的重要手段,从蛋白质的氨基酸序列出发对膜蛋白的类型进行预测有重要意义。文章基于蛋白质的氨基酸序列,将组合离散增量和伪氨基酸组分信息共同作为预测参数,采用随机森林分类器,对8类膜蛋白进行了预测。在Jackknife检验下的预测精度为86.3%,独立检验的预测精度为93.8%,取得了好于前人的预测结果。     

使用伪氨基酸组成和模糊支持向量机预测蛋白质结构类

蛋白质结构类预测是生物信息和蛋白质科学中重要的研究领域.基于Chou提出的伪氨基酸离散模型框架,从蛋白质序列出发,设计一种新的伪氨基酸组成方法表示蛋白质序列样本.抽取氨基酸组合(10-D)在序列中出现的频率和疏水氨基酸模式(6-D)表示蛋白质序列的附加特征,用和传统的氨基酸组成(20-D)一起构成的36维的伪氨基酸组成向量来表示蛋白质序列的特征.使用遗传算法来优化附加特征的权重系数.伪氨基酸组成向量作为输入数据,模糊支持向量机作为预测工具.使用三个常用的标准数据集来验证算法的性能.Jack-knife检验结果说明本方法具有较高的准确率,有望成为潜在的预测蛋白质功能的工具.     

基于氨基酸组成分布的蛋白质同源寡聚体分类研究

基于一种新的特征提取方法——氨基酸组成分布,使用支持向量机作为成员分类器,采用“一对一”的多类分类策略,从蛋白质一级序列对四类同源寡聚体进行分类研究。结果表明,在10-CV检验下,基于氨基酸组成分布,其总分类精度和精度指数分别达到了86.22%和67.12%,比基于氨基酸组成成分的传统特征提取方法分别提高了5.74和10.03个百分点,比二肽组成成分特征提取方法分别提高了3.12和5.63个百分点,说明氨基酸组成分布对于蛋白质同源寡聚体分类是一种非常有效的特征提取方法;将氨基酸组成分布和蛋白质序列长度特征组合,其总分类精度和精度指数分别达到了86.35%和67.23%,说明蛋白质序列长度特征含有一定的空间结构信息。     

Ectogenesis and the case against the right to the death of the foetus

Ectogenesis, or the use of an artificial womb to allow a foetus to develop, will likely become a reality within a few decades, and could significantly affect the abortion debate. We first examine the implications for Judith Jarvis Thomson’s violinist analogy, which argues for a woman’s right to withdraw life support from the foetus and so terminate her pregnancy, even if the foetus is granted full moral status. We show that on Thomson’s reasoning, there is no right to the death of the foetus, and abortion is not permissible if ectogenesis is available, provided it is safe and inexpensive. This raises the question of whether there are persuasive reasons for the right to the death of the foetus that could be exercised in the context of ectogenesis. Eric Mathison and Jeremy Davis have examined several arguments for this right, doubting that it exists, while Joona Räsänen has recently criticized their reasoning. We respond to Räsänen’s analysis, concluding that his arguments are unsuccessful, and that there is no right to the death of the foetus in these circumstances.     

On the diversity of the Cladocera in the tropics

The mythical concept of an impoverished tropical cladoceran fauna is refuted. On a planetary scale, around half of the cladoceran species presently known occur exclusively in the tropics-subtropics, often with considerable restriction to particular geographical subzones. On a regional (political) scale, the situation is often unclear because of the continued fragmentary nature of studies, and because political units are not a good basis for biogeographical comparisons. At the finest level of resolution (lake-perlake comparisons), there appears to be an upper limit of c. 50 cladoceran species per individual lake. No significant difference between lakes in the temperate zone and in the tropics could be established here. Daphnia is largely absent from the tropics, but is replaced by more Sidids, Moinids, and Bosminids, such that the average cladoceran community in the limnetic zone of a tropical lake is not characterized by less species but rather by lower population densities. This, in turn, is considered a consequence of higher prevalent predation levels in the tropics.     

Tubular networks in the terminal endings of the visual receptor cells in the human,the monkey,the cat and the dog

Summary A tubular network was found in the terminal endings of the visual receptor cells in the human, the monkey (Macaca mulatta), the cat and the dog. These tubules are arranged in close groups in the vicinity of the synaptic lamellae and the invaginated dendrites. According to the form, diameter, density of the tubules and to the consistence of the network formed by them one can distinguish at these places an initial type (type I), a transitory (type II) and a vesicular one (type III). In the the type III branching, bizarre forms are frequent. The diameter of all the tubules reaches 500–600 Å, their density and walls being the same as in the synaptic vesicles.Similar networks also occur in the axons of the visual receptor cells of the monkey.

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Zusammenfassung In den Endigungen der Photorezeptorzellen von Mensch, Affe (Macaca mulatta), Katze und Hund kommen aus Tubuli bestehende Komplexe vor. Organellenartig in geschlossenen Gruppen angeordnet, liegen sie in Nähe der synaptischen Lamellen und der invaginierten Dendriten. An diesen Stellen kann man nach Form, Durchmesser, Dichte und Konsistenz der von den Tubuli gebildeten Komplexe drei Typen unterscheiden: 1. einen initialen (Typus I), 2. einen Übergangstypus (Typus II) und 3. einen vesiculären Typus (Typus III). In letzterem kommen häufig verzweigte, bizarre Formen vor. Der Durchmesser sämtlicher Tubuli erreicht 500–600 Å. Ihre Dichte und ihre Wand gleicht denen der synaptischen Vesikel.Ähnliche Komplexe fanden wir auch in den Axonen der Photorezeptorzellen vom Affen.

     

Assessing the Physiological State of the Fucoids from the Barents Sea Littoral by the End of the Polar Night

Methods of amperometry and potentiometric titration were used to follow dark respiration (DR) and apparent photosynthesis (AP) in the fucoids Ascophyllum nodosum (L.) Le Jol, Fucus vesiculosus L., and F. serratus L. from the Barents Sea littoral by the end of the 40-day-long polar night. The macroalgae were shown to manifest species-specific low rates of photosynthesis and respiration. However, in spite of their low photosynthetic status due to the effects of subzero temperature and prolonged low or zero illumination, the macroalgae have been able to restore DR and AP to the initial level already by the day 9; the ability to restore AP depended on the level of illumination. The study of the changes in the carbonate–bicarbonate system in the light and darkness demonstrated that the macroalgae grown in darkness, in contrast to those grown in twilight, could absorb bicarbonate in darkness; however, they lost this capacity after two-day-long illumination at an irradiance of 7 mol/(m² s). Bicarbonate uptake in darkness and the capacity to restore the systems of photosynthesis and respiration in fucoid cells are discussed in the context of algal energy metabolism under the polar night conditions.     

Arranging the elements of the potassium channel: the T1 domain occludes the cytoplasmic face of the channel

The voltage-gated potassium channel is currently one of the few membrane proteins where functional roles have been mapped onto specific segments of sequence. Although high-resolution structures of the transmembrane portions of three bacterial potassium channels, the tetramerization domain and the cytoplasmic ball are available, their relative spatial arrangement in mammalian channels remains a matter of ongoing debate. Cryo-electron microscopic images of the six transmembrane voltage-gated Kv channel have been reconstructed at up to 18 Å resolution, revealing that the T1 domain tetramerizes and is suspended below the transmembrane segments. However, the resolution of these images is insufficient to reveal the location of the third piece of the puzzle, the inactivating ball domain. We have used the aberrant interactions observed in a series of chimæric channels to establish that an assembled T1 domain restricts access to the cytoplasmic face of the channel, suggesting that the N-terminal ball and chain may be confined in the space between the T1 domain and the transmembrane portion of the channel.     

Feeding the vertebrate retina from the Cambrian to the Tertiary

The retina of the vertebrate eye is metabolically active and requires nutritive support. During the last 540 million years it has evolved into forms as complicated and nutritionally demanding as those found in avian or primate eyes. Diffusion from the choroid is generally able to supply the metabolic needs of thin retinae. However, when the thickness exceeds the limits of diffusion, structures are needed to supplement the vascular supply from the choroid. These supplemental nutritive devices include the choroidal gland, the falciform process and preretinal vascular plexus of fish, the conus papillaris of lizards, the pecten oculi of birds, the intraretinal vessels of mammals and a few novel systems that remain difficult to classify. These vascular systems are among the most variable features of the vertebrate eye. Here, we review classical and recent findings regarding such retinal nutrition systems, propose a three category classification for them based on histologic origins and speculate on the evolutionary forces which drove their development.     

Observations on the permeability of the choriocapillaris of the eye

Summary The choriocapillaris is a fenestrated capillary bed located posterior to the retinal pigment epithelium. It serves as the main source of supply to the photoreceptors, retinal pigment epithelium, and other cells of the outer retina. The permeability of these capillaries to intravenously injected ferritin (MW — approx. 480,000; mol. diam. 11 nm) was examined in the mouse, rabbit, and guinea pig, each of which is characterized by a different type of retinal vascularization. In all three species, the bulk of the ferritin remained in the capillary lumina, where it appeared to be blocked at the level of the diaphragmed fenestrae. Some ferritin was present in endothelial cell vacuoles. The results confirm previous work on the rat choriocapillaris and indicate that the barrier function of the choriocapillary endothelium is present even among species in which the retinal circulation differs significantly.Supported by NIH grant EY03418     

Separation of the pineal vesicle from the wall of the third ventricle during the post-hatching development of the chicken

Summary According to light- and electron-microscopic observations the pineal organ of the 3-day-old chicken consists of a prominent end vesicle and a tapering parenchymal stalk. During this stage the pineal lumen is in open communication with the third ventricle. However, in the 40-day-old chicken, which still possesses a well-developed end vesicle, the proximal portion of the pineal stalk displays regressive changes leading to local fragmentation. At this stage the pineal stalk is reduced, and the pineal lumen is missing. In 1-year-old chickens the parenchyma of the proximal portion of the stalk is further diminished, and in 3-year-old domestic fowl is completely displaced by bundles of collagenous fibers, only some nerve fibers being present. This post-hatching pineal development may reflect the sequence of changes leading from pineal sense organs to pineal glands.This work was supported by a grant-in-aid for Scientific Research from the Ministry of Education, Science and Culture of Japan