A knowledge-based scale for amino acid membrane propensity

In this article, a membrane-propensity scale for amino acids is derived using only two ingredients: (i) a set of transmembrane helices segments from membrane protein crystal structures and (ii) the request that each component of the set has a free energy lower than that of a typical soluble protein sequence of the same length. Although the most widely used hydropathy scales satisfy this request, we use an optimization procedure that allows for extraction of an optimal scale, which correlates equally well with those scales. We show that, if the choice of the sequence database is accurate, significant knowledge-based scales, which are robust with respect to changes in the learning set, can be easily derived. The obtained scales can be used for transmembrane helices prediction. The predictive power of one of these scales is tested on membrane proteins, soluble proteins, and signal peptides databases, finding that its performances is comparable with those of the hydropathy scales.     

Structural peculiarities of the tubercles in the skin of the turbot,Scophthalmus maximus (L., 1758) (Osteichthyes,Pleuronectiformes, Scophthalmidae)

The structure of the bony tubercles of the turbot, Scophthalmus maximus (L., 1758), was examined using ground sections, microradiography, SEM, and TEM. The tubercles are small, isolated, mineralized conical plates randomly distributed in the eyed side of the body. They are composed of three layers: the outer limiting layer, the external layer, and the basal plate, which make up the thin and flat elasmoid scales of Teleostei. The main difference between regular elasmoid scales and bony tubercles lies in the organization and the growth of the basal plate. Indeed, the conical shape of the tubercle is the result of a prominent thickening of the central part of the basal plate where the collagen matrix is organized in a complicated three-dimensional network. Densely packed thick collagen fibrils form superimposed plies organized in a plywood-like structure that resembles that of the elasmoid scales but it is criss-crossed by numerous vertical sheets of thin collagen fibrils. The tubercles originate from thin and flat plates located in the skin of larvae and juveniles, whose structure is that of regular-developing elasmoid scales. Thus, the tubercles of Scophthalmus maximus could be considered as modified elasmoid scales rather than bony structures. They might be the result of specific arrangements related to the general trend of reduction of the dermal skeleton in the teleostean lineage.     

The reliability of approximate reduction techniques in population models with two time scales

As a result of the complexity inherent in some natural systems, mathematical models employed in ecology are often governed by a large number of variables. For instance, in the study of population dynamics we often find multiregional models for structured populations in which individuals are classified regarding their age and their spatial location. Dealing with such structured populations leads to high dimensional models. Moreover, in many instances the dynamics of the system is controlled by processes whose time scales are very different from each other. For example, in multiregional models migration is often a fast process in comparison to the growth of the population.Approximate reduction techniques take advantage of the presence of different time scales in a system to introduce approximations that allow one to transform the original system into a simpler low dimensional system. In this way, the dynamics of the original system can be approximated in terms of that of the reduced system. This work deals with the study of that approximation. In particular, we work with a non-autonomous discrete time model previously presented in the literature and obtain different bounds for the error we incur when we describe the dynamics of the original system in terms of the reduced one.The results are illustrated by some numerical simulations corresponding to the reduction of a Leslie type model for a population structured in two age classes and living in a two patch system.     

Strontium content of scales as a marker for distinguishing between sea trout and brown trout

Strontium was determined in trout scales from a river where it is often difficult to distinguish between sea trout and resident brown trout by coloration or other visual marks. Sr values were compared with values in scales from brown trout caught above the anadromous stretch of the same river and in scales from a river where sea trout coloration is typical. In the first river, the Sr concentration was generally low, and as a mean only 50 ppm higher in scales from individuals classified as sea trout from the anadromous stretch than in brown trout scales from the upper stretch. There was no consistency between fish coloration and Sr concentration in scales from presumed sea trout on the anadromous stretch. Individuals with a typical sea trout coloration could have a lower concentration of Sr than individuals that were classified as uncertain sea trout by coloration. Fish weight did not seem to influence Sr levels. The mean Sr concentration in scales from the typical sea trout colored population in the second river was 2.8 times higher than that of the anadromous part of the first river. The high variability of Sr concentration in sea trout scales may be explained by differences in individual and population life history. The Sr levels reflect differences in saltwater exposure, either expressed by length of stay or concentration of salt in marine habitats. The study has shown that fish coloration is an inadequate mean to distinguish between resident and migratory trout. Nor is Sr determination of scales alone sufficient, because of low inter-group and high intra-group variability in some rivers. However, Sr values can give valuable information on individual and population migration on a large scale.     

黄河三角洲县域绿色经济效率的时空演变与驱动机制

综合测度黄河三角洲地区的绿色经济效率,可为实现黄河三角洲地区生态保护和高质量发展提供参考依据。本研究依托多源遥感数据构建了县域绿色经济效率评价体系,采用考虑非期望产出的Super-EBM模型对黄河三角洲县域绿色经济效率进行了综合测度,运用核密度函数估计等方法刻画了时空演变特征,最后利用系统广义矩估计法识别其影响因素。结果表明: 2000—2015年黄河三角洲县域绿色经济综合效率和纯技术效率呈现波动上升态势,规模效率呈快速提升后保持平稳的类“Γ”型趋势,综合效率的提升由规模-技术驱动向技术主导转变;黄河三角洲县域绿色经济综合效率和纯技术效率呈现由“俱乐部收敛”向“整体收敛”演进趋势,低效率县区对高效率县区形成“追赶效应”,规模效率趋向均衡平稳发展;绿色经济综合效率及其分解效率空间上形成中部高、两翼低的“山”字型格局,高值区集中于黄河三角洲岬角处和莱州湾沿岸,且高值区呈西北-东南向偏移的特征,黄河三角洲东西两翼形成低值塌陷区;产业结构、人口集聚水平、固定资产投资强度对绿色经济效率具有正向影响,人口城镇化率对绿色经济效率具有负向作用,绿色经济效率与经济发展水平之间存在明显的“环境库兹涅茨”效应。     

祁连山国家公园青海片区山水林田湖草的时空分异

祁连山国家公园被确定为我国国家公园体制试点之后,对其生态环境保护、管制、修复提出了更高、更精准的要求。基于1980—2018年遥感影像数据,构建山水林田湖草空间信息格局图谱,分析祁连山国家公园青海片区一般控制区和核心保护区山水林田湖草的时空分异特征。结果表明: 研究期间,草地是公园主体景观,面积为8174.93 km²,其中,核心保护区草地面积是一般控制区的1.2倍;裸岩石质地是未利用土地的主要类型,分别占核心保护区和一般控制区未利用土地面积的86.7%和79.4%;一般控制区的林地面积大于核心保护区;核心保护区的水域面积是一般控制区的4.9倍,核心保护区90.4%的水域面积为永久性冰川雪地;旱地主要集中在一般控制区。1980—2018年间,水域面积呈降低趋势,减少186.75 km²,其中,永久性冰川雪地下降最明显,一般控制区和核心保护区分别下降12.05和175.88 km²;林地、草地整体呈增加趋势,核心保护区高、中、低覆盖度草地的变化趋势均大于一般控制区,1990—2000年变化最明显,1980—2018年一般控制区高、中覆盖度草地和核心保护区高、低覆盖度草地存在退化现象;裸岩石质地呈上升趋势,而永久性冰川雪地呈下降趋势。永久性冰川雪地和裸岩石质地是公园内变化最明显的地类,核心保护区冰川退缩速度比一般控制区退缩速度明显,其转为裸岩石质地主要发生在1980—1990和2000—2010年。     

Ontogenetic variation in the stratum granulosum of the epidermis of Chaetophractus vellerosus (Xenarthra,Dasypodidae) in relation to the development of cornified scales

The epidermis of mammals is characterized by having a stratum granulosum that produces an orthokeratotic stratum corneum, different from the typical reptilian parakeratotic stratum. Nonetheless, some mammals show distinct degrees of parakeratosis in epidermal regions with few or no pilose follicles (e.g., areas subjacent to cornified scales). With respect to the epidermis and the development of cornified scales in the Dasypodidae, previous studies have supported the presence of a continuous stratum granulosum without any variations during ontogeny. This condition, in which the cornified scales develop without a loss of the stratum granulosum, was interpreted as primitive for eutherians. The present contribution expands the knowledge on the epidermis of Chaetophractus vellerosus in distinct ontogenetic stages in order to determine whether the cornified scales show the same developmental pattern as in other eutherians. The presence of a stratum granulosum in C. vellerosus neonates and its reduction in more advanced ontogenetic stages, in direct relationship with cornified scale development, supports the hypothesis that the partial parakeratosis in the xenarthran integument is secondary, as in other eutherians, and can be interpreted as a derived character state.     

Morphological and molecular characterization of the small armoured dinoflagellate Heterocapsa minima (Peridiniales,Dinophyceae)

The dinophycean genus Heterocapsa is of considerable interest as it contains a number of bloom-forming and/or harmful species. Fine structure of organic body scales is regarded as the most important morphological feature for species determination but currently is unknown for the species H. minima described by Pomroy 25 years ago. Availability of a culture of H. minima collected in the south-west of Ireland allowed us to provide important information for this species, including cell size, cell organelle location, thecal plate pattern, body scale fine structure and molecular phylogeny. Light microscopy revealed the presence of one reticulate chloroplast, an elongated centrally located nucleus, and the presence of one pyrenoid surrounded by a starch sheath. Scanning electron microscopy (SEM) of the thecal plate pattern indicated that Pomroy erroneously designated the narrow first cingular plate as a sulcal plate. In addition, SEM revealed as yet unreported details of the apical pore complex and uncommon ornamentations of hypothecal plates. Organic body scales of H. minima were about 400 nm in size, roundish, with a small central hole and one central, six peripheral and three radiating spines. They differ from other body scales described within this genus allowing for positive identification of H. minima. Heterocapsa minima shares gross cell morphological features (hyposome smaller than episome, elongated nucleus in the middle of the cell, one pyrenoid located in the episome on its left side) with H. arctica (both subspecies H. arctica subsp. arctica and H. arctica subsp. frigida), H. lanceolata and H. rotundata. These relationships are reflected in the phylogenetic trees based on LSU and ITS rDNA sequence data, which identified H. arctica (both subspecies), H. rotundata and H. lanceolata as close relatives of H. minima.     

Impact of plasma-protein binding on receptor occupancy: an analytical description

In this paper we analyse the dynamics of an inhibitor I which can either bind to a receptor R or to a plasma protein P. Assuming typical association and dissociation rates, we find that after an initial dose of inhibitor, there are three time scales: a short one, measured in fractions of seconds, in which the inhibitor concentration and the plasma-protein complex jump to quasi-stationary values, a medium one, measured in seconds in which the receptor complex rises to an equilibrium value and a large one, measured in hours in which the inhibitor-receptor complex slowly drops down to zero. We show that the average receptor occupancy, the pharmacologically relevant quantity, taken over, say, 24 h reaches a maximal value for a specific value of the plasma-protein binding constant. Potentially, understanding and exploiting this optimum could be of great interest to those involved in drug discovery and development.     

Courtship dances in the flies of the genus Lispe (Diptera: Muscidae): from the fly's viewpoint

Two predatory fly species, Lispe consanguinea Loew, 1858 and L. tentaculata DeGeer, 1776, inhabit the supralittoral zone at the shore of a fresh-water reservoir. Both species look alike and possess similar "badges," reflective concave silvery scales on the face. Flies occupy different lek habitats. Males of the first species patrol the bare wet sand on the beach just above the surf. Males of the second species reside on the more textured heaps of algae and stones. Courtship and aggressive behaviour of males was video-recorded and analysed frame by frame. Visual stimuli provided by the conspecific partner were computed in the body-fixed space of a fly observer. Males of L. consanguinea perform long pedestrian dances of pendulating circular arcs (frequency 2 s(-1), median radius 2.5 cm, linear velocity 0.130 m/s). Right and left side runs are equally probable. Circular runs are interrupted by standby intervals of average duration 0.35 s. The female views the male as a target covering 2 by 2 ommatidia, moving abruptly with the angular velocity over 200 degrees/s in a horizontal direction down the path of about 50 degrees till the next standpoint. Dancing is evenly distributed around the female. On the contrary, the male fixates the image of the female within the narrow front sector (median +/-10 degrees); the target in his view has 6-7 times less angular velocity and angular span of oscillations, and its image in profile overlays 6-8 by 2 ommatidia. If the female walks, the male combines tracking with voluntary circular dances. Rival males circle about one another at a distance shorter than 15 mm, but not in close contact. Males of L. tentaculata are capable of similar circular courting dances, but do so rarely. Usually they try to mount any partner immediately. In the latter species, male combat consists of fierce wrestling. Flies of both species often walk sideward and observe the partner not in front but at the side.