Cichlid spawning structures – bowers or nests?

Males of mouthbrooding cichlids build sand-castle or sand-scrape structures. These are used as display sites to attract females, eggs are laid and inseminated there and then taken away by the female for brooding elsewhere. It has been suggested that the structure be called a bower because it has the same role as the bowerbird's bower. Thew word bower is restricted in ornithological literature to complex structures which reminded Gould (1840) of garden bowers. Simpler display sites of other bowerbirds and other bird families are called courts. Bowerbirds use separate nests for egg-laying, cichlids do not. Other birds, e.g. many weavers, use nests for display purposes. The cichlid structure is the same as nests used by other non mouthbrooding fishes, but mouthbrooding has freed females from the need to stay in the nest. It is unacceptable to use the word bower for the cichlid structure because it is not a bower as defined in ornithological literature, and it is used for egg laying as well as display. Weaver birds use nests for display in a similar way to cichlids, thus the word nest should be retained for the cichlid sand structure. This revised version was published online in July 2006 with corrections to the Cover Date.     

Artificial intelligence-guided analysis of cytologic data

A design for the integration of artificial intelligence (AI) technology with large databases of clinical and objective cytologic data, such as are on file at the University of Chicago, is presented. Among the key features of this approach are the use of a knowledge representation structure based upon an associative network, the use of a Bayesian belief network as a method of managing uncertainty in the system, and the use of neural networks and unsupervised learning algorithms as a means of discovering patterns within this database. Such an automated approach is necessary, given the complexity and interdependence of these data, to gain an understanding of their dependence structure and to assist in their exploration and analysis.     

Use of infrared spectroscopy to monitor protein structure and stability

One of the most versatile methods for monitoring the structure of proteins, either in solution or in the solid state, is Fourier transform infrared spectroscopy. Also known as mid-range infrared, which covers the frequency range from 4000 to 400 cm^-1, this wavelength region includes bands that arise from three conformationally sensitive vibrations within the peptide backbone (amide I, II and III). Of these vibrations, amide I is the most widely used and can provide information on secondary structure composition and structural stability. One of the advantages of infrared spectroscopy is that it can be used with proteins that are either in solution or in the solid state. The use of infrared to monitor protein structure and stability is summarized herein. In addition, specialized infrared methods are presented, such as techniques for the study of membrane proteins and oriented samples. In addition, there is a growing body of literature on the use of infrared to follow reaction kinetics and ligand binding in proteins, as well as a number of infrared studies on protein dynamics. Finally, the potential for using near-infrared spectroscopy to study protein structure is introduced.     

Protein function prediction using local 3D templates

The prediction of a protein's function from its 3D structure is becoming more and more important as the worldwide structural genomics initiatives gather pace and continue to solve 3D structures, many of which are of proteins of unknown function. Here, we present a methodology for predicting function from structure that shows great promise. It is based on 3D templates that are defined as specific 3D conformations of small numbers of residues. We use four types of template, covering enzyme active sites, ligand-binding residues, DNA-binding residues and reverse templates. The latter are templates generated from the target structure itself and scanned against a representative subset of all known protein structures. Together, the templates provide a fairly thorough coverage of the known structures and ensure that if there is a match to a known structure it is unlikely to be missed. A new scoring scheme provides a highly sensitive means of discriminating between true positive and false positive template matches. In all, the methodology provides a powerful new tool for function prediction to complement those already in use.     

Use of infrared spectroscopy to monitor protein structure and stability

One of the most versatile methods for monitoring the structure of proteins, either in solution or in the solid state, is Fourier transform infrared spectroscopy. Also known as mid-range infrared, which covers the frequency range from 4000 to 400 cm(-1), this wavelength region includes bands that arise from three conformationally sensitive vibrations within the peptide backbone (amide I, II and III). Of these vibrations, amide I is the most widely used and can provide information on secondary structure composition and structural stability. One of the advantages of infrared spectroscopy is that it can be used with proteins that are either in solution or in the solid state. The use of infrared to monitor protein structure and stability is summarized herein. In addition, specialized infrared methods are presented, such as techniques for the study of membrane proteins and oriented samples. In addition, there is a growing body of literature on the use of infrared to follow reaction kinetics and ligand binding in proteins, as well as a number of infrared studies on protein dynamics. Finally, the potential for using near-infrared spectroscopy to study protein structure is introduced.     

旅游生态安全约束下张家界市土地利用优化

土地利用多以经济、社会和生态效益最大化为目标进行数量结构优化,很少对旅游生态安全约束下的土地利用进行空间结构优化,鉴于此,为提高旅游城市土地利用综合效益和改善生态环境,在旅游生态安全约束下,不仅对土地利用数量结构进行优化,而且实现了土地利用空间结构优化。以典型旅游城市张家界为例,构建旅游生态安全评价指标体系,运用灰色线性规划法中的Lingo模型求取旅游生态安全约束下的最优土地利用结构,并根据分布规则把优化后的数量结构配置在空间上,借助CLUE-S模型进行土地利用空间优化。结果表明:(1)2015年旅游生态安全综合指数为0.7394,旅游环境状况和旅游人文社会响应的安全度均比旅游资源环境压力低。(2)在数量结构优化下,林地、水域、建设用地面积增幅明显,耕地、草地和未利用地的面积有所减少,2025年旅游生态安全综合指数为0.8196,比2015年提高了0.0802,处于安全的状态。(3)在空间结构优化下,林地主要分布在桑植县和慈利县的山地丘陵区、武陵源区以及永定区南部;建设用地主要集中在慈利县、桑植县及永定区城区;草地主要位于桑植县和慈利县的山区以及武陵源区;耕地主要分布在慈利县和永定区的平原和丘陵地区;未利用地零星分布在慈利县、桑植县及永定区。研究结果可为张家界市土地资源永续利用和旅游生态安全建设提供规划指导和技术借鉴。     

Topology of Type II REases revisited; structural classes and the common conserved core

Type II restriction endonucleases (REases) are deoxyribonucleases that cleave DNA sequences with remarkable specificity. Type II REases are highly divergent in sequence as well as in topology, i.e. the connectivity of secondary structure elements. A widely held assumption is that a structural core of five beta-strands flanked by two alpha-helices is common to these enzymes. We introduce a systematic procedure to enumerate secondary structure elements in an unambiguous and reproducible way, and use it to analyze the currently available X-ray structures of Type II REases. Based on this analysis, we propose an alternative definition of the core, which we term the alphabetaalpha-core. The alphabetaalpha-core includes the most frequently observed secondary structure elements and is not a sandwich, as it consists of a five-strand beta-sheet and two alpha-helices on the same face of the beta-sheet. We use the alphabetaalpha-core connectivity as a basis for grouping the Type II REases into distinct structural classes. In these new structural classes, the connectivity correlates with the angles between the secondary structure elements and with the cleavage patterns of the REases. We show that there exists a substructure of the alphabetaalpha-core, namely a common conserved core, ccc, defined here as one alpha-helix and four beta-strands common to all Type II REase of known structure.     

Habitat preference in the critically endangered yellow‐tailed woolly monkey (Lagothrix flavicauda) at La Esperanza,Peru

Habitat loss is one of the main threats to wildlife. Therefore, knowledge of habitat use and preference is essential for the design of conservation strategies and identification of priority sites for the protection of endangered species. The yellow‐tailed woolly monkey (Lagothrix flavicauda Humboldt, 1812), categorized as Critically Endangered on the IUCN Red List, is endemic to montane forests in northern Peru where its habitat is greatly threatened. We assessed how habitat use and preference in L. flavicauda are linked to forest structure and composition. The study took place near La Esperanza, in the Amazonas region, Peru. Our objective was to identify characteristics of habitat most utilized by L. flavicauda to provide information that will be useful for the selection of priority sites for conservation measures. Using presence records collected from May 2013 to February 2014 for one group of L. flavicauda, we classified the study site into three different use zones: low‐use, medium‐use, and high‐use. We assessed forest structure and composition for all use zones using 0.1 ha Gentry vegetation transects. Results show high levels of variation in plant species composition across the three use zones. Plants used as food resources had considerably greater density, dominance, and ecological importance in high‐use zones. High‐use zones presented similar structure to medium‐ and low‐use zones; thus it remains difficult to assess the influence of forest structure on habitat preference. We recommend focusing conservation efforts on areas with a similar floristic composition to the high‐use zones recorded in this study and suggest utilizing key alimentation species for reforestation efforts.     

Prediction of RNA secondary structure by free energy minimization

RNA secondary structure is often predicted from sequence by free energy minimization. Over the past two years, advances have been made in the estimation of folding free energy change, the mapping of secondary structure and the implementation of computer programs for structure prediction. The trends in computer program development are: efficient use of experimental mapping of structures to constrain structure prediction; use of statistical mechanics to improve the fidelity of structure prediction; inclusion of pseudoknots in secondary structure prediction; and use of two or more homologous sequences to find a common structure.     

Saltmarsh as habitat for fish and nektonic crustaceans: Challenges in sampling designs and methods

This is a review of research into the ecological role of saltmarsh as habitat used directly by fish and nektonic crustaceans such as shrimp (prawns) and portunid crabs. The quality of information about direct use of saltmarshes by nekton is poor, with even the most influential works suffering from obvious limitations. Attempts to generalize about nekton use of saltmarshes are hampered by sampling difficulties, poor sampling design, and inconsistent reporting of flooding regime and landscape structure. The difficulty in sampling nekton from shallow, vegetated marsh flats while inundated contributes to the fragmentary results of nekton work. A range of sampling methods have been described that vary in portability, size, amount of above-ground structure, escape rates of nekton, and expense; none has yet become standard. Poor experimental design in studies of saltmarsh nekton includes lack of replication, limited spatial scale, and lack of baseline data before management changes are made. Attempts to determine effects on commercial fisheries of losses in area or quality of saltmarsh by correlations between catch data and marsh loss should use active adaptive management. A second type of study, aimed at understanding how the saltmarsh is important to fisheries, can be tackled usefully at a smaller scale. To assist in the comparison of results from different studies, flooding regime should be reported as a proportion of time the marsh is submerged, and landscape structure as proportions of the marsh that are covered by intertidal flats, pools and drainage creeks. Flooding regime and landscape structure at the sites and at the time of sampling should then be put in the context of the typical pattern for the marsh under study.     

The structure of G117H mutant of butyrylcholinesterase: Nerve agents scavenger

Organophosphate ester (OP) compounds are known for their ubiquitous use as insecticides. At the same time, these chemicals are highly toxic and can be used as nerve agents. G117H mutant of human Butyrylcholinesterase (BChE) was found to be capable of hydrolyzing certain OPs and protect against their toxicity. However, for therapeutic use, the rate of hydrolysis is too low. Its catalytic power can be improved by rational design, but the structure of the G117H mutant is first required. In this work, we determined, computationally, the three dimensional structure of the G117H BChE mutant. The structure was then validated by simulating acetylation of acetylthiocholine (ATC). Several plausible conformers of G117H BChE were examined but only the (62,?75) conformer fully reproduced catalytic effect. The (62,?75) conformer is, therefore, suggested as the structure adopted by the G117H BChE mutant. This conformer is shown to explain the loss of esterase activity observed for the G122H Acetylcholinesterase mutant together with its recovery when additional mutations are placed turning the enzyme also into an OP hydrolase. Furthermore, similarity of the structure to the structure of RNase A, which is known to hydrolyze the O? P bond in RNA, grants it further credibility and suggests a mechanism for the OP hydrolysis. Proteins 2009. © 2009 Wiley‐Liss, Inc.     

Fold recognition without folds

Fold recognition predicts protein three-dimensional structure by establishing relationships between a protein sequence and known protein structures. Most methods explicitly use information derived from the secondary and tertiary structure of the templates. Here we show that rigorous application of a sequence search method (PSI-BLAST) with no reference to secondary or tertiary structure information is able to perform as well as traditional fold recognition methods. Since the method, SENSER, does not require knowledge of the three-dimensional structure, it can be used to infer relationships that are not tractable by methods dependent on structural templates.     

The conformation of alpha-human atrial natriuretic polypeptide in solution

The three-dimensional structure of alpha-human ANP in solution was determined through the combined use of nuclear magnetic resonance spectroscopy and distance geometry. The results are based on distance constraints determined by nuclear Overhauser effect measurements and one disulfide bond. The structure is as follows. Three separate regions, which are Ser1-Cys7, Arg11-Ile15, and Gln18-Tyr28 each have some ordered structure. The remaining parts in the sequences of Gly9-Gly10 and Gly16-Ala17 act as hinges. And the C-terminal part is folded back toward the cyclic moiety. The conformation of alpha-hANP reported here is expected to give a better understanding of the relationships between its biological activities and three-dimensional structure.     

Sequence-structure mapping errors in the PDB: OB-fold domains

The Protein Data Bank (PDB) is the single most important repository of structural data for proteins and other biologically relevant molecules. Therefore, it is critically important to keep the PDB data, as much as possible, error-free. In this study, we have analyzed PDB crystal structures possessing oligonucleotide/oligosaccharide binding (OB)-fold, one of the highly populated folds, for the presence of sequence-structure mapping errors. Using energy-based structure quality assessment coupled with sequence analyses, we have found that there are at least five OB-structures in the PDB that have regions where sequences have been incorrectly mapped onto the structure. We have demonstrated that the combination of these computation techniques is effective not only in detecting sequence-structure mapping errors, but also in providing guidance to correct them. Namely, we have used results of computational analysis to direct a revision of X-ray data for one of the PDB entries containing a fairly inconspicuous sequence-structure mapping error. The revised structure has been deposited with the PDB. We suggest use of computational energy assessment and sequence analysis techniques to facilitate structure determination when homologs having known structure are available to use as a reference. Such computational analysis may be useful in either guiding the sequence-structure assignment process or verifying the sequence mapping within poorly defined regions.     

Phylogenetic comparative analysis and the secondary structure of ribonuclease P RNA--a review

The most incisive a priori approach to inferring the higher order structure of large RNAs has proven to be the use of phylogenetic comparisons. This article provides guidelines to the method, using as an illustration the elucidation of the secondary structure of the catalytic RNA subunit of ribonuclease P (RNase P). The resultant structure is compared to the possibilities that are predicted thermodynamically for the RNase P RNA sequences of nine eubacteria.     

Utilization of phenol by hydrocarbon assimilating yeasts

77 Ascomycetous, basidiomycetous as well as imperfect yeast strains of 46 different species and 20 genera were tested for growth with the substrates n-octane, n-hexadecane, and phenol. Of 59 yeast strains with ascomycetous cell wall structure 33 grew on hydrocarbons and 32 on phenol. No yeast strain out of 26 which are unable to use n-alkanes as a source of carbon and energy grew on phenol. In comparison with the latter 32 out of 33 n-hexadecane assimilating yeasts were also capable of using phenol. All n-octane utilizing yeasts of this group also assimilate phenol as a carbon source for growth.The correlation of the hydrocarbon assimilation with the phenol assimilation seems to be not so strong in the basidiomycetous yeasts. 7 out of 18 strains from this group grew on n-hexadecane and 13 on phenol.Furthermore, it could be shown that the use of hydrocarbons and phenol (as well as methanol) is strongly correlated with the coenzyme Q structure of the respective yeast strain.The results are discussed with respect to the particular chemical properties of the substrates used and the fact that coenzyme Q structure is considered to be an important marker of evolutionary relationships among yeasts.     

Long-term patterns of change in a vanishing cultural landscape: A GIS-based assessment

The specific patterns of land use change that can be observed in many economically developed countries have fundamental implications on landscape structure and geomorphological processes. Areas characterized by widespread erosion such as badlands are often sensitive to anthropic modifications and of large interest in the analysis of the topographic determinants of land use change. This work aims to analyse the land use and landscape structure changes occurred in a Mediterranean landscape by analysing historical maps and infer the underlying processes that contribute to the pattern of change. First we carried out a comparative examination of three historical image datasets (1820, 1954, 2005) through overlay image processing and cross-classification analysis. Then we analysed the relationships between the detected land-use transformations and topographic parameters. Finally we determined the landscape structure change patterns through the use of GIS-based landscape metrics. The results showed how the study areas have experienced significant land use changes, mainly due to the abandonment of traditional rural systems. We found semi-natural areas distribution to be closely connected with terrain-shaping processes. The processes that underlie the multi-temporal landscape structure change have produced an overall increase of the landscape complexity. The work is one of the first attempts to use historical cartographic data to quantitatively assess changes in land use and landscape structure in the Mediterranean area. The proposed integrated methodology can support decision-making in landscape planning and may represent a useful tool to define effective strategies for biodiversity conservation.     

The Land Gini Coefficient and Its Application for Land Use Structure Analysis in China

We introduce the Gini coefficient to assess the rationality of land use structure. The rapid transformation of land use in China provides a typical case for land use structure analysis. In this study, a land Gini coefficient (LGC) analysis tool was developed. The land use structure rationality was analyzed and evaluated based on statistical data for China between 1996 and 2008. The results show: (1)The LGC of three major land use types–farmland, built-up land and unused land–was smaller when the four economic districts were considered as assessment units instead of the provinces. Therefore, the LGC is spatially dependent; if the calculation unit expands, then the LGC decreases, and this relationship does not change with time. Additionally, land use activities in different provinces of a single district differed greatly. (2) At the national level, the LGC of the three main land use types indicated that during the 13 years analyzed, the farmland and unused land were evenly distributed across China. However, the built-up land distribution was relatively or absolutely unequal and highlights the rapid urbanization in China. (3) Trends in the distribution of the three major land use types are very different. At the national level, when using a district as the calculation unit, the LGC of the three main land use types increased, and their distribution became increasingly concentrated. However, when a province was used as the calculation unit, the LGC of the farmland increased, while the LGC of the built-up and unused land decreased. These findings indicate that the distribution of the farmland became increasingly concentrated, while the built-up land and unused land became increasingly uniform. (4) The LGC analysis method of land use structure based on geographic information systems (GIS) is flexible and convenient.     

Calculation of protein conformations by proton-proton distance constraints. A new efficient algorithm

We have developed a method to determine the three-dimensional structure of a protein molecule from such a set of distance constraints as can be determined by nuclear magnetic resonance studies. The currently popular methods for distance geometry based on the use of the metric matrix are applicable only to small systems. The method developed here is applicable to large molecules, such as proteins, with all atoms treated explicitly. This method works in the space of variable dihedral angles and determines a three-dimensional structure by minimization of a target function. We avoid difficulties hitherto inherent in this type of approach by two new devices: the use of variable target functions; and a method of rapid calculation of the gradient of the target functions. The method is applied to the determination of the structures of a small globular protein, bovine pancreatic trypsin inhibitor, from several artificial sets of distance constraints extracted from the X-ray crystal structure of this molecule. When a good set of constraints was available for both short- and long-range distances, the crystal structure was regenerated nearly exactly. When some ambiguities, such as those expected in experimental information, are allowed, the protein conformation can be determined up to a few local deformations. These ambiguities are mainly associated with the low resolving power of the short-range information.