Functional demands of dynamic biological adhesion: an integrative approach

Climbing organisms are constantly challenged to make their way rapidly and reliably across varied and often novel terrain. A diversity of morphologically and mechanically disparate attachment strategies have evolved across widely distributed phylogenetic groups to aid legged animals in scaling these surfaces, notable among them some very impressive adhesive pads. Despite the differences between, for example, the dry fibrillar pads of geckos and the smooth, secretion-aided pads of stick insects, I hypothesize that they face similar functional demands in their environment. I outline three broad criteria defining dynamic biological adhesion: reusability, reversibility, and substrate tolerance. Organismal adhesive pads must be able to attach repeatedly without significant decline in performance, detach easily at will, and adhere strongly to the broadest possible range of surfaces in their habitat. A survey of the literature suggests that evidence for these general principles can be found in existing research, but that many gaps remain to be filled. By taking a comparative, integrative approach to biological dynamic adhesion, rather than focusing on a few model organisms, investigators will continue to discover new and interesting attachment strategies in natural systems.     

Oblique scanning 2‐photon light‐sheet fluorescence microscopy for rapid volumetric imaging

Light‐sheet fluorescence microscopy (LSFM) is a powerful tool for biological studies because it allows for optical sectioning of dynamic samples with superior temporal resolution. However, LSFM using 2 orthogonally co‐aligned objectives requires a special sample geometry, and volumetric imaging speed is limited due to physical sample translation. This paper describes an oblique scanning 2‐photon LSFM (OS‐2P‐LSFM) that eliminates these limitations by using a single objective near the sample and a refractive scanning‐descanning system. This system also provides improved light‐sheet confinement against scattering by using a 2‐photon Bessel beam. The OS‐2P‐LSFM hold promise for studying structural, functional and dynamic aspects of living tissues and organisms because it allows for high‐speed, translation‐free and scattering‐robust 3D imaging of large biological specimens.      

Organisms as Functional Machines: A Connectivity Explanation

Living organisms exist as a complex set of levels of organizationarranged in a pattern of strong ordering with none of theselevels being more important than others for a full understandingof life. Central to biological strong ordering is the organismallevel. Individual organisms are of special interest to biologistsbecause they are relevant to all biological processes regardlessof the operational level of the process. This is especiallytrue for investigations of the morphological-physiological propertiesof organisms. For such studies, living organisms must be consideredas complex machines with all of the sophisticated integrationand multifarious interactions of component parts typical ofcomplex systems. Understanding of the properties of any individualfeature in an organism depends as much, or possibly even more,on an appreciation of its connections and interactions withother features of that organism than on an understanding ofits intrinsic attributes. Learning the connectivity skills,including the modes of thinking, needed to comprehend the integrationof diverse components of any complex system requires a differenttraining than that needed to determine the detailed attributesof individual parts; both are necessary, however, to achieveproper advances in biological knowledge. Case studies of severalvertebrate features will be used to illustrate types of interactionswhich exist between structural/functional attributes, and howtheir recognition can lead to new and interesting questions.This "feeling for the organism" may be the major factor separatingthose biologists who are able to make important discoveriesfrom those who will only provide the subsequent, less excitingdetails of normal science.     

Meta-analysis reveals negative yet variable effects of ocean acidification on marine organisms

Ocean acidification is a pervasive stressor that could affect many marine organisms and cause profound ecological shifts. A variety of biological responses to ocean acidification have been measured across a range of taxa, but this information exists as case studies and has not been synthesized into meaningful comparisons amongst response variables and functional groups. We used meta-analytic techniques to explore the biological responses to ocean acidification, and found negative effects on survival, calcification, growth and reproduction. However, there was significant variation in the sensitivity of marine organisms. Calcifying organisms generally exhibited larger negative responses than non-calcifying organisms across numerous response variables, with the exception of crustaceans, which calcify but were not negatively affected. Calcification responses varied significantly amongst organisms using different mineral forms of calcium carbonate. Organisms using one of the more soluble forms of calcium carbonate (high-magnesium calcite) can be more resilient to ocean acidification than less soluble forms (calcite and aragonite). Additionally, there was variation in the sensitivities of different developmental stages, but this variation was dependent on the taxonomic group. Our analyses suggest that the biological effects of ocean acidification are generally large and negative, but the variation in sensitivity amongst organisms has important implications for ecosystem responses.     

S-layer-supported lipid membranes

Many prokaryotic organisms (archaea and bacteria) are covered by a regularly ordered surface layer (S-layer) as the outermost cell wall component. S-layers are built up of a single protein or glycoprotein species and represent the simplest biological membrane developed during evolution. Pores in S-layers are of regular size and morphology, and functional groups on the protein lattice are aligned in well-defined positions and orientations. Due to the high degree of structural regularity S-layers represent unique systems for studying the structure, morphogenesis, and function of layered supramolecular assemblies. Isolated S-layer subunits of numerous organisms are able to assemble into monomolecular arrays either in suspension, at air/water interfaces, on planar mono- and bilayer lipid films, on liposomes and on solid supports (e.g. silicon wafers). Detailed studies on composite S-layer/lipid structures have been performed with Langmuir films, freestanding bilayer lipid membranes, solid supported lipid membranes, and liposomes. Lipid molecules in planar films and liposomes interact via their head groups with defined domains on the S-layer lattice. Electrostatic interactions are the most prevalent forces. The hydrophobic chains of the lipid monolayers are almost unaffected by the attachment of the S-layer and no impact on the hydrophobic thickness of the membranes has been observed. Upon crystallization of a coherent S-layer lattice on planar and vesicular lipid membranes, an increase in molecular order is observed, which is reflected in a decrease of the membrane tension and an enhanced mobility of probe molecules within an S-layer-supported bilayer. Thus, the terminology 'semifluid membrane' has been introduced for describing S-layer-supported lipid membranes. The most important feature of composite S-layer/lipid membranes is an enhanced stability in comparison to unsupported membranes.     

Unique modifications of translation elongation factors

Covalent modifications of proteins often modulate their biological functions or change their subcellular location. Among the many known protein modifications, three are exceptional in that they only occur on single proteins: ethanolamine phosphoglycerol, diphthamide and hypusine. Remarkably, the corresponding proteins carrying these modifications, elongation factor 1A, elongation factor 2 and initiation factor 5A, are all involved in elongation steps of translation. For diphthamide and, in part, hypusine, functional essentiality has been demonstrated, whereas no functional role has been reported so far for ethanolamine phosphoglycerol. We review the biosynthesis, attachment and physiological roles of these unique protein modifications and discuss common and separate features of the target proteins, which represent essential proteins in all organisms.     

The influence of low surface energy materials on bioadhesion — a review

Investigations on the adhesion of a diverse range of biological systems including proteins, tissues, microbes, algae and invertebrates all indicate that minimal long-term adhesion is associated with surfaces having initial surface tensions between 20 and 30 dynes/cm (mN/m), i.e. low energy surfaces. However, all surfaces rapidly become modified on immersion in natural waters through the adsorption of ‘conditioning films’, which may influence subsequent adhesive events associated with the permanent attachment of organisms. In this review the various methods which have been used to measure the strength of attachment of both micro- and macrofouling to surfaces will be outlined and results presented for substrata with a range of surface energies. Data will be presented which show that surface energy can elicit different responses in different organisms. For most organisms, minimal adhesion is associated with low surface energy. Silicone elastomers and fluoropolymers have received most attention regarding their potential use as foul release coatings. Results on the antifouling performance of these classes of materials will be discussed.     

The quest for natural selection in the age of comparative genomics

Continued genome sequencing has fueled progress in statistical methods for understanding the action of natural selection at the molecular level. This article reviews various statistical techniques (and their applicability) for detecting adaptation events and the functional divergence of proteins. As large-scale automated studies become more frequent, they provide a useful resource for generating biological null hypotheses for further experimental and statistical testing. Furthermore, they shed light on typical patterns of lineage-specific evolution of organisms, on the functional and structural evolution of protein families and on the interplay between the two. More complex models are being developed to better reflect the underlying biological and chemical processes and to complement simpler statistical models. Linking molecular processes to their statistical signatures in genomes can be demanding, and the proper application of statistical models is discussed.     

Encoding of plant odour information in insects: peripheral and central mechanisms

Insects are suitable model organisms for studying mechanisms underlying olfactory coding and olfactory learning, by their unique adaptation to host plants in which the chemical senses are essential. Recent molecular biological studies have shown that a large number of genes in insects and other organisms are coding for olfactory receptor proteins. In general, one receptor type seems to be expressed in each neurone. The functional characterisations of olfactory receptor neurones have been extensive in certain insect species, demonstrating a fine-tuning of single neurones to biologically relevant odourants; both insect and plant produced volatiles. Stained neurones of the same functional type have been shown to project in one and the same glomerular unit in the primary olfactory centre, the antennal lobe. This corresponds to molecular biological studies, showing projections in one glomerulus by neurones expressing the same receptor type. Comparison of these findings with physiological and morphological characterisations of antennal lobe neurones has indicated correspondence between input and output of the glomerular units. Examples are presented from studies of heliothine moths. From the antennal lobe, the olfactory information is further conveyed to the mushroom bodies, particularly important for learning, and the lateral protocerebrum, a premotoric area. The three brain areas are regions of synaptic plasticity important in learning of odours, which is well studied in the honeybee but also in species of moths.     

植物可溶性N-乙基马来酰亚胺敏感因子连接物复合体(SNAREs)及其生物学功能研究进展

在真核生物细胞中, 各细胞器间物质和信息的交流是细胞生命活动的基本保证, 而囊泡转运是细胞器之间物质和信息交流的主要方式。大多数的囊泡融合过程是由可溶性的N-乙基马来酰亚胺敏感因子连接物复合体(Soluble N-ethyl-maleimide-sensitive fusion protein attachment protein receptors, SNAREs)介导的, 物种间的SNAREs具有高度保守的特性。与其他真核生物相比, 植物的基因组编码更多的SNAREs。研究证明, 植物的SNAREs是一个多功能的蛋白家族, 在植物的许多生理过程中都有着重要的作用。本文对植物SNAREs作用的分子机理及生物学功能的最新研究进展做一概述。     

Marine antifouling laboratory bioassays: an overview of their diversity

In aquatic environments, biofouling is a natural process of colonization of submerged surfaces, either living or artificial, involving a wide range of organisms from bacteria to invertebrates. Antifouling can be defined as preventing the attachment of organisms onto surfaces. This article reviews the laboratory bioassays that have been developed for studying the control of algae and invertebrates by epibiosis (chemical ecology) and the screening of new active compounds (natural products and biocides) to inhibit settlement or adhesion, ie fouling-release coatings. The assays utilize a range of organisms (mainly marine bacteria, diatoms, algae, barnacles). The main attributes of assays for micro- and macroorganisms are described in terms of their main characteristics and depending on the biological process assessed (growth, adhesion, toxicity, behavior). The validation of bioassays is also discussed.     

Refined phylogenetic profiles method for predicting protein-protein interactions

MOTIVATION: The increasing availability of complete genome sequences provides excellent opportunity for the further development of tools for functional studies in proteomics. Several experimental approaches and in silico algorithms have been developed to cluster proteins into networks of biological significance that may provide new biological insights, especially into understanding the functions of many uncharacterized proteins. Among these methods, the phylogenetic profiles method has been widely used to predict protein-protein interactions. It involves the selection of reference organisms and identification of homologous proteins. Up to now, no published report has systematically studied the effects of the reference genome selection and the identification of homologous proteins upon the accuracy of this method. RESULTS: In this study, we optimized the phylogenetic profiles method by integrating phylogenetic relationships among reference organisms and sequence homology information to improve prediction accuracy. Our results revealed that the selection of the reference organisms set and the criteria for homology identification significantly are two critical factors for the prediction accuracy of this method. Our refined phylogenetic profiles method shows greater performance and potentially provides more reliable functional linkages compared with previous methods.     

Computational Prediction of Genomic Functional Cores Specific to Different Microbes

Computational and experimental attempts tried to characterize a universial core of genes representing the minimal set of functional needs for an organism. Based on the increasing number of available complete genomes, comparative genomics has concluded that the universal core contains < 50 genes. In contrast, experiments suggest a much larger set of essential genes (certainly more than several hundreds, even under the most restrictive hypotheses) that is dependent on the biological complexity and environmental specificity of the organism. Highly biased genes, which are generally also the most expressed in translationally biased organisms, tend to be over represented in the class of genes deemed to be essential for any given bacterial species. This association is far from perfect; nevertheless, it allows us to propose a new computational method to detect, to a certain extent, ubiquitous genes, nonorthologous genes, environment-specific genes, genes involved in the stress response, and genes with no identified function but highly likely to be essential for the cell. Most of these groups of genes cannot be identified with previously attempted computational and experimental approaches. The large variety of life-styles and the unusually detectable functional signals characterizing translationally biased organisms suggest using them as reference organisms to infer essentiality in other microbial species. The case of small parasitic genomes is discussed. Data issued by the analysis are compared with previous computational and experimental studies. Results are discussed both on methodological and biological grounds. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editor: Martin Kreitman]     

Combination chemical genetics

Predicting the behavior of living organisms is an enormous challenge given their vast complexity. Efforts to model biological systems require large datasets generated by physical binding experiments and perturbation studies. Genetic perturbations have proven important and are greatly facilitated by the advent of comprehensive mutant libraries in model organisms. Small-molecule chemical perturbagens provide a complementary approach, especially for systems that lack mutant libraries, and can easily probe the function of essential genes. Though single chemical or genetic perturbations provide crucial information associating individual components (for example, genes, proteins or small molecules) with pathways or phenotypes, functional relationships between pathways and modules of components are most effectively obtained from combined perturbation experiments. Here we review the current state of and discuss some future directions for 'combination chemical genetics', the systematic application of multiple chemical or mixed chemical and genetic perturbations, both to gain insight into biological systems and to facilitate medical discoveries.     

Multi-level convergence of complex traits and the evolution of bioluminescence

Evolutionary convergence provides natural opportunities to investigate how, when, and why novel traits evolve. Many convergent traits are complex, highlighting the importance of explicitly considering convergence at different levels of biological organization, or ‘multi-level convergent evolution’. To investigate multi-level convergent evolution, we propose a holistic and hierarchical framework that emphasizes breaking down traits into several functional modules. We begin by identifying long-standing questions on the origins of complexity and the diverse evolutionary processes underlying phenotypic convergence to discuss how they can be addressed by examining convergent systems. We argue that bioluminescence, a complex trait that evolved dozens of times through either novel mechanisms or conserved toolkits, is particularly well suited for these studies. We present an updated estimate of at least 94 independent origins of bioluminescence across the tree of life, which we calculated by reviewing and summarizing all estimates of independent origins. Then, we use our framework to review the biology, chemistry, and evolution of bioluminescence, and for each biological level identify questions that arise from our systematic review. We focus on luminous organisms that use the shared luciferin substrates coelenterazine or vargulin to produce light because these organisms convergently evolved bioluminescent proteins that use the same luciferins to produce bioluminescence. Evolutionary convergence does not necessarily extend across biological levels, as exemplified by cases of conservation and disparity in biological functions, organs, cells, and molecules associated with bioluminescence systems. Investigating differences across bioluminescent organisms will address fundamental questions on predictability and contingency in convergent evolution. Lastly, we highlight unexplored areas of bioluminescence research and advances in sequencing and chemical techniques useful for developing bioluminescence as a model system for studying multi-level convergent evolution.     

基于直向同源序列的比较基因组学研究

直向同源序列在不同的物种中具有相近甚至相同的功能、相似的调控途径, 扮演相似甚至相同的角色, 而且, 绝大多数核心生物功能就是由相当数量的直向同源基因所承担, 它是基因组序列的功能注释与分析中最可靠的选择, 其特殊的生物学特性决定: 利用直向同源序列开展比较基因组学研究, 必将为探测不同生物在进化过程中重要功能基因的出现、表达和丢失提供线索。文章从直向同源基因的基本特性、直向同源序列与比较基因组学的关系、应用直向同源序列开展比较基因组学相关研究方法、现状等展开综述。关键词: 直向同源; 比较基因组学; 生物学特性; 数据库     

Neutralization of small RNA viruses by antibodies and antiviral agents

The 3-dimensional structures of a number of small animal RNA viruses are now known to near-atomic resolution. All these viruses have similar structures and have, in all probability, diverged from a common ancestral virus able to infect a variety of organisms. The structures have elucidated the site of attachment to host cell receptors and the mode of protection of this site against host immune pressure. An internal hydrophobic pocket in rhinoviruses is the site for binding of antiviral drugs that inhibit uncoating and can inhibit attachment in some viruses. The pocket is probably a functional necessity, and thus is a suitable target for well-designed antiviral agents in many viruses.     

PiNGO: a Cytoscape plugin to find candidate genes in biological networks

PiNGO is a tool to screen biological networks for candidate genes, i.e. genes predicted to be involved in a biological process of interest. The user can narrow the search to genes with particular known functions or exclude genes belonging to particular functional classes. PiNGO provides support for a wide range of organisms and Gene Ontology classification schemes, and it can easily be customized for other organisms and functional classifications. PiNGO is implemented as a plugin for Cytoscape, a popular network visualization platform. AVAILABILITY: PiNGO is distributed as an open-source Java package under the GNU General Public License (http://www.gnu.org/), and can be downloaded via the Cytoscape plugin manager. A detailed user guide and tutorial are available on the PiNGO website (http://www.psb.ugent.be/esb/PiNGO.     

Detection and functional characterization of early appearing antibodies in rabbits with experimental syphilis

Following testicular infection of rabbits with Treponema pallidum, different antibodies become detectable initially at the time of healing. Experiments were performed to determine a functional role for these antibodies. Rabbits were sacrificed after 4-8 days. Treponemal numbers steadily increased for 10-12 days. Thereafter, host defenses were sufficiently stimulated to begin clearing the organisms. Antibodies in serum and antibodies localized at the site of infection were quantitated using radioimmunoassay and enzyme-linked immunosorbent assay (ELISA) techniques. Anti-treponemal IgG was detected as early as day 4. Quantities of antibody correspondingly increased with time following infection. Treponema pallidum was harvested 7 and 14 days postinfection and tested for surface antibodies. With increasing days postinfection, more antibody was found on the organisms. Two functional properties of these antibodies were shown. Sera from 24 of 45 rabbits infected for 14 days immobilized T. pallidum in the presence of complement and 14-day sera blocked the attachment of T. pallidum to tissue culture cells. We suggest that antibody-mediated, complement-dependent immobilization of T. pallidum and blockage of attachment are at least partially responsible for healing of testicular lesions.