From the trap to the basket: getting to the bottom of the nuclear pore complex

Nuclear pore complexes (NPCs) are large supramolecular assemblies that perforate the double-membraned nuclear envelope and serve as the sole gateways of molecular exchange between the cytoplasm and the nucleus in interphase cells. Combining novel specimen preparation regimes with innovative use of high-resolution scanning electron microscopy, Hans Ris produced in the late eighties stereo images of the NPC with unparalleled clarity and structural detail, thereby setting new standards in the field. Since that time, efforts undertaken to resolve the molecular structure and architecture, and the numerous interactions that occur between NPC proteins (nucleoporins), soluble transport receptors, and the small GTPase Ran, have led to a deeper understanding of the functional role of NPCs in nucleocytoplasmic transport. In spite of these breakthroughs, getting to the bottom of the actual cargo translocation mechanism through the NPC remains elusive and controversial. Here, we review recent insights into NPC function by correlating structural findings with biochemical data. By introducing new experimental and computational results, we reexamine how NPCs can discriminate between receptor-mediated and passive cargo to promote vectorial translocation in a highly regulated manner. Moreover, we comment on the importance and potential benefits of identifying and experimenting with individual key components implicated in the translocation mechanism. We conclude by dwelling on questions that we feel are pertinent to a more rational understanding of the physical aspects governing NPC mechanics. Last but not least, we substantiate these uncertainties by boldly suggesting a new direction in NPC research as a means to verify such novel concepts, for example, a de novo designed ‘minimalist’ NPC. This article is dedicated to the memory of Hans Ris.     

Coral bleaching is linked to the capacity of the animal host to supply essential metals to the symbionts

Massive coral bleaching events result in extensive coral loss throughout the world. These events are mainly caused by seawater warming, but are exacerbated by the subsequent decrease in nutrient availability in surface waters. It has therefore been shown that nitrogen, phosphorus or iron limitation contribute to the underlying conditions by which thermal stress induces coral bleaching. Generally, information on the trophic ecology of trace elements (micronutrients) in corals, and on how they modulate the coral response to thermal stress is lacking. Here, we demonstrate for the first time that heterotrophic feeding (i.e. the capture of zooplankton prey by the coral host) and thermal stress induce significant changes in micro element concentrations and isotopic signatures of the scleractinian coral Stylophora pistillata. The results obtained first reveal that coral symbionts are the major sink for the heterotrophically acquired micronutrients and accumulate manganese, magnesium and iron from the food. These metals are involved in photosynthesis and antioxidant protection. In addition, we show that fed corals can maintain high micronutrient concentrations in the host tissue during thermal stress and do not bleach, whereas unfed corals experience a significant decrease in copper, zinc, boron, calcium and magnesium in the host tissue and bleach. In addition, the significant increase in δ⁶⁵Cu and δ⁶⁶Zn signature of symbionts and host tissue at high temperature suggests that these isotopic compositions are good proxy for stress in corals. Overall, present findings highlight a new way in which coral heterotrophy and micronutrient availability contribute to coral resistance to global warming and bleaching.     

Contribution of the FtsQ transmembrane segment to localization to the cell division site

The Escherichia coli cell division protein FtsQ is a central component of the divisome. FtsQ is a bitopic membrane protein with a large C-terminal periplasmic domain. In this work we investigated the role of the transmembrane segment (TMS) that anchors FtsQ in the cytoplasmic membrane. A set of TMS mutants was made and analyzed for the ability to complement an ftsQ mutant. Study of the various steps involved in FtsQ biogenesis revealed that one mutant (L29/32R;V38P) failed to functionally insert into the membrane, whereas another mutant (L29/32R) was correctly assembled and interacted with FtsB and FtsL but failed to localize efficiently to the cell division site. Our results indicate that the FtsQ TMS plays a role in FtsQ localization to the division site.     

The failure of morphology to contribute to the modern synthesis

How much, if anything, morphology contributed to the modern synthesis is partly a matter of how one defines that term. In the strict sense, morphology is a purely formal discipline and had very little to contribute. Morphology may also be considered a kind of data, and when it becomes functional a better case can be made for its role in evolutionary studies. Be that as it may, the incorporation of morphology into the synthesis was a later development. The initial focus was at the populational level, including the problems of speciation, which makes sense because that was where the opportunities seemed to be. As the synthesis evolved and matured it expanded its horizons and incorporated a larger range of topics. Very little discussion of morphology occurs in the canonical writings of the so-called architects. At the time when the synthesis was supposedly complete, which was around 1950, the incorporation of morphology into it was just beginning.     

Taking arrays from the lab to the field: trying to make sense of the unknown

With the rapid pace of nucleic acid microarray technology development and a renewed national emphasis on detecting and characterizing microorganisms in environmental samples, there is a rush to operationalize existing microarray technologies and apply them to uncharacterized environmental backgrounds. The purpose of this article is to pause and ask a basic question: what do microarray data actually mean in the face of uncharacterized sample backgrounds? In attempting to answer this question, we draw a clear distinction between hypothesis-driven fundamental science and operational uses of microarray technology; assess microarray technology assumptions in the face of uncharacterized environments; offer an environmental microbiologist's perspective on technology needs and requirements for quantitatively analyzing microbial communities; and hopefully stimulate a scientific and technical dialogue around the concept of analytical environmental microbiology and future technology development.     

Physical model of the plant tissue response to exposure to the microwave electromagnetic field

A hypothesis was suggested to explain the effect of biostimulation of seeds exposed to microwave electromagnetic field. It was shown that the assumption on the determining influence of the microwave field on the transport properties of the conducting system of a plant satisfactorily explains the phenomena observed in germinating seeds and growing plants. A physical model of the response of a plant cell to a microwave field is presented, which served as a basis for the method of calculating the maximum possible time of exposure of plant tissue.     

An approach to the study of intracellular proteins related to the excitability of the squid giant axon

The technique for covalently labeling proteins with 125I-labelled Bolton-Hunter reagent was used to determine the quantities of proteins released from the axoplasmic side of the squid axon membrane. The reagent could be introduced into the interior of the axon by the technique of intracellular perfusion, the radioiodination reaction being carried out in situ. Alternatively, the reaction could be carried out in vitro, i.e., by mixing the reagent with samples of proteins dissolved in the intracellular perfusion fluid collected from the axon. This technique was found to be sensitive enough to permit analysis of a large number of protein samples collected from a single axon. By the method of sodium dodecyl sulfate polyacrylamide gel electrophoresis, it was found that proteins of approx. 56 000 daltons were released into the perfusate when a solution of potassium chloride or potassium bromide was introduced into the interior of an axon. Suppression of axonal excitability was associated with this release of proteins. The significance of these findings in relation to the structure and function of the axon is discussed.     

Network-based method to infer the contributions of proteins to the etiology of drug side effects

Studying the molecular mechanisms that underlie the relationship between drugs and the side effects they produce is critical for drug discovery and drug development. Currently, however, computational methods are still unavailable to assess drug-protein interactions with the aim of globally inferring the contributions of various classes of proteins toward the etiology of side effects. In this work, we integrated data reflecting drug-side effect relationships, drug-target relationships, and protein-protein interactions to develop a novel network-based probabilistic model, SidePro, to evaluate the contributions of proteins toward the etiology of side effects. For a given side effect, the method applies an expectation---maximization algorithm and a diffusion kernel-based approach to estimate each protein’s contribution. We applied this method to a wide range of side effects and validated the results using cross-validation and records from the Side Effect Resource database. We also studied a specific side effect, nephrotoxicity, which is known to be associated with the irrational use of the Chinese herbal compound triptolide, a diterpenoid epoxide in the Thunder of God Vine, Tripterygium wilfordii Lei-Gong-Teng. Using triptolide as an example, we scored the target proteins of triptolide using our model and investigated the high-scoring proteins and their related biological processes. The results demonstrated that our model could differentiate between the potential side effect targets and therapeutic targets of triptolide. Overall, the proposed model could accurately pinpoint the molecular mechanisms of drug side effects, thus making contribution to safe and effective drug development.     

Exploring the acclimation to depth of Posidonia oceanica comparing the morphological variation to the histo-anatomical characteristics of the leaves

Posidonia oceanica is a marine plant that plays an important ecological role in marine ecosystems. Understanding the eco-physiology of this plant is fundamental for planning conservation and restoration actions covering this species and its habitat. The aim of this study was to explore the acclimation of P. oceanica to depth by examining the leaf morphological variation in a depth gradient. We measured leaf length, width and thickness, as well as the distance of fifth and sixth ribs from the margin and the central rib at different depths, comparing leaves morphology and histo-anatomy. Leaf length was the only morphological character clearly related to depth, whereas the overall morphological variation seems to be due to a change in the histo-anatomical characters. Depth-related characters showed a different variation pattern from that of not depth-related ones. Our results do not fit the model used to explain the seagrass responses to light variation; most morphological leaf traits are not directly linked to the acclimation of this species to depth. Finally, we hypothesise that the variation pattern of not depth-dependent characters is an expression of P. oceanica meadow genetic structure along the depth gradient.     

Approaches to the study of the cell secretome

The secretome, or secretomics, has recently emerged as a new term to describe the global study of proteins that are secreted by a cell, tissue or organism at any given time or under certain conditions. The secretome constitutes an important class of proteins that control and regulate a multitude of biological and physiological processes, thus making it a clinically relevant source for biomarkers and therapeutic target discoveries. There are several approaches that are being implemented to study such a class of proteins; however, each of these approaches has its advantages and limitations. While genome-wide studies using signal predictions can provide a comprehensive analysis of the secretome, the detection and quantification of the actual secreted proteins in a tissue would be more relevant. The goal of this review is to provide an overview of the methods currently used to analyze such a class of proteins, as well as the challenges encountered during the study of the secretome. The implication of studying the cell secretome together with its clinical relevance will be also covered.     

RNA kink turns to the left and to the right

A helix-loop-helix within the group I intron has most of the canonical sequence elements of a kink turn (K-turn), yet it bends in the opposite direction. The reverse K-turn kinks toward the major rather than the minor grooves of the flanking helices. This suggests that there are two distinct subclasses of tertiary structures that a K-turn secondary structure can adopt. The final structure may be specified by external factors, such as protein binding or the tertiary structural context, rather than the intrinsic conformation of the RNA.     

Introduction to the symposium: responses of organisms to climate change: a synthetic approach to the role of thermal adaptation

On a global scale, changing climates are affecting ecological systems across multiple levels of biological organization. Moreover, climates are changing at rates unprecedented in recent geological history. Thus, one of the most pressing concerns of the modern era is to understand the biological responses to climate such that society can both adapt and implement measures that attempt to offset the negative impacts of a rapidly changing climate. One crucial question, to understand organismal responses to climate, is whether the ability of organisms to adapt can keep pace with quickly changing environments. To address this question, a syntheses of knowledge from a broad set of biological disciplines will be needed that integrates information from the fields of ecology, behavior, physiology, genetics, and evolution. This symposium assembled a diverse group of scientists from these subdisciplines to present their perspectives regarding the ability of organisms to adapt to changing climates. Specifically, the goals of this symposia were to (1) highlight what each discipline brings to a discussion of organismal responses to climate, (2) to initiate and foster a discussion to break barriers in the transfer of knowledge across disciplines, and (3) to synthesize an approach to address ongoing issues concerning biological responses to climate.     

Contributions to the theoretical physics of the cell

Summary On thermodynamical basis it is shown, that regardless to any assumption about the surface phenomena, a cell the volume of which is the seat of chemical reactions as a result of which it grows, must divide in two after reaching a critical size.The order of magnitude of this critical size and the order of magnitude of the time necessary for a cell to divide are calculated and found in agreement with the actually observed values.     

From the Genome to the Phenome: Tools to Understand the Basic Biology of Plasmodium falciparum

Malaria plagues one out of every 30 humans and contributes to almost a million deaths, and the problem could worsen. Our current therapeutic options are compromised by emerging resistance by the parasite to our front line drugs. It is thus imperative to better understand the basic biology of the parasite and develop novel drugs to stem this disease. The most facile approach to analyse a gene's function is to remove it from the genome or inhibit its activity. Although genetic manipulation of the human malaria parasite Plasmodium falciparum is a relatively standard procedure, there is no optimal method to perturb genes essential to the intraerythrocytic development cycle—the part of the life cycle that produces the clinical manifestation of malaria. This is a severe impediment to progress because the phenotype we wish to study is exactly the one that is so elusive. In the absence of any utilitarian way to conditionally delete essential genes, we are prevented from investigating the parasite's most vulnerable points. This review aims to focus on the development of tools identifying essential genes of P. falciparum and our ability to elicit phenotypic mutation.     

Platyrrhine contribution to the phylogeny of the Primates

The morphology of the skeleton of both extant and fossil Platyrrhini often suggests an image of the ancestry of higher Primates, Man included. Here we give a survey of the characters of common origin to both groups. Reciprocally, a number of such original characters are seen to be maintained in modern Man, thereby placing him along a direct and singular evolutionary lineage.     

Contribution to the analysis of gaits: practical elements to complement the Hildebrand method

This paper suggests three additions to the Hildebrand method for gait-pattern specification. The first allows an extension of this method by the use of the forelimb as reference. Thus, dataset could be gathered indifferently from fore or hindlimbs cycles to identify a symmetrical gait or compare gaits of diverse species. On the basis of Hildebrand's definitions, the second suggestion permits to check the proportion of symmetrical and asymmetrical gaits adopted by different individuals of one or different species. The third addition makes a graphical clear-cut between four basic modes of gallops: rotary, transverse, half-bound and bound. These additions will facilitate extensive data comparison either to evaluate the range of variation within a single species or to specify the preferred gaits in diverse species.     

Reaction of the cell center to exposure to the calcium ionophore A-23187

Calcium ionophore A23187, taken at a concentration of 0.1 microgram/ml, quickly uncouples mitochondria in PE culture cells in medium 199. The cell ultrastructure undergoes reversible changes (especially that of mitochondria): maximum changes occur 2 hours after the start of the treatment; in 8 hours they become less pronounced. The adaptation of cells does not involve the ionophore inactivation in the medium. 10 micrograms/ml of A23187 induces gradual but irreversible alterations. Microtubules in PE cells are not destroyed when incubated in medium 199 containing 10 micrograms/ml of A23187 and 11 mM Ca2+. The addition of 10 micrograms/ml ionophore to the normal 199 medium (1.26 mM Ca2+) results in the formation of electron dense bodies in the cell center 30 minutes after the start of incubation. These bodies disappear in the course of a subsequent incubation. The number of cells with primary cilia decreases. The percentage of centrioles located perpendicularly to the substrate increases 30 minutes following treatment with 0.1 microgram/ml A23187 in medium 199. 2 hours after the start of treatment with 0.1 microgram/ml ionophore no such changes are detected; an electron dense halo appears around the centriolar cylinders. 8 hours after the start of treatment the structure of the cell center does not differ from the normal one.     

Contribution of the water-sediment interface to the transformation of biogenic substances: application to nitrogen compounds

Up to now the water-sediment interface (WSI) has not been considered by limnologists and oceanographers as a theoretical frontier between two phases, but as a variable layer comprising the overlying bottom water, the superficial sediment, and the bioturbed sediment. This heterogeneous benthic boundary layer forms a non-equilibrated assemblage of an aqueous phase, a mineral phase influencing the exchanges, and a dissolved gaseous phase regulating biological activity, detrital organic matter present as dissolved or adsorbed compounds and particles, and a living benthic community dominated by microorganisms. Biological activity and the equilibrium between these components are linked to depth, bottom currents, primary production and allochtonous inputs of organic matter. The settling rate of particulate matter in the water column, which depends on both the size and density of particles, is also an important factor. Settled organic matter is broken down mainly by heterotrophic microorganisms. In the first stage, dissolved or particulate matter is depolymerized by exoenzymes linked to the bacterial membrane. Other heterotrophic organisms, like flagellates and ciliates, contribute to the activity of bacterial populations or to a modification of the physical and chemical characteristics of organic matter like macrofauna. Bacterial activity in the WSI is one to two orders of magnitude higher than in overlying bottom water, depending on the density of the bacterial population, on the amount of available organic matter, and on the presence of predators grazing on bacteria and macrofauna and increasing oxygen and dissolved substrates. The WSI is now considered as a sink for particulate matter and biopolymers, and/or as a sink or source for organic monomers and NH₄ ⁺ depending on their concentrations. As a result of its contribution to mineral and organic cycles, the WSI is a crossroad for exchanges between aqueous and sediment layer. During the last decade, intensive work has been performed in this field, but progress has been slow due to the heterogeneity of the layer and the adsorptive properties of the mineral fraction.     

Relevant assay to study the adhesion of Plasmodium falciparum-infected erythrocytes to the placental epithelium

In placental malaria, Plasmodium falciparum-infected erythrocytes adhere to the apical plasma membrane of the placental epithelium, triggering an impairment of placental function detrimental to the fetus. The design of anti-adhesion intervention strategies requires a detailed understanding of the mechanisms involved. However, most adhesion assays lack in vivo relevance and are hardly quantitative. Here, we describe a flow cytometry-based adhesion assay that is fully relevant by using apical epithelial plasma membrane vesicles as the adhesion matrix, and being applicable to infected erythrocytes directly isolated from patients. Adhesion is measured both as the percentage of pathogens bound to epithelial membrane vesicles as well as the mean number of vesicles bound per infected erythrocytes. We show that adhesins alternative to those currently identified could be involved. This demonstrates the power of this assay to advance our understanding of epithelial adhesion of infected erythrocytes and in the design of intervention strategies.