Wza: a new structural paradigm for outer membrane secretory proteins?

Gram-negative bacteria need to be able to transport a large variety of macromolecules across their outer membranes. In Escherichia coli, the passage of the group 1 capsular polysaccharide is mediated by an integral outer membrane protein, Wza. The crystal structure of Wza, determined recently, reveals a novel transmembrane alpha-helical barrel and a large central cavity within the core of the vase-shaped protein complex. The structure has similarities with that of the secretin protein, PilQ, which mediates the transition of type IV pili across the outer membrane. We propose that the large internal chamber, which can accommodate the secreted assembled macromolecule, is likely to be a common feature found in other outer membrane proteins involved in secretion processes.     

Problems with essential fatty acids: time for a new paradigm?

The term ‘essential fatty acid’ is ambiguous and inappropriately inclusive or exclusive of many polyunsaturated fatty acids. When applied most rigidly to linoleate and -linolenate, this term excludes the now well accepted but conditional dietary need for two long chain polyunsaturates (arachidonate and docosahexaenoate) during infancy. In addition, because of the concomitant absence of dietary -linolenate, essential fatty acid deficiency is a seriously flawed model that has probably led to significantly overestimating linoleate requirements. Linoleate and -linolenate are more rapidly β-oxidized and less easily replaced in tissue lipids than the common ‘non-essential’ fatty acids (palmitate, stearate, oleate). Carbon from linoleate and -linolenate is recycled into palmitate and cholesterol in amounts frequently exceeding that used to make long chain polyunsaturates. These observations represent several problems with the concept of ‘essential fatty acid’, a term that connotes a more protected and important fatty acid than those which can be made endogenously. The metabolism of essential and non-essential fatty acids is clearly much more interconnected than previously understood. Replacing the term ‘essential fatty acid’ by existing but less biased terminology, i.e. polyunsaturates, ω3 or ω6 polyunsaturates, or naming the individual fatty acid(s) in question, would improve clarity and would potentially promote broader exploration of the functional and health attributes of polyunsaturated fatty acids.     

Intra-Golgi transport: a way to a new paradigm?

The morpho-functional principles of intra-Golgi transport are, surprisingly, still not clear, which is in marked contrast to our advanced knowledge of the underlying molecular machineries. Recently, the conceptual and technological hindrances that had delayed progress in this area have been disappearing, and a cluster of powerful morphological techniques has been revealing new glimpses of the organization of traffic in intact cells. Here, we discuss the new concepts around the present models of intra-Golgi transport.     

Apoptosis initiated by dependence receptors: a new paradigm for cell death?

A distinct group of receptors including DCC, UNC5, RET and Ptc1 is known to function in ligand-dependent neuronal growth and differentiation or axon guidance. Acting as "dependence receptors", they may also regulate neuronal cell survival by inducing apoptosis in the absence of cognate ligand. Receptor-initiated apoptosis requires proteolytic (caspase) cleavage and exposure of a pro-apoptotic region in the cytoplasmic domains of the receptors. In contrast, classical apoptosis induced by growth factor or cytokine deprivation involves loss of survival signaling without receptor cleavage. DCC, UNC5, RET and Ptc1 are downregulated or mutated in diverse cancers, and show properties characteristic of tumor suppressors, consistent with their ability to promote neuronal cell death. Dysfunctional dependence receptors have been linked to the loss of specific neurons in certain inherited and neurodegenerative diseases. Dependence receptor-initiated apoptosis represents a novel paradigm for the controlled removal of specific cells during neural development and elimination of malignant cells that have strayed beyond regions of ligand availability.     

Bacteriorhodopsin: a paradigm for proton pumps?

Recent studies of the photochemistry of wild type and mutant bacteriorhodopsins, their proton release and uptake kinetics, and their X-ray diffraction structure have suggested a hypothesis for the way energy is coupled in this light-driven proton pump. The first and critical step in converting light energy to a vectorial proton potential is the transfer of the Schiff base proton to D85 which causes dissociation of the Schiff base-counterion complex. Removal of this primarily coulombic interaction destabilizes the protein structure, and results in transition to an alternative conformation in which the two proton conduction pathways between the active site and the membrane surfaces are reorganized. Recovery of the initial charge state of the Schiff base and D85 must therefore occur through a series of unidirectional proton transfers that create a transmembrane electrochemical proton gradient. Passage of the transported proton through the two peripheral protein domains appears to utilize hydrogen bonded networks containing aspartate, arginine and bound water. This kind of mutual interaction between the active site and the protein conformation that determines the conductive pathways to the two membrane surfaces may have relevance to ion pumps in general.     

Liver metastases and SBRT: A new paradigm?

BackgroundThe outstanding innovations made by early diagnosis, novel surgical techniques, effective chemotherapy regimens and conformal radiotherapy, have significantly improved patients overall survival and quality of life. Multidisciplinary approach to cancer has also led to an increased prevalence of patients with few, organ-confined metastases, who can experience long-term survival even if their disease is no longer localized. Liver is one of the most common site for metastatic disease from several cancers, and when metastatic disease is confined to liver, given the ability of this organ to regenerate almost to its optimal volume, surgical resection represents the standard of care because is associated with a better prognosis. Approximately 70–90% of liver metastases, however, are unresectable and a safe, effective alternative therapeutic option is necessary for these patients.Materials and methodsA review of the current literature was performed to analyze the role of SBRT in treating liver metastases from different cancers. A literature search using the terms “SBRT” and “liver metastases” was carried out in PUBMED.ResultsStereotactic body radiation therapy has shown to provide promising results in the treatment of liver metastases, thanks to the ability of this procedure to deliver a conformal high dose of radiation to the target lesion and a minimal dose to surrounding critical tissues.ConclusionStereotactic body radiation therapy is a non-invasive, well-tolerated and effective treatment for patients with liver metastases not suitable for surgical resection.     

Vascular cell biology in vivo: a new piscine paradigm?

Understanding how blood vessels form has become increasingly important in recent years yet remains difficult to study. The architecture and context of blood vessels are difficult to reproduce in vitro, and most developing blood vessels in vivo are relatively inaccessible to observation and experimental manipulation. Zebrafish, however, provide several advantages. They have small, accessible, transparent embryos and larvae, facilitating high-resolution imaging in vivo. In addition, genetic and experimental tools and methods are available for functional manipulation of the entire organism, vascular tissues or even single vascular- or non-vascular cells. Together, these features make the fish amenable to 'in vivo vascular cell biology'.     

Gating the bacterial mechanosensitive channels: MscS a new paradigm?

Mechanosensitive channels play major roles in protecting bacteria from hypo-osmotic shock. In the millisecond timescale they must achieve the transition from tightly closed oligomers to large, relatively non-discriminating pores. The crystal structure for MscL, combined with genetic and biochemical analysis, provided the initial insights for the mechanism by which this structural transition might be made. Discovery of the gene for a second class of mechanosensitive channel, MscS, and its subsequent crystallisation, has provided a new paradigm for mechanosensation, enabling a deeper understanding of the mechanisms of sensing membrane tension.     

InvertNet: a new paradigm for digital access to invertebrate collections

InvertNet, one of the three Thematic Collection Networks (TCNs) funded in the first round of the U.S. National Science Foundation's Advancing Digitization of Biological Collections (ADBC) program, is tasked with providing digital access to ~60 million specimens housed in 22 arthropod (primarily insect) collections at institutions distributed throughout the upper midwestern USA. The traditional workflow for insect collection digitization involves manually keying information from specimen labels into a database and attaching a unique identifier label to each specimen. This remains the dominant paradigm, despite some recent attempts to automate various steps in the process using more advanced technologies. InvertNet aims to develop improved semi-automated, high-throughput workflows for digitizing and providing access to invertebrate collections that balance the need for speed and cost-effectiveness with long-term preservation of specimens and accuracy of data capture. The proposed workflows build on recent methods for digitizing and providing access to high-quality images of multiple specimens (e.g., entire drawers of pinned insects) simultaneously. Limitations of previous approaches are discussed and possible solutions are proposed that incorporate advanced imaging and 3-D reconstruction technologies. InvertNet couples efficient digitization workflows with a highly robust network infrastructure capable of managing massive amounts of image data and related metadata and delivering high-quality images, including interactive 3-D reconstructions in real time via the Internet.     

G protein-coupled receptors in and on the cell nucleus: a new signaling paradigm?

Signaling from internalizing and endosomal receptors has almost become a classic GPCR paradigm in the last several years. However, it has become clear in recent years that GPCRs also elicit signals when resident at other subcellular sites including the endoplasmic reticulum, Golgi apparatus, and the nucleus. In this review we discuss the nature, function, and trafficking of nuclear GPCR signaling complexes, as well as potential sources of endogenous and exogenous ligands. Finally, we pose a series of questions that will need to be answered in the coming years to confirm and extend this as a new paradigm for GPCR signaling.     

Vertebrate somitogenesis: a novel paradigm for animal segmentation?

In vertebrates, the primary segmented tissue of the body axis is the paraxial mesoderm, which lies bilaterally to the axial organs, neural tube and notochord. The segmental pattern of the paraxial mesoderm is established during embryogenesis through the production of the somites which are transient embryonic segments giving rise to the vertebrae, the skeletal muscles and the dorsal dermis. Somitogenesis can be subdivided into three major phases (see Fig. 1). First a growth phase during which new paraxial mesoderm cells are produced by a growth zone (epiblast and blastopore margin or primitive streak and later on tail bud) and become organized as two rods of mesenchymal tissue,forming the presomitic mesoderm. Second a patterning phase occuring in the PSM, during which the segmental pattern is established at the molecular level. Third, the somitic boundaries are formed during the morphological segmentation phase. In all vertebrates, all cells of the paraxial mesoderm, during their maturation in the PSM, go successively through these three phases, which are tightly regulated at the spatio-temporal level. The first phase of paraxial mesoderm production falls out of the scope of this review, as it essentially pertains to the gastrulation process. Here, I essentially discuss the segmental patterning phase in vertebrates. Recent data suggest that establishment of the segmental pattern relies on a clock and wavefront mechanism which has been conserved in vertebrates. Furthermore, conservation of this system could extend to invertebrates, suggesting that the clock and wavefront is an ancestral mechanism.     

Quantitative genetics of Aedes aegypti vector competence for dengue viruses: towards a new paradigm?

Similar to many other host-pathogen interactions, the vector competence of Aedes aegypti for dengue viruses appears to be determined by genotype-by-genotype interactions, whereby the outcome of infection depends on the specific combination of mosquito and virus genotypes. This can complicate efforts to dissect the genetic basis of vector competence in nature because it obscures mapping between genotype and phenotype and brings into question the notion of universal mosquito resistance or susceptibility. Conversely, it offers novel opportunities to better define compatible vector-pathogen associations based on integration of both vector and pathogen genomics, which should eventually improve understanding of pathogen transmission dynamics and the risk of vector-borne disease emergence.     

Pseudomonad replication origins: a paradigm for bacterial origins?

Structural features of three analysed bacterial DNA replication origin classes (six enteric origins, three pseudomonad origins, and the Bacillus subtilis origin region) are compared in order to deduce characteristics common to all bacterial origins and characteristics that distinguish the three origin classes. The two Pseudomonas aeruginosa origins are shown to map within 10 kb of each other, and correlations are drawn with four potential origin regions in B. subtilis. The enteric origin class is further distinguished from the other two classes by its genetic organization, the presence of GATC sites, and the role of Dam methylation in enteric initiation. The pseudomonad origin class has the most features that are common to all of these bacterial origins, and hence may be the paradigm bacterial origin class.     

Role of motor cortex in coordinating multi-joint movements: is it time for a new paradigm?

Reaching movements to spatial targets require motor patterns at the shoulder to be coordinated carefully with those at the elbow to smoothly move the hand through space. While the motor cortex is involved in this volitional task, considerable debate remains about how this cortical region participates in planning and controlling movement. This article reviews two opposing interpretations of motor cortical function during multi-joint movements. On the one hand, studies performed predominantly on single-joint movement generally support the notion that motor cortical activity is intimately involved in generating motor patterns at a given joint. In contrast, studies on reaching demonstrate correlations between motor cortical activity and features of movement related to the hand, suggesting that the motor cortex may be involved in more global features of the task. Although this latter paradigm involves a multi-joint motor task in which neural activity is correlated with features of movement related to the hand, this neural activity is also correlated to other movement variables. Therefore it is difficult to assess if and how the motor cortex contributes to the coordination of motor patterns at different joints. In particular, present paradigms cannot assess whether motor cortical activity contributes to the control of one joint or multiple joints during whole-arm tasks. The final point discussed in this article is the development of a new experimental device (KINARM) that can both monitor and manipulate the mechanics of the shoulder and elbow independently during multi-joint motor tasks. It is hoped that this new device will provide a new approach for examining how the motor cortex is involved in motor coordination.