Hox genes: Did the vertebrate ancestor have a Hox14?

A new group of vertebrate Hox genes, Hox14, has been discovered in two fish, the horn shark and the coelacanth. This reveals that ancestrally all jawed vertebrates may have had fourteen Hox paralogue groups rather than the thirteen groups of mammals and teleost fish.     

Signaling at the vertebrate synapse: new roles for embryonic morphogens?

The formation of synapses is critical for functional neuronal connectivity. The coordinated assembly at both sides of the synapse is fundamental for the proper apposition of the neurotransmitter release machinery on the presynaptic neuron and the clustering of neurotransmitter receptors and ion channels on the receptive postsynaptic cell. This process requires bidirectional communication between the presynaptic neuron and its postsynaptic target, another neuron, or muscle fiber. Extracellular signals such as WNT, TGF-beta, and FGF factors are emerging as key target-derived signals required for the initial stages of synaptic assembly. Studies in invertebrates are also providing new insights into the function of these signals in synaptic growth and homeostasis. During early embryonic patterning, WNT, TGF-beta, and FGF factors function as typical morphogens in a concentration-dependent manner to regulate cell fate decisions. This mode of action raises the provocative idea that these same morphogens might also provide a coordinate system for axons to establish the distance to their targets during axon guidance and synapse formation.     

What are the roles of substrate-assisted catalysis and proximity effects in peptide bond formation by the ribosome?

The action of the peptidyl transferase center of the large ribosomal unit presents a fundamental step in the evolution from the RNA world to the protein world. Thus, it is important to understand the origin of the catalytic power of this ancient enzyme. Earlier studies suggested that the ribosome catalyzes peptide bond formation by using one of its groups as a general base, while more recent works have proposed that the catalysis is due to proximity effects or to substrate-assisted catalysis. However, the actual nature of the catalytic mechanism remains controversial. This work addresses the origin of the catalytic power of the ribosome by using computer simulation approaches and comparing the energetics of the peptide bond formation in the ribosome and in water. It is found that a significant part of the observed activation entropy of the reference solution reaction is due to solvation entropy, and that the proximity effect is smaller than previously thought. It is also found that the 2'-OH of the A76 ribose, which is associated with a large rate acceleration in the ribosome reaction, does not catalyze peptide bond formation in water. Thus, the catalytic effect cannot be attributed to substrate-assisted catalysis but rather to the effect of the ribosome on the reacting system. Overall, our calculations indicate that the reduction of the activation free energy is mainly due to electrostatic effects. The nature of these effects and their relationship to catalytic factors in modern enzymes is analyzed and discussed.     

What are the characteristics of lionfish and other fishes that influence their association in diurnal refuges?

In Caribbean reefs, the lionfish Pterois volitans is an invasive species that causes severe negative ecological effects, especially as this crepuscular predator consumes very diverse prey. Lionfish are not active during the day and stay in their refuges, sharing these spaces with various other fishes. The aim of this study is to determine which fishes are associated with the lionfish in their shelters, and what characteristics of both the invasive and native species may influence and explain such coexistence between a predator and its potential prey. Through diving and snorkelling, we visited 141 lionfish refuges, mostly caves, where we observed 204 lionfish and 494 other fish from 16 native species. We recorded species and abundance, as well as lionfish size and abundance. Half of the lionfish were observed in groups and the majority were large-sized. The association with most fish species seems fortuitous, but three species, Gramma loreto, Chromis cyanea and Canthigaster rostrata, were frequently observed in association with lionfish. Numerous fish juveniles, most likely Scarus coeruleus, were also observed together with the invasive predator. The more commonly associated fishes, particularly G. loreto, are mostly associated with large-sized lionfish that were found in groups. The associated fishes are also generally found in groups. Gramma loreto is a potential cleaner of the lionfish; the reasons for the association between these fish species and the invasive lionfish may be more complex than a simple predator-prey relationship and are discussed based on their biological traits and previously reported lionfish trophic ecology and predation behaviour.     

What are definitions of life good for? Transdisciplinary and other definitions in astrobiology

The attempt to define life has gained new momentum in the wake of novel fields such as synthetic biology, astrobiology, and artificial life. In a series of articles, Cleland, Chyba, and Machery claim that definitions of life seek to provide necessary and sufficient conditions for applying the concept of life—something that such definitions cannot, and should not do. We argue that this criticism is largely unwarranted. Cleland, Chyba, and Machery approach definitions of life as classifying devices, thereby neglecting their other epistemic roles. We identify within the discussions of the nature and origin of life three other types of definitions: theoretical, transdisciplinary, and diagnostic definitions. The primary aim of these definitions is not to distinguish life from nonlife, although they can also be used for classificatory purposes. We focus on the definitions of life within the budding field of astrobiology, paying particular attention to transdisciplinary definitions, and diagnostic definitions in the search for biosignatures from other planets.     

HLA complex genes in type 1 diabetes and other autoimmune diseases. Which genes are involved?

The predisposition to develop a majority of autoimmune diseases is associated with specific genes within the human leukocyte antigen (HLA) complex. However, it is frequently difficult to determine which of the many genes of the HLA complex are directly involved in the disease process. The main reasons for these difficulties are the complexity of associations where several HLA complex genes might be involved, and the strong linkage disequilibrium that exists between the genes in this complex. The latter phenomenon leads to secondary disease associations, or what has been called 'hitchhiking polymorphisms'. Here, we give an overview of the complexity of HLA associations in autoimmune disease, focusing on type 1 diabetes and trying to answer the question: how many and which HLA genes are directly involved?     

The organization of the β-globin gene of the bivalve mollusc Anadara trapezia and its evolutionary relationship to other invertebrate and vertebrate globin genes

Three pairs of oligonucleotide primers based on partial DNA and amino acid sequences were used in a combination of PCR experiments to amplify the -globin gene of the bivalve mollusc Anadara trapezia. The sequence of 2,139 by presented contains the whole of the -globin gene with the exception of the 5 flanking sequence. This gene possesses the three-exon-and-two-intron gene structure typical of vertebrate globin genes but the lengths of the introns (762 by and 690 bp, respectively) are only approximately half the size of those present in a -variant gene previously characterized from this organism. The encoded amino acid sequence shows two changes when compared to the previously published amino acid sequence. Correspondence to: A.G. Mackinlay     

Recognition memory: what are the roles of the perirhinal cortex and hippocampus?

The hallmark of medial temporal lobe amnesia is a loss of episodic memory such that patients fail to remember new events that are set in an autobiographical context (an episode). A further symptom is a loss of recognition memory. The relationship between these two features has recently become contentious. Here, we focus on the central issue in this dispute--the relative contributions of the hippocampus and the perirhinal cortex to recognition memory. A resolution is vital not only for uncovering the neural substrates of these key aspects of memory, but also for understanding the processes disrupted in medial temporal lobe amnesia and the validity of animal models of this syndrome.     

What are the relative costs,limits and correlates of increased degree of serotiny?

There is variability in the period that serotinous species retain seeds in protective closed cones and in the sizes of the cones. Seed predation and inter‐fire recruitment have been suggested to be reasons for this variability. I argue against these two reasons. Variation in annual rates of increase in fecundity and in numbers of flowering episodes before fire should be correlated with the degree of serotiny. These two attributes are a consequence of cone size, plant architecture and degree of serotiny.     

Mammalian DSCAMs: roles in the development of the spinal cord,cortex, and cerebellum?

Central nervous system (CNS) development involves neural patterning, neuronal and axonal migrations, and synapse formation. DSCAM, a chromosome 21 axon guidance molecule, is expressed by CNS neurons during development and throughout adult life. We now report that DSCAM and its chromosome 11 paralog DSCAML1 exhibit inverse ventral-dorsal expression patterns in the developing spinal cord and distinct, partly inverse, expression patterns in the developing cortex, beginning in the Cajal-Retzius cells. In the adult cortex, DSCAM predominates in layer 3/5 pyramidal cells and DSCAML1 predominates in layer 2 granule cells. In the cerebellum, DSCAM is stronger in the Purkinje cells and DSCAML1 in the granule cells. Finally, we find that the predicted DSCAML1 protein contains 60 additional N-terminal amino acids which may contribute to its distinct expression pattern and putative function. We propose that the DSCAMs comprise novel elements of the pathways mediating dorsal-ventral patterning and cell-fate specification in the developing CNS.