Telomeres--what's new at the end?

Telomeres are specialized chromatin domains located at the ends of chromosomes. They are involved in chromosome replication, stability and localization in the nucleus. In addition to these functions, recent work suggests that telomeres are involved in such superficially diverse cellular phenomena as ageing, cancer, nuclear architecture and nuclear/cellular division.     

Neurocomputers: a dead end?

The last decade saw a proliferation of research into the design of neurocomputers. Although such work still continues, much of it is never beyond the prototype-machine stage. In this paper, we argue that, on the whole, neurocomputers are no longer viable; like, say, database computers before them, their time has passed before they became a common reality. We consider the implementation of hardware neural networks, from the level of arithmetic to complete individual processors and parallel processors and show that currents trends in computer architecture and implementation are not supportive of a case for custom neurocomputers. We argue that in the future, neural-network processing ought to be mostly restricted to general-purpose processors or to processors that have been designed for other widely-used applications. There are just one or two, rather narrow, exceptions to this.     

The end of autophagic cell death?

In the mammalian system, cell death is often preceded or accompanied by autophagic vacuolization, a finding that initially led to the widespread belief that so-called "autophagic cell death" would be mediated by autophagy. Thanks to the availability of genetic tools to disable the autophagic machinery, it has become clear over recent years that autophagy usually constitutes a futile attempt of dying cells to adapt to lethal stress rather than a mechanism to execute a cell death program. Recently, we systematically addressed the question as to whether established or prospective anticancer agents may induce "autophagic cell death". Although a considerable portion among the 1,400 compounds that we evaluated induced autophagic puncta and actually increased autophagic flux, not a single one turned out to kill tumor cells through the induction of autophagy. Thus, knockdown of essential autophagy genes (such as ATG5 and ATG7) failed to prevent and rather accelerated chemotherapy-induced cell death, in spite of the fact that this manipulation efficiently inhibits autophagosome formation. Herein, we review these finding and--polemically--raise doubts as to the very existence of "autophagic cell death".     

Microbrachiopods and the end‐Ordovician event

Millimetre sized chitinophosphatic brachiopods ("microbrachiopods") largely, but by no means entirely, centred around the family Acrotretidae are commonly regarded as being in decline after the early Ordovician. Work on Irish Upper Ordovician limestones however shows that this is not the case, material recovered showing both numerical abundance and taxonomic diversity in beds of Ashgill age. Although forms are known from the Devonian, the published record of these neglected fossils from the Silurian is sparse, so that the effects, if any, of the end‐Ordovician event on this ecologically enigmatic group cannot as yet be determined.     

Dead end for auxin conjugates in Physcomitrella?

For proper development of plants auxin levels need to be tightly controlled. For this, several routes have evolved and it is plausible that different organisms use these differently. To determine whether members of the family of GH3 proteins, which partially act as auxin conjugate synthetases in Arabidopsis thaliana, have similar roles in the moss Physcomitrella patens, we have investigated the in vitro activity of the two GH3 members in moss. We showed that both proteins can form amino acid conjugates with indole-3-acetic acid (IAA) but also with jasmonic acid (JA). Confirming these findings, single and double knockout-mutants showed lower levels of IAA conjugates than wild type. We discuss the results in light of the possible functions of IAA conjugate formation in lower land plants.Key words: Arabidopsis thaliana, auxin metabolism, jasmonic acid, GH3 genes, moss, Physcomitrella patensAuxins play diverse roles in many aspects of plant growth and development. Their activity is relying on the correct concentration in a given tissue and developmental stage.¹ If higher levels of indole-3-acetic acid (IAA) are present, the hormone can also have an inhibitory effect on growth processes.² Therefore, the tight control of IAA concentrations is absolutely necessary. To this end plants have evolved different mechanisms.³ First, biosynthesis is contributing to increasing IAA concentrations, mostly in young tissues such as meristems. Second, IAA can be transported in a polar way, depending on transport molecules, from cell to cell, away from the site of synthesis, thereby forming an auxin gradient along the plant axis. Third, IAA can be degraded, and fourth, IAA can be reversibly inactivated by conjugation to small molecules such as amino acids or sugars, but also be linked to larger molecules such as peptides or proteins.⁴ The inactive IAA conjugates can be hydrolyzed to yield free (i.e., active) IAA if needed. In higher plants the levels of free IAA constitutes between 5 and 20% depending on the tissue or age of the plant, whereas the conjugated form constitutes the major part.⁴ However, it is not yet clear in which way auxin homeostasis has evolved. The hypothesis that auxin has to be present during the evolution of a body plan has been tested by using different lower land plants which were compared in their mechanism to control auxin homeostasis. In algae, e.g., charophytes, the major metabolic way of controlling IAA is via biosynthesis. In bryophytes, the formation of IAA conjugates has been shown, although the amount was lower than for example in seed plants such as Arabidopsis thaliana.^5,6 Since the molecular biology of auxin homeostasis in Arabidopsis is most advanced, we will use this model plant to compare the knowledge on seed plants with that in the moss Physcomitrella patens. The recent publication of the Physcomitrella genome⁷ gives the possibility to investigate components of the machinery controlling IAA levels in a lower land plant.In general, there seem to be high levels of redundancy involved in the pathways leading to decrease or increase of IAA, respectively. In Figure 1 we compare the current knowledge about genes related to IAA concentrations in Physcomitrella with Arabidopsis. While in Arabidopsis many different biosynthetic routes leading to IAA were identified,⁸ in the Physcomitrella genome homologs of the YUCCA genes have been detected.⁷ The presence of auxin conjugate synthetases has been experimentally verified in the moss (see below) and additional evidence for ester conjugate synthesis comes from sequence homology to UDP-glucosyl transferases.⁷ There is also the possibility of degradation of either IAA or an amino acid conjugate with IAA^9,10 as discussed below.Open in a separate windowFigure 1Comparison of possibilities to regulate auxin homeostasis in Physcomitrella (solid lines) and Arabidopsis (dotted lines). Biosynthesis—AO, aldehyde oxidase; AMI1, amidase; CYP, cytochrome P450; NIT, nitrilase; TAA1, tryptophan aminotransferase; YUCCA, flavin monooxygenase; transport—AUX/LAX, auxin influx facilitator family; PIN, auxin efflux carrier family; PGP, ABC transporter type auxin efflux carrier family; conjugation/hydrolysis—UGT, UDP-glucosyl transferase; GH3, auxin conjugate synthetase family; ILR/IAR, auxin conjugate hydrolase family; Ox-IAA, oxindole-3-acetic acid; Ox-IAAsp, oxindole-3-aspartic acid.So far our work has focussed on the characterization of two members of the so called GH3 family, of which several from Arabidopsis can form conjugates of IAA with a variety of amino acids.¹¹ While 19 members of this family have been described in Arabidopsis, only two are present in Physcomitrella.¹² The Arabidopsis family clusters in three groups: group I containing the jasmonic acid conjugate synthetase JAR1 and a few others with as yet unkown function, group II the auxin conjugate synthetases, and group III with mostly as yet uncharacterized members.^11,13 Sequence similarity of the GH3 genes from Physcomitrella showed that both cluster within the JAR1 group.¹² Therefore, we analyzed the enzymatic activity of the two Physcomitrella GH3 proteins (PpGH3-1 and PpGH3-2) in vitro¹⁴ and found that both were active on jasmonic acid and a variety of different amino acids, whereas PpGH3-2 was active mostly with IAA. PpGH3-1 showed only weak activity with IAA and only two amino acids. For this reason, it could be assumed that the two Physcomitrella genes evolved by gene duplication, from which the initial activities would be for IAA and jasmonic acid. One of these genes might have evolved into a jasmonate conjugate synthetase (maybe AtJAR1),¹³ thereby loosing its activity on IAA. The second may have given rise to the auxin conjugate synthetase family in Arabidopsis,¹¹ but the conjugate synthetases of Physcomitrella have still activity with both hormones. Interestingly, there is no evidence as yet that jasmonic acid itself has a role during Physcomitrella development, although a possible function of JA-conjugates has not been closely investigated. Since in Arabidopsis the JA conjugate with isoleucine is the active compound to be recognized by the COI1 receptor protein,¹⁵ it could be the case that JA itself has no effect in Physcomitrella. However, in our growth experiments a small growth promoting effect of JA, independently on the presence of GH3 genes was found. Similar observations were made with gibberellins in Physcomitrella.¹⁶Further characterization of single and double KO mutants in each of the PpGH3 genes has led to the hypothesis that GH3 proteins are indeed involved in regulating the auxin homeostasis in Physcomitrella.¹⁴ Both single KO mutants were more sensitive to increasing IAA concentrations in the medium than the wild type. Furthermore, the levels of free IAA were higher and the levels of conjugated IAA concomitantly dropped. A double KO mutant had almost no IAA conjugates when compared to the wild type. However, this mutant was still able to synthesize ester conjugates with IAA. Interestingly, the role of GH3 proteins in auxin conjugation seemed to be only important in the gametophore stage, whereas protonema cultures of GH3 KO mutants did not show any changes in auxin homeostasis. Therefore, we hypothesize that the role of GH3 proteins is dependent on a certain developmental stage of the moss. Additionally, we propose other detoxification mechanisms for example, export or degradation, in protonema.In higher plants the ester conjugate formation of IAA has been shown to be dependent on UDP-glucosyl transferases (AtUGT84B1 for Arabidopsis¹⁷ and ZmIAGLU for maize¹⁸). In the genome of Physcomitrella we could detect candidate sequence(s) for these genes, indicating that Physcomitrella has indeed the potential to synthesise the ester conjugates found in the gametophores in addition to amide conjugates. However, in the Physcomitrella genome, no homolog for an auxin conjugate hydrolase was found. In higher plants, auxin conjugate hydrolysis is thought to contribute to free IAA and depending on the plant species, large gene families with overlapping but distinct substrate preferences for individual amino acid conjugates with IAA are present.^19,20 Since this is not the case for Physcomitrella, one has to ask the question whether the conjugation of auxin is a one-way road for inactivation of excess auxin and whether auxin conjugate hydrolysis has evolved later during plant evolution.In the Selaginella moellendorffii genome (http://genome.jgi-psf.org/Selmo1/Selmo1.home.html), an auxin conjugate hydrolase sequence related to higher plant ones, has been found based on homology searches, but the completion of the genome has to be awaited to draw final conclusions. Likewise, it is not clear, if this effect is specific for Physcomitrella, or found in bryophytes in general. Therefore, additional sequenced bryophyte genomes are needed.²¹Since in Arabidopsis the degradation of the IAA-Aspartate conjugate to Ox-IAA-Asp (see Fig. 1) has been described,^9,10 a similar scenario could be suggested to occur in Physcomitrella with the amino acid conjugates formed. Alternatively, the hydrolysis of IAA conjugates by members of the M20 dipeptidase family can be envisioned. However, this would need the activity of enzymes with very low sequence conservation to auxin conjugate hydrolases. These questions will be addressed in future research by studying the metabolism of IAA and IAA conjugates of Physcomitrella in more detail.     

Drosophila olfaction: the end of stereotypy?

Recent work has demonstrated substantial wiring and functional stereotypy in the fly olfactory system. In this issue of Neuron, Murthy et al. demonstrate that in the mushroom body, a site of olfactory associative learning, this initial peripheral stereotypy gives way to functionally nonstereotyped circuits.     

The end of the adaptive landscape metaphor?

The concepts of adaptive/fitness landscapes and adaptive peaks are a central part of much of contemporary evolutionary biology; the concepts are introduced in introductory texts, developed in more detail in graduate-level treatments, and are used extensively in papers published in the major journals in the field. The appeal of visualizing the process of evolution in terms of the movement of populations on such landscapes is very strong; as one becomes familiar with the metaphor, one often develops the feeling that it is possible to gain deep insights into evolution by thinking about the movement of populations on landscapes consisting of adaptive valleys and peaks. But, since Wright first introduced the metaphor in 1932, the metaphor has been the subject of persistent confusion, from equivocation over just what the features of the landscape are meant to represent to how we ought to expect the landscapes to look. Recent advances—conceptual, empirical, and computational—have pointed towards the inadequacy and indeed incoherence of the landscapes as usually pictured. I argue that attempts to reform the metaphor are misguided; it is time to give up the pictorial metaphor of the landscape entirely and rely instead on the results of formal modeling, however difficult such results are to understand in ‘intuitive’ terms.

Genetic viability and population history of the giant panda, putting an end to the "evolutionary dead end"?

The giant panda (Ailuropoda melanoleuca) is currently threatened by habitat loss, fragmentation, and human persecution. Its dietary specialization, habitat isolation, and reproductive constraints have led to a perception that this is a species at an "evolutionary dead end," destined for deterministic extinction in the modern world. Here we examine this perception by a comprehensive investigation of its genetic diversity, population structure, and demographic history across its geographic range. We present analysis of 655 base pairs of mitochondrial (mt) control region (CR) DNA and 10 microsatellite loci for samples from its 5 extant mountain populations (Qinling, Minshan, Qionglai, Liangshan, and Lesser Xiangling). Surprisingly, extant populations display average to high levels of CR and microsatellite diversity compared with other bear species. Genetic differentiation among populations was significant in most cases but was markedly higher between Qinling and the other mountain ranges, suggesting, minimally, that the Qinling population should comprise a separate management unit for conservation purposes. Recent demographic inference using microsatellite markers demonstrated a clear genetic signature for population decline starting several thousands years ago or even further back in the past, and being accelerated and enhanced by the expansion of human populations. Importantly, these data suggest that the panda is not a species at an evolutionary "dead end," but in common with other large carnivores, has suffered demographically at the hands of human pressure. Conservation strategies should therefore focus on the restoration and protection of wild habitat and the maintenance of the currently substantial regional genetic diversity, through active management of disconnected populations.     

Lateral gene transfer: when will adolescence end?

The scope and impact of horizontal gene transfer (HGT) in Bacteria and Archaea has grown from a topic largely ignored by the microbiological community to a hot-button issue gaining staunch supporters (on particular points of view) at a seemingly ever-increasing rate. Opinions range from HGT being a phenomenon with minor impact on overall microbial evolution and diversification to HGT being so rampant as to obfuscate any opportunities for elucidating microbial evolution - especially organismal phylogeny - from sequence comparisons. This contentious issue has been fuelled by the influx of complete genome sequences, which has allowed for a more detailed examination of this question than previously afforded. We propose that the lack of common ground upon which to formulate consensus viewpoints probably stems from the absence of answers to four critical questions. If addressed, they could clarify concepts, reject tenuous speculation and solidify a robust foundation for the integration of HGT into a framework for long-term microbial evolution, regardless of the intellectual camp in which you reside. Here, we examine these issues, why their answers shape the outcome of this debate and the progress being made to address them.     

Prion hypothesis: the end of the controversy?

Forty-three years have passed since it was first proposed that a protein could be the sole component of the infectious agent responsible for the enigmatic prion diseases. Many discoveries have strongly supported the prion hypothesis, but only recently has this once heretical hypothesis been widely accepted by the scientific community. In the past 3 years, researchers have achieved the 'Holy Grail' demonstration that infectious material can be generated in vitro using completely defined components. These breakthroughs have proven that a misfolded protein is the active component of the infectious agent, and that propagation of the disease and its unique features depend on the self-replication of the infectious folding of the prion protein. In spite of these important discoveries, it remains unclear whether another molecule besides the misfolded prion protein might be an essential element of the infectious agent. Future research promises to reveal many more intriguing features about the rogue prions.     

Catecholamine sulfates: end products or metabolic intermediates?

Dopamine-beta-hydroxylase catalyzes the beta-oxidation of dopamine to noradrenaline while phenylethanolamine-N-methyltransferase converts noradrenaline to adrenaline. Since catecholamine sulfates represent the predominant form of catecholamines in human tissues, we have studied the role of dopamine sulfate and noradrenaline sulfate as alternate substrates for dopamine-beta-hydroxylase and phenylethanolamine-N-methyltransferase, respectively. Dopamine 3-sulfate, dopamine 4-sulfate and noradrenaline 3-sulfate were chemically synthesized and exhaustively purified by ion-exchange chromatography. Dopamine-beta-hydroxylase and phenylethanolamine-N-methyltransferase were partially purified from human adrenals. Using tyramine as substrate, dopamine-beta-hydroxylase is slightly inhibited by dopamine 3-sulfate according to some irreversible or mixed mechanisms. When dopamine-beta-hydroxylase was incubated with dopamine 3-sulfate or dopamine 4-sulfate, we were not able to find any synthesis of either noradrenaline sulfate or free noradrenaline. Using phenylethanolamine as substrate, the enzymatic activity of phenylethanolamine-N-methyltransferase remains unchanged with addition of dopamine 3-sulfate, dopamine 4-sulfate or noradrenaline 3-sulfate. It was concluded that dopamine sulfate is not an alternate substrate for either dopamine-beta-hydroxylase or phenylethanolamine-N-methyltransferase nor is noradrenaline 3-sulfate an alternate substrate for phenylethanolamine-N-methyltransferase.