Neuroscience: how is three-dimensional space encoded in the brain?

A recent study in the rat has shown that hippocampal place cells and entorhinal grid cells exhibit vertically-elongated firing fields, indicating that the rat's brain may encode the animal's elevation less accurately than its horizontal position.     

mTOR signaling in protein homeostasis: Less is more?

A proper balance between synthesis, maturation and degradation of cellular proteins is crucial for cells to maintain physiological functions. The costly process of protein synthesis is tightly coupled to energy status and nutrient levels by the mammalian target of rapamycin (mTOR), whereas the quality of newly synthesized polypeptides is largely maintained by molecular chaperones and the ubiquitin-proteasome system. There is a wealth of evidence indicating close ties between the nutrient signaling pathway and the intracellular stress response. Dysregulation of both systems has been implicated in aging and age-associated pathologies. In this review, we describe molecular mechanisms underlying the connection between mTOR and the chaperone network and discuss the importance of their functional interaction in growth and aging.Key words: target of rapamycin, stress response, ribosome, chaperone, translation, folding, degradation, aging     

How complex is GTPase signaling in trypanosomes?

Many signaling pathways in higher eukaryotes use Ras-like small GTPases. Here, we ask how complex are these small GTPase signaling pathways in trypanosomes? We seek to address this issue by comparisons with the representation of both the GTPase molecules and their accessory factors in several genomes.     

Why is the microtubule lattice helical?

Microtubules polymerize from identical tubulin heterodimers, which form a helical lattice pattern that is the microtubule. This pattern always has left-handed chirality, but it is not known why. But as tubulin, similar to other proteins, evolved for a purpose, the question of the title of this artcile appears to be meaningful. In a computer simulation that explores the 'counterfactual biology' of microtubules without helicity, we demonstrate that these have the same mechanical properties as Nature's microtubules with helicity. Thus only a dynamical reason for helicity is left as potential explanation. We find that helicity solves 'the problem of the blind mason', i.e. how to correctly build a structure, guided only by the shape of the bricks. This answer in turn raises some new questions for researchers to address.     

mTORC1 signaling under hypoxic conditions is controlled by ATM-dependent phosphorylation of HIF-1α

The mTOR complex-1 (mTORC1) coordinates cell growth and metabolism, acting as a restriction point under stress conditions such as low oxygen tension (hypoxia). Hypoxia suppresses mTORC1 signaling. However, the signals by which hypoxia suppresses mTORC1 are only partially understood, and a direct link between hypoxia-driven physiological stress and the regulation of mTORC1 signaling is unknown. Here we show that hypoxia results in ataxia telangiectasia mutated (ATM)-dependent phosphorylation of hypoxia-inducible factor 1-alpha (HIF-1α) on serine(696) and mediates downregulation of mTORC1 signaling. Deregulation of these pathways in pediatric solid tumor xenografts suggests a link between mTORC1 dysregulation and solid tumor development and points to an important role for hypoxic regulation of mTORC1 activity in tumor development.     

Natural variation in phosphorylation of photosystem II proteins in Arabidopsis thaliana: is it caused by genetic variation in the STN kinases?

Reversible phosphorylation of photosystem II (PSII) proteins is an important regulatory mechanism that can protect plants from changes in ambient light intensity and quality. We hypothesized that there is natural variation in this process in Arabidopsis (Arabidopsis thaliana), and that this results from genetic variation in the STN7 and STN8 kinase genes. To test this, Arabidopsis accessions of diverse geographical origins were exposed to two light regimes, and the levels of phospho-D1 and phospho-light harvesting complex II (LHCII) proteins were quantified by western blotting with anti-phosphothreonine antibodies. Accessions were classified as having high, moderate or low phosphorylation relative to Col-0. This variation could not be explained by the abundance of the substrates in thylakoid membranes. In genotypes with atrazine-resistant forms of the D1 protein, low D1 and LHCII protein phosphorylation was observed, which may be due to low PSII efficiency, resulting in reduced activation of the STN kinases. In the remaining genotypes, phospho-D1 levels correlated with STN8 protein abundance in high-light conditions. In growth light, D1 and LHCII phosphorylation correlated with longitude and in the case of LHCII phosphorylation also with temperature variability. This suggests a possible role of natural variation in PSII protein phosphorylation in the adaptation of Arabidopsis to diverse environments.     

Episodic memory in nonhumans: what, and where, is when?

Episodic memory is defined as the recollection of specific events in one's past, accompanied by the experience of having been there personally. This definition presents high hurdles to the investigation of episodic memory in nonhumans. Recent studies operationalize episodic memory as memory for when and where an event occurred, for the order in which events occurred, or for an animal's own behavior. None of these approaches has yet generalized across species, and each fails to capture features of human episodic memory. Nonetheless, the study of episodic memory in nonhumans seems less daunting than it did five years ago. To demonstrate a correspondence between human episodic memory and nonhuman memory, progress is needed in three areas. Putative episodic memories in nonhumans should be shown to be; first, represented in long-term memory, rather than short-term or working memory; second, explicit, or accessible to introspection; and third, distinct from semantic memory, or general knowledge about the world.     

All signaling is local?

The mechanism of signal transmission following ligand stimulation of receptor tyrosine kinases in living cells is poorly understood. Recent studies have visualized the spatio-temporal pattern of EGF signaling, indicating that receptor density is an important factor in the mechanism of lateral propagation of local EGF signaling.     

Gamma-tubulin: the microtubule organizer?

Microtubules are composed predominantly of two related proteins: alpha- and beta-tubulin. These proteins form the tubulin heterodimer, which is the basic building block of microtubules. Surprisingly, recent molecular genetic studies have revealed the existence of gamma-tubulin, a new member of the tubulin family. Like alpha- and beta-tubulin, gamma-tubulin is essential for microtubule function but, unlike alpha- and beta-tubulin, it is not a component of microtubules. Rather, it is located at microtubule-organizing centres and may function in the nucleation of microtubule assembly and establishment of microtubule polarity.     

Mitochondrial oxidative phosphorylation is regulated by fructose 1,6-bisphosphate. A possible role in Crabtree effect induction?

In numerous cell types, tumoral cells, proliferating cells, bacteria, and yeast, respiration is inhibited when high concentrations of glucose are added to the culture medium. This phenomenon has been named the Crabtree effect. We used yeast to investigate (i) the short term event(s) associated with the Crabtree effect and (ii) a putative role of hexose phosphates in the inhibition of respiration. Indeed, yeast divide into Crabtree-positive, where the Crabtree effect occurs, and Crabtree-negative, where it does not. In mitochondria isolated from these two categories of yeast, we found that low, physiological concentrations of glucose 6-phosphate and fructose 6-phosphate slightly (20%) stimulated the respiratory flux and that this effect was strongly antagonized by fructose 1,6-bisphosphate (F16bP). On the other hand, F16bP by itself was able to inhibit mitochondrial respiration only in mitochondria isolated from a Crabtree-positive strain. Using permeabilized spheroplasts from Crabtree-positive yeast, we have shown that the sole effect observed at physiological concentrations of hexose phosphates is an inhibition of oxidative phosphorylation by F16bP. This F16bP-mediated inhibition was also observed in isolated rat liver mitochondria, extending this process to mammalian cells. From these results and taking into account that F16bP is able to accumulate in the cell cytoplasm, we propose that F16bP regulates oxidative phosphorylation and thus participates in the establishment of the Crabtree effect.     

Prospective and retrospective duration memory in the hippocampus: is time in the foreground or background?

Psychologists have long distinguished between prospective and retrospective timing to highlight the difference between our sense of duration during an experience in passing and our sense of duration in hindsight. Humans and other animals use prospective timing in the seconds-to-minutes range in order to learn durations, and can organize their behaviour based upon this knowledge when they know that duration information will be important ahead of time. By contrast, when durations are estimated after the fact, thus precluding the subject from consciously attending to temporal information, duration information must be extracted from other memory representations. The accumulated evidence from prospective timing research has generally led to the hippocampus (HPC) being casted in a supporting role with prefrontal–striatal, cortical or cerebellar circuits playing the lead. Here, I review findings from the animal and human literature that have led to this conclusion and consider that the contribution of the HPC to duration memory is understated because we have little understanding about how we remember duration.     

Kinetics of protein tyrosine phosphorylation in sperm selected by binding to homologous and heterologous oviductal explants: how specific is the regulation by the oviduct?

Essential steps of the capacitation process take place in the oviductal isthmus. A crucial step in the process of capacitation is the phosphorylation of membrane proteins. The aims of this work were (1) to study the effect of dog sperm binding to oviductal epithelium on tyrosine phosphorylation and (2) to investigate the specificity of regulation of molecular changes by the oviduct of different species by comparing the numbers of canine sperm bound to heterologous (porcine) and homologous epithelium, and the kinetics of tyrosine phosphorylation. Semen was collected from four healthy dogs and washed through a Percoll gradient. Explants, small pieces of epithelium, were cut from porcine and estrous bitch oviducts. During 6 h of coincubation in Tyrode medium, the numbers of bound sperm were counted by microvideographic observation, and the state of tyrosine phosphorylation was determined immunocytochemically after 3, 30, 90, 180 and 360 min. Canine sperm bound in similar numbers to homologous and heterologous explants. Increasing tyrosine phosphorylation of tail proteins and subsequent phosphorylation of sperm head proteins were observed. Binding occurred mainly in sperm with non-phosphorylated heads (approximately 2% phosphorylated), while higher proportions of head-phosphorylated cells were found in unbound populations (approximately 40-60%;P<0.05). The head phosphorylation progressed significantly during incubation in unbound spermatozoa (P<0.05), while it was suppressed in bound suspensions. The rate of tyrosine phosphorylation of sperm tail proteins was higher in cells bound to explants than in unbound cells or in those incubated in control medium. There were no significant differences with respect to the kinetics of tyrosine phosphorylation between the two coincubation systems. These observations support the hypothesis that spermatozoa with non-phosphorylated heads preferentially attach to epithelial cells. Tyrosine phosphorylation of sperm head proteins and capacitation are delayed in spermatozoa in close contact with oviductal epithelium. This mechanism appears to be species-independent, as sperm bound similarly to pig and dog oviduct explants, and similar phosphorylation kinetics were observed in both types of tissue.     

Sulfur signaling: is the agent sulfide or sulfane?

Triplex-forming oligonucleotides (TFOs) are sequence-dependent DNA binders that may be useful for DNA targeting and detection. A sensitive and convenient method to monitor triplex formation by a TFO and its target DNA duplex is required for the application of TFO probes. Here we describe a novel design by which triplex formation can be monitored homogeneously without prelabeling the target duplex. The design uses a TFO probe tagged with a fluorophore that undergoes fluorescence resonance energy transfer with fluorescent dyes that intercalate into the target duplex. Through color compensation analysis, the specific emission of the TFO probe reveals the status of the triple helices. We used this method to show that triple helix formation with TFOs is magnesium dependent. We also demonstrated that the TFO probe can be used for detection of sequence variation in melting analysis and for DNA quantitation in real-time polymerase chain reaction.     

Herd size in large herbivores: encoded in the individual or emergent?

In large mammalian herbivores, the increase of group size with habitat openness was first assumed to be an adaptive response, encoded in the individual. However, it could, alternatively, be an emergent property: if groups were nonpermanent units, often fusing and splitting up, then any increase of the distance at which animals perceive one another could increase the rate of group fusion and thus mean group size. Dynamical models and empirical data support this second hypothesis. This is not to say that adaptive modifications of mean herd size cannot occur. However, this changes the way in which we can envisage the history of gregariousness in large herbivores during the Tertiary.     

Enhanced electron transfer by GTP: cross-membrane electron signaling by G-proteins?

Activation of several receptor types is followed by their binding to a G-protein. Prior to transmission of the agonist signal, the G-protein which had affinity for guanosine 5-diphosphate (GDP) binds guanosine 5-triphosphate (GTP) instead. Because evidence exists that several agonist groups activate their receptors by reduction, we evaluated whether the nucleotide associated with G-proteins could enhance electron flow. Using a model system of ferrous iron and ferric cytochrome c, it was determined that substitution of GTP for GDP led to an enhanced reduction of ferric cytochrome c. These results support the concept that cellular activation by certain receptors may involve reductive activation with the participation of GTP and G-proteins. We speculate that GTP, when bound to G-protein, can facilitate electron transfer perhaps from the receptor or the G-protein to the catalytic subunit of the adenylate cyclase enzyme.