Functional context, biosynthesis, and genetic encoding of pyrrolysine

In Methanosarcina spp., amber codons in methylamine methyltransferase genes are translated as the 22nd amino acid, pyrrolysine. The responsible pyl genes plus amber-codon containing methyltransferase genes have been identified in four archaeal and five bacterial genera, including one human pathogen. In Escherichia coli, the recombinant pylBCD gene products biosynthesize pyrrolysine from two molecules of lysine and the pylTS gene products direct pyrrolysine incorporation into protein. In the proposed biosynthetic pathway, PylB forms methylornithine from lysine, which is joined to another lysine by PylC, and oxidized to pyrrolysine by PylD. Structures of the catalytic domain of pyrrolysyl-tRNA synthetase (archaeal PylS or bacterial PylSc) revealed binding sites for tRNAPyl and pyrrolysine. PylS and tRNAPyl are now being exploited as an orthogonal pair in recombinant systems for introduction of useful modified amino acids into proteins.     

Sensory-perceptual episodic memory and its context: autobiographical memory

Episodic memory is reconceived as a memory system that retains highly detailed sensory perceptual knowledge of recent experience over retention intervals measured in minutes and hours. Episodic knowledge has yet to be integrated with the autobiographical memory knowledge base and so takes as its context or referent the immediate past of the experiencing self (or the 'I'). When recalled it can be accessed independently of content and is recollectively experienced. Autobiographical memory, in contrast, retains knowledge over retention intervals measured in weeks, months, years, decades and across the life span. Autobiographical knowledge represents the experienced self (or the 'me'), is always accessed by its content and, when accessed, does not necessarily give rise to recollective experience. Instead, recollective experience occurs when autobiographical knowledge retains access to associated episodic memories. In this reworking of the 'episodic memory' concept autobiographical memory provides the instantiating context for sensory-perceptual episodic memory.     

Second-order relational manipulations affect both humans and monkeys

Recognition and individuation of conspecifics by their face is essential for primate social cognition. This ability is driven by a mechanism that integrates the appearance of facial features with subtle variations in their configuration (i.e., second-order relational properties) into a holistic representation. So far, there is little evidence of whether our evolutionary ancestors show sensitivity to featural spatial relations and hence holistic processing of faces as shown in humans. Here, we directly compared macaques with humans in their sensitivity to configurally altered faces in upright and inverted orientations using a habituation paradigm and eye tracking technologies. In addition, we tested for differences in processing of conspecific faces (human faces for humans, macaque faces for macaques) and non-conspecific faces, addressing aspects of perceptual expertise. In both species, we found sensitivity to second-order relational properties for conspecific (expert) faces, when presented in upright, not in inverted, orientation. This shows that macaques possess the requirements for holistic processing, and thus show similar face processing to that of humans.     

Reward context determines risky choice in pigeons and humans

Whereas humans are risk averse for monetary gains, other animals can be risk seeking for food rewards, especially when faced with variable delays or under significant deprivation. A key difference between these findings is that humans are often explicitly told about the risky options, whereas non-human animals must learn about them from their own experience. We tested pigeons (Columba livia) and humans in formally identical choice tasks where all outcomes were learned from experience. Both species were more risk seeking for larger rewards than for smaller ones. The data suggest that the largest and smallest rewards experienced are overweighted in risky choice. This observed bias towards extreme outcomes represents a key step towards a consilience of these two disparate literatures, identifying common features that drive risky choice across phyla.     

Enhanced intersubject correlations during movie viewing correlate with successful episodic encoding

While much has been learned regarding the neural substrates supporting episodic encoding using highly controlled experimental protocols, relatively little is known regarding the neural bases of episodic encoding of real-world events. In an effort to examine this issue, we measured fMRI activity while observers viewed a novel TV sitcom. Three weeks later, subsequent memory (SM) for the narrative content of movie events was assessed. We analyzed the encoding data for intersubject correlations (ISC) based on subjects' subsequent memory (ISC-SM) performance to identify brain regions whose BOLD response is significantly more correlated across subjects during portions of the movie that are successfully as compared to unsuccessfully encoded. These regions include the parahippocampal gyrus, superior temporal gyrus, anterior temporal poles, and the temporal-parietal junction. Further analyses reveal (1) that these correlated regions can display distinct activation profiles and (2) that the results seen with the ISC-SM analysis are complementary to more traditional linear models and allow analysis of complex time course data. Thus, the ISC-SM analysis extends traditional subsequent memory findings to a rich, dynamic and more ecologically valid situation.     

Memory consolidation during sleep involves context reinstatement in humans

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Effects of context on judgements of odor intensities in humans

This study evaluated whether the intensity of previously smelled odors could unintentionally influence the subsequent judgement of odor intensity. The predicted context effect was based on the adaptation- level theory. Before and 25 min after either WEAK or STRONG biasing odor concentrations, 51 subjects were required to rate the intensity of 10 different odor concentrations of California Orange Oil. After the WEAK bias, subjects judged the odor intensity as being stronger than they did after the STRONG bias. Thus the intensity of odors smelled 25 min earlier can unintentionally influence subsequent odor intensity judgement. The findings are discussed in the light of two alternative explanations, namely, a central implicit memory process and a stimulus- level-based change at the peripheral level.      

Effect of episodic hypoxia on upper airway mechanics in humans during NREM sleep.

We hypothesized that long-term facilitation (LTF) is due to decreased upper airway resistance (Rua). We studied 11 normal subjects during stable non-rapid eye movement sleep. We induced brief isocapnic hypoxia (inspired O(2) fraction = 8%) (3 min) followed by 5 min of room air. This sequence was repeated 10 times. Measurements were obtained during control, hypoxia, and at 20 min of recovery (R(20)) for ventilation, timing, and Rua. In addition, nine subjects were studied in a sham study with no hypoxic exposure. During the episodic hypoxia study, inspiratory minute ventilation (VI) increased from 7.1 +/- 1.8 l/min during the control period to 8.3 +/- 1.8 l/min at R(20) (117% of control; P < 0.05). Conversely, there was no change in diaphragmatic electromyogram (EMG(dia)) between control (16.1 +/- 6.9 arbitrary units) and R(20) (15.3 +/- 4.9 arbitrary units) (95% of control; P > 0.05). In contrast, increased VI was associated with decreased Rua from 10.7 +/- 7.5 cmH(2)O. l(-1). s during control to 8.2 +/- 4.4 cmH(2)O. l(-1). s at R(20) (77% of control; P < 0.05). No change was noted in VI, Rua, or EMG(dia) during the recovery period relative to control during the sham study. We conclude the following: 1) increased VI in the recovery period is indicative of LTF, 2) the lack of increased EMG(dia) suggests lack of LTF to the diaphragm, 3) reduced Rua suggests LTF of upper airway dilators, and 4) increased VI in the recovery period is due to "unloading" of the upper airway by LTF of upper airway dilators.     

Genes encoding longevity: from model organisms to humans

Ample evidence from model organisms has indicated that subtle variation in genes can dramatically influence lifespan. The key genes and molecular pathways that have been identified so far encode for metabolism, maintenance and repair mechanisms that minimize age-related accumulation of permanent damage. Here, we describe the evolutionary conserved genes that are involved in lifespan regulation of model organisms and humans, and explore the reasons of discrepancies that exist between the results found in the various species. In general, the accumulated data have revealed that when moving up the evolutionary ladder, together with an increase of genome complexity, the impact of candidate genes on lifespan becomes smaller. The presence of genetic networks makes it more likely to expect impact of variation in several interacting genes to affect lifespan in humans. Extrapolation of findings from experimental models to humans is further complicated as phenotypes are critically dependent on the setting in which genes are expressed, while laboratory conditions and modern environments are markedly dissimilar. Finally, currently used methodologies may have only little power and validity to reveal genetic variation in the population. In conclusion, although the study of model organisms has revealed potential candidate genetic mechanisms determining aging and lifespan, to what extent they explain variation in human populations is still uncertain.     

Differential encoding of behavior and spatial context in deep and superficial layers of the neocortex

Rodent hippocampal activity is correlated with spatial and behavioral context, but how context affects coding in association neocortex is not well understood. The cellular distribution of the neural activity-regulated immediate-early gene Arc was used to monitor the activity history of cells in CA1, and in deep and superficial layers of posterior parietal and gustatory cortices (which encode movement and taste, respectively), during two behavioral epochs in which spatial and behavioral context were independently manipulated while gustatory input was held constant. Under conditions in which the hippocampus strongly differentiated behavioral and spatial contexts, deep parietal and gustatory layers did not discriminate between spatial contexts, whereas superficial layers in both neocortical regions discriminated well. Deep parietal cells discriminated behavioral context, whereas deep gustatory cortex neurons encoded the two conditions identically. Increased context sensitivity of superficial neocortical layers, which receive more hippocampal outflow, may reflect a general principle of neocortical organization for memory retrieval.     

Social context hinders humans but not ravens in a short-term memory task

Using resources shared within a social group—either in a cooperative or a competitive way—requires keeping track of own and others’ actions, which, in turn, requires well-developed short-term memory. Although short-term memory has been tested in social mammal species, little is known about this capacity in highly social birds, such as ravens. We compared ravens (Corvus corax) with humans in spatial tasks based on caching, which required short-term memory of one's own and of others’ actions. Human short-term memory has been most extensively tested of all social mammal species, hence providing an informative benchmark for the ravens. A recent study on another corvid species (Corvus corone) suggests their capacity to be similar to the humans’, but short-term memory skills have, to date, not been compared in a social setting. We used spatial setups based on caches of foods or objects, divided into individual and social conditions with two different spatial arrangements of caches (in a row or a 3 × 3 matrix). In each trial, a set of three up to nine caches was presented to an individual that was thereafter allowed to retrieve all items. Humans performed better on average across trials, but their performance dropped, when they had to keep track of partner's actions. This differed in ravens, as keeping track of such actions did not impair their performance. However, both humans and ravens demonstrated more memory-related mistakes in the social than in the individual conditions. Therefore, whereas both the ravens’ and the humans’ memory suffered in the social conditions, the ravens seemed to deal better with the demands of these conditions. The social conditions had a competitive element, and one might speculate that ravens’ memory strategies are more attuned to such situations, in particular in caching contexts, than is the case for humans.     

A relational database for the discovery of genes encoding amino acid biosynthetic enzymes in pathogenic fungi

Fungal phytopathogens continue to cause major economic impact, either directly, through crop losses, or due to the costs of fungicide application. Attempts to understand these organisms are hampered by a lack of fungal genome sequence data. A need exists, however, to develop specific bioinformatics tools to collate and analyse the sequence data that currently is available. A web-accessible gene discovery database (http://cogeme.ex.ac.uk/biosynthesis.html) was developed as a demonstration tool for the analysis of metabolic and signal transduction pathways in pathogenic fungi using incomplete gene inventories. Using Bayesian probability to analyse the currently available gene information from pathogenic fungi, we provide evidence that the obligate pathogen Blumeria graminis possesses all amino acid biosynthetic pathways found in free-living fungi, such as Saccharomyces cerevisiae. Phylogenetic analysis was also used to deduce a gene history of succinate-semialdehyde dehydrogenase, an enzyme in the glutamate and lysine biosynthesis pathways. The database provides a tool and methodology to researchers to direct experimentation towards predicting pathway conservation in pathogenic microorganisms.     

Peripheral chemoreflex responsiveness is increased at elevated levels of carbon dioxide after episodic hypoxia in awake humans.

We hypothesized that the acute ventilatory response to hypoxia is enhanced after exposure to episodic hypoxia in awake humans. Eleven subjects completed a series of rebreathing trials before and after exposure to eight 4-min episodes of hypoxia. During the rebreathing trials, subjects initially hyperventilated to reduce the partial pressure of carbon dioxide (Pet(CO(2))) below 25 Torr. Subjects then breathed from a bag containing normocapnic (42 Torr), low (50 Torr), or high oxygen (140 Torr) gas mixtures. During the trials, Pet(CO(2)) increased while a constant oxygen level was maintained. The point at which ventilation began to rise in a linear fashion as Pet(CO(2)) increased was considered to be the ventilatory recruitment threshold. The ventilatory response below and above the recruitment threshold was determined. Ventilation did not persist above baseline values immediately after exposure to episodic hypoxia; however, Pet(CO(2)) levels were reduced compared with baseline. In contrast, compared with baseline, the ventilatory response to progressive increases in carbon dioxide during rebreathing trials in the presence of low but not high oxygen levels was increased after exposure to episodic hypoxia. This increase occurred when carbon dioxide levels were above but not below the ventilatory recruitment threshold. We conclude that long-term facilitation of ventilation (i.e., increases in ventilation that persist when normoxia is restored after episodic hypoxia) is not expressed in awake humans in the presence of hypocapnia. Nevertheless, despite this lack of expression, the acute ventilatory response to hypoxia in the presence of hypercapnia is increased after exposure to episodic hypoxia.     

Elongation as a factor in artefacts of humans and other animals: an Acheulean example in comparative context

Elongation is a commonly found feature in artefacts made and used by humans and other animals and can be analysed in comparative study. Whether made for use in hand or beak, the artefacts have some common properties of length, breadth, thickness and balance point, and elongation can be studied as a factor relating to construction or use of a long axis. In human artefacts, elongation can be traced through the archaeological record, for example in stone blades of the Upper Palaeolithic (traditionally regarded as more sophisticated than earlier artefacts), and in earlier blades of the Middle Palaeolithic. It is now recognized that elongation extends to earlier Palaeolithic artefacts, being found in the repertoire of both Neanderthals and more archaic humans. Artefacts used by non-human animals, including chimpanzees, capuchin monkeys and New Caledonian crows show selection for diameter and length, and consistent interventions of modification. Both chimpanzees and capuchins trim side branches from stems, and appropriate lengths of stave are selected or cut. In human artefacts, occasional organic finds show elongation back to about 0.5 million years. A record of elongation achieved in stone tools survives to at least 1.75 Ma (million years ago) in the Acheulean tradition. Throughout this tradition, some Acheulean handaxes are highly elongated, usually found with others that are less elongated. Finds from the million-year-old site of Kilombe and Kenya are given as an example. These findings argue that the elongation need not be integral to a design, but that artefacts may be the outcome of adjustments to individual variables. Such individual adjustments are seen in animal artefacts. In the case of a handaxe, the maker must balance the adjustments to achieve a satisfactory outcome in the artefact as a whole. It is argued that the need to make decisions about individual variables within multivariate objects provides an essential continuity across artefacts made by different species.     

The approximation method,relational biology and organismic sets

It is pointed out that the approximation method for diffusion problems, developed by N. Rashevsky in 1937 and successfully used since then by many authors, was in a sense a precursor of relational biology. The connection between the approximation method, relational biology, and the theory of organismic sets, developed in a series of recent papers by N. Rashevsky, is discussed. A number of conclusions known to hold experimentally, are then derived from relational considerations and some of them are applied to organismic sets.     

Self‐ownership,relational dignity,and organ sales

Material property has traditionally been conceived of as separable from its owner and thus alienable in an exchange. So it seems that you could sell your watch or even your kidney because it can be removed from your wrist or abdomen and transferred to another. However, if we are each identical to a living human animal, self‐ownership is impossible for self‐separation is impossible. We thus cannot sell our parts if we don't own the whole that they compose. It would be incoherent to own all of your body's parts but not the whole body; and it would be arbitrary to own some but not all of your removable parts. These metaphysical obstacles to organ sales do not apply to the selling of the organs of the deceased. The human being goes out of existence at death and is not identical to the body's remains. Any objections to selling the organs of the deceased must instead be due to dignity rather than metaphysical or conceptual considerations. But the remains lack the intrinsic dignity of the human being, instead possessing, at best, relational dignity. Relational dignity would not provide sufficient reason to prohibit life‐saving sales.