Arbitrariness is not enough: towards a functional approach to the genetic code

Arbitrariness in the genetic code is one of the main reasons for a linguistic approach to molecular biology: the genetic code is usually understood as an arbitrary relation between amino acids and nucleobases. However, from a semiotic point of view, arbitrariness should not be the only condition for definition of a code, consequently it is not completely correct to talk about “code” in this case. Yet we suppose that there exist a code in the process of protein synthesis, but on a higher level than the nucleic bases chains. Semiotically, a code should be always associated with a function and we propose to define the genetic code not only relationally (in basis of relation between nucleobases and amino acids) but also in terms of function (function of a protein as meaning of the code). Even if the functional definition of meaning in the genetic code has been discussed in the field of biosemiotics, its further implications have not been considered. In fact, if the function of a protein represents the meaning of the genetic code (the sign’s object), then it is crucial to reconsider the notion of its expression (the sign) as well. In our contribution, we will show that the actual model of the genetic code is not the only possible and we will propose a more appropriate model from a semiotic point of view.     

Restricted attentional capacity within but not between sensory modalities: an individual differences approach

Background

Most people show a remarkable deficit to report the second of two targets when presented in close temporal succession, reflecting an attentional blink (AB). An aspect of the AB that is often ignored is that there are large individual differences in the magnitude of the effect. Here we exploit these individual differences to address a long-standing question: does attention to a visual target come at a cost for attention to an auditory target (and vice versa)? More specifically, the goal of the current study was to investigate a) whether individuals with a large within-modality AB also show a large cross-modal AB, and b) whether individual differences in AB magnitude within different modalities correlate or are completely separate.

Methodology/Principal Findings

While minimizing differential task difficulty and chances for a task-switch to occur, a significant AB was observed when targets were both presented within the auditory or visual modality, and a positive correlation was found between individual within-modality AB magnitudes. However, neither a cross-modal AB nor a correlation between cross-modal and within-modality AB magnitudes was found.

Conclusion/Significance

The results provide strong evidence that a major source of attentional restriction must lie in modality-specific sensory systems rather than a central amodal system, effectively settling a long-standing debate. Individuals with a large within-modality AB may be especially committed or focused in their processing of the first target, and to some extent that tendency to focus could cross modalities, reflected in the within-modality correlation. However, what they are focusing (resource allocation, blocking of processing) is strictly within-modality as it only affects the second target on within-modality trials. The findings show that individual differences in AB magnitude can provide important information about the modular structure of human cognition.     

Ancestry trumps experience: Transgenerational but not early life stress affects the adult physiological stress response

Exposure to stressors can affect an organism's physiology and behavior as well as that of its descendants (e.g. through maternal effects, epigenetics, and/or selection). We examined the relative influence of early life vs. transgenerational stress exposure on adult stress physiology in a species that has populations with and without ancestral exposure to an invasive predator. We raised offspring of eastern fence lizards (Sceloporus undulatus) from sites historically invaded (high stress) or uninvaded (low stress) by predatory fire ants (Solenopsis invicta) and determined how this different transgenerational exposure to stress interacted with the effects of early life stress exposure to influence the physiological stress response in adulthood. Offspring from these high- and low-stress populations were exposed weekly to either sub-lethal attack by fire ants (an ecologically relevant stressor), topical treatment with a physiologically-appropriate dose of the stress-relevant hormone, corticosterone (CORT), or a control treatment from 2 to 43 weeks of age. Several months after treatments ended, we quantified plasma CORT concentrations at baseline and following restraint, exposure to fire ants, and adrenocorticotropic hormone (ACTH) injection. Exposure to fire ants or CORT during early life did not affect lizard stress physiology in adulthood. However, offspring of lizards from populations that had experienced multiple generations of fire ant-invasion exhibited more robust adult CORT responses to restraint and ACTH-injection compared to offspring from uninvaded populations. Together, these results indicate that transgenerational stress history may be at least as important, if not more important, than early life stress in affecting adult physiological stress responses.     

'Your true and proper gender': the Barr body as a good enough science of sex

In the late 1940s, a microanatomist from London Ontario, Murray Barr, discovered a mark of sex chromosome status in bodily tissues, what came to be known as the 'Barr body'. This discovery offered an important diagnostic technology to the burgeoning clinical science community engaged with the medical interpretation and management of sexual anomalies. It seemed to offer a way to identify the true, underlying sex in those whose bodies or lives were sexually anomalous (intersexuals, homosexuals and transsexuals). The hypothesis that allowed the Barr body to stand in for 'chromosomal' or 'genetic' sex was provisional, but it supported the expectation that genetic information established one's primary identity, and the conviction that the animal world could be neatly divided into two, and only two, sexes. Ultimately, this provisional hypothesis, and its status as an unambiguous arbiter of true sex, was overturned. But during much of the 1950s, Barr's thesis about the identity of the Barr body was consistent with a coherent set of theories and evidence explaining sexual development and sexual pathology. Though provisional, the scientific status of the sex chromatin within this system of knowledge was good enough to support a flourishing research enterprise in the clinical sciences.     

Morphine suppresses the ovarian steroid hormone-dependent lordosis response of female guinea pigs: reversal by naloxone but not clonidine.

The opiate agonist morphine caused a dose- and time-dependent suppression of lordosis responding in ovariectomized guinea pigs treated with estradiol-17 beta and progesterone. The suppression of lordosis by morphine appears to be mediated by opiate receptors since the opiate antagonist naloxone blocked its effects both in terms of the percentage of animals showing lordosis and the duration of individual responses. Naloxone, when given alone, did not affect lordosis responding in estradiol-17 beta + progesterone-primed animals and did not induce lordosis in animals primed with estradiol-17 beta alone. Thus, endogenous opioids might not tonically inhibit lordosis under the physiological conditions examined. The alpha-noradrenergic agonist clonidine did not reverse the effects of morphine on lordosis. Thus, the inhibitory effects of morphine on this behavior might be independent of its presynaptic effects on norepinephrine release in brain.     

Nitrogen fluxes from treefrogs to tank epiphytic bromeliads: an isotopic and physiological approach

Diverse invertebrate and vertebrate species live in association with plants of the large Neotropical family Bromeliaceae. Although previous studies have assumed that debris of associated organisms improves plant nutrition, so far little evidence supports this assumption. In this study we used isotopic (¹⁵N) and physiological methods to investigate if the treefrog Scinax hayii, which uses the tank epiphytic bromeliad Vriesea bituminosa as a diurnal shelter, contributes to host plant nutrition. In the field, bromeliads with frogs had higher stable N isotopic composition (δ¹⁵N) values than those without frogs. Similar results were obtained from a controlled greenhouse experiment. Linear mixing models showed that frog feces and dead termites used to simulate insects that eventually fall inside the bromeliad tank contributed, respectively, 27.7% (±0.07 SE) and 49.6% (±0.50 SE) of the total N of V. bituminosa. Net photosynthetic rate was higher in plants that received feces and termites than in controls; however, this effect was only detected in the rainy, but not in the dry season. These results demonstrate for the first time that vertebrates contribute to bromeliad nutrition, and that this benefit is seasonally restricted. Since amphibian–bromeliad associations occur in diverse habitats in South and Central America, this mechanism for deriving nutrients may be important in bromeliad systems throughout the Neotropics.     

Cell adhesion in tumor invasion and metastasis: loss of the glue is not enough.

Tumor cells often show a decrease in cell-cell and/or cell-matrix adhesion. An increasing body of evidence indicates that this reduction in cell adhesion correlates with tumor invasion and metastasis. Two main groups of adhesion molecules, cadherins and CAMs, have been implicated in tumor malignancy. However, the specific role that these proteins play in the context of tumor progression remains to be elucidated. In this review, we discuss recent data pointing to a causal relationship between the loss of cell adhesion molecules and tumor progression. In addition, the direct involvement of these molecules in specific signal transduction pathways will be considered, with particular emphasis on the alterations of such pathways in transformed cells. Finally, we review recent observations on the molecular mechanisms underlying metastatic dissemination. In many cases, spreading of tumor cells from the primary site to distant organs has been characterized as an active process involving the loss of cell-cell adhesion and gain of invasive properties. On the other hand, various examples of metastases exhibiting a relatively benign (i.e. not invasive) phenotype have been reported. Together with our recent results on a mouse tumor model, these findings indicate that 'passive' metastatic dissemination can occur, in particular as a consequence of impaired cell-matrix adhesion and of tumor tissue disaggregation.     

Low O2 avoidance is associated with physiological perturbation but not exhaustion in the snapper (Pagrus auratus: Sparidae)

It is already known that the New Zealand snapper (Pagrus auratus, Sparidae) does not avoid hypoxia until reaching an oxygen partial pressure (PO(2)) of 3.1±1.2 kPa at 18 °C. Avoidance at this level of PO(2) and temperature is below the critical oxygen partial pressure of the species (P(crit)=5.8±0.6 kPa, 43.5±4.5 mmHg) and is therefore expected to result in major physiological stress. Results from the current study showed that avoidance was associated with numerous physiological perturbations, including a significant endocrine response, haematological changes, osmoregulatory disturbance and metabolic adjustments in the heart, liver and muscle. Snapper clearly experienced physiological stress at the point of avoidance but they were not however in a state of physiological exhaustion since some fuel reserves were still available. In addition to avoidance, snapper also showed a subtle reduction in swimming speed - this energy-saving response may have helped snapper minimise the physiological challenge of low O(2) residence. It is therefore concluded that snapper can reside in water below their P(crit) threshold for brief periods of time and, without any evidence of physiological exhaustion at the point of avoidance, fish should recover quickly once normoxia is selected. Lastly, with signs of anaerobic metabolism in cardiac tissue at the point of avoidance, we tentatively suggest that snapper may leave hypoxia to protect heart function.     

Cultural differences in investing in others and in the future: why measuring trust is not enough

Standard measures of generalized trust in others are often taken to provide reliable indicators of economic attitudes in different countries. Here we compared three highly distinct groups, in Kenya, China and the US, in terms of more specific attitudes, [a] people's willingness to invest in the future, [b] their willingness to invest in others, and [c] their trust in institutions. Results suggest that these measures capture deep differences in economic attitudes that are not detected by standard measures of generalized trust.     

Spatial heterogeneity of mortality and temporal fluctuation in fertility promote coexistence but not vice versa: a random-community approach

Both spatial heterogeneity and temporal fluctuation of the environment are important mechanisms promoting species coexistence, but they work in different manners. We consider many pairs of species with randomly generated survivorship and fertility in the lottery model, and examine how the variability in demographic processes affects the outcome of competition. The results are: [1] Coexistence is easier if habitat difference in mortality is greater, or if year-to-year variation in reproductive rate is larger. But neither habitat-difference in fertility nor temporal variation in mortality promotes coexistence. [2] Mean fertility does not affect the outcome if CV remains constant. In contrast, enhanced mean mortality decreases the fraction of coexisting pairs if the environment fluctuates temporally. [3] We also investigate the effect of limited dispersal of propagules between habitats. Compared with the complete mixing case, the fraction of coexisting pairs is clearly enhanced if the spatial heterogeneity is the major source of environmental variation, but shows slight increase if the temporal fluctuation is dominant. We conclude that spatial heterogeneity is likely to work more effectively in promoting species coexistence than temporal fluctuation, especially when the species suffer relatively high mortality, and disperse their propagules in a limited spatial scale.     

Maternal overnutrition suppresses the phosphorylation of 5'-AMP-activated protein kinase in liver, but not skeletal muscle, in the fetal and neonatal sheep

Epidemiological studies have shown that infants exposed to an increased supply of nutrients before birth are at increased risk of type 2 diabetes in later life. We have investigated the hypothesis that fetal overnutrition results in reduced expression and phosphorylation of the cellular fuel sensor, AMP-activated kinase (AMPK) in liver and skeletal muscle before and after birth. From 115 days gestation, ewes were fed either at or approximately 55% above maintenance energy requirements. Postmortem was performed on lamb fetuses at 139-141 days gestation (n = 14) and lambs at 30 days of postnatal age (n = 21), and liver and quadriceps muscle were collected at each time point. The expression of AMPKalpha1 and AMPKalpha2 mRNA was determined by quantitative RT-PCR (qRT-PCR). The abundance of AMPKalpha and phospho-AMPKalpha (P-AMPKalpha) was determined by Western blot analysis, and the proportion of the total AMPKalpha pool that was phosphorylated in each sample (%P-AMPKalpha) was determined. The ratio of AMPKalpha2 to AMPKalpha1 mRNA expression was lower in fetuses compared with lambs in both liver and muscle, independent of maternal nutrition. Hepatic %P-AMPKalpha was lower in both fetuses and lambs in the Overfed group and %P-AMPKalpha in the lamb liver was inversely related to plasma glucose concentrations in the first 24 h after birth (r = 0.73, P < 0.025). There was no effect of maternal overnutrition on total AMPKalpha or P-AMPKalpha abundance in liver or skeletal muscle. We have, therefore, demonstrated that AMPKalpha responds to signals of increased nutrient availability in the fetal liver. Suppression of hepatic AMPK phosphorylation may contribute to increased glucose production, and basal hyperglycemia, present in lambs of overfed ewes in early postnatal life.     

Synonymous but not the same: the causes and consequences of codon bias

Despite their name, synonymous mutations have significant consequences for cellular processes in all taxa. As a result, an understanding of codon bias is central to fields as diverse as molecular evolution and biotechnology. Although recent advances in sequencing and synthetic biology have helped to resolve longstanding questions about codon bias, they have also uncovered striking patterns that suggest new hypotheses about protein synthesis. Ongoing work to quantify the dynamics of initiation and elongation is as important for understanding natural synonymous variation as it is for designing transgenes in applied contexts.     

2-Deoxyglucose: an anticancer and antiviral therapeutic, but not any more a low glucose mimetic

2-Deoxyglucose (2-DG), a non-metabolizable glucose analogue, blocks glycolysis and inhibits protein glycosylation. It has been tested in multiple studies for possible application as an anticancer or antiviral therapeutic. The inhibitory effect of 2-DG on ATP generation made it a good candidate molecule as a calorie restriction mimetic as well. Furthermore, 2-DG has been utilized in numerous studies to simulate a condition of glucose starvation. Because 2-DG disrupts glucose metabolism, protein glycosylation, and ER quality control at the same time, a cellular or pathologic outcome could be easily misinterpreted without clear understanding of 2-DG's effect on each of these aspects. However, the effect of 2-DG on protein glycosylation has rarely been investigated. A recent study suggested that 2-DG causes hyperGlcNAcylation of proteins, while low glucose supply causes hypoGlcNAcylation. In certain aspects of cellular physiology, this difference could be disregarded, but in others, this may possibly cause totally different outcomes.     

Xenopus ElrB, but not ElrA, binds RNA as an oligomer: possible role of the linker

We have shown that ElrA and ElrB, Xenopus ELAV homologues, bind the Vg1 mRNA 3'UTR translation element in Xenopus oocytes and implicated ElrB in mediating translational repression during oogenesis. Here we report that, while ElrA and ElrB are 69% identical and both exhibit RNA binding in the nM range, recombinant ElrB, but not ElrA, is able to oligomerise. This oligomerisation is also seen with the endogenous protein. Both RNA binding and oligomerisation require the linker region flanked with two RNA recognition motifs. Our data demonstrate a novel and unique property of ElrB which may be important for its function as a translational regulator.