How is the balance between protein synthesis and degradation achieved?

Unlike most substances that cells manufacture, proteins are not produced and broken down by a common series of chemical reactions, but by completely different (independent and disconnected) mechanisms that possess no intrinsic means of making the rates of the two processes equal and attaining steady state concentrations. Balance between them is achieved extrinsically and is often imagined today to be the result of the actions of chemical feedback agents. But however instantiated, chemical feedback or any similar mechanism can only rectify induced imbalances in a system previously balanced by other means. Those "other means" necessarily involve reversible mass action or equilibrium-based interactions between native and altered forms of protein molecules somewhere in time and space between their synthesis and degradation.     

Effects of uni- and bilateral destructions of the caudate nucleus head by kainic acid on electroencephalogram in the wakefulness—sleep cycle in wistar rats

Changes in characteristics of the wakefulness—sleep cycle were studied in Wistar rats after a uni- and bilateral destruction of the head of nucleus caudatus by kainic acid that produces a selective destruction of neuronal elements but does not damage conducting pathways passing through this structure. It is established that changes of the cycle after injections of the acid did not last long (not more than 4 days) and were due to the presence of foci of paroxysmal activity resulted from a strong excitatory effect of this selective neurotoxin. It is revealed that the consequences of the bilateral injury of the nucleus caudatus were less pronounced and easier tolerated by animals than those of the unilateral one. The appearance of spindle-like discharges on rat EEG during the fast wave sleep was observed after the unilateral but not the bilateral destruction. A possible role in the genesis of this activity played by a disbalance in the work of the system of the caudate inhibitory control of the activity of non-specific thalamic nuclei is discussed.     

On the influence of prenatal hypoxia on formation of the orexinergic system and sleep–wake cycle in early ontogenesis of rats

The role of orexin in the organization of the sleep–wake cycle (SWC) is well known. The aim of this study was to examine the timing of the orexinergic system formation in rat postnatal ontogenesis and to assess the role of orexin A in the SWC organization under normal conditions and after prenatal hypoxia undergone on days 14 and 19 of embryogenesis. The SWC was investigated in 30-day-old rats with electrodes implanted into the somatosensory and occipital cortex. Immunoreactivity within the orexigenic structures of the lateral hypothalamus was analyzed. It was shown that in control 14-day-old animals the orexinergic structures were in their formative stage, whereas in 30-day-old rats they were already as formed as in adults. In 14-day-old rats, prenatal hypoxia evoked retarded formation of the orexinergic system. In 30-day-old animals, hypoxia undergone in the prenatal period increased the activity of the orexinergic system, which was higher in animals exposed to hypoxia on day 19 than on day 14 of gestation. In 30-day-old rats, these changes were reflected in the SWC formation in the form of shorter slow-wave sleep, more fitful sleep and increased number of transitions from slow- to fast-wave sleep. The results obtained are discussed in the light of the adaptive-compensatory role of the orexigenic system in postnatal ontogenesis after prenatal damage to the central nervous system.     

How essential is the ‘essential’ active-site lysine in dihydrodipicolinate synthase?

Dihydrodipicolinate synthase (DHDPS, E.C. 4.2.1.52), a validated antibiotic target, catalyses the first committed step in the lysine biosynthetic pathway: the condensation reaction between (S)-aspartate β-semialdehyde [(S)-ASA] and pyruvate via the formation of a Schiff base intermediate between pyruvate and the absolutely conserved active-site lysine. Escherichia coli DHDPS mutants K161A and K161R of the active-site lysine were characterised for the first time. Unexpectedly, the mutant enzymes were still catalytically active, albeit with a significant decrease in activity. The k_cat values for DHDPS-K161A and DHDPS-K161R were 0.06 ± 0.02 s⁻¹ and 0.16 ± 0.06 s⁻¹ respectively, compared to 45 ± 3 s⁻¹ for the wild-type enzyme. Remarkably, the K_M values for pyruvate increased by only 3-fold for DHDPS-K161A and DHDPS-K161R (0.45 ± 0.04 mM and 0.57 ± 0.06 mM, compared to 0.15 ± 0.01 mM for the wild-type DHDPS), while the K_M values for (S)-ASA remained the same for DHDPS-K161R (0.12 ± 0.01 mM) and increased by only 2-fold for DHDPS-K161A (0.23 ± 0.02 mM) and the K_i for lysine was unchanged. The X-ray crystal structures of DHDPS-K161A and DHDPS-K161R were solved at resolutions of 2.0 and 2.1 Å respectively and showed no changes in their secondary or tertiary structures when compared to the wild-type structure. The crystal structure of DHDPS-K161A with pyruvate bound at the active site was solved at a resolution of 2.3 Å and revealed a defined binding pocket for pyruvate that is thus not dependent upon lysine 161. Taken together with ITC and NMR data, it is concluded that although lysine 161 is important in the wild-type DHDPS-catalysed reaction, it is not absolutely essential for catalysis.     

Does childhood experience of attention-deficit hyperactivity disorder symptoms increase sleep/wake cycle disturbances as measured with actigraphy in adult patients with bipolar disorder?

ABSTRACT

Childhood attention-deficit hyperactivity disorder (ADHD) is a common precursor of adult bipolar disorders (BD). Furthermore, actigraphy studies demonstrate that each disorder may be associated with abnormalities in sleep and activity patterns. This study investigates whether the presence or absence of self-reported childhood experiences of ADHD symptoms is associated with different sleep and activity patterns in adults with BD. A sample of 115 euthymic adult patients with BD was assessed for childhood ADHD symptoms using the Wender Utah Rating Scale (WURS) and then completed 21 days of actigraphy monitoring. Actigraphic measures of sleep quantity and variability and daytime activity were compared between BD groups classified as ADHD+ (n = 24) or ADHD? (n = 91), defined according to established cutoff scores for the WURS; then we examined any associations between sleep–wake cycle parameters and ADHD dimensions (using the continuous score on the WURS). Neither approach revealed any statistically significant associations between actigraphy parameters and childhood ADHD categories or dimensions. We conclude that the sleep and activity patterns of adult patients with BD do not differ according to their self-reported history of ADHD symptoms. We discuss the implications of these findings and suggest how future studies might confirm or refute our findings.     

How is the relationship between TWIST-1 and BCR-ABL1 gene expressions in chronic myeloid leukaemia patients?

Background: The activation and increased expression of BCR-ABL1 lead to malignant chronic myelogenous leukaemia (CML) cells, as well as the resistance to antitumour agents and apoptosis inducers. Moreover, TWIST-1 protein is a prognostic factor of leukemogenesis, and its level is raised in CML patients with cytogenetic resistance to imatinib. So, there is a likely relationship between BCR-ABL1 and TWIST-1 genes.

Objective: The aim of the study was to assess the relationship between TWIST-1 and BCR-ABL1 expressions.

Methods: Peripheral blood samples were obtained from 44 CML patients under treatment and also from ten healthy subjects as normal controls. The expression of TWIST-1 and BCR-ABL1 genes was measured using real-time PCR, and ABL1 was used as the reference gene. The gene expression was evaluated by REST software.

Results: The expression levels of TWIST-1 and BCR-ABL1 genes in CML patients was changed 40.23?±?177.75-fold and 6?±?18-fold, respectively.

Discussion: No significant relationship was observed between the expressions of TWIST-1 and BCR-ABL1 genes. All patients with TWIST-1 expression levels?≥100-fold had failure of response to treatment.

Conclusion: The probability of the relationship between BCR-ABL1 and TWIST-1 is still debatable, and the average of TWIST-1 expression has been higher in patients without response to treatment. Definitive conclusion needs further investigations.     

How specialized is the plant–pollinator association between Eucalyptus globulus ssp. globulus and the swift parrot Lathamus discolor?

Abstract The swift parrot Lathamus discolor (Shaw) (Psittacidae) evolved from granivorous ancestors to become a specialized flower‐feeder in a monotypic genus. Its reproduction is dependent largely on flowers of Eucalyptus globulus Labill. ssp. globulus (Myrtaceae), the birds migrating to breed within the natural distribution of this tree. This paper investigates the extent to which this dependence of L. discolor on E. globulus is mirrored by dependence of the tree on the bird. It was found that L. discolor carried significantly more eucalypt pollen within 22 mm of its bill tip than did the New Holland honeyeater, Phylidonyris novaehollandiae (Latham) (Meliphagidae), and that pollen was concentrated on the regions of the head of L. discolor that consistently contact stigmas. Larger pollen loads on L. discolor can be attributed to it consuming both pollen and nectar, while honeyeaters take nectar only. The short thick bill of L. discolor necessitates regular stigmatic contact while the long slender bills of honeyeaters are unlikely to contact stigmas as often in these bowl‐shaped flowers. These factors suggest that L. discolor has a greater capacity to deposit pollen on stigmas of E. globulus than do honeyeaters. However, the characteristics of L. discolor that make it such an effective pollinator of E. globulus are also exhibited by a lorikeet (Psittacidae) that feeds on flowers of E. globulus. The association between E. globulus and L. discolor is therefore only moderately specialized because the flowers are also adapted to the more recently associated lorikeet and are almost certainly also pollinated by honeyeaters.     

Life cycle abbreviation in trematode parasites and the developmental time hypothesis: is the clock ticking?

The typical multi‐host life cycle of many parasites, although conferring several advantages, presents the parasites with a highly hazardous transmission route. As a consequence, parasites have evolved various adaptations increasing their chances of transmission between the different hosts of the life cycle. Some trematode species like the opecoelid Coitocaecum parvum have adopted a more drastic alternative strategy whereby the definitive host is facultatively dropped from the cycle, resulting in a shorter, hence easier to complete, life cycle. Like other species capable of abbreviating their life cycle, C. parvum does so through progenetic development within its intermediate host. Laboratory‐reared C. parvum can modulate their developmental strategy inside the second intermediate host according to current transmission opportunities, though this ability is not apparent in natural C. parvum populations. Here we show that this difference is likely due to the time C. parvum individuals spend in their intermediate hosts in the natural environment. Although transmission opportunities, i.e. chemical cues of the presence of definitive hosts, promoted the adoption of a truncated life cycle in the early stages of infection, individuals that remained in their amphipod host for a relatively long time had a similar probability of adopting progenesis and the abbreviated cycle, regardless of the presence or absence of chemical cues from the predator definitive host. These results support the developmental time hypothesis which states that parasites capable of facultative life cycle abbreviation should eventually adopt progenesis regardless of transmission opportunities, and provide further evidence of the adaptive plasticity of parasite transmission strategies.     

How is autonomic nervous system activity in subjects who are sleepy but are unable to sleep in the daytime?

We investigated changes in the activity of the autonomic nervous system (ANS) in the relaxed condition in subjects who felt sleepy, but were unable to sleep. A total of 1021 subjects underwent daytime polysomnography. The sleep latency (SL) and the visual analog scale (VAS) were used to assess “immediate” objective and subjective sleepiness, respectively. The subjects were assigned to an “Alert-Alert” group (VAS ≤ 25 mm, SL ≥ 8 min), a “Sleepy-Alert” group (VAS ≥ 75 mm, SL ≥ 8 min), or a “Sleepy-Sleepy” group (VAS ≥ 75 mm, SL ≤ 4 min). In order to assess the ANS, the spectral analysis and the geometric method were used. The ANS data collected during the relaxed condition (after lights off, post-LO) was compared to that obtained during the control condition (before lights off, pre-LO). From the spectral analysis, a significant decrease of sympathetic function and an increase of parasympathetic function at post-LO in the Sleepy-Sleepy group, a tendency for sympathetic function decrease at post-LO in the Alert-Alert group, and no significant changes to sympathetic and parasympathetic function in the Sleepy-Alert group were observed. The results from the geometric method supported the results of the spectral analysis in the Alert-Alert group and the Sleepy-Sleepy group. The results of this study suggest that the ANS plays a role in individuals who are unable to sleep even though they feel sleepy and are given the opportunity to sleep.

     

How much further should we go to develop and establish sleep medicine in Japan? (Through a comparison between Japan and the US)

Sleep and Biological Rhythms -     

How dim is dim? Precision of the celestial compass in moonlight and sunlight

Prominent in the sky, but not visible to humans, is a pattern of polarized skylight formed around both the Sun and the Moon. Dung beetles are, at present, the only animal group known to use the much dimmer polarization pattern formed around the Moon as a compass cue for maintaining travel direction. However, the Moon is not visible every night and the intensity of the celestial polarization pattern gradually declines as the Moon wanes. Therefore, for nocturnal orientation on all moonlit nights, the absolute sensitivity of the dung beetle's polarization detector may limit the precision of this behaviour. To test this, we studied the straight-line foraging behaviour of the nocturnal ball-rolling dung beetle Scarabaeus satyrus to establish when the Moon is too dim--and the polarization pattern too weak--to provide a reliable cue for orientation. Our results show that celestial orientation is as accurate during crescent Moon as it is during full Moon. Moreover, this orientation accuracy is equal to that measured for diurnal species that orient under the 100 million times brighter polarization pattern formed around the Sun. This indicates that, in nocturnal species, the sensitivity of the optical polarization compass can be greatly increased without any loss of precision.     

How common is the funnel‐like energy landscape in protein‐protein interactions?

The goal of this study is to verify the concept of the funnel-like intermolecular energy landscape in protein-protein interactions by use of a series of computational experiments. Our preliminary analysis revealed the existence of the funnel in many protein-protein interactions. However, because of the uncertainties in the modeling of these interactions and the ambiguity of the analysis procedures, the detection of the funnels requires detailed quantitative approaches to the energy landscape analysis. A number of such approaches are presented in this study. We show that the funnel detection problem is equivalent to a problem of distinguishing between distributions of low-energy intermolecular matches in the funnel and in the low-frequency landscape fluctuations. If the fluctuations are random, the decision about whether the minimum is the funnel is equivalent to determining whether this minimum is significantly different from a would-be random one. A database of 475 nonredundant cocrystallized protein-protein complexes was used to re-dock the proteins by use of smoothed potentials. To detect the funnel, we developed a set of sophisticated models of random matches. The funnel was considered detected if the binding area was more populated by the low-energy docking predictions than by the matches generated in the random models. The number of funnels detected by use of different random models varied significantly. However, the results confirmed that the funnel may be the general feature in protein-protein association.     

How do the Fat–Dachsous and core planar polarity pathways act together and independently to coordinate polarized cell behaviours?

Planar polarity describes the coordinated polarization of cells within the plane of a tissue. This is controlled by two main pathways in Drosophila: the Frizzled-dependent core planar polarity pathway and the Fat–Dachsous pathway. Components of both of these pathways become asymmetrically localized within cells in response to long-range upstream cues, and form intercellular complexes that link polarity between neighbouring cells. This review examines if and when the two pathways are coupled, focusing on the Drosophila wing, eye and abdomen. There is strong evidence that the pathways are molecularly coupled in tissues that express a specific isoform of the core protein Prickle, namely Spiny-legs. However, in other contexts, the linkages between the pathways are indirect. We discuss how the two pathways act together and independently to mediate a diverse range of effects on polarization of cell structures and behaviours.     

Testing agreement between a new method and the gold standard—How do we test?

Data analysis can be the most challenging aspect of a research study. Having been taught statistical techniques that tend to be based on finding significant differences or significant relationships, difficulties arise when trying to determine if a newly developed method is equally as good as the established method (the gold standard).     

How important is the relationship between Protea humiflora (Proteaceae) and its non-flying mammal pollinators?

The interaction between Protea humiflora and its non-flying mammal pollinators was investigated with the aim of quantifying the relationship for both the plants and mammals involved. We manipulated flower density by inflorescence removal and determined the effect upon mammal captures, and excluded mammals to determine their effect upon seed set. Of three mammal species captured frequently, the smallest, Acomys subspinosus (18dž SD g, Rodentia: Muridae), demonstrated the strongest relationship with P. humiflora. Breeding coincided with flowering, and pollen constituted 33.5ᆯ.5% by volume (max 80%, n=19) of winter scats. Acomys captures on control grids were twice those on inflorescence-removal grids during flowering. Aethomys namaquensis (51ᆢ g, Rodentia: Muridae) included flower products in its diet (pollen comprising 3.2dž.9% of winter scats, n=73), but captures were not affected by inflorescence removal. Aethomys is a seasonal breeder and juveniles entered the population 2 months after flowering. Elephantulus edwardii, although an insectivore (48lj g, Macroscelidea: Macroscelididae), carried more pollen grains on its nose than the rodents, acquired while foraging in inflorescences for insects. Pollen comprised 3.1LJ.4% (n=23) of winter scats. From the plant perspective, seed set was significantly reduced in caged inflorescences and in those >20 cm above the ground, presumably due to limited accessibility by terrestrial animals. We conclude that small mammals are responsible for around half (56%) of the effective seed set in P. humiflora.     

Analysis of stable states in global savannas: is the CART pulling the horse? – a comment

In their recent paper, Hanan et al. (Global Ecology and Biogeography, 2014, 23 , 259–263) argue that the use of classification and regression trees (CARTs) to calibrate global remote sensing datasets, including the MODIS VCF tree‐cover dataset, makes these data inappropriate for analysing the frequency distribution of tree cover. While we agree with their most general point – that the use of remote sensing products should be informed and deliberate – their analysis overlooks a few key aspects of the use of CARTs in generating global tree‐cover data. Firstly, while their presentation of flaws in the use of CARTs is compelling, their use of hypothetical data obscures the reasons why CARTs are a useful tool. Secondly, they do not actually examine the error distributions of the MODIS VCF tree‐cover data. Such an analysis, which we perform, revealed the following: (1) the MODIS VCF product may not be useful for differentiating over small ranges of tree cover (less than c. 10%); (2) that the bimodality of low and high tree cover, with a frequency minimum at intermediate tree cover, is not attributable to bias in MODIS VCF tree‐cover calibrations; and (3) that the MODIS VCF is not well‐resolved below c. 20–30% tree cover, such that MODIS cannot be used with any confidence to evaluate multimodality in tree cover in that range. Further validation and calibration are likely to be helpful and, at low tree cover, necessary for improving MODIS VCF tree‐cover estimates. However, the MODIS VCF – which has facilitated major steps in our ability to examine ecological phenomena at global scales – remains a useful tool for well‐informed ecological analysis.     

How strict is the correlation between STIM1 and Orai1 expression, puncta formation, and ICRAC activation?

Stromal interaction molecule 1 (STIM1) and Orai1 have been identified as crucial elements of the store-operated Ca(2+) entry (SOCE) pathway, but the mechanism of their functional interaction remains controversial. It is now well established that, upon depletion of the stores, both molecules can accumulate and colocalize in specific areas (puncta) where the endoplasmic reticulum comes in close proximity to the plasma membrane. Some models propose a direct interaction between STIM1 and Orai1 as the most straightforward mechanism for signal transduction from the stores to the plasma membrane. To test some of the predictions of a conformational coupling model, we assessed how tight the relationships are between STIM1 and Orai1 expression, puncta formation, and SOCE activation. Here we present evidence that STIM1 accumulates in puncta equally well in the presence or absence of Orai1 expression, that STIM1 accumulation is not sufficient for Orai1 accumulation in the same areas, and that normal Ca(2+) release-activated Ca(2+) current (I(CRAC)) can be activated in STIM1-deficient cells. These data challenge the idea of direct conformational coupling between STIM1 and Orai1 as a viable mechanism of puncta formation and SOCE activation and uncover greater complexity in their relationship, which may require additional intermediate elements.