Remembrance of things past: maintaining gene expression patterns with altered chromatin

Eukaryotic organisms have evolved mechanisms to stably preserve the gene expression patterns that determine cell fate. Recent advances have been made in understanding the DNA sequences and protein factors required to propagate gene activation or silencing. These studies suggest that, after gene activity states are selected during development, maintenance protein complexes provide a molecular memory of those states by altering a local domain of chromatin structure.     

Caught in self-interaction: evolutionary and functional mechanisms of protein homooligomerization

Many soluble and membrane proteins form homooligomeric complexes in a cell which are responsible for the diversity and specificity of many pathways, may mediate and regulate gene expression, activity of enzymes, ion channels, receptors, and cell adhesion processes. The evolutionary and physical mechanisms of oligomerization are very diverse and its general principles have not yet been formulated. Homooligomeric states may be conserved within certain protein subfamilies and might be important in providing specificity to certain substrates while minimizing interactions with other unwanted partners. Moreover, recent studies have led to a greater awareness that transitions between different oligomeric states may regulate protein activity and provide the switch between different pathways. In this paper we summarize the biological importance of homooligomeric assemblies, physico-chemical properties of their interfaces, experimental and computational methods for their identification and prediction. We particularly focus on homooligomer evolution and describe the mechanisms to develop new specificities through the formation of different homooligomeric complexes. Finally, we discuss the possible role of oligomeric transitions in the regulation of protein activity and compile a set of experimental examples with such regulatory mechanisms.     

To Perceive or Not Perceive: The Role of Gamma-band Activity in Signaling Object Percepts

The relation of gamma-band synchrony to holistic perception in which concerns the effects of sensory processing, high level perceptual gestalt formation, motor planning and response is still controversial. To provide a more direct link to emergent perceptual states we have used holistic EEG/ERP paradigms where the moment of perceptual “discovery” of a global pattern was variable. Using a rapid visual presentation of short-lived Mooney objects we found an increase of gamma-band activity locked to perceptual events. Additional experiments using dynamic Mooney stimuli showed that gamma activity increases well before the report of an emergent holistic percept. To confirm these findings in a data driven manner we have further used a support vector machine classification approach to distinguish between perceptual vs. non perceptual states, based on time-frequency features. Sensitivity, specificity and accuracy were all above 95%. Modulations in the 30–75 Hz range were larger for perception states. Interestingly, phase synchrony was larger for perception states for high frequency bands. By focusing on global gestalt mechanisms instead of local processing we conclude that gamma-band activity and synchrony provide a signature of holistic perceptual states of variable onset, which are separable from sensory and motor processing.     

Epigenetic inheritance in Arabidopsis: selective silence

Eukaryotic organisms have the remarkable ability to inherit states of gene activity without altering the underlying DNA sequence. This epigenetic inheritance can persist over thousands of years, providing an alternative to genetic mutations as a substrate for natural selection. Epigenetic inheritance might be propagated by differences in DNA methylation, post-translational histone modifications, and deposition of histone variants. Mounting evidence also indicates that small interfering RNA (siRNA)-mediated mechanisms play central roles in setting up and maintaining states of gene activity. Much of the epigenetic machinery of many organisms, including Arabidopsis, appears to be directed at silencing viruses and transposable elements, with epigenetic regulation of endogenous genes being mostly derived from such processes.     

The behavioural state in human perinatal life

Behavioural states are easy to recognise in healthy neonates with a gestational age of 36 weeks or more. In younger neonates stable behavioural states, as seen at full-term, are not present, but activity cycles exist. In utero stable behavioural states can also be recognised from 36 to 38 weeks onwards. The existence of awake states in utero remains controversial. A close relationship exists between neural mechanisms regulating the behavioural state cycling and those modulating breathing. Our understanding of these is still very limited. The absence of behavioural states or of activity cycles is a very sensitive but non-specific sign of nervous system dysfunction in human perinatal life.     

Development states associated with the floral transition.

Floral initiation can be analyzed from a developmental perspective by focusing upon how developmental fates are imprinted, remembered, and expressed. This is not an altogether new perspective, since people studying flowering have been concerned for a long time with the commitment of meristems to form flowers and the morphological, cellular, and molecular changes associated with this commitment. What is novel is the emphasis on developmental states as opposed to physiological processes. This developmental focus indicates that there appear to be at least three major developmental states that are acquired and expressed in the process of a meristem initiating floral morphogenesis. The meristem cells must first become competent to respond to a developmental signal that evokes them into a florally determined state. The leaves are the usual source of this signal and a specific leaf may or may not have the capacity to be inductively active. When a leaf does develop the capacity for inductive activity, this capacity is usually correlated with the ontogeny of the leaf. Inductive activity, however, may be continually expressed as in some day-neutral plants or may be latent as in plants where the photoperiod is the external cue for activity. Competent shoot apical meristems respond to inductive leaf signal by being evoked into a florally determined state. Under permissive conditions this florally determined state is expressed as the initiation of floral morphogenesis. Many mechanisms have evolved to regulate entry into and expression of these developmental states. As we learn more about the developmental states associated with flowering and how they are acquired and expressed, we will understand better how the various patterns of flowering are related to one another as well as which developmental processes are common to all angiosperms.     

Promoting remyelination: A case study in regenerative medicine

Therapeutics that modulate regenerative mechanisms by targeting the activity of endogenous (adult) stem cell populations have the potential to revolutionize medicine. In many human disease states, capacity to repair damaged tissue underlies progressive decline and disease progression. Recent insights derived from efforts aimed at promoting remyelination for the treatment of multiple sclerosis (MS) highlight the importance of considering the limiting factors and underlying mechanisms associated with all aspects of disease onset, progression and recovery, during both the discovery and clinical stages of developing a regenerative medicine. This perspective presents general considerations for the development of regenerative therapies, using remyelination as a case study.     

Motor Activity of Eyelids as a Functional State Indicator

The authors consider an insufficiently studied indicator, i.e., motor activity of eyelids, recorded with or without miniature contacts in infrared rays for the visual analyzer states eyes open / eyes closed. Eyelid movement characteristics are highly informative in diagnosing the functional state and evaluating operator activity quality under monotonous conditions. The authors discuss possible mechanisms of the influence of such functional states on the motor activity of eyelids.     

Recent advances in mechanisms regulating glucose oxidation at the level of the pyruvate dehydrogenase complex by PDKs

The mitochondrial pyruvate dehydrogenase complex (PDC) catalyzes the oxidative decarboxylation of pyruvate, linking glycolysis to the tricarboxylic acid cycle and fatty acid (FA) synthesis. Knowledge of the mechanisms that regulate PDC activity is important, because PDC inactivation is crucial for glucose conservation when glucose is scarce, whereas adequate PDC activity is required to allow both ATP and FA production from glucose. The mechanisms that control mammalian PDC activity include its phosphorylation (inactivation) by a family of pyruvate dehydrogenase kinases (PDKs 1-4) and its dephosphorylation (activation, reactivation) by the pyruvate dehydrogenase phosphate phosphatases (PDPs 1 and 2). Isoform-specific differences in kinetic parameters, regulation, and phosphorylation site specificity of the PDKs introduce variations in the regulation of PDC activity in differing endocrine and metabolic states. In this review, we summarize recent significant advances in our knowledge of the mechanisms regulating PDC with emphasis on the PDKs, in particular PDK4, whose expression is linked with sustained changes in tissue lipid handling and which may represent an attractive target for pharmacological interventions aimed at modulating whole body glucose, lipid, and lactate homeostasis in disease states.     

Electron microscopic-cytochemical heterogeneity of succinate dehydrogenase activity in rat cardiomyocytes

The ultrastructural localization of succinate dehydrogenase in white rat heart myocytes is studied and heterogeneity of reaction products in separate mitochondria and their groups is described. The enzyme activity is cardiomyocyte electron density dependent. This dependence, in all probability, is the result of different structural and functional states of cells and their organelles, that is revealed by electron microscopy as different electron density of these. It is found that middle electron density cells have the maximum enzyme activity. The mechanisms of enzyme activity dependence of cell electron density are discussed.     

Molecular Dynamics Simulations and Classical Multidimensional Scaling Unveil New Metastable States in the Conformational Landscape of CDK2

Protein kinases are key regulatory nodes in cellular networks and their function has been shown to be intimately coupled with their structural flexibility. However, understanding the key structural mechanisms of large conformational transitions remains a difficult task. CDK2 is a crucial regulator of cell cycle. Its activity is finely tuned by Cyclin E/A and the catalytic segment phosphorylation, whereas its deregulation occurs in many types of cancer. ATP competitive inhibitors have failed to be approved for clinical use due to toxicity issues raised by a lack of selectivity. However, in the last few years type III allosteric inhibitors have emerged as an alternative strategy to selectively modulate CDK2 activity. In this study we have investigated the conformational variability of CDK2. A low dimensional conformational landscape of CDK2 was modeled using classical multidimensional scaling on a set of 255 crystal structures. Microsecond-scale plain and accelerated MD simulations were used to populate this landscape by using an out-of-sample extension of multidimensional scaling. CDK2 was simulated in the apo-form and in complex with the allosteric inhibitor 8-anilino-1-napthalenesulfonic acid (ANS). The apo-CDK2 landscape analysis showed a conformational equilibrium between an Src-like inactive conformation and an active-like form. These two states are separated by different metastable states that share hybrid structural features with both forms of the kinase. In contrast, the CDK2/ANS complex landscape is compatible with a conformational selection picture where the binding of ANS in proximity of the αC helix causes a population shift toward the inactive conformation. Interestingly, the new metastable states could enlarge the pool of candidate structures for the development of selective allosteric CDK2 inhibitors. The method here presented should not be limited to the CDK2 case but could be used to systematically unmask similar mechanisms throughout the human kinome.     

Neural Correlates of Attentional Flexibility during Approach and Avoidance Motivation

Dynamic, momentary approach or avoidance motivational states have downstream effects on eventual goal success and overall well being, but there is still uncertainty about how those states affect the proximal neurocognitive processes (e.g., attention) that mediate the longer-term effects. Attentional flexibility, or the ability to switch between different attentional foci, is one such neurocognitive process that influences outcomes in the long run. The present study examined how approach and avoidance motivational states affect the neural processes involved in attentional flexibility using fMRI with the aim of determining whether flexibility operates via different neural mechanisms under these different states. Attentional flexibility was operationalized as subjects’ ability to switch between global and local stimulus features. In addition to subjects’ motivational state, the task context was manipulated by varying the ratio of global to local trials in a block in light of recent findings about the moderating role of context on motivation-related differences in attentional flexibility. The neural processes involved in attentional flexibility differ under approach versus avoidance states. First, differences in the preparatory activity in key brain regions suggested that subjects’ preparedness to switch was influenced by motivational state (anterior insula) and the interaction between motivation and context (superior temporal gyrus, inferior parietal lobule). Additionally, we observed motivation-related differences the anterior cingulate cortex during switching. These results provide initial evidence that motivation-induced behavioral changes may arise via different mechanisms in approach versus avoidance motivational states.     

The physiology of follicular maturation in the pig

Exogenous gonadotrophin (eg. PMSG) treatment results in follicular growth in most reproductive states, and suggests that lack of FSH and LH-like activity is a likely cause of arrested-follicular development in the pig. Endogenous changes in gonadotrophins between reproductive and non-reproductive states are consistent with this concept. However, changes in the pattern of LH secretion, rather than clearly defined changes in FSH release, appear to be the effective trigger for follicular recruitment. In other situations in vivo, follicular growth is initiated in the absence of demonstrable changes in LH or FSH secretion, suggesting that other hormones interact to sensitize the ovary to gonadotrophins. Such effects have been reported for insulin, cortisol, thyroxine and IGF-1 in vitro, and the steroid environment of follicles also affects gonadotrophin receptors and receptor-mediated mechanisms. Once initiated, the regulation of follicle maturation also involves interactions between gonadotrophins and steroids, as well as other intra-ovarian regulators. Co-operation exists between theca and granulosa in the synthesis of steroids and androgen precursor availability is an important regulator of the oestrogenic activity of follicles. Considerable heterogeneity exists in the morphological and biochemical maturity of preovulatory follicles and inter-follicular regulation via endocrine and paracrine mechanisms may be an essential component of the selection process.     

Correlations and apparent contradictions in assessment of oxidant stress status in vivo.

Oxidative modifications of biological molecules are essential, but uncontrolled or excessive oxidative activities appear to contribute to many disease states. The mechanisms through which excess oxidant activities cause injury have been studied most extensively for acute responses, particularly for drug-induced tissue damage and cell death, but substantial evidence suggests that chronically elevated oxidative activity may contribute to the development of diseases such as cancer. It is important that the correlation between oxidant stress status and cancer risk be examined directly in humans. A number of methods have been developed for assessing oxidant activities by measuring oxidized products in biological systems, but cross-comparison studies of these different methods are needed. In studies of mechanisms of acute hepatotoxicity, assessments of oxidant stress responses by different analytical methods often have provided data that appear at first glance to be contradictory. Marked oxidant stress responses may be indicated by one or more methods of analysis despite the lack of detectable change in other parameters, whereas in a second experimental model the responses may be reversed. These observations emphasize the need to integrate different analytical approaches into the assessment of oxidant activity in vivo and illustrate the importance for developing a better understanding of the chemical and physiological mechanisms through which the analytical methodologies are related.     

Peroxiredoxins,a new family of antioxidant proteins

Current ideas are discussed about the structures and mechanisms of action of proteins that have been united at present into a family of thiol-specific antioxidants or peroxiredoxins, which protect the cells of different organisms from the action of hydrogen peroxide. Peroxiredoxins fulfill the same function as antioxidant enzymes such as catalases and glutathione-dependent peroxidases; however, their catalytic activity is lower than that of these enzymes. The level of expression of genes of peroxiredoxins is increased in many pathological states accompanied by oxidative stress, and today there is direct evidence for the important role of peroxiredoxins in the vital activity of cells.     

Riboregulators in kidney development and function

The discovery of microRNAs has brought in another level of intricacy in gene regulation. These microRNAs are small non-coding RNAs that have dual ability to act as repressors or inducers of gene activity. MicroRNAs have been implicated in a wide spectrum of biological processes and their expressions have been found to be dysregulated in several diseases. Recently, microRNAs have emerged as a new area of interest in renal development and pathology. MicroRNA profilings have revealed a number of microRNAs that are specific to the kidney or restricted to certain regions of the organ suggesting possible exclusive roles therein. Recently, knockout studies have shown that these riboregulators are critical for normal renal growth and functional renal system. Individual microRNAs have also been identified in renal disease models including kidney cancers, diabetic nephropathy and polycystic kidney disease. Several mechanisms of modulating microRNA activity have also been introduced in recent years. Further progress in the understanding of microRNA activity, identification of microRNA signatures in different states as well as advancement of microRNA manipulation techniques will be valuable for kidney research.     

Conformational similarity in the activation of caspase-3 and -7 revealed by the unliganded and inhibited structures of caspase-7

Caspase-mediated apoptosis has important roles in normal cell differentiation and aging and in many diseases including cancer, neuromuscular disorders and neurodegenerative diseases. Therefore, modulation of caspase activity and conformational states is of therapeutic importance. We report crystal structures of a new unliganded conformation of caspase-7 and the inhibited caspase-7 with the tetrapeptide Ac-YVAD-Cho. Different conformational states and mechanisms for substrate recognition have been proposed based on unliganded structures of the redundant apoptotic executioner caspase-3 and -7. The current study shows that the executioner caspase-3 and -7 have similar conformations for the unliganded active site as well as the inhibitor-bound active site. The new unliganded caspase-7 structure exhibits the tyrosine flipping mechanism in which the Tyr230 has rotated to block entry to the S2 binding site similar to the active site conformation of unliganded caspase-3. The inhibited structure of caspase-7/YVAD shows that the P4 Tyr binds the S4 region specific to polar residues at the expense of a main chain hydrogen bond between the P4 amide and carbonyl oxygen of caspase-7 Gln 276, which is similar to the caspase-3 complex. This new knowledge of the structures and conformational states of unliganded and inhibited caspases will be important for the design of drugs to modulate caspase activity and apoptosis.     

The insider's guide to leukocyte integrin signalling and function

The activation of leukocyte integrins through diverse receptors results in transformation of the integrin from a bent, resting form to an extended conformation, which has at least two states of ligand-binding activity. This highly regulated activation process is essential for T cell migration and the formation of an immunological synapse. The signalling events that drive integrin activation are complex. Some key players have been well-characterized, but other aspects of the signalling mechanisms involved are still unclear. This Review focuses on the integrin lymphocyte function-associated antigen 1 (LFA1; also known as αLβ2 integrin), which is expressed by T cells, and explores how disparate signalling pathways synergize to regulate LFA1 activity.