Origin and diversity of the Sox transcription factor gene family: genome-wide analysis in Fugu rubripes

The SOX family of transcription factors are found throughout the animal kingdom and are important in a variety of developmental contexts. Genome analysis has identified 20 Sox genes in human and mouse, which can be subdivided into 8 groups, based on sequence comparison and intron-exon structure. Most of the SOX groups identified in mammals are represented by a single SOX sequence in invertebrate model organisms, suggesting a duplication and divergence mechanism has operated during vertebrate evolution. We have now analysed the Sox gene complement in the pufferfish, Fugu rubripes, in order to shed further light on the diversity and origins of the Sox gene family. Major differences were found between the Sox family in Fugu and those in humans and mice. In particular, Fugu does not have orthologues of Sry, Sox,15 and Sox30, which appear to be specific to mammals, while Sox19, found in Fugu and zebrafish but absent in mammals, seems to be specific to fishes. Six mammalian Sox genes are represented by two copies each in Fugu, indicating a large-scale gene duplication in the fish lineage. These findings point to recent Sox gene loss, duplication and divergence occurring during the evolution of tetrapod and teleost lineages, and provide further evidence for large-scale segmental or a whole-genome duplication occurring early in the radiation of teleosts. (C) 2004 Elsevier B.V. All rights reserved.

Nur77 regulates lipolysis in skeletal muscle cells - Evidence for cross-talk between the beta-adrenergic and an orphan nuclear hormone receptor pathway

Skeletal muscle is a major mass peripheral tissue that accounts for similar to 40% of total body weight and 50% of energy expenditure and is a primary site of glucose disposal and fatty acid oxidation. Consequently, muscle has a significant role in insulin sensitivity, obesity, and the blood-lipid profile. Excessive caloric intake is sensed by the brain and induces beta-adrenergic receptor (beta-AR)- mediated adaptive thermogenesis. beta-AR null mice develop severe obesity on a high fat diet. However, the target gene(s), target tissues(s), and molecular mechanism involved remain obscure. We observed that 30 - 60 min of beta-AR agonist ( isoprenaline) treatment of C2C12 skeletal muscle cells strikingly activated (> 100-fold) the expression of the mRNA encoding the nuclear hormone receptor, Nur77. In contrast, the expression of other nuclear receptors that regulate lipid and carbohydrate metabolism was not induced. Stable transfection of Nur77-specific small interfering RNAs (siNur77) into skeletal muscle cells repressed endogenous Nur77 mRNA expression. Moreover, we observed attenuation of gene and protein expression associated with the regulation of energy expenditure and lipid homeostasis, for example AMP-activated protein kinase gamma 3, UCP3, CD36,adiponectin receptor 2, GLUT4, and caveolin-3. Attenuation of Nur77 expression resulted in decreased lipolysis. Finally, in concordance with the cell culture model, injection and electrotransfer of siNur77 into mouse tibialis cranialis muscle resulted in the repression of UCP3 mRNA expression. This study demonstrates regulatory cross-talk between the nuclear hormone receptor and beta-AR signaling pathways. Moreover, it suggests Nur77 modulates the expression of genes that are key regulators of skeletal muscle lipid and energy homeostasis. In conclusion, we speculate that Nur77 agonists would stimulate lipolysis and increase energy expenditure in skeletal muscle and suggest selective activators of Nur77 may have therapeutic utility in the treatment of obesity.

Network topology and the evolution of dynamics in an artificial genetic regulatory network model created by whole genome duplication and divergence

Topological measures of large-scale complex networks are applied to a specific artificial regulatory network model created through a whole genome duplication and divergence mechanism. This class of networks share topological features with natural transcriptional regulatory networks. Specifically, these networks display scale-free and small-world topology and possess subgraph distributions similar to those of natural networks. Thus, the topologies inherent in natural networks may be in part due to their method of creation rather than being exclusively shaped by subsequent evolution under selection. The evolvability of the dynamics of these networks is also examined by evolving networks in simulation to obtain three simple types of output dynamics. The networks obtained from this process show a wide variety of topologies and numbers of genes indicating that it is relatively easy to evolve these classes of dynamics in this model. (c) 2006 Elsevier Ireland Ltd. All rights reserved.

An evolutionary framework for studies of hibernation and short-term torpor

Data from diverse studies endorse ideas that short term torpor and hibernation are expressions of ancient characters. In evolutionary terms, their basic mechanisms are probably plesiomorphic (= ancestral/primitive) and physiologically similar. This contrasts with the alternate view that they are apomorphic (= derived, specialized), arising independently in many taxa from homeothermic ancestry by numerous apparent convergences. This paper explores some of the implications of accepting the plesiomorphic interpretation. Hibernation is, of course, a complex phenomenon that has undergone variations and refinements in different mammalian lineages. The argument is not that hibernation in total is a plesiomorphic character, but that it is built upon fundamental processes that are. Taking this view provides a framework for research that emphasizes the value of comparative studies, particularly of reptiles and birds. Studies of reptiles, for example, might unravel the mystery about periodic arousals. A plesiomorphic framework also explains the most extreme examples of hibernation as derived specializations from ancestry in which heterothermy is more about energy management than escape from cold. It cautions against using low body temperature (Tb) alone to diagnose torpor, emphasizes the need to distinguish between constitutional eurythermy (plesiomorphic) and constitutional stenothermy (apomorphic), and leads to a parsimonious theory about the evolution of endothermy. The paper proposes that brown adipose tissue (BAT) is apomorphic within eutheria and highlights the conundrum posed by the occurrence of both nonshivering thermogenesis (NST) and rapid arousal from hibernation in noneutherian mammals that lack BAT and uncoupling protein 1 (UCP1). It endorses the likely existence of a different, ancient and widespread mechanism for regulatory NST in mammals.

RSA-Grid: A grid computing based framework for power system reliability and security analysis

Grid computing is an emerging technology for providing the high performance computing capability and collaboration mechanism for solving the collaborated and complex problems while using the existing resources. In this paper, a grid computing based framework is proposed for the probabilistic based power system reliability and security analysis. The suggested name of this computing grid is Reliability and Security Grid (RSA-Grid). Then the architecture of this grid is presented. A prototype system has been built for further development of grid-based services for power systems reliability and security assessment based on probabilistic techniques, which require high performance computing and large amount of memory. Preliminary results based on prototype of this grid show that RSA-Grid can provide the comprehensive assessment results for real power systems efficiently and economically.

Mechanisms of Mycoplasma-induced inflammation and cellular transformation

There is a growing interest in “medical gasses” for their antibacterial and anti-inflammatory properties. Hydrogen sulfide (H2S), a member of the family of gasotransmitters, is in fact increasingly being recognized as an important signaling molecule, but its precise role in the regulation of the inflammatory response is still not clear. For this reason, the aim of the first part of this thesis was to investigate the effects of H2S on the expression of pro-inflammatory cytokines, such as MCP-1, by using an in vitro model composed by both primary monocytes-derived macrophages cultures and the human monocytic cell line U937 infected with Mycoplasma fermentans, a well-known pro-inflammatory agent. In our experiments, we observed a marked increase in the production of pro-inflammatory cytokines in infected cells. In particular, MCP-1 was induced both at the RNA and at the protein level. To test the effects of H2S on infected cells, we treated the cells with two different H2S donors (NaHS and GYY4137), showing that both H2S treatments had anti-inflammatory effects in Mycoplasma-infected cells: the levels of MCP-1, both mRNA expression and protein production, were reduced. Our subsequent studies aimed at understanding the molecular mechanisms responsible for these effects, focused on two specific molecular pathways, both involved in inflammation: the NF-κB and the Nrf2 pathway. After treatment with pharmacological inhibitors, we demonstrated that Mycoplasma fermentans induces MCP-1 expression through the TLR-NF-κB pathway with the nuclear translocation of its subunits, while treatment with H2S completely blocked the nuclear translocation of NF-κB heterodimer p65/p50. Then, once infected cells were treated with H2S donors, we observed an increased protective effect of Nrf2 and also a decrease in ROS production. These results highlight the importance of H2S in reducing the inflammatory process caused by Mycoplasma fermentans. To this regard, it should be noted that several projects are currently ongoing to develop H2S-releasing compounds as candidate drugs capable of alleviating cell deterioration and to reduce the rate of decline in organ function. In the second part of this study, we investigated the role of Mycoplasma infection in cellular transformation. Infectious agents are involved in the etiology of many different cancers and a number of studies are still investigating the role of microbiota in tumor development. Mycoplasma has been associated with some human cancers, such as prostate cancer and non-Hodgkin’s lymphoma in HIV-seropositive people, and its potential causative role and molecular mechanisms involved are being actively investigated. To this regard, in vitro studies demonstrated that, upon infection, Mycoplasma suppresses the transcriptional activity of p53, key protein in the cancer suppression. As a consequence, infected cells were less susceptible to apoptosis and proliferated more than the uninfected cells. The mechanism(s) responsible for the Mycoplasma-induced inhibitory effect on p53 were not determined. Aim of the second part of this thesis was to better understand the tumorigenic role of the microorganism, by investigating more in details the effect(s) of Mycoplasma on p53 activity in an adenocarcinoma HCT116 cell line. Treatment of Mycoplasma-infected cells with 5FU or with Nutlin, two molecules that induce p53 activity, resulted in cellular proliferation comparable to untreated controls. These results suggested that Mycoplasma infection inhibited p53 activity. Immunoprecipitation of p53 with specific antibodies, and subsequent Gas Chromatography and Mass Spectroscopy (GC-MS) assays, allowed us to identify several Mycoplasma-specific proteins interacting with p53, such as DnaK, a prokaryotic heat shock protein and stress inducible chaperones. In cells transfected with DnaK we observed i) reduced p53 protein levels; ii) reduced activity and expression of p21, Bax and PUMA, iii) a marked increase in cells leaving G1 phase. Taken together, these data show an interaction between the human p53 and the Mycoplasma protein DnaK, with the consequent decreased p53 activity and decreased capability to respond to DNA damage and prevent cell proliferation. Our data indicate that Mycoplasma could be involved in cancer formation and the mechanism(s) has the potential to be a target for cancer diagnosis and treatment(s).

Advances in (poly)phenol research: novel sources, bioavailability, bioaccumulation and bioactivity

In the last decades, increasing scientific evidence has correlated the regular consumption of (poly)phenol-rich foods to a potential reduction of chronic disease incidence and mortality. However, epidemiological evidence on the role of (poly)phenol intake against the risk of some chronic diseases is promising, but not conclusive. In this framework a proper approach to (poly)phenol research is requested, using a step by step strategy. The plant kingdom produces an overwhelming array of structurally diverse secondary metabolites, among which flavonoids and related phenolic and (poly)phenolic compounds constitute one of the most numerous and widely distributed group of natural products. To date, more than 8000 structures have been classified as members of the phytochemical class of (poly)phenol, and among them over 4000 flavonoids have been identified. For this reason, a detailed food (poly)phenolic characterization is essential to identify the compounds that will likely enter the human body upon consumption, to predict the metabolites that will be generated and to unravel the potential effects of phenolic rich food sources on human health. In the first part of this work the attention was focused on the phenolic characterization of fruit and vegetable supplements, considering the increasing attention recently addressed to the so called "nutraceuticals", and on the main coffee industry by-product, namely coffee silverskin. The interest oriented toward (poly)phenols is then extended to their metabolism within the human body, paramount in the framework of their putative health promoting effects. Like all nutrients and non-nutrients, once introduced through the diet, (poly)phenols are subjected to an intense metabolism, able to convert the native compounds into similar conjugated, as well as smaller and deeply modified molecules, which in turn could be further conjugated. Although great strides have been made in the last decades, some steps of the (poly)phenol metabolism remain unclear and are interesting points of research. In the second part of this work the research was focused on a specific bran fraction, namely aleurone, added in feed pellets and in bread to investigate the absorption, metabolism and bioavailability of its phenolic compounds in animal and humans, with a preliminary in vitro step to determine their potential bioaccesibility. This part outlines the best approaches to assess the bioavailability of specific phenolics in several experimental models. The physiological mechanisms explaining the epidemiological and observational data on phenolics and health, are still far from being unraveled or understood in full. Many published results on phenolic actions at cell levels are biased by the fact that aglycones or native compounds have been used, not considering the previously mentioned chemical and biological transformations. In the last part of this thesis work, a new approach in (poly)phenol bioactivity investigation is proposed, consisting of a medium-long term treatment of animals with a (poly)phenol source, in this specific case resveratrol, the detection of its metabolites to determine their possible specific tissue accumulation, and the evaluation of specific parameters and/or mechanism of action at target tissue level. To conclude, this PhD work has contributed to advancing the field, as novel sources of (poly)phenols have been described, the bioavailability of (poly)phenols contained in a novel specific bran fraction used as ingredient has been evaluated in animal and in humans, and, finally, the tissue accumulation of specific (poly)phenol metabolites and the evaluation of specific parameters and/or mechanism of action has been carried out. For these reasons, this PhD work should be considered an example of adequate approach to the investigation of (poly)phenols and of their bioactivity, unavoidable in the process of unequivocally defining their effects on human health.

Opening returns, noise and overreaction

In this article a partial-adjustment model, which shows how equity prices fail to adjust instantaneously to new information, is estimated using a Kalman filter. For the components of the Dow Jones Industrial 30 index I aim to identify whether overreaction or noise is the cause of serial correlation and high volatility associated with opening returns. I find that the tendency for overreaction in opening prices is much stronger than for closing prices; therefore, overreaction rather than noise may account for differences in the return behavior of opening and closing returns.

Protein oxidation:role in signalling and detection by mass spectrometry

Proteins can undergo a wide variety of oxidative post-translational modifications (oxPTM); while reversible modifications are thought to be relevant in physiological processes, non-reversible oxPTM may contribute to pathological situations and disease. The oxidant is also important in determining the type of oxPTM, such as oxidation, chlorination or nitration. The best characterized oxPTMs involved in signalling modulation are partial oxidations of cysteine to disulfide, glutathionylated or sulfenic acid forms that can be reversed by thiol reductants. Proline hydroxylation in HIF signalling is also quite well characterized, and there is increasing evidence that specific oxidations of methionine and tyrosine may have some biological roles. For some proteins regulated by cysteine oxidation, the residues and molecular mechanism involved have been extensively studied and are well understood, such as the protein tyrosine phosphatase PTP1B and MAP3 kinase ASK1, as well as transcription factor complex Keap1-Nrf2. The advances in understanding of the role oxPTMs in signalling have been facilitated by advances in analytical technology, in particular tandem mass spectrometry techniques. Combinations of peptide sequencing by collisionally induced dissociation and precursor ion scanning or neutral loss to select for specific oxPTMs have proved very useful for identifying oxidatively modified proteins and mapping the sites of oxidation. The development of specific labelling and enrichment procedures for S-nitrosylation or disulfide formation has proved invaluable, and there is ongoing work to establish analogous methods for detection of nitrotyrosine and other modifications.

Studies on the mechanism of action on antitumour imidazotetrazinones

The imidazotetrazinones are clinically active antitumour agents, temozolomide currently proving successful in the treatment of melanomas and gliomas. The exact nature of the biological processes underlying response are as yet unclear.This thesis attempts to identify the cellular targets important to the cytotoxicity of imidazotetrazinones, to elucidate the pathways by which this damage leads to cell death, and to identify mechanisms by which tumour cells may circumvent this action. The levels of the DNA repair enzymes O6-alkylguanine-DNA-alkyltransferase (O6-AGAT) and 3-methyladenine-DNA-glycosylase (3MAG) have been examined in a range of murine and human cell lines with differential sensitivity to temozolomide. All the cell lines were proficient in 3MAG despite there being 40-fold difference in sensitivity to temozolomide. This suggests that while 3-methyladenine is a major product of temozolomide alkylation of DNA it is unlikely to be a cytotoxic lesion. In contrast, there was a 20-fold variation in O6-AGAT levels and the concentration of this repair enzyme correlated with variations in cytotoxicity. Furthermore, depletion of this enzyme in a resistant, O6-AGAT proficient cell line (Raji), by pre-treatment with the free base O6-methylguanine resulted in 54% sensitisation to the effects of temozolomide. These observations have been extended to 3 glioma cell lines; results that support the view that the cytotoxicity of temozolomide is related to alkylation at the O6-position of guanine and that resistance to this drug is determined by efficient repair of this lesion. It is clear, however, the other factors may influence tumour response since temozolomide showed little differential activity towards 3 established solid murine tumours in vivo, despite different tumour O6-AGAT levels. Unlike mitozolomide, temozolomide is incapable of cross-linking DNA and a mechanism by which O6-methylguanine may exert lethality is unclear. The cytotoxicity of the methyl group may be due to its disruption of DNA-protein interactions, or alternatively cell death may not be a direct result of the alkyl group itself, but manifested by DNA single-strand breaks. Enhanced alkaline elution rates were found for the DNA of Raji cells treated with temozolomide following alkyltransferase depletion, suggesting a relationship between O6-methylguanine and the induction single-strand breaks. Such breaks can activate poly(ADP-ribose) synthetase (ADPRT) an enzyme capable of rapid and lethal depletion of cellular NAD levels. However, at concentrations of temozolomlde relevant in vivo little change in adenine nucleotides was detected in cell lines, although this enzyme would appear important in modulating DNA repair since inhibition of ADPRT potentiated temozolomide cytotoxicity in Raji cells but not O6-AGAT deficient GM892A cells. Cell lines have been reported that are O6-AGAT deficient yet resistant to methylating agents. Thus, resistance to temozolomide may arise not only by removal of the methyl group from the O6-position of guanine, but also from another mechanism involving caffeine-sensitive post-replication repair or mismatch repair activity. A modification of the standard Maxam Gilbert sequencing technique was used to determine the sequence specificity of guanine-N7 alkylation. Temozolomide preferentially alkylated runs of guanines with the intensity of reaction increasing with the number of adjacent guanines in the DNA sequence. Comparable results were obtained with a polymerase-stop assay, although neither technique elucidates the sequence specificity of O6-guanine alkylation. The importance of such specificity to cytotoxicity is uncertain, although guanine-rich sequences are common to the promoter regions of oncogenes. Expression of a plasmid reporter gene under the control of the Ha-ras proto~oncogene promoter was inhibited by alkylation with temozolomide when transfected into cancer cell lines, However, this inhibition did not appear to be related to O6~guanine alkylation and therefore would seem unimportant to the chemotherapeutic activity of temozolomide.

Visual signs and symptoms of progressive supranuclear palsy

Progressive supranuclear palsy is a rare, degenerative brain disorder and the second most common syndrome in which the patient exhibits 'parkinsonism', that is, a variety of symptoms involving problems with movement. General symptoms include difficulties with gait and balance; the patient walking clumsily and often falling backwards. The syndrome can be difficult to diagnose and visual signs and symptoms can help to separate it from closely related movement disorders such as Parkinson's disease, multiple system atrophy, dementia with Lewy bodies and corticobasal degeneration. A combination of the presence of vertical supranuclear gaze palsy, fixation instability, lid retraction, blepharospasm and apraxia of eyelid opening and closing may be useful visual signs in the identification of progressive supranuclear palsy. As primary eye-care practitioners, optometrists should be able to identify the visual problems of patients with this disorder and be expected to work with patients and their carers to manage their visual welfare.

Rapid aquaporin translocation regulates cellular water flow:the mechanism of hypotonicity-induced sub-cellular localization of the aquaporin 1 water channel

The control of cellular water flow is mediated by the aquaporin (AQP) family of membrane proteins. The family's structural features and the mechanism of selective water passage through the AQP pore are established, but there remains a gap in our knowledge of how water transport is regulated. Two broad possibilities exist. One is controlling the passage of water through the AQP pore, but this has only been observed as a phenomenon in some plant and microbial AQPs. An alternative is controlling the number of AQPs in the cell membrane. Here we describe a novel pathway in mammalian cells whereby a hypotonic stimulus directly induces intracellular calcium elevations, through transient receptor potential channels, that trigger AQP1 translocation. This translocation, which has a direct role in cell volume regulation, occurs within 30s and is dependent on calmodulin activation and phosphorylation of AQP1 at two threonine residues by protein kinase C. This direct mechanism provides a rationale for the changes in water transport that are required in response to constantly-changing local cellular water availability. Moreover, since calcium is a pluripotent and ubiquitous second messenger in biological systems, the discovery of its role in the regulation of AQP translocation has ramifications for diverse physiological and pathophysiological processes, as well as providing an explanation for the rapid regulation of water flow that is necessary for cell homeostasis.

Eye movement problems and differential diagnosis of the parkinsonian syndromes

Differential clinical diagnosis of the parkinsonian syndromes, viz., Parkinson’s disease (PD), progressive supranuclear palsy (PSP), dementia with Lewy bodies (DLB), and multiple system atrophy (MSA) can be difficult. Eye movement problems, however, are a chronic complication of many of these disorders and may be a useful aid to diagnosis. Hence, the presence in PSP of vertical supranuclear gaze palsy, fixation instability, lid retraction, blepharospasm, and apraxia of eyelid opening and closing is useful in separating PD from PSP. Moreover, atypical features of PSP include slowing of upward saccades, moderate slowing of downward saccades, the presence of a full range of voluntary vertical eye movements, a curved trajectory of oblique saccades, and absence of square-wave jerks. Downgaze palsy is probably the most useful diagnostic clinical symptom of PSP. By contrast, DLB patients are specifically impaired in both reflexive and saccadic execution and in the performance of more complex saccadic eye movement tasks. Problems in convergence in DLB are also followed by akinesia and rigidity. Abnormal ocular fixation may occur in a significant proportion of MSA patients along with excessive square-wave jerks, a mild supranuclear gaze palsy, a gaze-evoked nystagmus, a positioning down-beat nystagmus, mild-moderate saccadic hypometria, impaired smooth pursuit movements, and reduced vestibulo-ocular reflex (VOR) suppression. There may be considerable overlap between the eye movement problems characteristic of the various parkinsonian disorders, but taken together with other signs and symptoms, can be a useful aid in differential diagnosis, especially in the separation of PD and PSP.

HOCl-modified phosphatidylcholines induce apoptosis and redox imbalance in HUVEC-ST cells

Electrophilic attack of hypochlorous acid on unsaturated bonds of fatty acyl chains is known to result mostly in chlorinated products that show cytotoxicity to some cell lines and were found in biological systems exposed to HOCl. This study aimed to investigate more deeply the products and the mechanism underlying cytotoxicity of phospholipid-HOCl oxidation products, synthesized by the reaction of HOCl with 1-stearoyl-2-oleoyl-, 1-stearoyl-2-linoleoyl-, and 1-stearoyl-2-arachidonyl-phosphatidylcholine. Phospholipid chlorohydrins were found to be the most abundant among obtained products. HOCl-modified lipids were cytotoxic towards HUVEC-ST (endothelial cells), leading to a decrease of mitochondrial potential and an increase in the number of apoptotic cells. These effects were accompanied by an increase of the level of active caspase-3 and caspase-7, while the caspase-3/-7 inhibitor Ac-DEVD-CHO dramatically decreased the number of apoptotic cells. Phospholipid-HOCl oxidation products were shown to affect cell proliferation by a concentration-dependent cell cycle arrest in the G/G phase and activating redox sensitive p38 kinase. The redox imbalance observed in HUVEC-ST cells exposed to modified phosphatidylcholines was accompanied by an increase in ROS level, and a decrease in glutathione content and antioxidant capacity of cell extracts. © 2014 Elsevier Inc. All rights reserved.