Determining day length and temperature regulation of flowering: a molecular and modelling approach

Thesis (Ph.D.)--University of Washington, 2016-08

Post-translational lysine-acetylation of Ran and its regulation by Sirtuin deacetylases

Through recent advances in high-throughput mass spectrometry it has become evident that post-translational N-(epsilon)-lysine-acetylation is a modification found on thousands of proteins of all cellular compartments and all essential physiological processes. Many aspects in the biology of lysine-acetylation are poorly understood, including its regulation by lysine-acetyltransferases and lysine-deacetylases (KDACs). Here, the role of this modification was investigated for the small GTP-binding protein Ran, which, inter alia, is essential for the regulation of nucleocytoplasmic transport. To this end, site-specifically acetylated Ran was produced in E. coli by genetic code expansion. For five previously identified sites, Ran acetylation was tested regarding its impact on the intrinsic GTP hydrolysis rate, the assembly of export complexes (modeled in vitro with the export receptor CRM1 and the export substrate Spn1) and the interaction of Ran with its GTPase activation protein RanGAP and RanBP1. Overall, mild effects of Ran acetylation were observed for intrinsic and RanGAP-stimulated GTP hydrolysis rates. The interaction of active Ran with RanBP1 was negatively influenced by Ran acetylation at K159. Moreover, CRM1 bound to Ran acetylated at K37, K99 or K159 interacted more strongly with Spn1. Thus, lysine-acetylation interferes with essential aspects of Ran function. An in vitro screen was performed to identify potential Ran KDACs. The NAD+-dependent KDACs of the Sirtuin class showed activity towards two acetylation sites of Ran, K37 and K71. The specificity of Sirtuins was further analyzed based on an additional Ran acetylation site, K38. Since deacetylation of RanAcK38 was much slower compared to RanAcK37, di-acetylated RanAcK37/38 was tested next. The deacetylation rate of di-acetylated Ran was comparable to that of RanAcK37. Deacetylation experiments under single turnover conditions revealed that deacetylation occurs first at the K38 site in the di-acetylated RanAcK37/38 background. The ability of Sirtuins to deacetylate two adjacent AcKs was further investigated based on two proteins, which had previously been found to be di-acetylated and targeted by Sirtuins, namely the tumor suppressor protein p53 and phosphoenolpyruvate carboxykinase 1 (PEPCK1). p53 was readily deacetylated at two di-acetylation sites (K372/372 and K381/382), whereas PEPCK1 was not deacetylated in vitro. Taken together, these results have important implications for the substrate specificity of Sirtuins.

Hemoglobin conformational properties and ionic composition of red blood cells in vascular diseases patients

This is an abstract of a presented talk at the European Biotechnology Conference held in Latvia during 05–07 May 2016

Epigenetic and oncogenic regulation of SLC16A7 (MCT2) results in protein over-expression, impacting on signalling and cellular phenotypes in prostate cancer

Monocarboxylate Transporter 2 (MCT2) is a major pyruvate transporter encoded by the SLC16A7 gene. Recent studies pointed to a consistent overexpression of MCT2 in prostate cancer (PCa) suggesting MCT2 as a putative biomarker and molecular target. Despite the importance of this observation the mechanisms involved in MCT2 regulation are unknown. Through an integrative analysis we have discovered that selective demethylation of an internal SLC16A7/MCT2 promoter is a recurrent event in independent PCa cohorts. This demethylation is associated with expression of isoforms differing only in 5'-UTR translational control motifs, providing one contributing mechanism for MCT2 protein overexpression in PCa. Genes co-expressed with SLC16A7/MCT2 also clustered in oncogenic-related pathways and effectors of these signalling pathways were found to bind at the SLC16A7/MCT2 gene locus. Finally, MCT2 knock-down attenuated the growth of PCa cells. The present study unveils an unexpected epigenetic regulation of SLC16A7/MCT2 isoforms and identifies a link between SLC16A7/MCT2, Androgen Receptor (AR), ETS-related gene (ERG) and other oncogenic pathways in PCa. These results underscore the importance of combining data from epigenetic, transcriptomic and protein level changes to allow more comprehensive insights into the mechanisms underlying protein expression, that in our case provide additional weight to MCT2 as a candidate biomarker and molecular target in PCa.

Efeitos bioquímicos e fisiológicos da exposição ao níquel no caranguejo euraliano neohelice granulata

Em invertebrados eurialinos, a exposição a metais pode induzir distúrbios respiratórios, iônicos e osmóticos, bem como estresse oxidativo. Diversos estudos sobre o efeito combinado da salinidade da água e a exposição a metais em invertebrados estuarinos estão relatados na literatura, porém a maioria destes estudos estão focados em apenas alguns metais como Cd, Cu, Pb e Zn. Entretanto, poucos estudos avaliaram as respostas bioquímicas e fisiológicas de invertebrados eurialinos à exposição ao Ni em diferentes salinidades. No presente estudo, o caranguejo estuarino Neohelice granulata foi mantido sob condições controle (sem adição de Ni na água) ou exposto (96 h) a concentrações subletais de Ni (100 e 1000 µg/L) em duas salinidades (2 e 30). Após exposição, o consumo de oxigênio corporal foi medido e amostras de tecidos (hemolinfa, hepatopâncreas, músculo, e brânquias anteriores e posteriores) foram coletadas para análises posteriores. A concentração osmótica e a composição iônica (Na+ , Cl- , Ca2+, Mg2+ e K+ ) foram determinadas nas amostras de hemolinfa. A atividade da lactato desidrogenase (LDH) foi medida na hemolinfa, hepatopâncreas e músculo, enquanto a peroxidação lipídica (LPO) foi analisada no hepatopâncreas, músculo e brânquias (anteriores e posteriores). Os caranguejos controle não apresentaram diferença na concentração osmótica em função da salinidade, porém aqueles aclimatados à salinidade 2 apresentaram menores concentrações hemolinfáticas de Na+ , K + e Mg2+, bem como maiores níveis de LPO nas brânquias (anteriores e posteriores) e hepatopâncreas do que aqueles aclimatados à salinidade 30. O consumo de oxigênio corporal e a atividade tecidual da LDH foram semelhantes nos caranguejos controles aclimatados a 2 e 30. Estes resultados indicam que, após duas semanas de manutenção em laboratório, N. granulata apresenta ajustes fisiológicos da concentração osmótica (2‰: hiper-regulação; 30‰: hipo-regulação), composição iônica hemolinfática e taxas 4 metabólicas (aeróbica e anaeróbica) em função da salinidade, com conseqüente maior dano oxidativo em lipídios durante a hiper-regulação em baixa salinidade. Quanto à exposição ao Ni, houve aumento do consumo de oxigênio corporal, da atividade da LDH hemolinfática e da concentração hemolinfática de K+ na salinidade 2. Na salinidade 30 foi observado um aumento da atividade da LDH hemolinfática, da concentração osmótica e de Cl- hemolinfática, bem como uma diminuição das concentrações hemolinfáticas de K+ e Mg2+. Nos caranguejos aclimatados à salinidade 2, os efeitos do Ni parecem estar associados a distúrbios metabólicos (aeróbico e anaeróbico), enquanto distúrbios osmóticos e ionoregulatórios foram mais evidentes nos caranguejos aclimatados e expostos ao Ni na salinidade 30.

The effects of the quality of social relationships and emotion regulation ability on the happiness of introvert individuals

Previous research has shown that extraverts are happier than introverts and, although happy introverts exist, it is unclear under what conditions they can achieve happiness. The aim of the present study is to analyze the quality of social relationships and emotion regulation ability as a possible factor for happiness in introvert individuals. 1006 adults (42% males) completed measures of extraversion, neuroticism, quality of social relationships, emotion regulation ability and happiness. Results shows that introverts have significantly lower happiness, quality of life, quality of social relationship and emotion regulation ability scores than extraverts. Besides, those individuals with high quality social relationships or high emotion regulation ability were happier. Introverts were happier when they had high scores for quality of social relationships and emotion regulation ability, however the effect size was small. These results suggest that emotion regulation and social relationships are important to understand the relationships between introversion and happiness.

Altered transcriptional and epigenetic regulation affects brain cells proliferation and differentiation in the ultra-rare genetic demyelinating disease AGC1 deficiency: a study on in vitro models

AGC1 deficiency is a rare demyelinating disease caused by mutations in the SLC25A12 gene, which encodes for the mitochondrial glutamate-aspartate carrier 1 (AGC1/Alarar), highly expressed in the central nervous system. In neurons, impairment in AGC1 activity leads to reduction in N-acetyl-aspartate, the main lipid precursor for myelin synthesis (Profilo et al., 2017); in oligodendrocytes progenitors cells, AGC1 down regulation has been related to early arrest proliferation and premature differentiation (Petralla et al., 2019). Additionally, in vivo AGC1 deficiency models i.e., heterozygous mice for AGC1 knock-out and neurospheres from their subventricular zone, respectively, showed a global decrease in cells proliferation and a switch in neural stem cells (NSCs) commitment, with specific reduction in OPCs number and increase in neural and astrocytic pools (Petralla et al., 2019). Therefore, the present study aims to investigate the transcriptional and epigenetic regulation underlying the alterations observed in OPCs and NSCs biological mechanisms, in either AGC1 deficiency models of Oli-neu cells (murine immortalized oligodendrocytes precursors cells), partially silenced by a shRNA for SLC25A12 gene, and SVZ-derived neurospheres from AGC1+/- mice. Western blot and immunofluorescence analysis revealed significant variations in the expression of transcription factors involved in brain cells’ proliferation and differentiation, in association with altered histone post-translational modifications, as well as histone acetylases (HATs) and deacetylases (HDACs) activity/expression, suggesting an improper transcriptional and epigenetic regulation affecting both AGC1 deficiency in vitro models. Furthermore, given the large role of acetylation in controlling in specific time-windows OPC maturation (Hernandez and Casaccia; 2015), pharmacological HATs/HDACs inhibitions were performed, confirming the involvement of chromatin remodelling enzymes in the altered proliferation and early differentiation observed in the AGC1 deficiency models of siAGC1 Oli-neu cells and AGC1+/- mice-derived neurospheres.

Kidney and cloaca function in the estuarine crocodile (Crocodylus porosus) at different salinities: Evidence for solute-linked water uptake

Kidney function and the role of the cloacal complex in osmoregulation was investigated in estuarine crocodile (Crocodylus porosus) exposed to three environmental salinities: hypo-, iso- and hyperosmotic to the plasma. Plasma homeostasis was maintained over the range of salinities. Antidiuresis occurred with increased salinity. Although urine from the kidneys retained an osmotic pressure between 77% and 82% of the plasma, over 93% and 98% of plasma chloride filtered at the glomeruli was reabsorbed during passage through the kidneys under hypo and hyperosmotic conditions, respectively, and only 64% in iso-osmotic water. The kidneys were the primary site of sodium reabsorption under hypo-and hyperosmotic conditions. Secondary processing of urine during storage in the cloaca varied with salinity. During post renal storage of urine, the difference in urine osmotic pressure increased from -26.1 +/- 15.5 to 35.66 +/- 9.29 mOsM with increased salinity, and potassium concentration of urine increased over 3-fold in C. porosus from freshwater. The almost complete reabsorption of both sodium and chloride under hyperosmotic conditions indicates the necessity for secretory activity by the lingual salt glands. The osmoregulatory response of the kidneys and cloacal complex to environmental salinity is both plastic and complementary. (C) 1998 Elsevier Science Inc.

HYPOTHALAMIC COCAINE- AND AMPHETAMINE-REGULATED TRANSCRIPT AND CORTICOTROPHIN RELEASING FACTOR NEURONS ARE STIMULATED BY EXTRACELLULAR VOLUME AND OSMOTIC CHANGES

Several studies suggest that hypothalamic cocaine- and amphetamine-regulated transcript (CART) may interact with the hypothalamic-pituitary-adrenal (HPA) axis in the control of neuroendocrine function and may also participate in cardiovascular regulation. Therefore, this study aimed to evaluate, in experimental models of isotonic (I-EVE) and hypertonic (H-EVE) extracellular volume expansion and water deprivation (WD), the activation of CART- and corticotrophin releasing factor (CRF)-immunoreactive neurons, as well as the relative expression of CART and CRF mRNAs in the paraventricular (PVN) and supraoptic (SON) nuclei of the hypothalamus. Both H-EVE (0.30M NaCl, 2mL/100g of body weight, in 1 minute) and 24 hours of WD significantly increased plasma sodium concentrations, producing, respectively, either an increase or a decrease in extracellular volume. I-EVE (0.15M NaCl, 2mL/100g of body weight, in 1 minute) evoked a significant increase in the circulating volume accompanied by unaltered plasma concentrations of sodium. CART-expressing neurons of both magnocellular and parvocellular hypothalamic divisions were activated to produce Fos in response to H-EVE but not in response to I-EVE. Furthermore, increased expression of CART mRNA was found in the PVN of H-EVE but not I-EVE rats. These data show for the first time that EVE not only activates hypothalamic CRF neurons but also increases CRF mRNA expression in the PVN. In contrast, WD increases the number of CART-immunoreactive neurons activated to produce Fos in the PVN and SON but does not change the number of neurons double labeled for Fos and CRF or expression of CRF mRNA in the PVN. These findings provided new insights into the participation of CART in diverse processes within the PVN and SON, including its possible involvement in activation of the HPA axis and cardiovascular regulation in response to changes in extracellular volume and osmolality. (C) 2011 IBRO. Published by Elsevier Ltd. All rights reserved.

Ionic and Histological Studies of Salivary Glands in Rats with Diabetes and Their Glycemic State After Laser Irradiation

Objectives: To evaluate the effect of laser irradiation (LI) on the glycemic state and the histological and ionic parameters of the parotid and submandibular glands in rats with diabetes. Methods: One hundred twenty female rats were divided into eight groups. Diabetes was induced by administration of streptozotocin and confirmed later according to results of glycemia testing. Twenty-nine days after the induction, the parotid and submandibular glands of the rats were irradiated with 5, 10, and 20 J/cm(2) using a laser diode (660nm/100mW) (without diabetes: C5, C10, and C20; with diabetes: D5, D10, and D20, respectively). On the following day, the rats were euthanized, and blood glucose determined. Histological and ionic analyses were performed. Results: Rats with diabetes without irradiation (D0) showed lipid droples accumulation in the parotid gland, but accumulation decreased after 5, 10, and 20 J/cm(2) of laser irradiation. A decrease in fasting glycemia level from 358.97 +/- 56.70 to 278.33 +/- 87.98mg/dL for D5 and from 409.50 +/- 124.41 to 231.80 +/- 120.18 mg/dL for D20 (p < 0.05) was also observed. Conclusion: LI should be explored as an auxiliary therapy for control of complications of diabetes because it can alter the carbohydrate and lipid metabolism of rats with diabetes.

The peripheral pro-nociceptive state induced by repetitive inflammatory stimuli involves continuous activation of protein kinase A and protein kinase C epsilon and its Na(v)1.8 sodium channel functional regulation in the primary sensory neuron

In the present study, the participation of the Na(v)1.8 sodium channel was investigated in the development of the peripheral pro-nociceptive state induced by daily intraplantar injections of PGE(2) in rats and its regulation in vivo by protein kinase A (PKA) and protein kinase C epsilon (PKC epsilon) as well. In the prostaglandin E(2) (PGE(2))-induced persistent hypernociception, the Na(v)1.8 mRNA in the dorsal root ganglia (DRG) was up-regulated. The local treatment with dipyrone abolished this persistent hypernociception but did not alter the Na(v)1.8 mRNA level in the DRG. Daily intrathecal administrations of antisense Na(v)1.8 decreased the Na(v)1.8 mRNA in the DRG and reduced ongoing persistent hypernociception. once the persistent hypernociception had been abolished by dipyrone, but not by Na(v)1.8 antisense treatment, a small dose of PGE(2) restored the hypernociceptive plateau. These data show that, after a period of recurring inflammatory stimuli, an intense and prolonged nociceptive response is elicited by a minimum inflammatory stimulus and that this pro-nociceptive state depends on Na(v)1.8 mRNA up-regulation in the DRG. in addition, during the persistent hypernociceptive state, the PKA and PKC epsilon expression and activity in the DRG are up-regulated and the administration of the PKA and PKC epsilon inhibitors reduce the hypernociception as well as the Na(v)1.8 mRNA level. In the present study, we demonstrated that the functional regulation of the Na(v)1.8 mRNA by PKA and PKC epsilon in the primary sensory neuron is important for the development of the peripheral pro-nociceptive state induced by repetitive inflammatory stimuli and for the maintenance of the behavioral persistent hypernociception. (C) 2008 Elsevier Inc. All rights reserved.

Regulation of yeast acetohydroxyacid synthase by valine and ATP

The first step in the common pathway for the biosynthesis of branched-chain amino acids is catalysed by acetohydroxyacid synthase (AHAS; EC 4.1.3.18). The enzyme is found in plants, fungi and bacteria, and is regulated by controls on transcription and translation, and by allosteric modulation of catalytic activity. It has long been known that the bacterial enzyme is composed of two types of subunit, and a similar arrangement has been found recently for the yeast and plant enzymes. One type of subunit contains the catalytic machinery, whereas the other has a regulatory function. Previously, we have shown [Pang and Duggleby (1999) Biochemistry 38, 5222-5231] that yeast AHAS can be reconstituted from its separately purified subunits. The, reconstituted enzyme is inhibited by valine, and ATP reverses this inhibition. In the present work, we further characterize the structure and the regulatory properties of reconstituted yeast AHAS. High phosphate concentrations are required for reconstitution and it is shown that these conditions are necessary for physical association between the catalytic and regulatory subunits. It is demonstrated by CD spectral changes that ATP binds to the regulatory subunit alone, most probably as MgATP. Neither valine nor MgATP causes dissociation of the regulatory subunit from the catalytic subunit. The specificity of valine inhibition and MgATP activation are examined and it is found that the only effective analogue of either regulator of those tested is the non-hydrolysable ATP mimic, adenosine 5 '-[beta,gamma -imido]triphosphate. The kinetics of regulation are studied in detail and it is shown that the activation by MgATP depends on the valine concentration in a complex manner that is consistent with a proposed quantitative model.

Environmental regulation of land use and public compensation: principles, and Swiss and Australian examples

The authors discuss the regulation of rural land use and compensation for property-rights restrictions, both of which appear to have become more commonplace in recent years but also more contested. The implications of contemporary theories in relation to this matter are examined, including: the applicability of new welfare economics; the relevance of the neoclassical theory of politics; and the implications of contemporary theories of social conflict resolution and communication. Examination of examples of Swiss and Australian regulation of the use of rural properties, and the ensuing conflicts, reveals that many decisions reflect a mixture of these elements. Rarely, if ever, are social decisions in this area made solely on the basis of welfare economics, for instance social cost-benefit analysis. Only some aspects of such decisions can be explained by the neoclassical theory of politics. Theories of social conflict resolution suggest why, and in what way, approaches of discourse and participation may resolve conflicts regarding regulation and compensation. These theories and their practical application seem to gain in importance as opposition to government decisions increases. The high degree of complexity of most conflicts concerning regulation and compensation cannot be tackled with narrow economic theories. Moreover, the Swiss and Australian examples show that approaches involving conflict resolution may favour environmental standards.

Cytokine regulation of syndecan-1 and-2 gene expression in human periodontal fibroblasts and osteoblasts

Cell-surface proteoglycans participate in several biological functions including interactions with a variety of growth factors and cytokines. Regulation of syndecan-1 and -2 gene expression was investigated in human periodontal ligament fibroblasts (PDLF), osteoblasts (OB) and gingival fibroblasts (GF), in response to platelet-derived growth factor (PDGF-BB), transforming growth factor (TGF-beta(1)), and interleukin (IL-1beta) by Northern blot analyses. We also compared the effect of PDGF-BB and TGF-beta(1), separately and in combination, in the prolonged presence of IL-1beta on the expression of both syndecan genes. The results demonstrated that the three cell lines regulated the expression of syndecan-1 and -2 in response to growth factors and cytokines in different manners. These cell lines increased syndecan-1 mRNA levels in response to either PDGF-BB or TGF-beta(1) and decreased levels in response to IL-1beta. The effect of IL-1beta on syndecan-1 mRNA synthesis was partially reversed after adding PDGF-BB and TGF-beta(1), separately or in combination, in the presence of IL-1beta. In contrast, syndecan-2 mRNA level was markedly upregulated in response to either TGF-beta(1) or IL-1beta in OB when compared with the other two cell lines. However, the stimulatory effect of TGF-beta(1) on syndecan-2 mRNA production in OB was abolished in the prolonged presence of IL-1beta. These findings lend support to the notion that syndecan-1 and syndecan-2 have distinct functions which correlate with their source and functions within the periodontium.