Abnormal alterations in the Ca2+/CaV1.2/calmodulin/caMKII signaling pathway in a tremor rat model and in cultured hippocampal neurons exposed to Mg2+-free solution

Voltage-dependent calcium channels (VDCCs) are key elements in epileptogenesis. There are several binding-sites linked to calmodulin (CaM) and several potential CaM-dependent protein kinase II (CaMKII)-mediated phosphorylation sites in CaV1.2. The tremor rat model (TRM) exhibits absence‑like seizures from 8 weeks of age. The present study was performed to detect changes in the Ca2+/CaV1.2/CaM/CaMKII pathway in TRMs and in cultured hippocampal neurons exposed to Mg2+‑free solution. The expression levels of CaV1.2, CaM and phosphorylated CaMKII (p‑CaMKII; Thr‑286) in these two models were examined using immunofluorescence and western blotting. Compared with Wistar rats, the expression levels of CaV1.2 and CaM were increased, and the expression of p‑CaMKII was decreased in the TRM hippocampus. However, the expression of the targeted proteins was reversed in the TRM temporal cortex. A significant increase in the expression of CaM and decrease in the expression of CaV1.2 were observed in the TRM cerebellum. In the cultured neuron model, p‑CaMKII and CaV1.2 were markedly decreased. In addition, neurons exhibiting co‑localized expression of CaV1.2 and CaM immunoreactivities were detected. Furthermore, intracellular calcium concentrations were increased in these two models. For the first time, o the best of our knowledge, the data of the present study suggested that abnormal alterations in the Ca2+/CaV1.2/CaM/CaMKII pathway may be involved in epileptogenesis and in the phenotypes of TRMs and cultured hippocampal neurons exposed to Mg2+‑free solution.

Donor chimaerism is a strong indicator of disease free survival following bone marrow transplantation for chronic myeloid leukaemia

Although Chronic Myeloid Leukaemia (CML) can be treated successfully with allogeneic bone marrow transplantation (BMT), leukaemia relapse remains a significant clinical problem. Molecular monitoring of the post transplant marrow can be useful in predicting relapse particularly in CML patients where the Philadelphia chromosome or its molecular counterpart, the BCR-ABL fusion messenger RNA can be used as a leukaemia specific marker of minimal residual disease (MRD). We have investigated chimaerism (using polymerase chain reaction of short tandem repeat sequences (STR-PCR)) and MRD status (using reverse transcriptase PCR of the BCR-ABL fusion mRNA) in a serial fashion in 18 patients who were in clinical and haematological remission post allogeneic BMT for chronic phase CML. Eleven patients exhibited complete donor chimaerism with no evidence of minimal residual disease. Five patients had transient or low level stable MC. Late MC and MRD was observed in two patients who relapsed > 6 years after T cell depleted BMT for CML. Thus STR-PCR is an appropriate screening test in the post transplant setting for CML patients, but those patients exhibiting mixed haemopoietic chimaerism should also be monitored using a leukaemia specific sensitive molecular assay.

Studies on hemopoietic chimerism following allogeneic bone marrow transplantation in the molecular biology era

Donor hematopoiesis or donor chimerism in the host following allogeneic bone marrow transplantation (BMT) has appeared crucial to the engraftment process. However, as molecular techniques exploiting neutral variation in human genetic material have been used in the study of chimerism, the detection of residual host cells or mixed hemopoietic chimerism has indicated that donor chimerism is not obligatory following BMT. This review focuses on the detection and significance of mixed chimerism (MC) in patients transplanted for both malignant and non-malignant hemopoietic disease and attempts to tease out the contribution of MC to engraftment, leukemia relapse, graft rejection and long-term disease-free survival.

Tailoring Plasmonic Metamaterials for Ultrasenstive Detection of Mercury Trace Contaminants via Molecular Logic Gates

Structural and functional information encoded in DNA combined with unique properties of nanomaterials could be of use for the construction of novel biocomputational circuits and intelligent biomedical nanodevices. However, at present their practical applications are still limited by either low reproducibility of fabrication, modest sensitivity, or complicated handling procedures. Here, we demonstrate the construction of label-free and switchable molecular logic gates (AND, INHIBIT, and OR) that use specific conformation modulation of a guanine- and thymine-rich DNA, while the optical readout is enabled by the tunable metamaterials which serve as a substrate for surface enhanced Raman spectroscopy (MetaSERS). Our MetaSERS-based DNA logic is simple to operate, highly reproducible, and can be stimulated by ultra-low concentration of the external inputs, enabling an extremely sensitive detection of mercury ions down to 2×10-4 ppb, which is four orders of magnitude lower than the exposure limit allowed by United States Environmental Protection Agency

Label-free based quantitative proteomics analysis of primary neonatal porcine Leydig cells exposed to the persistent contaminant 3-methylsulfonyl-DDE

Evidence that persistent environmental pollutants may target the male reproductive system is increasing. The male reproductive system is regulated by secretion of testosterone by testicular Leydig cells, and perturbation of Leydig cell function may have ultimate consequences. 3-Methylsulfonyl-DDE (3-MeSO₂-DDE) is a potent adrenal toxicants formed from the persistent insecticide DDT. Although studies have revealed the endocrine disruptive effect of 3-MeSO₂-DDE, the underlying mechanisms at cellular level in steroidogenic Leydig cells remains to be established. The current study addresses the effect of 3-MeSO₂-DDE on viability, hormone production and proteome response of primary neonatal porcine Leydig cells. The AlamarBlue™ assay was used to evaluate cell viability. Solid phase radioimmunoassay was used to measure concentration of hormones produced by both unstimulated and Luteinizing hormone (LH)-stimulated Leydig cells following 48h exposure. Protein samples from Leydig cells exposed to a non-cytotoxic concentration of 3-MeSO₂-DDE (10μM) were subjected to nano-LC-MS/MS and analyzed on a Q Exactive mass spectrometer and quantified using label-free quantitative algorithm. Gene Ontology (GO) and Ingenuity Pathway Analysis (IPA) were carried out for functional annotation and identification of protein interaction networks. 3-MeSO₂-DDE regulated Leydig cell steroidogenesis differentially depending on cell culture condition. Whereas its effect on testosterone secretion at basal condition was stimulatory, the effect on LH-stimulated cells was inhibitory. From triplicate experiments, a total of 6804 proteins were identified in which the abundance of 86 proteins in unstimulated Leydig cells and 145 proteins in LH-stimulated Leydig cells was found to be significantly regulated in response to 3-MeSO₂-DDE exposure. These proteins not only are the first reported in relation to 3-MeSO₂-DDE exposure, but also display small number of proteins shared between culture conditions, suggesting the action of 3-MeSO₂-DDE on several targeted pathways, including mitochondrial dysfunction, oxidative phosphorylation, EIF2-signaling, and glutathione-mediated detoxification. Further identification and characterization of these proteins and pathways may build our understanding to the molecular basis of 3-MeSO₂-DDE induced endocrine disruption in Leydig cells.

A Molecular Mechanism for Sequential Activation of a G Protein-Coupled Receptor

Ligands targeting G protein-coupled receptors (GPCRs) are currently classified as either orthosteric, allosteric, or dualsteric/bitopic. Here, we introduce a new pharmacological concept for GPCR functional modulation: sequential receptor activation. A hallmark feature of this is a stepwise ligand binding mode with transient activation of a first receptor site followed by sustained activation of a second topographically distinct site. We identify 4-CMTB (2-(4-chlorophenyl)-3-methyl-N-(thiazol-2-yl)butanamide), previously classified as a pure allosteric agonist of the free fatty acid receptor 2, as the first sequential activator and corroborate its two-step activation in living cells by tracking integrated responses with innovative label-free biosensors that visualize multiple signaling inputs in real time. We validate this unique pharmacology with traditional cellular readouts, including mutational and pharmacological perturbations along with computational methods, and propose a kinetic model applicable to the analysis of sequential receptor activation. We envision this form of dynamic agonism as a common principle of nature to spatiotemporally encode cellular information.

Probing confinement resonances by photoionizing Xe inside a C60+ molecular cage

Double photoionization accompanied by loss of n C atoms (n=0, 2, 4, 6) was investigated by merging beams of Xe@C60+ ions and synchrotron radiation and measuring the yields of product ions. The giant 4d dipole resonance of the caged Xe atom has a prominent signature in the cross section for these product channels, which together account for 6.2 ± 1.4 of the total Xe 4d oscillator strength of 10. Compared to that for a free Xe atom, the oscillator strength is redistributed in photon energy due to multipath interference of outgoing Xe 4d photoelectron waves that may be transmitted or reflected by the spherical C60+ molecular cage, yielding so-called confinement resonances. The data are compared with an earlier measurement and with theoretical predictions for this single-molecule photoelectron interferometer system. Relativistic R-matrix calculations for the Xe atom in a spherical potential shell representing the fullerene cage show the sensitivity of the interference pattern to the molecular geometry. © 2013 American Physical Society.

Challenging the cancer molecular stratification dogma: Intratumoral heterogeneity undermines consensus molecular subtypes and potential diagnostic value in colorectal cancer

Purpose:
A number of independent gene expression profiling studies have identified transcriptional subtypes in colorectal cancer (CRC) with potential diagnostic utility, culminating in publication of a CRC Consensus Molecular Subtype classification. The worst prognostic subtype has been defined by genes associated with stem-like biology. Recently, it has been shown that the majority of genes associated with this poor prognostic group are stromal-derived. We investigated the potential for tumor misclassification into multiple diagnostic subgroups based on tumoral region sampled.

Experimental Design:
We performed multi-region tissue RNA extraction/transcriptomic analysis using Colorectal Specific Arrays on invasive front, central tumor and lymph node regions selected from tissue samples from 25 CRC patients.

Results:
We identified a consensus 30 gene list which represents the intratumoral heterogeneity within a cohort of primary CRC tumors. Using a series of online datasets, we showed that this gene list displays prognostic potential (HR=2.914 (CI 0.9286-9.162) in stage II/III CRC patients, but in addition we demonstrated that these genes are stromal derived, challenging the assumption that poor prognosis tumors with stem-like biology have undergone a widespread Epithelial Mesenchymal Transition (EMT). Most importantly, we showed that patients can be simultaneously classified into multiple diagnostically relevant subgroups based purely on the tumoral region analysed.

Conclusions:
Gene expression profiles derived from the non-malignant stromal region can influence assignment of CRC transcriptional subtypes, questioning the current molecular classification dogma and highlighting the need to consider pathology sampling region and degree of stromal infiltration when employing transcription-based classifiers to underpin clinical decision-making in CRC.

Modelação molecular de associações entre aniões e receptores sintéticos

A aplicação de simulações de mecânica e dinâmica molecular ao estudo de sistemas supramoleculares tem adquirido, ao longo dos últimos anos, enorme relevância. A sua utilização não só tem levado a uma melhor compreensão dos mecanismos de formação desses mesmos sistemas, como também tem fornecido um meio para o desenvolvimento de novas arquitecturas supramoleculares. Nesta tese são descritos os trabalhos de mecânica e dinâmica molecular desenvolvidos no âmbito do estudo de associações supramoleculares entre aniões e receptores sintéticos do tipo [2]catenano, [2]rotaxano e pseudorotaxano. São ainda estudados complexos supramoleculares envolvendo receptores heteroditópicos do tipo calix[4]diquinona e pares iónicos formados por aniões halogeneto e catiões alcalinos e amónio. Os estudos aqui apresentados assentam essencialmente em duas vertentes: no estudo das propriedades dinâmicas em solução dos vários complexos supramoleculares considerados e no cálculo das energias livres de Gibbs de associação relativas dos vários iões aos receptores sintéticos. As metodologias utilizadas passaram por dinâmica molecular convencional e REMD (Replica Exchange Molecular Dynamics), para o estudo das propriedades em solução, e por cálculos de integração termodinâmica e MMPBSA (Molecular Mechanics – Poisson Boltzmann Surface Area), para a computação das energias livres de associação relativas. Os resultados obtidos, além de terem permitido uma visão mais detalhada dos mecanismos envolvidos no reconhecimento e associação dos vários receptores aos aniões e pares iónicos abordados, encontram-se, globalmente, de acordo com os análogos determinados experimentalmente, validando assim as metodologias empregadas. Em jeito de conclusão, investigou-se ainda a capacidade de um dos receptores heteroditópicos estudados para assistir favoravelmente na migração do par iónico KCl através da interface água-clorofórmio. Para tal, foram utilizadas simulações SMD (Steered Molecular Dynamics) para a computação do perfil de energia livre de Gibbs associada à migração do par iónico através da interface.

Estudo de receptores sintéticos no reconhecimento molecular de substratos aniónicos e iões metálicos

O trabalho descrito insere-se no âmbito da Química Supramolecular e consistiu no desenvolvimento de receptores artificiais, na forma protonada ou complexada, para o reconhecimento molecular de substratos aniónicos derivados de ácidos carboxílicos incluindo os herbicidas PMG2-, ATCP- e 2,4-D-. Foram investigadas duas séries de aniões, uma alifática (ox2-, mal2-, suc2-, glu2-, adip2-, cit3- e cta3-) e outra aromática (bzc-, naphc-, anthc-, pyrc-, ph2-, iph2-, tph2-, btc3-, dihyac2-, 4,4-dibzc2-, 3-nitrobzc- e 4-nitrobzc-). Foram sintetizados sete novos ligandos macrocíclicos simétricos constituídos por anéis aromáticos piridina ou fenantrolina ligados por cadeias de poliaminas saturadas. O comportamento ácido-base destes macrociclos foi investigado em solução aquosa e as constantes de protonação correspondentes determinadas por métodos potenciométricos e de RMN de 1H. As propriedades de complexação destes ligandos com os iões metálicos Ni2+, Cu2+, Zn2+, Cd2+ e Pb2+ foram também estudadas por métodos potenciométricos nas mesmas condições experimentais, tendo revelado que os macrociclos de dimensão média são capazes de acomodar um ou dois iões metálicos. O complexo dinuclear de Cu(II) derivado do macrociclo com dois grupos piridina foi utilizado como receptor de aniões carboxilato originando complexos ternários. Todos os complexos foram caracterizados em solução por espectroscopias de UV/vis/IVpróx e de RMN. As espécies paramagnéticas foram também caracterizadas por espectroscopia de RPE. A formação de espécies ternárias foi ainda investigada por espectrometria de massa ESI-MS e ESI-MS/MS. As estruturas cristalinas de alguns dos complexos foram determinadas por difracção de raios-X. As formas protonadas dos macrociclos foram utilizadas como receptores de uma grande variedade de aniões carboxilato. O reconhecimento molecular entre os receptores e os substratos aniónicos foi investigado em solução por métodos potenciométricos e de espectroscopia de RMN com determinação das constantes de associação. Os agregados supramoleculares foram caracterizados no estado sólido por difracção de raios-X. Finalmente as associações supramoleculares foram estudadas em solução por métodos de dinâmica molecular com determinação dos termos entrópicos e entálpicos das energias livres de ligação. Em resumo, nesta tese apresentam-se os resultados de estudos realizados com duas famílias de macrociclos: desde a síntese dos compostos, passando por estudos em solução e finalizando com simulação molecular. Este estudo sistemático através da conjugação de metodologias complementares permitiu caracterizar ao nível macroscópico e microscópico as associações moleculares.

Development of a Piggybac based direct reprogramming system for derivation of integration free induced pluripotent stem cells

Induced pluripotent stem cells (iPSc) have great potential for applications in regenerative medicine, disease modeling and basic research. Several methods have been developed for their derivation. The original method of Takahashi and Yamanaka involved the use of retroviral vectors which result in insertional mutagenesis, presence in the genome of potential oncogenes and effects of residual transgene expression on differentiation bias of each particular iPSc line. Other methods have been developed, using different viral vectors (adenovirus and Sendai virus), transient plasmid transfection, mRNA transduction, protein transduction and use of small molecules. However, these methods suffer from low efficiencies; can be extremely labor intensive, or both. An additional method makes use of the piggybac transposon, which has the advantage of inserting its payload into the host genome and being perfectly excised upon re-expression of the transposon transposase. Briefly, a policistronic cassette expressing Oct4, Sox2, Klf4 and C-Myc flanked by piggybac terminal repeats is delivered to the cells along with a plasmid transiently expressing piggybac transposase. Once reprogramming occurs, the cells are re-transfected with transposase and subclones free of tranposon integrations screened for. The procedure is therefore very labor intensive, requiring multiple manipulations and successive rounds of cloning and screening. The original method for reprogramming with the the PiggyBac transposon was created by Woltjen et al in 2009 (schematized here) and describes a process with which it is possible to obtain insert-free iPSc. Insert-free iPSc enables the establishment of better cellular models of iPS and adds a new level of security to the use of these cells in regenerative medicine. Due to the fact that it was based on several low efficiency steps, the overall efficiency of the method is very low (<1%). Moreover, the stochastic transfection, integration, excision and the inexistence of an active way of selection leaves this method in need of extensive characterization and screening of the final clones. In this work we aime to develop a non-integrative iPSc derivation system in which integration and excision of the transgenes can be controlled by simple media manipulations, avoiding labor intensive and potentially mutagenic procedures. To reach our goal we developed a two vector system which is simultaneously delivered to original population of fibroblasts. The first vector, Remo I, carries the reprogramming cassette and GFP under the regulation of a constitutive promoter (CAG). The second vector, Eneas, carries the piggybac transposase associated with an estrogen receptor fragment (ERT2), regulated in a TET-OFF fashion, and its equivalent reverse trans-activator associated with a positive-negative selection cassette under a constitutive promoter. We tested its functionality in HEK 293T cells. The protocol is divided in two the following steps: 1) Obtaining acceptable transfection efficiency into human fibroblasts. 2) Testing the functionality of the construct 3) Determining the ideal concentration of DOX for repressing mPB-ERT2 expression 4) Determining the ideal concentration of TM for transposition into the genome 5) Determining the ideal Windows of no DOX/TM pulse for transposition into the genome 6) 3, 4 and 5) for transposition out of the genome 7) Determination of the ideal concentration of GCV for negative selection We successfully demonstrated that ENEAS behaved as expected in terms of DOX regulation of the expression of mPB-ERT2. We also demonstrated that by delivering the plasmid into 293T HEK cells and manipulating the levels of DOX and TM in the medium, we could obtain puromycin resistant lines. The number of puromycin resistant colonies obtained was significantly higher when DOX as absent, suggesting that the colonies resulted from transposition events. Presence of TM added an extra layer of regulation, albeit weaker. Our PCR analysis, while not a clean as would be desired, suggested that transposition was indeed occurring, although a background level of random integration could not be ruled out. Finally, our attempt to determine whether we could use GVC to select clones that had successfully mobilized PB out of the genome was unsuccessful. Unexpectedly, 293T HEK cells that had been transfected with ENEAS and selected for puromycin resistance were insensitive to GCV.

Molecular structure and functional analysis of runx3 in zebrafish

Tese de doutoramento, Ciências Biomédicas, Universidade do Algarve, Departamento de Ciências Biomédicas e Medicina, 2014

Molecular determinants of the cellular internalization of crotamine-derived peptides

Tese de doutoramento, Ciências Biomédicas (Bioquímica Médica), Universidade de Lisboa, Faculdade de Medicina, 2014

Molecular mobility, composition and structure analysis in glycerol plasticised chitosan films

This study was developed with the purpose to investigate the effect of polysaccharide/plasticiser concentration on the microstructure and molecular dynamics of polymeric film systems, using transmission electron microscope imaging (TEM) and nuclear magnetic resonance (NMR) techniques. Experiments were carried out in chitosan/glycerol films prepared with solutions of different composition. The films obtained after drying and equilibration were characterised in terms of composition, thickness and water activity. Results show that glycerol quantities used in film forming solutions were responsible for films composition; while polymer/total plasticiser ratio in the solution determined the thickness (and thus structure) of the films. These results were confirmed by TEM. NMR allowed understanding the films molecular rearrangement. Two different behaviours for the two components analysed, water and glycerol were observed: the first is predominantly moving free in the matrix, while glycerol is mainly bounded to the chitosan chain. (C) 2013 Elsevier Ltd. All rights reserved.

Molecular cloning and restriction endonuclease analysis of bovine adenovirus type 3

Bovine adenovirus type 3 (BAV3) is a medium size DNA virus that causes respiratory and gastrointestinal disorders in cattle. The viral genome consists of a 35,000 base pair, linear, double-stranded DNA molecule with inverted terminal repeats and a 55 kilodalton protein covalently linked to each of the 5' ends. In this study, the viral genome was cloned in the form of subgenomic restriction fragments. Five EcoRI internal fragments spanning 3.4 to 89.0 % and two Xb a I internal fragments spanning 35.7 to 82.9 % of the viral genome were cloned into the EcoRI and Xbal sites of the bacterial vector pUC19. To generate overlap between cloned fragments, ten Hi n dIll internal fragments spanning 3.9 to 84.9 and 85.5 to 96% and two BAV3 BamHI internal fragments spanning 59.8 to 84.9% of the viral genome were cloned into the HindllI and BamHI sites of pUC19. The HindlII cloning strategy also resulted in six recombinant plasmids carrying two or more Hi ndII I fragments. These fragments provided valuable information on the linear orientation of the cloned fragments within the viral genome. Cloning of the terminal fragments required the removal of the residual peptides that remain attached to the 5' ends of the genome. This was accomplished by alkaline hydrolysis of the DNA-peptide bond. BamH I restriction fragments of the peptide-free DNA were cloned into pUC19 and resulted in two plasmids carrying the BAV3 Bam HI terminal fragments spanning 0 to 53.9% and 84.9 to 100% of the viral genome.