Electrochemical aptasensor for human osteopontin detection using a DNA aptamer selected by SELEX

A DNA aptamer with affinity and specificity for human osteopontin (OPN), a potential breast cancer biomarker, was selected using the SELEX process, considering its homology rate and the stability of its secondary structures. This aptamer exhibited a satisfactory affinity towards OPN, showing dissociation constants lower than 2.5 nM. It was further used to develop a simple, label-free electrochemical aptasensor against OPN. The aptasensor showed good sensitivity towards OPN in standard solutions, being the square wave voltammetry (SWV), compared to the cyclic voltammetry, the most sensitive technique with detection and quantification limits of 1.4 ± 0.4 nM and 4.2 ± 1.1 nM, respectively. It showed good reproducibility and acceptable selectivity, exhibiting low signal interferences from other proteins, as thrombin, with 2.610 times lower current signals-off than for OPN. The aptasensor also successfully detected OPN in spiked synthetic human plasma. Using SWV, detection and quantification limits (1.3 ± 0.1 and 3.9 ± 0.4 nM) within the OPN plasma levels reported for patients with breast cancer (0.44.5 nM) or with metastatic or recurrent breast cancer (0.98.4 nM) were found. Moreover, preliminary assays, using a sample of human plasma, showed that the aptasensor and the standard ELISA method quantified similar OPN levels (2.2 ± 0.7 and 1.7 ± 0.1 nM, respectively). Thus, our aptasensor coupled with SWV represents a promising alternative for the detection of relevant breast cancer biomarkers.The authors acknowledge the financial support from the Strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684), and from project BioTecNorte (project number NORTE-01-0145-FEDER-000004). This work was also financially supported by Project POCI-01–0145-FEDER-006984 – Associate Laboratory LSRE-LCM and by Project UID/QUI/00616/2013 – CQ-VR both funded by FEDER - Fundo Europeu de Desenvolvimento Regional through COMPETE2020 - Programa Operacional Competitividade e Internacionalização (POCI) – and by national funds through FCT - Fundação para a Ciência e a Tecnologia, Portugal. S. Meirinho also acknowledges the research grant provided by Project UID/EQU/50020/2013.info:eu-repo/semantics/publishedVersio

QTLs for oil yield components in an elite oil palm (Elaeis guineensis) cross

Increased modern farming of superior types of the oil palm, Elaeis guineensis Jacq., which has naturally efficient oil biosynthesis, has made it the world’s foremost edible oil crop. Breeding improvement is, however, circumscribed by time and costs associated with the tree’s long reproductive cycle, large size and 10–15 years of field testing. Marker-assisted breeding has considerable potential for improving this crop. Towards this, quantitative trait loci (QTL) linked to oil yield component traits were mapped in a high-yield population. In total, 164 QTLs associated with 21 oil yield component traits were discovered, with cumulative QTL effects increasing in tandem with the number of QTL markers and matching the QT+ alleles for each trait. The QTLs confirmed all traits to be polygenic, with many genes of individual small effects on independent loci, but epistatic interactions are not ruled out. Furthermore, several QTLs maybe pleiotropic as suggested by QTL clustering of inter-related traits on almost all linkage groups. Certain regions of the chromosomes seem richer in the genes affecting a particular yield component trait and likely encompass pleiotropic, epistatic and heterotic effects. A large proportion of the identified additive effects from QTLs may actually arise from genic interactions between loci. Comparisons with previous mapping studies show that most of the QTLs were for similar traits and shared similar marker intervals on the same linkage groups. Practical applications for such QTLs in marker-assisted breeding will require seeking them out in different genetic backgrounds and environments

Biosynthesis of CdS Quantum Dots Mediated by Volatile Sulfur Compounds Released by Antarctic Pseudomonas fragi

Previously we reported the biosynthesis of intracellular cadmium sulfide quantum dots (CdS QDs) at low temperatures by the Antarctic strain Pseudomonas fragi GC01. Here we studied the role of volatile sulfur compounds (VSCs) in the biosynthesis of CdS QDs by P. fragi GC01. The biosynthesis of nanoparticles was evaluated in the presence of sulfate, sulfite, thiosulfate, sulfide, cysteine and methionine as sole sulfur sources. Intracellular biosynthesis occurred with all sulfur sources tested. However, extracellular biosynthesis was observed only in cultures amended with cysteine (Cys) and methionine (Met). Extracellular nanoparticles were characterized by dynamic light scattering, absorption and emission spectra, energy dispersive X-ray, atomic force microscopy, transmission electron microscopy, X-ray diffraction and X-ray photoelectron spectroscopy. Purified QDs correspond to cubic nanocrystals of CdS with sizes between 2 and 16 nm. The analysis of VSCs revealed that P. fragi GC01 produced hydrogen sulfide (H2S), methanethiol (MeSH) and dimethyl sulfide (DMS) in the presence of sulfate, Met or Cys. Dimethyl disulfide (DMDS) was only detected in the presence of Met. Interestingly, MeSH was the main VSC produced in this condition. In addition, MeSH was the only VSC for which the concentration decreased in the presence of cadmium (Cd) of all the sulfur sources tested, suggesting that this gas interacts with Cd to form nanoparticles. The role of MeSH and DMS on Cds QDs biosynthesis was evaluated in two mutants of the Antarctic strain Pseudomonas deceptionensis M1T: megL- (unable to produce MeSH from Met) and mddA- (unable to generate DMS from MeSH). No biosynthesis of QDs was observed in the megL- strain, confirming the importance of MeSH in QD biosynthesis. In addition, the production of QDs in the mddA- strain was not affected, indicating that DMS is not a substrate for the biosynthesis of nanoparticles. Here, we confirm a link between MeSH production and CdS QDs biosynthesis when Met is used as sole sulfur source. This work represents the first report that directly associates the production of MeSH with the bacterial synthesis of QDs, thus revealing the importance of different VSCs in the biological generation of metal sulfide nanostructures

Insufficient OPC migration into demyelinated lesions is a cause of poor remyelination in MS and mouse models

Failure of remyelination of multiple sclerosis (MS) lesions contributes to neurodegeneration that correlates with chronic disability in patients. Currently, there are no available treatments to reduce neurodegeneration, but one therapeutic approach to fill this unmet need is to promote remyelination. As many demyelinated MS lesions contain plentiful oligodendrocyte precursor cells (OPCs), but no mature myelinating oligodendrocytes, research has previously concentrated on promoting OPC maturation. However, some MS lesions contain few OPCs, and therefore, remyelination failure may also be secondary to OPC recruitment failure. Here, in a series of MS samples, we determined how many lesions contained few OPCs, and correlated this to pathological subtype and expression of the chemotactic molecules Semaphorin (Sema) 3A and 3F. 37 % of MS lesions contained low numbers of OPCs, and these were mostly chronic active lesions, in which cells expressed Sema3A (chemorepellent). To test the hypothesis that differential Sema3 expression in demyelinated lesions alters OPC recruitment and the efficiency of subsequent remyelination, we used a focal myelinotoxic mouse model of demyelination. Adding recombinant (r)Sema3A (chemorepellent) to demyelinated lesions reduced OPC recruitment and remyelination, whereas the addition of rSema3F (chemoattractant), or use of transgenic mice with reduced Sema3A expression increased OPC recruitment and remyelination. We conclude that some MS lesions fail to remyelinate secondary to reduced OPC recruitment, and that chemotactic molecules are involved in the mechanism, providing a new group of drug targets to improve remyelination, with a specific target in the Sema3A receptor neuropilin-1. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00401-013-1112-y) contains supplementary material, which is available to authorized users

New Roles for Old Glue: Astrocyte Function in Synaptic Plasticity and Neurological Disorders

Previously believed to solely play a supportive role in the central nervous system, astrocytes are now considered active players in normal brain function. Evidence in recent decades extends their contributions beyond the classically held brain glue role; it’s now known that astrocytes act as a unique excitable component with functions extending into local network modulation, synaptic plasticity, and memory formation, and postinjury repair. In this review article, we highlight our growing understanding of astrocyte function and physiology, the increasing role of gliotransmitters in neuron-glia communication, and the role of astrocytes in modulating synaptic plasticity and cognitive function. Owing to the duality of both beneficial and deleterious roles attributed to astrocytes, we also discuss the implications of this new knowledge as it applies to neurological disorders including Alzheimer disease, epilepsy, and schizophrenia

Pengaturcaraan Web Hypertext Preprocessor (PHP)

Buku ini memperkenalkan kepada pembaca tentang asas pengaturcaraan web dalam Hypertext Preprocessor (PHP). Perbincangan awal dimula dengan memperkenalkan teknologi web dan perisian sumber terbuka. Kemudiannya, diikuti pengenalan kepada PHP yang merangkumi konsep, sejarah dan keperluan asas sebelum menulis atur cara PHP. Selain itu, terdapat beberapa bab yang menghuraikan pelbagai elemen bahasa pengaturcaraan. Antaranya struktur kawalan, fungsi, rentetan, dan tatasusunan. Bab akhir buku ini pula menerangkan tentang cara membangunkan aplikasi web menggunakan PHP, iaitu sistem penjanaan nombor dan variasi rawak. Buku ini juga turut menyediakan contoh atur cara dan latihan pengaturcaraan bagi memahir dan mengukuhkan lagi penguasaan pembaca dalam pengaturcaraan web. Buku ini sesuai sebagai bahan pengajaran dan pembelajaran oleh pensyarah dan pelajar, kepada pengaturcara yang ingin mempelajari bahasa penulisan skrip PHP dengan lebih mendalam, serta pembaca umum yang berminat untuk mengenali PHP dan ingin mempelajari asas pengaturcaraan web dengan mudah dan berkesan

In silico transcriptional regulation and functional analysis of dengue shock syndrome associated SNPs in PLCE1 and MICB genes

YesSingle nucleotide polymorphisms (SNPs) in PLCE1 and MICB genes increase risk for the development of dengue shock syndrome (DSS). We used Bioinformatics tools to predict alterations at the transcriptional and posttranslational levels driven by PLCE1 and MICB SNPs associated with DSS. Functional and phenotypic analysis conducted to determine deleterious SNPs and impact of amino acid substitution on the structure and function of proteins identified rs2274223 (H1619R) as deleterious to protein coding as it induces structural change in the C2 domain of PLCε, with the mutant residue more positively charged than the wild-type residue (RMSD score, 1.75 Å).Moreover, rs2274223 condenses the chromatinrepressing PLCε expression in DSS. Briefly, this study presents the impact of a single nucleotide transition at SNPs associated with DSS on differential protein binding patterns with PLCE1 and MICB genes and on protein structure modification and their possible role in the pathogenesis of DSS

Voltammetric aptasensors for protein disease biomarkers detection: a review

"Available online 24 May 2016"An electrochemical aptasensor is a compact analytical device where the bioreceptor (aptamer) is coupled to a transducer surface to convert a biological interaction into a measurable signal (current) that can be easily processed, recorded and displayed. Since the discovery of the Systematic Evolution of Ligands by Enrichment (SELEX) methodology, the selection of aptamers and their application as bioreceptors has become a promising tool in the design of electrochemical aptasensors. Aptamers present several advantages that highlight their usefulness as bioreceptors such as chemical stability, cost effectiveness and ease of modification towards detection and immobilization at different transducer surfaces. In this review, a special emphasis is given to the potential use of electrochemical aptasensors for the detection of protein disease biomarkers using voltammetry techniques. Methods for the immobilization of aptamers onto electrode surfaces are discussed, as well as different electrochemical strategies that can be used for the design of aptasensors.The authors acknowledge the financial support from the Strategic funding of UID/BIO/04469/2013 unit, from Project POCI-01-0145- FEDER-006984 – Associate Laboratory LSRE-LCM funded by FEDER funds through COMPETE2020 - Programa Operacional Competitividade e Internacionalização (POCI) – and by national funds through FCT - Fundação para a Ciência e a Tecnologia and project ref. RECI/BBB-EBI/ 0179/2012 (project number FCOMP-01-0124-FEDER-027462) and S. Meirinhos's doctoral grant (ref SFRH/BD/65021/2009) funded by Fundação para a Ciência e a Tecnologia

Improved identification of abdominal aortic aneurysm using the Kernelized Expectation Maximization algorithm

Abdominal aortic aneurysm (AAA) monitoring and risk of rupture is currently assumed to be correlated with the aneurysm diameter. Aneurysm growth, however, has been demonstrated to be unpredictable. Using PET to measure uptake of [18F]-NaF in calcified lesions of the abdominal aorta has been shown to be useful for identifying AAA and to predict its growth. The PET low spatial resolution, however, can affect the accuracy of the diagnosis. Advanced edge-preserving reconstruction algorithms can overcome this issue. The kernel method has been demonstrated to provide noise suppression while retaining emission and edge information. Nevertheless, these findings were obtained using simulations, phantoms and a limited amount of patient data. In this study, the authors aim to investigate the usefulness of the anatomically guided kernelized expectation maximization (KEM) and the hybrid KEM (HKEM) methods and to judge the statistical significance of the related improvements. Sixty-one datasets of patients with AAA and 11 from control patients were reconstructed with ordered subsets expectation maximization (OSEM), HKEM and KEM and the analysis was carried out using the target-to-blood-pool ratio, and a series of statistical tests. The results show that all algorithms have similar diagnostic power, but HKEM and KEM can significantly recover uptake of lesions and improve the accuracy of the diagnosis by up to 22% compared to OSEM. The same improvements are likely to be obtained in clinical applications based on the quantification of small lesions, like for example cancer