Conical refraction in generalized biaxial media: A geometric algebra approach

It is well-know that conical refraction occurs for electric anisotropic biaxial crystals when the wave vector has the direction of the medium optic axes. In this paper, we show that conical refraction occurs in an analogous away for a more general type of biaxial media that have simultaneously electric and magnetic anisotropies. Furthermore, the new coordinate-free approach based on geometric algebra, developed by the authors in previous papers to address anisotropy, is shown to shed new light on this classic topic of optics that is conical refraction.info:eu-repo/semantics/acceptedVersio

Histological and mutational profile of diffuse gastric cancer: current knowledge and future challenges

Gastric cancer (GC) pathogenesis is complex and heterogeneous, reflecting morphological, molecular and genetic diversity. Diffuse gastric cancer (DGC) and intestinal gastric cancer (IGC) are the major histological types. GC may be sporadic or hereditary; sporadic GC is related to environmental and genetic low-risk factors and hereditary GC is caused by inherited high-risk mutations, so far identified only for the diffuse histotype. DGC phenotypic heterogeneity challenges the current understanding of molecular mechanisms underlying carcinogenesis. The definition of a DGC-specific mutational profile remains controversial, possibly reflecting the heterogeneity of DGC-related histological subtypes [signet-ring cell carcinoma (SRCC) and poorly cohesive carcinoma not otherwise specified (PCC-NOS)]. Indeed, DGC and DGC-related subtypes may present specific mutational profiles underlying the particularly aggressive behaviour and dismal prognosis of DGC vs IGC and PCC-NOS vs SRCC. In this systematic review, we revised the histological presentations, molecular classifications and approved therapies for gastric cancer, with a focus on DGC. We then analysed results from the most relevant studies, reporting mutational analysis data specifying mutational frequencies, and their relationship with DGC and IGC histological types, and with specific DGC subtypes (SRCC and PCC-NOS). We aimed at identifying histology-associated mutational profiles with an emphasis in DGC and its subtypes (DGC vs IGC; sporadic vs hereditary DGC; and SRCC vs PCC-NOS). We further used these mutational profiles to identify the most commonly affected molecular pathways and biological functions, and explored the clinical trials directed specifically to patients with DGC. This systematic analysis is expected to expose a DGC-specific molecular profile and shed light into potential targets for therapeutic intervention, which are currently missing.The authors acknowledge the support of the National Infrastructure ‘GenomePT’ – National Laboratory for Genome Sequencing and Analysis (POCI-01-0145-FEDER-022184). J.G-P acknowledges the support of Faculty of Medicine from University of Porto, specifically by the Doctoral Programme in Biomedicine and the Solve-RD Project (H2020-SC1-2017-Single-Stage-RTD) for his PhD fellowship. R.B-M. acknowledges the support of Institute of Biomedical Sciences Abel Salazar from University of Porto, specifically by the Doctoral Programme BiotechHealth and the FCT – Fundação para a Ciência e a Tecnologia for her PhD fellowship (ref. SFRH/BD/145132/2019). This research and its authors were funded by FEDER – Fundo Europeu de Desenvolvimento Regional funds through the COMPETE 2020 – Operacional Programme for Competitiveness and Internationalization (POCI), Portugal 2020, and by Portuguese funds through FCT – Fundação para a Ciência e a Tecnologia/Ministério da Ciência, Tecnologia e Inovação in the framework of the project ‘Institute for Research and Innovation in Health Sciences’ (POCI-01-0145-FEDER-007274). This work was also financed by the projects NORTE-01-0145-FEDER-000003 (DOCnet) and NORTE-01-0145-FEDER-000029 (CANCER) – supported by Norte Portugal Regional Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF) – project POCI-01-0145-FEDER-016390 (CancelStem) and PTDC/BTM-TEC/30164/2017 (3DChroMe), funded by ERDF, POCI and FCT

Control and comparison of the antioxidant capacity of beers

The purpose of the present work is to determine the antioxidant capacity (AC) of 27 commercial beers. The AC indicates the degree of protection of a certain organism against oxidative damage provoked by reactive oxygen and nitrogen species. Assays were carried out by the following methods: (i) total radical trapping antioxidant parameter (TRAP); (ii) trolox equivalent antioxidant capacity (TEAC); (iii) trolox equivalent antioxidant capacity (DPPH); (iv) ferric-ion reducing antioxidant parameter (FRAP); (v) cupric reducing antioxidant capacity (CUPRAC); (vi) oxygen radical absorbance capacity (ORAC). Ascorbic acid (AA), gallic acid (GA) and trolox (TR) were used as standards. All beers showed antioxidant power, but a wide range of ACs was observed. The effect of several factors upon these differences was studied. Statistical differences were found between ACs of beers of different colours. ORAC method provided always higher experimental ACs, of significant statistical differences to other assays

Parâmetros reprodutivos de cabras mestiças Anglo-nubiana x Saanen infectadas e não infectadas com o vírus da artrite-encefalite caprina.

Objetivou-se com esse estudo avaliar os parâmetros reprodutivos de cabras mestiças Anglo-Nubiana x Saanen infectadas e não infectadas com o vírus da Artrite-Encefalite Caprina (CAEV). Foram utilizadas 100 matrizes mestiças Anglo-Nubiana x Saanen, sendo 38 soro-positivas e 62 soro-negativas para CAEV e quatro machos de mesmo grupo genético e soro-negativo, diagnosticados pelo IDGA e WB.Os parâmetros avaliados foram: taxa de gestação (Tg); duração da gestação (DG); fertilidade (Fe); fertilidade ao parto (FP); serviços por concepção (SC); prolificidade (Pl); taxa de gemelaridade (TG); peso vivo (PV) dos cabritos ao nascimento e a desmama; sexo das crias; e número de aborto e de natimorto. Não foi observada diferença estatística significativa entre as positivas e as negativas quando os seguintes parâmetros foram comparados: DG, PV das crias ao nascer e a desmama, Fe, sexo das crias e Pl. Quanto ao tipo de parto verificou-se que o as cabras positivas apresentaram freqüência de parto duplo significativamente mais elevada. Não foi observadas ocorrência de partos distórcicos nem retenção de placenta. Com base nesses resultados conclui-se que o vírus da Artrite-Encefalite Caprina não afetou os parâmetros reprodutivos das cabras infectadas, nas condições experimentais deste estudo

Rizobactérias multifuncionais atuam também no controle da mosca-branca.

Este trabalho teve como objetivo testar a eficiência das bactérias benéficas Pseudomonas fluorescens e Burkholderia pyrrocina no controle de ninfas de mosca-branca

Comparação entre protocolos para extração de DNA de cupuaçu (Theobroma grandiflorum).

O cupuaçu é uma espécie nativa na região Amazônica que se encontra em estágio inicial de domesticação, apresentando ampla variabilidade genética para as diversas características. Contudo, poucos são os estudos que envolvem avaliações moleculares nesta espécie. A otimização de um protocolo para extração de DNA é pré-requisito básico para etapas subseqüentes da análise molecular. Com o objetivo realizar amplificação e melhoria da qualidade e quantidade de DNA obtido dessa espécie, o presente trabalho compara protocolos de extração de DNA do cupuaçu. Os protocolos utilizados foram o de Doyle e Doyle (1990), modificado por FIGUEIRA et al. (1997) com a utilização de proteinase K, e o Doyle e Doyle (1990), modificado por FERREIRA GRA TTAP AGLIA (1998) estabelecido para várias espécies e já utilizado no setor de Biologia Molecular do Laboratório de Morfogênese e Biologia Molecular da EMBRAPA-Acre, em ambos os protocolos também foram feitos os testes com beads de cerâmica e de tungstênio. Os resultados obtidos na quantificação das amostras mostraram que o emprego da proteinase K produziu um DNA mais limpo. Porém, quando se compara esta metodologia com a que não utilizou a proteinase K, verificou-se uma menor quantidade de DNA extraído. A utilização das beads de cerâmica proporcionou um aumento significativo na quantidade de DNA, no entanto, não se obteve boa qualidade, apresentando DNA fragmentado. Em meio a esses resultados pode-se constatar que o uso das beads de tungstênio e sem o emprego da proteinase K possibilitaram a extração de um DNA com melhor qualidade e quantidade. Cupuassu is a native species in the Amazon region that finds in initial stage of domesticated, that has ample genetic variability for the diverse characteristics. However, few studies that involve molecular evaluations in this species. The optimization of a protocol of DNA extraction is basic prerequisite for subsequent steps the molecular analysis. With the objective J of realization the amplification and improvement of the quality and amount in DNA of this species, the present work compares two protocols of DNA extraction. The protocols of extraction ofDNA that utilized were Doyle and Doyle (1990), modified for FIGUEIRA et al. (1997) with the use of proteinase K, and the Doyle and Doyle (1990), modified for FERRERIA and GRA TTAP AGLIA (1998) established for some species and used in the sector of Molecular Biology in the Laboratory of Morphogenesis and Molecular Biology of EMBRAPA-Acre, in both of protocols also were made the tests with ceramics and tungsten beads. The results obtained in quantification of samples had shown that the used of proteinase K produced a cleaner DNA. However, when this methodology is compared with that did not use proteinase K, was verified a few amount of extracted DNA. The use of beads of ceramics provided a significant increase in the DNA amount, however, did not get good quality, shown DNA fragmented. These results evidenced that the use of tungsten beads and no utilization of proteinase K makes possible the better quality and amount in DNA extration

Genetic and epigenetic alterations of cdh1 regulatory regions in hereditary and sporadic gastric cancer

E-cadherin is a key player in gastric cancer (GC) and germline alterations of CDH1, its encoding gene, are responsible for Hereditary Diffuse Gastric Cancer (HDGC) syndrome. This study aimed at elucidating the role of genetic variants and DNA methylation of CDH1 promoter and enhancers in the regulation of gene expression. For this purpose, we analyzed genetic variants of the CDH1 gene through Next-Generation Sequencing (NGS) in a series of GC cell lines (NCI-N87, KATO-III, SNU-1, SNU-5, GK2, AKG, KKP) and the corresponding CDH1 expression levels. By bisulfite genomic sequencing, we analyzed the methylation status of CDH1 regulatory regions in 8 GC cell lines, in a series of 13 sporadic GC tissues and in a group of 20 HDGC CDH1-negative patients and 6 healthy controls. The NGS analysis on CDH1 coding and regulatory regions detected genetic alterations in 3 out of 5 GC cell lines lacking functional E-cadherin. CDH1 regulatory regions showed different methylation patterns in patients and controls, GC cell lines and GC tissues, expressing different E-cadherin levels. Our results showed that alterations in terms of genetic variants and DNA methylation patterns of both promoter and enhancers are associated with CDH1 expression levels and have a role in its regulation.This research and its authors were funded by IRCCS IRST (G.T., C.M., R.D. V.A., M.R., F.R., M.C., S.P., G.M., D.C., P.U.) and by FEDER-Fundo Europeu de Desenvolvimento Regional funds through the COMPETE 2020–Operacional Programme for Competitiveness and Internationalization (POCI), Portugal 2020, and by Portuguese funds through FCT–Fundação para a Ciência e a Tecnologia/Ministério da Ciência, Tecnologia e Inovação in the framework of the project “Institute for Research and Innovation in Health Sciences” (POCI-01-0145-FEDER-007274) (C.S.J., R.B.-M., A.A., C.O.). This work was also financed by the project NORTE-01-0145-FEDER-000029 (CANCER)-supported by Norte Portugal Regional Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF)–project POCI-01-0145-FEDER-016390 (CancelStem) and PTDC/BTM-TEC/30164/2017 (3DChroMe), funded by ERDF, POCI and FCT

The cdh1 c.1901c>t variant: A founder variant in the portuguese population with severe impact in mrna splicing

Hereditary diffuse gastric cancer (HDGC) caused by CDH1 variants predisposes to early-onset diffuse gastric (DGC) and lobular breast cancer (LBC). In Northern Portugal, the unusually high number of HDGC cases in unrelated families carrying the c.1901C>T variant (formerly known as p.A634V) suggested this as a CDH1-founder variant. We aimed to demonstrate that c.1901C>T is a bona fide truncating variant inducing cryptic splicing, to calculate the timing of a potential founder effect, and to characterize tumour spectrum and age of onset in carrying families. The impact in splicing was proven by using carriers’ RNA for PCR-cloning sequencing and allelic expression imbalance analysis with SNaPshot. Carriers and noncarriers were haplotyped for 12 polymorphic markers, and the decay of haplotype sharing (DHS) method was used to estimate the time to the most common ancestor of c.1901C>T. Clinical information from 58 carriers was collected and analysed. We validated the cryptic splice site within CDH1-exon 12, which was preferred over the canonical one in 100% of sequenced clones. Cryptic splicing induced an out-of-frame 37bp deletion in exon 12, premature truncation (p.Ala634ProfsTer7), and consequently RNA mediated decay. The haplotypes carrying the c.1901C>T variant were found to share a common ancestral estimated at 490 years (95% Confidence Interval 445–10,900). Among 58 carriers (27 males (M)–31 females (F); 13–83 years), DGC occurred in 11 (18.9%; 4M–7F; average age 33 ± 12) and LBC in 6 females (19.4%; average age 50 ± 8). Herein, we demonstrated that the c.1901C>T variant is a loss-of-function splice-site variant that underlies the first CDH1-founder effect in Portugal. Knowledge on this founder effect will drive genetic testing of this specific variant in HDGC families in this geographical region and allow intrafamilial penetrance analysis and better estimation of variant-associated tumour risks, disease age of onset, and spectrum.This research and its authors were funded by FEDER—Fundo Europeu de Desenvolvi-mento Regional funds through the COMPETE 2020—Operational Programme for Competitiveness and Internationalization (POCI), Portugal 2020, and by Portuguese funds through FCT—Fundação para a Ciência e a Tecnologia/Ministério da Ciência, Tecnologia e Inovação in the framework of the project “Institute for Research and Innovation in Health Sciences” (POCI-01-0145-FEDER-007274) and LEGOH (PTDC/BTM-TEC/6706/2020). This work was also financed by the projects NORTE-01-0145-FEDER-000003 (DOCnet)—supported by Norte Portugal Regional Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF)—project POCI-01-0145-FEDER-016390 (CancelStem) and PTDC/BTM-TEC/30164/2017 (3DChroMe), funded by ERDF, POCI, and FCT

PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries

BACKGROUND: Biological function is greatly dependent on the interactions of proteins with other proteins and genes. Abstracts from the biomedical literature stored in the NCBI's PubMed database can be used for the derivation of interactions between genes and proteins by identifying the co-occurrences of their terms. Often, the amount of interactions obtained through such an approach is large and may mix processes occurring in different contexts. Current tools do not allow studying these data with a focus on concepts of relevance to a user, for example, interactions related to a disease or to a biological mechanism such as protein aggregation. RESULTS: To help the concept-oriented exploration of such data we developed PESCADOR, a web tool that extracts a network of interactions from a set of PubMed abstracts given by a user, and allows filtering the interaction network according to user-defined concepts. We illustrate its use in exploring protein aggregation in neurodegenerative disease and in the expansion of pathways associated to colon cancer. CONCLUSIONS: PESCADOR is a platform independent web resource available at: http://cbdm.mdc-berlin.de/tools/pescador