Lyophilization of Molecular Biology Reactions: A Review.

Molecular biology is a widely used and widespread technique in research and as a laboratory diagnostic tool, aiming to investigate targets of interest from the obtainment, identification, and analysis of genetic material. In this context, methods, such as Polymerase Chain Reaction (PCR), Reverse Transcription Polymerase Chain Reaction (RT-PCR), real-time PCR, loopmediated isothermal amplification (LAMP), and loop-mediated isothermal amplification with reverse transcription (RT-LAMP), can be cited. Such methods use enzymes, buffers, and thermosensitive reagents, which require specific storage conditions. In an attempt to solve this problem, the lyophilization procedure (dehydration process by sublimation) can be applied, aiming to preserve and prolong the useful life of the reaction components in cases of temperature variation. In this review, we present a synthesis of the lyophilization process, describing the events of each step of the procedure and providing general information about the technique. Moreover, we selected lyophilization protocols found in the literature, paying attention to the conditions chosen by the authors for each step of the procedure, and structured the main data in tables, facilitating access to information for researchers who need material to produce new functional protocols.

Biologia molecular de leveduras e sua aplicação biotecnológica para estudo de mecanismos celulares do câncer e seu tratamento / Molecular biology of yeast and its biotechnological application to study the cellular mechanisms of cancer and its treatment

A levedura Saccharomyces cerevisiae é o eucarioto mais bem caracterizado quanto às vias metabólicas, celulares e funções de genes. Calcula-se que dos 6.000 genes codificadores de proteínas, pelo menos 3.000 tenham homologia com genes humanos. Além disso, mesmo quando não há homologia direta, os mecanismos moleculares são conservados e em ensaios de complementação de função é possível caracterizar funções análogas em humanos. Leveduras apresentam além de mecanismos conservados, diversas semelhanças metabólicas com células tumorais; talvez a mais marcante delas seja a repressão catabólica por glicose. Esse fenômeno causa uma superativação da via glicolítica e inibição da cadeia respiratória, o que lembra muito o efeito Warburg apresentado pelas células tumorais. Esse comportamento metabólico tem relação estreita com a homeostase redox celular. Estes fatores mostram o quanto à caracterização dessas células fúngicas pode ser aplicada ao entendimento e tratamento do câncer. Mesmo assim, 20 anos após o término do sequenciamento do genoma de S. cerevisiae, mais de 1.000 genes continuam anotados como não caracterizados. Além disso, as leveduras têm papel fundamental na produção biotecnológica de insumos farmacêuticos. Nesse texto sistematizado relato as contribuições dos meus estudos, juntamente com os resultados do meu grupo de pesquisa, usando a biologia molecular das leveduras, para responder questões aplicadas à compreensão de funções celulares (com destaque à resposta antioxidante), mecanismos moleculares de resposta aos antitumorais e produção de biofármacos. Além de modelo celular, as leveduras representam excelentes plataformas para expressão heteróloga de proteínas de interesse Biotecnológico-Farmacêutico

The yeast Saccharomyces cerevisiae is the most well characterized eukaryote for metabolic, cellular and gene functions. It is estimated that of the 6,000 protein-encoding genes, at least 3,000 have homology to human genes. Moreover, even when there is no direct homology, the molecular mechanisms are conserved and through function complementation assays it is possible to characterize analogous functions in humans. Yeasts present, in addition to conserved mechanisms, diverse metabolic similarities with tumor cells; perhaps the most remarkable of them is the catabolic repression by glucose. This phenomenon causes an over activation of the glycolytic pathway and inhibition of the respiratory chain, which strongly resembles the Warburg effect presented by tumor cells. This metabolic behavior is closely related to cellular redox homeostasis. These factors show how much the characterization of these fungal cells can be applied to the understanding and treatment of cancer. Even so, 20 years after the end of the sequencing of the S. cerevisiae genome, more than 1,000 genes remain annotated as uncharacterized. In addition, yeasts play a key role in the biotechnological production of pharmaceutical inputs. In this systematized text I show the contributions of my studies, together with the results of my research group, using molecular biology of yeast to answer questions applied to understanding cellular functions (with emphasis on the antioxidant response), molecular response mechanisms to antitumor drugs and biopharmaceutical production. In addition to cellular model, yeasts represent excellent platforms for the heterologous expression of proteins of Biotechnological-Pharmaceutical interes

Identifying human disease genes: advances in molecular genetics and computational approaches.

The human genome project is one of the significant achievements that have provided detailed insight into our genetic legacy. During the last two decades, biomedical investigations have gathered a considerable body of evidence by detecting more than 2000 disease genes. Despite the imperative advances in the genetic understanding of various diseases, the pathogenesis of many others remains obscure. With recent advances, the laborious methodologies used to identify DNA variations are replaced by direct sequencing of genomic DNA to detect genetic changes. The ability to perform such studies depends equally on the development of high-throughput and economical genotyping methods. Currently, basically for every disease whose origen is still unknown, genetic approaches are available which could be pedigree-dependent or -independent with the capacity to elucidate fundamental disease mechanisms. Computer algorithms and programs for linkage analysis have formed the foundation for many disease gene detection projects, similarly databases of clinical findings have been widely used to support diagnostic decisions in dysmorphology and general human disease. For every disease type, genome sequence variations, particularly single nucleotide polymorphisms are mapped by comparing the genetic makeup of case and control groups. Methods that predict the effects of polymorphisms on protein stability are useful for the identification of possible disease associations, whereas structural effects can be assessed using methods to predict stability changes in proteins using sequence and/or structural information.

Um novo gene de Pseudomonas aeruginosa envolvido em percepção de quórum / A novel gene involved in Pseudomonas aeruginosa quorum sensing

Pseudomonas aeruginosa é uma gamaproteobactéria com capacidade de colonizar diversos tipos de ambiente e infectar hospedeiros filogeneticamente distintos. Em humanos, comporta-se como um patógeno oportunista,estando frequentemente relacionada à infecções em indivíduos imunocomprometidos e indivíduos portadores de fibrose cística. Um mecanismo importante para a versatilidade de P. aeruginosa é o sistema de percepção de quórum (QS), onde a bactéria pode vincular expressão gênica à densidade populacional e às características do ambiente. Atualmente, sabe-se que muitos outros reguladores estão interligados com QS, entre eles, a proteína reguladora RsmA e os pequenos RNAs RsmZ e RsmY. Além disso, diversos fatores importantes para a patogenicidade da bactéria são reguladas por QS. Em P. aeruginosa PA14, um fator importante para a patogenicidade em diversos hospedeiros é a proteína KerV, cujo envolvimento com QS foi descrito pela primeira vez neste trabalho. A linhagem D12, que possui uma deleção no gene kerV, mostrou alterações em fenótipos regulados por QS, como a maior produção de piocianina, composto que contribui para virulência e persistência das infecções causada por P. aeruginosa. Por ser facilmente detectável e pela regulação de sua síntese não ter sido completamente explorada em PA14, a expressão dos genes responsáveis pela produção de piocianina é um interessante repórter na investigação do possível envolvimento de KerV com QS. Além de piocianina, D12 apresenta níveis reduzidos de ramnolipídeos. Esses fenótipos somados se assemelham aos fenótipos da mutação de rsmA, sugerindo o envolvimento de KerV com os sistemas QS e Gac-Rsm direta ou indiretamente. Neste trabalho, mostramos que KerV exerce um efeito negativo na regulação dos operons phz1 e phz2, responsáveis pela síntese de piocianina, alterando a expressão desses genes. KerV exerce também um efeito positivo na expressão da proteína RsmA, responsável pela repressão de diversos genes alvos, onde RsmA se liga ao sítio de ligação ao ribossomo no mRNA, impedindo a tradução. Ensaios de gel shift mostraram que a ligação direta de RsmA na sequência líder de phzA1 e phzA2 ocorre, elucidando a maneira pela qual KerV está envolvido na regulação da expressão dos operons phz em P. aeruginosa PA14. Mostramos também que phz2 é ativo e contribui para a síntese de piocianina, pois na ausência de phz1, os níveis do pigmento são maiores do que aqueles detectados em PA14. Isso sugere uma maior expressão de phz2 e uma regulação diferencial dos operons de acordo com as condições ambientais como possível estratégia para manter os níveis desse composto. Uma evidência dessa regulação diferencial é vista no mutante lasR. Na fase inicial de crescimento, esse mutante não produz piocianina, porém quando exposto a tempos mais longos de cultivo, a produção de piocianina é maior quando comparada a PA14. Isso é reflexo da ativação da expressão de phz1 no mutante lasR em fase estacionária tardia, enquanto phz2 permanece não expresso. Isso indica que phz2 é dependente de LasR, ainda que indiretamente. Já phz1, embora tenha sua expressão influenciada por LasR no estágio inicial de crescimento, na fase estacionária é regulado por outros fatores independentes de las

Pseudomonas aeruginosa is a gammaproteobacterium that colonizes several environments and infects phylogenetically distinct hosts. It behaves as an opportunistic pathogen in humans, often related to infection in immunocompromised individuals and cystic fibrosis patients. An important mechanism for P. aeruginosa versatility is the quorum sensing (QS) network, that allows bacteria to link gene expression to population density and environmental traits. Several additional regulators are interconnected with QS, as the regulatory mRNA binding protein RsmA and the non-coding small RNAs RsmZ and RsmY. Futhermore, key factors for pathogenicity are QS-regulated. In P. aeruginosa PA14, an important pathogenicity-related factor is the KerV protein, described for the first time here as involved in QS. D12 strain, that harbor a deletion in the kerV gene, shows alterations in QS-regulated phenotypes, such as high production of pyocyanin, a compound that contributes to virulence and persistence of P. aeruginosa infections. As the production of pyocyanin is easily detected and all mechanisms involved in its synthesis regulation are not fully described, the expression of genes responsible for production of this pigment is a good reporter to investigate KerV involvement in the QS network. Additionally, D12 also shows lower levels of rhamnolipids, another QS-regulated trait. Taken together, these phenotypes resemble the effects of a rsmA mutation, suggesting KerV involvement with QS and Gac-Rsm systems. In this work, we propose that KerV exerts a negative effect in the regulation of phz1 and phz2 operons, responsible for pyocyanin synthesis, by alterating the expression of these genes. KerV also has a positive effect on rsmA expression, responsible for the repression of several genes by blocking the ribosome binding site preventing the translation. Gel shift assays showed that RsmA binds directly in the leader sequence of phzA1 and phzA2, elucidating the manner in which KerV is involved in the regulation of phz operons expression in P. aeruginosa PA14. We also demonstrate that phz2 is actively expressed and contributes to pyocyanin production in PA14, since in the phz1 mutant the levels of pyocyanin are even higher than in the wild type strain. This suggests a phz2 higher expression and a differential regulation of phz operons according to environmental changes as a mechanism to maintain the levels of pyocyanin synthesis. An evidence for this regulation is the synthesis of pyocyanin by the lasR mutant, which does not make pyocyanin at early growth stages. However, at late stationary phase, pyocyanin production is even higher than in the wild-type strain, reflecting the LasR-independent regulation of phz1 expression, while phz2 operon remains silent

A novel and highly efficient method for genetic transformation of fungi employing shock waves.

Genetic transformation of filamentous fungi is an essential tool in many areas such as biotechnology, medicine, phytopathology and genetics. However, available protocols to transform fungi are inefficient, laborious and have low reproducibility. We report the use of underwater shock waves as a novel method to transform filamentous fungi. An experimental piezoelectric shock wave generator was designed to expose fungal conidia to heterologous DNA. The device was successfully tested in Aspergillus niger, Fusarium oxysporum, Trichoderma reesei and Phanerochaete chrysosporium. The transformation frequency per number of conidia was between two and four orders of magnitude higher in comparison to previously published methods. For example, the frequency of transformation in A. niger was improved up to 5400-fold as compared with Agrobacterium protocols. Transformation was verified by expression of the green fluorescent protein, PCR and Southern blot. Our method offers new possibilities for fast, easy and efficient genetic manipulation of diverse fungal species.

Robust and inexpensive SSR markers analyses using LI-COR DNA analyzer.

Plant genotyping is performed for different purposes which dictate to a large extent the type of molecular makers and platform to be used. The level of throughput, the technical capacity of the genotyping facility, and the availability of reagents are also part of the decision towards a particular genotyping system. SSR markers are quite popular markers because they are easily implementable in standard laboratories, can be used on manual gel electrophoresis, require inexpensive reagents, are mostly randomly distributed in the genome, can be located within genes, have a good discriminatory power, and are codominant with Mendelian inheritance. These features have made SSR the marker of choice for low-resolution genetic mapping and genetic diversity studies including genetic identity verification. The LI-COR platform offers both qualitative and quantitative improvements over the conventional assays based on agarose and polyacrylamide (PAGE) gels with DNA stained with ethidium bromide and silver or radiolabeled. A fast run coupled with an automated detection system using fluorophores makes possible to achieve routinely in our genotyping facility five runs per day using the same gel up to four times which results in 48 genotypes genotyped with ten SSR markers (two per gel electrophoresis using low-cost M13-tailed primers). This gel-base, low cost per sample and equipment, and medium throughput makes the LI-COR platform -particularly useful for laboratories with intermediate skills and expectations in molecular genetics.

Métodos de avaliação da morfologia e função espermática: momento atual e desafios futuros / Methods of the assessment of morphology and function of sperm: actual moment and future challenges

Com o propósito de obter resultados que demonstrem maior repetibilidade na avaliação da morfologia tanto quanto na função espermática, diversas técnicas laboratoriais tem sido desenvolvidas. Surgiram sistemas que utilizam a análise computadorizada de imagens, métodos de “coloração” empregando corantes fluorescentes (sondas fluorescentes) em microscopia de epifluorescência ou citometria de fluxo, que aumentaram a possibilidade de uma análise mais criteriosa da integridade estrutural dos espermatozóides. Os autores descrevem experiências, por mais de uma década, com a utilização destas biotécnicas, fazendo uma análise crítica, bem como apontando os desafios futuros, inclusive na área de biologia molecular espermática.

In order to obtain results showing greater repeatability in morphology and sperm function assessment, several laboratorial techniques have been developed continuously. Systems that utilize computerized image analysis, staining methods using fluorescent dies (fluorescent probes) in epifluorescence microscopy or flow cytometry, that allowed a more judicious evaluation of sperm structure integrity arose. Authors describe experiences, over a decade, with the use of these biotechiques, critically analyzing and pointing out future challenges, including the field of sperm molecular biology.

Métodos de avaliação da morfologia e função espermática: momento atual e desafios futuros / Methods of the assessment of morphology and function of sperm: actual moment and future challenges

Com o propósito de obter resultados que demonstrem maior repetibilidade na avaliação da morfologia tanto quanto na função espermática, diversas técnicas laboratoriais tem sido desenvolvidas. Surgiram sistemas que utilizam a análise computadorizada de imagens, métodos de “coloração” empregando corantes fluorescentes (sondas fluorescentes) em microscopia de epifluorescência ou citometria de fluxo, que aumentaram a possibilidade de uma análise mais criteriosa da integridade estrutural dos espermatozóides. Os autores descrevem experiências, por mais de uma década, com a utilização destas biotécnicas, fazendo uma análise crítica, bem como apontando os desafios futuros, inclusive na área de biologia molecular espermática.(AU)

In order to obtain results showing greater repeatability in morphology and sperm function assessment, several laboratorial techniques have been developed continuously. Systems that utilize computerized image analysis, staining methods using fluorescent dies (fluorescent probes) in epifluorescence microscopy or flow cytometry, that allowed a more judicious evaluation of sperm structure integrity arose. Authors describe experiences, over a decade, with the use of these biotechiques, critically analyzing and pointing out future challenges, including the field of sperm molecular biology.(AU)

Biotecnologia translacional: hemopressina e outros peptídeos intracelulares / Translational biotechnology: hemopressin and other intracellular peptides

A biotecnologia é uma prática antiga, sendo utilizada desde o antigo Egito para a produção de pão e cerveja. No mundo contemporâneo, a biotecnologia tem sido utilizada de diversas formas, incluindo o tratamento de doenças. No universo acadêmico, a biotecnologia tem permitido um avanço rápido do conhecimento. Neste artigo, fazemos um breve resumo sobre o que é biotecnologia, sua relação com o processo de inovação e produção de biofármacos. No universo acadêmico, a biotecnologia tem contribuído de forma decisiva para a descoberta de novas moléculas bioativas, como no caso da hemopressina e de diversos outros peptídeos intracelulares.

Biotechnology has been used since ancient Egypt for the production of bread and beer. In the modern world, biotechnology has been used in several ways, including for the treatment of diseases. In academia, biotechnology has allowed a rapid advance of knowledge. In this article, we make a brief summary of what is biotechnology and its relation to the process of innovation and production of biopharmaceuticals. In academia, biotechnology has contributed decisively to the discovery of new bioactive molecules, such as in hemopressin and several other intracellular peptides.