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1.
J Fungi (Basel) ; 10(6)2024 Jun 06.
Article in English | MEDLINE | ID: mdl-38921397

ABSTRACT

Komagataella phaffii (formerly Pichia pastoris) is a methylotrophic yeast widely used in laboratories around the world to produce recombinant proteins. Given its advantageous features, it has also gained much interest in the context of modern biotechnology. In this review, we present the utilization of K. phaffii as a platform to produce several products of economic interest such as biopharmaceuticals, renewable chemicals, fuels, biomaterials, and food/feed products. Finally, we present synthetic biology approaches currently used for strain engineering, aiming at the production of new bioproducts.

2.
Rev. enferm. UERJ ; 31: e71389, jan. -dez. 2023.
Article in English, Portuguese | LILACS, BDENF - Nursing | ID: biblio-1437983

ABSTRACT

Objetivos: analisar a qualidade de vida no trabalho (QVT) na Estratégia Saúde da Família durante o período pandêmico e identificar na visão dos trabalhadores sugestões para promoção da qualidade de vida no ambiente laboral. Métodos: estudo transversal e quantitativo, realizado entre outubro de 2020 a junho de 2021 nas Unidades Básicas de Saúde de Palmas, capital do Tocantins, Brasil. Investigou-se o perfil sociodemográfico, a QVT por meio do Quality of Working Life Questionnaire (QOLWQbref) e sugestões para sua melhoria. Resultados: a QVT foi satisfatória para 91,96% dos 112 participantes, com níveis médios a altos em todos os domínios. Aqueles que não consideravam o trabalho estressante alcançaram melhor QVT. Entre as 113 sugestões para promoção da QVT, destacaram-se aspectos relacionados à Condições de Trabalho (29,19%) e Relacionamento na Equipe (19,46%). Conclusão: apesar da pandemia, a maioria dos participantes avaliaram QVT como satisfatória. As sugestões dos trabalhadores podem colaborar para manutenção e melhoria da QVT, protegendo a saúde do trabalhador(AU)


Objective: to analyze the quality of life at work QoWL in the Family Health Strategy during the pandemic period and to identify suggestions for promoting quality of life in the work environment from the workers' point of view. Methods: quantitative study, carried out between October/2020 and June/2021 in the Primary Care Units of a Palmas, capital in Tocantins, Brazil. The sociodemographic profile, QoWL through the Quality of Working Life Questionnaire (QoWLQ-bref) and suggestions for its improvement were investigated. Results: the QoWL was satisfactory for 91.96% of the 112 participants, with medium to high levels in all domains. Those who did not consider work stressful achieved better QoWL. Of the 113 suggestions for promoting QoWL, aspects related to Working Conditions (29.19%) and Team Relationships (19.46%) stood out. Conclusion: despite the pandemic, most participants rated QoWL as satisfactory. Workers' suggestions can collaborate to maintain and improve QoWL, protecting workers' health(AU)


Objetivo: analizar la calidad de vida en el trabajo (CVT) en la Estrategia de Salud de la Familia durante el período pandémico e identificar sugerencias para la promoción de la calidad de vida en el ambiente laboral desde la perspectiva de los trabajadores. Métodos: estudio cuantitativo, realizado entre octubre/2020 y junio/2021 en las Unidades Básicas de Salud de Palmas, capital del Tocantins, Brasil. Se investigó el perfil sociodemográfico, la CVL a través del Cuestionario de Calidad de Vida Laboral - Quality of Working Life Questionnaire (QoWLQ-bref) y sugerencias para su mejora. Resultados: la CVL fue satisfactoria para el 91,96% de los 112 participantes, cuyos niveles fueron de medios a altos en todos los dominios. Aquellos que no consideraban el trabajo estresante lograron mejor CVT. De las 113 sugerencias para promover la CVT, se destacaron aspectos relacionados con las Condiciones de Trabajo (29,19%) y las Relaciones de Equipo (19,46%). Conclusión: a pesar de la pandemia, la mayoría de los participantes calificaron la CVT como satisfactoria. Las sugerencias de los trabajadores pueden colaborar para mantener y mejorar la CVT, protegiendo la salud de los trabajadores(AU)


Subject(s)
Humans , Male , Female , Adult , Middle Aged , Quality of Life , National Health Strategies , Occupational Health , Health Personnel/psychology , Working Conditions , Health Centers , Cross-Sectional Studies , Surveys and Questionnaires , COVID-19
3.
Biotechnol Adv ; 54: 107839, 2022.
Article in English | MEDLINE | ID: mdl-34592347

ABSTRACT

Optogenetics involves the use of light to control cellular functions and has become increasingly popular in various areas of research, especially in the precise control of gene expression. While this technology is already well established in neurobiology and basic research, its use in bioprocess development is still emerging. Some optogenetic switches have been implemented in yeasts for different purposes, taking advantage of a wide repertoire of biological parts and relatively easy genetic manipulation. In this review, we cover the current strategies used for the construction of yeast strains to be used in optogenetically controlled protein or metabolite production, as well as the operational aspects to be considered for the scale-up of this type of process. Finally, we discuss the main applications of optogenetic switches in yeast systems and highlight the main advantages and challenges of bioprocess development considering future directions for this field.


Subject(s)
Optogenetics , Yeasts , Gene Expression , Proteins/genetics , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Yeasts/genetics
4.
Genes (Basel) ; 12(9)2021 09 17.
Article in English | MEDLINE | ID: mdl-34573415

ABSTRACT

Although Autism Spectrum Disorders (ASD) is recognized as being heavily influenced by genetic factors, the role of epigenetic and environmental factors is still being established. This study aimed to identify ASD vulnerability components based on familial history and intrauterine environmental stress exposure, explore possible vulnerability subgroups, access DNA methylation age acceleration (AA) as a proxy of stress exposure during life, and evaluate the association of ASD vulnerability components and AA to phenotypic severity measures. Principal Component Analysis (PCA) was used to search the vulnerability components from 67 mothers of autistic children. We found that PC1 had a higher correlation with psychosocial stress (maternal stress, maternal education, and social class), and PC2 had a higher correlation with biological factors (psychiatric family history and gestational complications). Comparing the methylome between above and below PC1 average subgroups we found 11,879 statistically significant differentially methylated probes (DMPs, p < 0.05). DMPs CpG sites were enriched in variably methylated regions (VMRs), most showing environmental and genetic influences. Hypermethylated probes presented higher rates in different regulatory regions associated with functional SNPs, indicating that the subgroups may have different affected regulatory regions and their liability to disease explained by common variations. Vulnerability components score moderated by epigenetic clock AA was associated with Vineland Total score (p = 0.0036, adjR2 = 0.31), suggesting risk factors with stress burden can influence ASD phenotype.


Subject(s)
Autism Spectrum Disorder/epidemiology , Autism Spectrum Disorder/genetics , Circadian Clocks/genetics , Gene-Environment Interaction , Adolescent , Adult , Age Factors , Autism Spectrum Disorder/etiology , Autism Spectrum Disorder/pathology , Brazil/epidemiology , Child , Child, Preschool , DNA Methylation/physiology , Disease Susceptibility , Environment , Epigenesis, Genetic , Female , Genetic Heterogeneity , Humans , Infant , Infant, Newborn , Male , Middle Aged , Parturition , Pregnancy , Risk Factors , Vulnerable Populations/statistics & numerical data , Young Adult
5.
Genes, v. 12, n. 9, 1433, set. 2021
Article in English | Sec. Est. Saúde SP, SESSP-IBPROD, Sec. Est. Saúde SP | ID: bud-3963

ABSTRACT

Although Autism Spectrum Disorders (ASD) is recognized as being heavily influenced by genetic factors, the role of epigenetic and environmental factors is still being established. This study aimed to identify ASD vulnerability components based on familial history and intrauterine environmental stress exposure, explore possible vulnerability subgroups, access DNA methylation age acceleration (AA) as a proxy of stress exposure during life, and evaluate the association of ASD vulnerability components and AA to phenotypic severity measures. Principal Component Analysis (PCA) was used to search the vulnerability components from 67 mothers of autistic children. We found that PC1 had a higher correlation with psychosocial stress (maternal stress, maternal education, and social class), and PC2 had a higher correlation with biological factors (psychiatric family history and gestational complications). Comparing the methylome between above and below PC1 average subgroups we found 11,879 statistically significant differentially methylated probes (DMPs, p < 0.05). DMPs CpG sites were enriched in variably methylated regions (VMRs), most showing environmental and genetic influences. Hypermethylated probes presented higher rates in different regulatory regions associated with functional SNPs, indicating that the subgroups may have different affected regulatory regions and their liability to disease explained by common variations. Vulnerability components score moderated by epigenetic clock AA was associated with Vineland Total score (p = 0.0036, adjR2 = 0.31), suggesting risk factors with stress burden can influence ASD phenotype.

6.
PLoS One ; 15(7): e0235532, 2020.
Article in English | MEDLINE | ID: mdl-32614905

ABSTRACT

The yeast Komagataella phaffii is widely used as a microbial host for heterologous protein production. However, molecular tools for this yeast are basically restricted to a few integrative and replicative plasmids. Four sequences that have recently been proposed as the K. phaffii centromeres could be used to develop a new class of mitotically stable vectors. In this work, we designed a color-based genetic assay to investigate plasmid stability in K. phaffii and constructed vectors bearing K. phaffii centromeres and the ADE3 marker. These genetic tools were evaluated in terms of mitotic stability by transforming an ade2/ade3 auxotrophic strain and regarding plasmid copy number by quantitative PCR (qPCR). Our results confirmed that the centromeric plasmids were maintained at low copy numbers as a result of typical chromosome-like segregation during cell division. These features, combined with in vivo assembly possibilities, prompt these plasmids as a new addition to the K. phaffii genetic toolbox.


Subject(s)
Centromere/genetics , Colorimetry/methods , Pichia/genetics , Plasmids/analysis , DNA, Fungal/metabolism , Plasmids/genetics , Plasmids/metabolism , Real-Time Polymerase Chain Reaction
7.
Meat Sci ; 160: 107962, 2020 Feb.
Article in English | MEDLINE | ID: mdl-31683256

ABSTRACT

Two studies were carried out, the first with the objective to evaluate performance, beef quality and expression of genes involved in lipid metabolism in the muscle of bulls fed with or without low-fat dried distillers grains with solubles (DDGS, 21% DM) in the diet. In the second, eight rumen-fistulated bulls were assigned in a switch back design to evaluate the fatty acid profile of omasal fluid. We hypothesized that bulls fed DDGS may have an improved fatty acid profile and expression of genes involved in lipid metabolism may be altered, without affecting performance. Bulls fed DDGS had greater (P < .05) concentrations of PUFA n-6 in the omasum and muscle. CLA t10, c12 content was higher and there was lower expression of the LPL gene (P = .05) in the muscle of animals fed DDGS (P = .03). In conclusion, DDGS can be used as a protein feedstuff because it maintains beef quality.


Subject(s)
Cattle/physiology , Diet/veterinary , Red Meat/analysis , Animal Feed/analysis , Animal Nutritional Physiological Phenomena , Animals , Edible Grain , Fatty Acids/metabolism , Gene Expression , Lipogenesis/genetics , Male , Omasum/chemistry
8.
Cien Saude Colet ; 24(7): 2667-2678, 2019 Jul 22.
Article in Portuguese | MEDLINE | ID: mdl-31340284

ABSTRACT

The scope of this article is to identify the prevalence of the loss of quality of sleep and associated factors among menopausal women. It is a quantitative, cross-sectional and analytical study, the variables of which were investigated by applying a structured/pre-tested questionnaire and the Pittsburgh Sleep Quality Index with 819 menopausal women cared for under the Family Health Strategy. Simple Poisson regression was used to screen the variables (p < 0.25). For multiple analysis, Poisson regression was used based on a hierarchical model, at a significance level of 5%. Loss of quality of sleep was identified in 67% of the sample. Variables such as advanced age (PR = 1.09; CI = 1.03-1.16), moderate and severe menopausal symptoms (PR = 1.18; CI = 1.10-1.27), moderate to severe anxiety (PR = 1.17; CI = 1.10-1.25), moderate to severe depression (PR = 1.08; CI = 1.01-1.15) and arthritis/arthrosis/rheumatism (PR = 1. 07; CI = 1.01 - 1.14) revealed statistically significant associations with loss of quality of sleep. The loss of quality of sleep was highly prevalent in the population studied. Factors associated with loss of quality of sleep were advanced age, moderate to severe menopausal symptoms, moderate to severe anxiety and depression, and the presence of arthritis/arthrosis/rheumatism.


O objetivo deste artigo é identificar a prevalência de perda da qualidade do sono em mulheres climatéricas e os fatores associados. Estudo quantitativo, transversal e analítico, cujas variáveis foram investigadas por questionário estruturado/pré-testado e pelo Índice de Qualidade do Sono de Pittsburgh, em 819 mulheres climatéricas assistidas pela Estratégia Saúde da Família. Regressão de Poisson simples foi utilizada para triagem das variáveis (p < 0, 25). Para a modelagem hierarquizada foi utilizada a regressão de Poisson, adotando nível de significância de 5%. Identificou-se perda de qualidade do sono em 67% da amostra. Variáveis como idade avançada (RP = 1,09; IC = 1,03 ­ 1,16), sintomas climatéricos moderados e intensos (RP = 1,18; IC = 1,10 ­ 1,27), ansiedade moderada e grave (RP = 1,17; IC = 1,10 ­ 1,25), depressão moderada/grave (RP = 1,08; IC = 1,01 ­ 1,15) e artrite/artrose/reumatismo (RP = 1,07; IC = 1,01 ­ 1,14) demonstraram associações estatisticamente significativas com a perda de qualidade do sono. A perda de qualidade do sono foi altamente prevalente na população estudada. Os fatores associados à perda da qualidade do sono foram idade avançada, sintomas climatéricos de moderados a intensos, ansiedade e depressão moderada a intensa e presença de artrite/artrose/reumatismo.


Subject(s)
Anxiety/epidemiology , Depression/epidemiology , Menopause , Rheumatic Diseases/epidemiology , Sleep Wake Disorders/epidemiology , Adult , Age Factors , Aged , Cross-Sectional Studies , Female , Humans , Middle Aged , Prevalence , Rheumatic Diseases/physiopathology , Risk Factors , Severity of Illness Index , Sleep , Sleep Wake Disorders/etiology , Surveys and Questionnaires
9.
Ciênc. Saúde Colet. (Impr.) ; 24(7): 2667-2678, jul. 2019. tab
Article in Portuguese | LILACS | ID: biblio-1011851

ABSTRACT

Resumo O objetivo deste artigo é identificar a prevalência de perda da qualidade do sono em mulheres climatéricas e os fatores associados. Estudo quantitativo, transversal e analítico, cujas variáveis foram investigadas por questionário estruturado/pré-testado e pelo Índice de Qualidade do Sono de Pittsburgh, em 819 mulheres climatéricas assistidas pela Estratégia Saúde da Família. Regressão de Poisson simples foi utilizada para triagem das variáveis (p < 0, 25). Para a modelagem hierarquizada foi utilizada a regressão de Poisson, adotando nível de significância de 5%. Identificou-se perda de qualidade do sono em 67% da amostra. Variáveis como idade avançada (RP = 1,09; IC = 1,03 - 1,16), sintomas climatéricos moderados e intensos (RP = 1,18; IC = 1,10 - 1,27), ansiedade moderada e grave (RP = 1,17; IC = 1,10 - 1,25), depressão moderada/grave (RP = 1,08; IC = 1,01 - 1,15) e artrite/artrose/reumatismo (RP = 1,07; IC = 1,01 - 1,14) demonstraram associações estatisticamente significativas com a perda de qualidade do sono. A perda de qualidade do sono foi altamente prevalente na população estudada. Os fatores associados à perda da qualidade do sono foram idade avançada, sintomas climatéricos de moderados a intensos, ansiedade e depressão moderada a intensa e presença de artrite/artrose/reumatismo.


Abstract The scope of this article is to identify the prevalence of the loss of quality of sleep and associated factors among menopausal women. It is a quantitative, cross-sectional and analytical study, the variables of which were investigated by applying a structured/pre-tested questionnaire and the Pittsburgh Sleep Quality Index with 819 menopausal women cared for under the Family Health Strategy. Simple Poisson regression was used to screen the variables (p < 0.25). For multiple analysis, Poisson regression was used based on a hierarchical model, at a significance level of 5%. Loss of quality of sleep was identified in 67% of the sample. Variables such as advanced age (PR = 1.09; CI = 1.03-1.16), moderate and severe menopausal symptoms (PR = 1.18; CI = 1.10-1.27), moderate to severe anxiety (PR = 1.17; CI = 1.10-1.25), moderate to severe depression (PR = 1.08; CI = 1.01-1.15) and arthritis/arthrosis/rheumatism (PR = 1. 07; CI = 1.01 - 1.14) revealed statistically significant associations with loss of quality of sleep. The loss of quality of sleep was highly prevalent in the population studied. Factors associated with loss of quality of sleep were advanced age, moderate to severe menopausal symptoms, moderate to severe anxiety and depression, and the presence of arthritis/arthrosis/rheumatism.


Subject(s)
Humans , Female , Adult , Aged , Anxiety/epidemiology , Sleep Wake Disorders/epidemiology , Menopause , Rheumatic Diseases/epidemiology , Depression/epidemiology , Sleep , Sleep Wake Disorders/etiology , Severity of Illness Index , Rheumatic Diseases/physiopathology , Prevalence , Cross-Sectional Studies , Surveys and Questionnaires , Risk Factors , Age Factors , Middle Aged
10.
Braz J Microbiol ; 50(2): 405-413, 2019 Apr.
Article in English | MEDLINE | ID: mdl-30827000

ABSTRACT

The effect of gene dosage on the production of Candida antarctica lipase B (CalB) in the methylotrophic yeast Komagataella phaffii, at high densities in a simple medium containing crude glycerin as the sole carbon source, is described. The use of crude glycerin, the main by-product of biodiesel production from vegetable oils, will reduce the production cost of the bioprocess. Two K. phaffii strains were constructed with one or three copies of LipB, an optimized version of the gene encoding CalB under the control of the constitutive PPGK1 promoter. These two constructs were tested and compared on batches using minimal-salts medium with crude glycerin. The strain with three copies achieved a higher enzyme yield (48,760 U/L, 2.3-fold higher than the one-copy strain), with 42 g/L biomass, with no effects on growth.


Subject(s)
Candida/enzymology , Candida/genetics , Fungal Proteins/biosynthesis , Fungal Proteins/genetics , Lipase/biosynthesis , Lipase/genetics , Pichia/genetics , Saccharomycetales/metabolism , Candida/metabolism , Gene Dosage/genetics , Glycerol/metabolism , Promoter Regions, Genetic/genetics , Saccharomycetales/genetics
11.
Am J Med Genet B Neuropsychiatr Genet ; 180(6): 390-414, 2019 09.
Article in English | MEDLINE | ID: mdl-30537354

ABSTRACT

The male-biased prevalence of certain neurodevelopmental disorders and the sex-biased outcomes associated with stress exposure during gestation have been previously described. Here, we hypothesized that genes distinctively targeted by only one or both homologous proteins highly conserved across therian mammals, SOX3 and SRY, could induce sexual adaptive changes that result in a differential risk for neurodevelopmental disorders. ChIP-seq/chip data showed that SOX3/SRY gene targets were expressed in different brain cell types in mice. We used orthologous human genes in rodent genomes to extend the number of SOX3/SRY set (1,721). These genes were later found to be enriched in five modules of coexpressed genes during the early and mid-gestation periods (FDR < 0.05), independent of sexual hormones. Genes with differential expression (24, p < 0.0001) and methylation (40, p < 0.047) between sexes were overrepresented in this set. Exclusive SOX3 or SRY target genes were more associated with the late gestational and postnatal periods. Using autism as a model sex-biased disorder, the SOX3/SRY set was enriched in autism gene databases (FDR ≤ 0.05), and there were more de novo variations from the male autism spectrum disorder (ASD) samples under the SRY peaks compared to the random peaks (p < 0.024). The comparison of coexpressed networks of SOX3/SRY target genes between male autism and control samples revealed low preservation in gene modules related to stress response (99 genes) and neurogenesis (78 genes). This study provides evidence that while SOX3 is a regulatory mechanism for both sexes, the male-exclusive SRY also plays a role in gene regulation, suggesting a potential mechanism for sex bias in ASD.


Subject(s)
Neurodevelopmental Disorders/genetics , SOXB1 Transcription Factors/genetics , Sex-Determining Region Y Protein/genetics , Animals , Autism Spectrum Disorder/genetics , DNA-Binding Proteins/genetics , Databases, Genetic , Female , Gene Expression Regulation/genetics , Gene Regulatory Networks , Genetic Predisposition to Disease , Humans , Male , Mice , Mice, Inbred C57BL , Risk Factors , SOXB1 Transcription Factors/metabolism , Sex Chromosomes/genetics , Sex Factors , Sex-Determining Region Y Protein/metabolism , Transcription Factors/genetics
12.
AMB Express ; 8(1): 82, 2018 May 21.
Article in English | MEDLINE | ID: mdl-29785587

ABSTRACT

Polymorphism is well known in Saccharomyces cerevisiae strains used for different industrial applications, however little is known about its effects on promoter efficiency. In order to test this, five different promoters derived from an industrial and a laboratory (S288c) strain were used to drive the expression of eGFP reporter gene in both cells. The ADH1 promoter (P ADH1 ) in particular, which showed more polymorphism among the promoters analyzed, also exhibited the highest differences in intracellular fluorescence production. This was further confirmed by Northern blot analysis. The same behavior was also observed when the gene coding for secreted α-amylase from Cryptococcus flavus was placed under the control of either P ADH1 . These results underline the importance of the careful choice of the source of the promoter to be used in industrial yeast strains for heterologous expression.

13.
Appl Microbiol Biotechnol ; 102(6): 2753-2761, 2018 Mar.
Article in English | MEDLINE | ID: mdl-29435619

ABSTRACT

We have investigated the use of the gene coding for acetamidase (amdS) as a recyclable dominant marker for the methylotrophic yeast Komagataella phaffii in order to broaden its genetic toolbox. First, the endogenous constitutive AMD2 gene (a putative acetamidase) was deleted generating strain LA1. A cassette (amdSloxP) was constructed bearing a codon-optimized version of the Aspergillus nidulans amdS gene flanked by loxP sites for marker excision with Cre recombinase. This cassette was successfully tested as a dominant selection marker for transformation of the LA1 strain after selection on plates containing acetamide as a sole nitrogen source. Finally, amdSloxP was used to sequentially disrupt the K. phaffii ADE2 and URA5 genes. After each disruption event, a Cre-mediated marker recycling step was performed by plating cells on medium containing fluoroacetamide. In conclusion, amdS proved to be a suitable tool for K. phaffii transformation and marker recycling thus providing a new antibiotic-free system for genetic manipulation of this yeast.


Subject(s)
Amidohydrolases/metabolism , Genetic Engineering/methods , Saccharomycetales/genetics , Selection, Genetic , Transformation, Genetic , Amidohydrolases/genetics , Gene Knockout Techniques , Recombination, Genetic
14.
Microb Cell Fact ; 16(1): 99, 2017 Jun 08.
Article in English | MEDLINE | ID: mdl-28595601

ABSTRACT

BACKGROUND: A commonly used approach to improve recombinant protein production is to increase the levels of expression by providing extra-copies of a heterologous gene. In Komagataella phaffii (Pichia pastoris) this is usually accomplished by transforming cells with an expression vector carrying a drug-resistance marker following a screening for multicopy clones on plates with increasingly higher concentrations of an antibiotic. Alternatively, defective auxotrophic markers can be used for the same purpose. These markers are generally transcriptionally impaired genes lacking most of the promoter region. Among the defective markers commonly used in Saccharomyces cerevisiae is leu2-d, an allele of LEU2 which is involved in leucine metabolism. Cells transformed with this marker can recover prototrophy when they carry multiple copies of leu2-d in order to compensate the poor transcription from this defective allele. RESULTS: A K. phaffii strain auxotrophic for leucine (M12) was constructed by disrupting endogenous LEU2. The resulting strain was successfully transformed with a vector carrying leu2-d and an EGFP (enhanced green fluorescent protein) reporter gene. Vector copy numbers were determined from selected clones which grew to different colony sizes on transformation plates. A direct correlation was observed between colony size, number of integrated vectors and EGFP production. By using this approach we were able to isolate genetically stable clones bearing as many as 20 integrated copies of the vector and with no significant effects on cell growth. CONCLUSIONS: In this work we have successfully developed a genetic system based on a defective auxotrophic which can be applied to improve heterologous protein production in K. phaffii. The system comprises a K. phaffii leu2 strain and an expression vector carrying the defective leu2-d marker which allowed the isolation of multicopy clones after a single transformation step. Because a linear correlation was observed between copy number and heterologous protein production, this system may provide a simple approach to improve recombinant protein productivity in K. phaffii.


Subject(s)
Genetic Markers/genetics , Pichia/genetics , Plasmids/genetics , Recombinant Proteins/genetics , Recombinant Proteins/metabolism
15.
Bioengineered ; 8(5): 441-445, 2017 Sep 03.
Article in English | MEDLINE | ID: mdl-28399696

ABSTRACT

Komagataella phaffii (formerly Pichia pastoris) is a well-known fungal system for heterologous protein production in the context of modern biotechnology. To obtain higher protein titers in this system many researchers have sought to optimize gene expression by increasing the levels of transcription of the heterologous gene. This has been typically achieved by manipulating promoter sequences or by generating clones bearing multiple copies of the desired gene. The aim of this work is to describe how these different molecular strategies have been applied in K. phaffii presenting their advantages and drawbacks.


Subject(s)
Ascomycota/genetics , Ascomycota/metabolism , Genetic Enhancement/methods , Promoter Regions, Genetic/genetics , Protein Engineering/methods , Recombinant Proteins/biosynthesis , Transcription Factors/biosynthesis , Cloning, Molecular/methods , Gene Dosage/genetics , Gene Expression Regulation, Fungal/genetics , Recombinant Proteins/genetics , Transcription Factors/genetics
16.
PLoS One ; 12(1): e0170386, 2017.
Article in English | MEDLINE | ID: mdl-28118382

ABSTRACT

It has been proposed that copy number variations (CNVs) are associated with increased risk of autism spectrum disorder (ASD) and, in conjunction with other genetic changes, contribute to the heterogeneity of ASD phenotypes. Array comparative genomic hybridization (aCGH) and exome sequencing, together with systems genetics and network analyses, are being used as tools for the study of complex disorders of unknown etiology, especially those characterized by significant genetic and phenotypic heterogeneity. Therefore, to characterize the complex genotype-phenotype relationship, we performed aCGH and sequenced the exomes of two affected siblings with ASD symptoms, dysmorphic features, and intellectual disability, searching for de novo CNVs, as well as for de novo and rare inherited point variations-single nucleotide variants (SNVs) or small insertions and deletions (indels)-with probable functional impacts. With aCGH, we identified, in both siblings, a duplication in the 4p16.3 region and a deletion at 8p23.3, inherited by a paternal balanced translocation, t(4, 8) (p16; p23). Exome variant analysis found a total of 316 variants, of which 102 were shared by both siblings, 128 were in the male sibling exome data, and 86 were in the female exome data. Our integrative network analysis showed that the siblings' shared translocation could explain their similar syndromic phenotype, including overgrowth, macrocephaly, and intellectual disability. However, exome data aggregate genes to those already connected from their translocation, which are important to the robustness of the network and contribute to the understanding of the broader spectrum of psychiatric symptoms. This study shows the importance of using an integrative approach to explore genotype-phenotype variability.


Subject(s)
Autism Spectrum Disorder/genetics , Chromosomes, Human, Pair 4/genetics , Chromosomes, Human, Pair 8/genetics , Comparative Genomic Hybridization , DNA Copy Number Variations , Exome/genetics , Genetic Association Studies , Translocation, Genetic , Child , Chromosomes, Human, Pair 4/ultrastructure , Chromosomes, Human, Pair 8/ultrastructure , Female , Gene Duplication , Gene Regulatory Networks , Humans , In Situ Hybridization, Fluorescence , Intellectual Disability/genetics , Learning Disabilities/genetics , Male , Megalencephaly/genetics , Nerve Tissue Proteins/genetics , Nucleic Acid Amplification Techniques , Sequence Deletion , Siblings , Syndrome
17.
Int J Mol Sci ; 17(3): 207, 2016 Feb 25.
Article in English | MEDLINE | ID: mdl-26927067

ABSTRACT

Many years have passed since the first genetically modified Saccharomyces cerevisiae strains capable of fermenting xylose were obtained with the promise of an environmentally sustainable solution for the conversion of the abundant lignocellulosic biomass to ethanol. Several challenges emerged from these first experiences, most of them related to solving redox imbalances, discovering new pathways for xylose utilization, modulation of the expression of genes of the non-oxidative pentose phosphate pathway, and reduction of xylitol formation. Strategies on evolutionary engineering were used to improve fermentation kinetics, but the resulting strains were still far from industrial application. Lignocellulosic hydrolysates proved to have different inhibitors derived from lignin and sugar degradation, along with significant amounts of acetic acid, intrinsically related with biomass deconstruction. This, associated with pH, temperature, high ethanol, and other stress fluctuations presented on large scale fermentations led the search for yeasts with more robust backgrounds, like industrial strains, as engineering targets. Some promising yeasts were obtained both from studies of stress tolerance genes and adaptation on hydrolysates. Since fermentation times on mixed-substrate hydrolysates were still not cost-effective, the more selective search for new or engineered sugar transporters for xylose are still the focus of many recent studies. These challenges, as well as under-appreciated process strategies, will be discussed in this review.


Subject(s)
Fermentation , Industrial Microbiology/methods , Saccharomyces cerevisiae/metabolism , Xylose/metabolism , Ethanol/metabolism , Saccharomyces cerevisiae/genetics
18.
Biotechnol Lett ; 38(3): 509-17, 2016 Mar.
Article in English | MEDLINE | ID: mdl-26585331

ABSTRACT

OBJECTIVES: To develop a new vector for constitutive expression in Pichia pastoris based on the endogenous glycolytic PGK1 promoter. RESULTS: P. pastoris plasmids bearing at least 415 bp of PGK1 promoter sequences can be used to drive plasmid integration by addition at this locus without affecting cell growth. Based on this result, a new P. pastoris integrative vector, pPICK2, was constructed bearing some features that facilitate protein production in this yeast: a ~620 bp PGK1 promoter fragment with three options of restriction sites for plasmid linearization prior to yeast transformation: a codon-optimized α-factor secretion signal, a new polylinker, and the kan marker for vector propagation in bacteria and selection of yeast transformants. CONCLUSIONS: A new constitutive vector for P. pastoris represents an alternative platform for recombinant protein production and metabolic engineering purposes.


Subject(s)
Gene Expression , Gene Targeting/methods , Genetic Vectors , Genetics, Microbial/methods , Phosphoglycerate Kinase/genetics , Pichia/genetics , Promoter Regions, Genetic , Pichia/enzymology , Plasmids
19.
Rev Chilena Infectol ; 31(4): 468-72, 2014 Aug.
Article in Spanish | MEDLINE | ID: mdl-25327202

ABSTRACT

Several species of black fungi have been reported as agents of subcutaneous phaeohyphomycosis. Although most of these fungi are considered opportunistic pathogens, they play an important role in phaeohyphomycosis, a disease considered an emergent mycosis among solid organ recipients. We report a case of phaeohyphomycosis caused by Alternaria infectoria of the left hand and the 4th finger of the right hand of a 68-year-old male who underwent a renal transplant 35 months before. The lesion was treated with surgical excision. One year later, the patient presented a new lesion on the 5th finger of the right hand, but this time caused by Colletotrichum gloeosporioides that was also removed surgically. Both lesions did not relapse after being removed. Antifungal susceptibility testing was performed against five antifungal drugs (amphotericin B, itraconazole, flucytosine, fluconazole and voriconazole). Alternaria infectoria was resistant to all five drugs and C. gloeosporioides was sensitive only to amphotericin B and voriconazole. We emphasize the need of histopathologic and microbiologic studies of new lesions of phaeohyphomycosis, since in this case the same patient was infected twice by two different fungi.


Subject(s)
Alternaria/isolation & purification , Colletotrichum/isolation & purification , Kidney Transplantation/adverse effects , Phaeohyphomycosis/diagnosis , Aged , Alternaria/drug effects , Antifungal Agents/pharmacology , Colletotrichum/drug effects , Humans , Immunocompromised Host , Male , Microbial Sensitivity Tests , Phaeohyphomycosis/surgery
20.
PLoS One ; 9(10): e110198, 2014.
Article in English | MEDLINE | ID: mdl-25303678

ABSTRACT

Copy number variations (CNVs) have been previously associated with several different neurodevelopmental psychiatric disorders, such as autism, schizophrenia, and attention deficit hyperactivity disorder (ADHD). The present study consisted of a pilot genome-wide screen for CNVs in a cohort of 16 patients with early-onset obsessive-compulsive disorder (OCD) and 12 mentally healthy individuals, using array-based comparative genomic hybridization (aCGH) on 44K arrays. A small rare paternal inherited microdeletion (∼64 kb) was identified in chromosome 15q13.3 of one male patient with very early onset OCD. The father did not have OCD. The deletion encompassed part of the FMN1 gene, which is involved with the glutamatergic system. This finding supports the hypothesis of a complex network of several genes expressed in the brain contributing for the genetic risk of OCD, and also supports the glutamatergic involvement in OCD, which has been previously reported in the literature.


Subject(s)
Chromosome Deletion , Chromosomes, Human, Pair 15 , Obsessive-Compulsive Disorder/genetics , Adolescent , Age of Onset , Case-Control Studies , Child , Child, Preschool , Comparative Genomic Hybridization , DNA Copy Number Variations , Fetal Proteins/genetics , Formins , Genetic Predisposition to Disease , Genome-Wide Association Study , Humans , Male , Microfilament Proteins/genetics , Nuclear Proteins/genetics
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