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1.
PLoS Comput Biol ; 16(1): e1007494, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31951609

RESUMO

The fixation probability of a single mutant invading a population of residents is among the most widely-studied quantities in evolutionary dynamics. Amplifiers of natural selection are population structures that increase the fixation probability of advantageous mutants, compared to well-mixed populations. Extensive studies have shown that many amplifiers exist for the Birth-death Moran process, some of them substantially increasing the fixation probability or even guaranteeing fixation in the limit of large population size. On the other hand, no amplifiers are known for the death-Birth Moran process, and computer-assisted exhaustive searches have failed to discover amplification. In this work we resolve this disparity, by showing that any amplification under death-Birth updating is necessarily bounded and transient. Our boundedness result states that even if a population structure does amplify selection, the resulting fixation probability is close to that of the well-mixed population. Our transience result states that for any population structure there exists a threshold r⋆ such that the population structure ceases to amplify selection if the mutant fitness advantage r is larger than r⋆. Finally, we also extend the above results to δ-death-Birth updating, which is a combination of Birth-death and death-Birth updating. On the positive side, we identify population structures that maintain amplification for a wide range of values r and δ. These results demonstrate that amplification of natural selection depends on the specific mechanisms of the evolutionary process.


Assuntos
Modelos Biológicos , Dinâmica Populacional/estatística & dados numéricos , Seleção Genética/fisiologia , Biologia Computacional , Mutação/fisiologia , Densidade Demográfica , Processos Estocásticos
2.
Vet Res ; 50(1): 71, 2019 Sep 24.
Artigo em Inglês | MEDLINE | ID: mdl-31551081

RESUMO

Eggs and raw or undercooked egg-containing food items are frequently identified as the bacterial source during epidemiolocal investigation of Salmonella outbreaks. Multi-locus variable number of tandem repeats analysis (MLVA) is a widely used Salmonella typing method enabling the study of diversity within populations of the same serotype. In vivo passage, however, has been linked with changes in MLVA type and more broadly the Salmonella genome. We sought to investigate whether in vivo passage through layer hens had an effect on MLVA type as well as the bacterial genome and whether any mutations affected bacterial virulence. Layer hens were infected with either Salmonella Typhimurium DT9 (03-24-11-11-523) as part of a single infection or were co-infected with an equal amount of Salmonella Mbandaka. Salmonella shedding in both single and co-infected birds was variable over the course of the 16-week experiment. Salmonella Typhimurium and Salmonella Mbandaka were identified in feces of co-infected birds. Salmonella colonies isolated from fecal samples were subtyped using MLVA. A single change in SSTR-6 was observed in Salmonella Typhimurium strains isolated from co-infected birds. Isolates of Salmonella Typhimurium of both the parent (03-24-11-11-523) and modified (03-24-12-11-523) MLVA type were sequenced and compared with the genome of the parent strain. Sequence analysis revealed that in vivo passaging resulted in minor mutation events. Passaged isolates exhibited significantly higher invasiveness in cultured human intestinal epithelial cells than the parent strain. The microevolution observed in this study suggests that changes in MLVA may arise more commonly and may have clinical significance.


Assuntos
Galinhas , Genoma Bacteriano/genética , Mutação/fisiologia , Doenças das Aves Domésticas/fisiopatologia , Salmonelose Animal/fisiopatologia , Salmonella typhimurium/fisiologia , Animais , Células CACO-2 , Coinfecção/microbiologia , Coinfecção/fisiopatologia , Coinfecção/veterinária , Fezes/microbiologia , Feminino , Humanos , Repetições Minissatélites , Tipagem de Sequências Multilocus/veterinária , Doenças das Aves Domésticas/microbiologia , Salmonelose Animal/microbiologia , Salmonella enterica/fisiologia , Salmonella typhimurium/genética , Inoculações Seriadas , Virulência
3.
PLoS Comput Biol ; 15(9): e1007319, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31504032

RESUMO

Kinetic models of metabolic networks offer the promise of quantitative phenotype prediction. The mechanistic characterization of enzyme catalyzed reactions allows for tracing the effect of perturbations in metabolite concentrations and reaction fluxes in response to genetic and environmental perturbation that are beyond the scope of stoichiometric models. In this study, we develop a two-step computational pipeline for the rapid parameterization of kinetic models of metabolic networks using a curated metabolic model and available 13C-labeling distributions under multiple genetic and environmental perturbations. The first step involves the elucidation of all intracellular fluxes in a core model of E. coli containing 74 reactions and 61 metabolites using 13C-Metabolic Flux Analysis (13C-MFA). Here, fluxes corresponding to the mid-exponential growth phase are elucidated for seven single gene deletion mutants from upper glycolysis, pentose phosphate pathway and the Entner-Doudoroff pathway. The computed flux ranges are then used to parameterize the same (i.e., k-ecoli74) core kinetic model for E. coli with 55 substrate-level regulations using the newly developed K-FIT parameterization algorithm. The K-FIT algorithm employs a combination of equation decomposition and iterative solution techniques to evaluate steady-state fluxes in response to genetic perturbations. k-ecoli74 predicted 86% of flux values for strains used during fitting within a single standard deviation of 13C-MFA estimated values. By performing both tasks using the same network, errors associated with lack of congruity between the two networks are avoided, allowing for seamless integration of data with model building. Product yield predictions and comparison with previously developed kinetic models indicate shifts in flux ranges and the presence or absence of mutant strains delivering flux towards pathways of interest from training data significantly impact predictive capabilities. Using this workflow, the impact of completeness of fluxomic datasets and the importance of specific genetic perturbations on uncertainties in kinetic parameter estimation are evaluated.


Assuntos
Isótopos de Carbono/metabolismo , Biologia Computacional/métodos , Escherichia coli , Redes e Vias Metabólicas , Modelos Biológicos , Algoritmos , Metabolismo dos Carboidratos , Escherichia coli/genética , Escherichia coli/metabolismo , Cinética , Redes e Vias Metabólicas/genética , Redes e Vias Metabólicas/fisiologia , Mutação/genética , Mutação/fisiologia
4.
Oncogene ; 38(38): 6491-6506, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31337866

RESUMO

Oncodriver genes are usually identified when mutations recur in multiple tumours. Different drivers often converge in the activation or repression of key cancer-relevant pathways. However, as many pathways contain multiple members of the same gene family, individual mutations might be overlooked, as each family member would necessarily have a lower mutation frequency and thus not identified as significant in any one-gene-at-a-time analysis. Here, we looked for mutated, functional sequence positions in gene families that were mutually exclusive (in patients) with another gene in the same pathway, which identified both known and new candidate oncodrivers. For instance, many inactivating mutations in multiple G-protein (particularly Gi/o) coupled receptors, are mutually exclusive with Gαs oncogenic activating mutations, both of which ultimately enhance cAMP signalling. By integrating transcriptomics and interaction data, we show that the Gs pathway is upregulated in multiple cancer types, even those lacking known GNAS activating mutations. This suggests that cancer cells may develop alternative strategies to activate adenylate cyclase signalling in multiple cancer types. Our study provides a mechanistic interpretation for several rare somatic mutations in multi-gene oncodrivers, and offers possible explanations for known and potential off-label cancer treatments, suggesting new therapeutic opportunities.


Assuntos
Mutação , Neoplasias/genética , Oncogenes/genética , Receptores Acoplados a Proteínas-G/genética , Cromograninas/genética , Biologia Computacional , Epistasia Genética , Subunidades alfa Gs de Proteínas de Ligação ao GTP/genética , Frequência do Gene , Redes Reguladoras de Genes/fisiologia , Genes Supressores de Tumor , Células HEK293 , Humanos , Modelos Moleculares , Família Multigênica/genética , Mutação/fisiologia , Neoplasias/mortalidade , Neoplasias/patologia , Receptores Acoplados a Proteínas-G/química , Receptores Acoplados a Proteínas-G/metabolismo , Transdução de Sinais/genética , Análise de Sobrevida , Fatores de Transcrição/genética
5.
Oncogene ; 38(34): 6184-6195, 2019 08.
Artigo em Inglês | MEDLINE | ID: mdl-31312025

RESUMO

Missense mutations in the TP53 gene are frequent in human cancers, giving rise to mutant p53 proteins that can acquire oncogenic properties. Gain of function mutant p53 proteins can enhance tumour aggressiveness by promoting cell invasion, metastasis and chemoresistance. Accumulating evidences indicate that mutant p53 proteins can also modulate cell homeostatic processes, suggesting that missense p53 mutation may increase resistance of tumour cells to intrinsic and extrinsic cancer-related stress conditions, thus offering a selective advantage. Here we provide evidence that mutant p53 proteins can modulate the Unfolded Protein Response (UPR) to increase cell survival upon Endoplasmic Reticulum (ER) stress, a condition to which cancer cells are exposed during tumour formation and progression, as well as during therapy. Mechanistically, this action of mutant p53 is due to enhanced activation of the pro-survival UPR effector ATF6, coordinated with inhibition of the pro-apoptotic UPR effectors JNK and CHOP. In a triple-negative breast cancer cell model with missense TP53 mutation, we found that ATF6 activity is necessary for viability and invasion phenotypes. Together, these findings suggest that ATF6 inhibitors might be combined with mutant p53-targeting drugs to specifically sensitise cancer cells to endogenous or chemotherapy-induced ER stress.


Assuntos
Fator 6 Ativador da Transcrição/genética , Estresse do Retículo Endoplasmático/genética , Neoplasias/genética , Proteína Supressora de Tumor p53/genética , Resposta a Proteínas não Dobradas/genética , Fator 6 Ativador da Transcrição/metabolismo , Animais , Células Cultivadas , Progressão da Doença , Retículo Endoplasmático/metabolismo , Regulação Neoplásica da Expressão Gênica , Humanos , Células MCF-7 , Camundongos , Camundongos Transgênicos , Mutação/fisiologia , Invasividade Neoplásica , Neoplasias/metabolismo , Neoplasias/patologia , Regulação para Cima
6.
Respir Res ; 20(1): 164, 2019 Jul 22.
Artigo em Inglês | MEDLINE | ID: mdl-31331328

RESUMO

BACKGROUND: Approximately 30% of patients with epidermal growth factor receptor (EGFR)-activating mutations have no response to EGFR-tyrosine kinase inhibitors (TKIs) (primary resistance). However, little is known about the molecular mechanism involved in primary resistance to EGFR-TKIs in EGFR-mutant non-small cell lung cancer (NSCLC). Programmed death ligand-1 (PD-L1) plays important regulatory roles in intracellular functions and leads to acquired resistance to EGFR-TKIs in NSCLC. Here, we investigated the mechanistic role of PD-L1 in primary resistance to EGFR-TKIs in EGFR-mutant NSCLC cells. METHODS: The expression levels of PD-L1 and the sensitivity to gefitinib in H1975, HCC827 and PC-9 cells were determined by quantitative real-time PCR analysis (qRT-PCR) and Cell Counting Kit-8 (CCK-8) assays, respectively. Molecular manipulations (silencing or overexpression) were performed to assess the effect of PD-L1 on sensitivity to gefitinib, and a mouse xenograft model was used for in vivo confirmation. Western blotting and qRT-PCR were used to analyse the expression of epithelial-mesenchymal transition (EMT) markers. The effect of PD-L1 on migratory and invasive abilities was evaluated using the Transwell assay and mice tail intravenous injection. RESULTS: Higher expression of PD-L1 was related to less sensitivity to gefitinib in EGFR-mutant NSCLC cell lines. The overexpression or knockdown of PD-L1 presented diametrical sensitivity to gefitinib in vitro and in vivo. Furthermore, the overexpression of PD-L1 led to primary resistance to gefitinib through the induction of EMT, which was dependent on the upregulation of Smad3 phosphorylation. Moreover, in the mouse model, the knockdown of PD-L1 inhibited transforming growth factor (TGF)-ß1-induced cell metastasis in vivo. CONCLUSION: PD-L1 contributes to primary resistance to EGFR-TKI in EGFR-mutant NSCLC cells, which may be mediated through the induction of EMT via the activation of the TGF-ß/Smad canonical signalling pathway.


Assuntos
Antígeno B7-H1/biossíntese , Carcinoma Pulmonar de Células não Pequenas/metabolismo , Receptores ErbB/biossíntese , Neoplasias Pulmonares/metabolismo , Proteínas Smad/metabolismo , Fator de Crescimento Transformador beta/metabolismo , Animais , Antineoplásicos/farmacologia , Antineoplásicos/uso terapêutico , Antígeno B7-H1/genética , Carcinoma Pulmonar de Células não Pequenas/tratamento farmacológico , Carcinoma Pulmonar de Células não Pequenas/genética , Linhagem Celular Tumoral , Receptores ErbB/antagonistas & inibidores , Receptores ErbB/genética , Feminino , Células HEK293 , Humanos , Neoplasias Pulmonares/tratamento farmacológico , Neoplasias Pulmonares/genética , Camundongos , Camundongos Endogâmicos BALB C , Camundongos Nus , Mutação/efeitos dos fármacos , Mutação/fisiologia , Inibidores de Proteínas Quinases/farmacologia , Inibidores de Proteínas Quinases/uso terapêutico , Distribuição Aleatória , Transdução de Sinais/efeitos dos fármacos , Transdução de Sinais/fisiologia , Proteínas Smad/genética , Fator de Crescimento Transformador beta/genética , Ensaios Antitumorais Modelo de Xenoenxerto/métodos
7.
Fluids Barriers CNS ; 16(1): 20, 2019 Jul 15.
Artigo em Inglês | MEDLINE | ID: mdl-31303172

RESUMO

BACKGROUND: Blood-brain barrier dysfunction is associated with many late-stage neurodegenerative diseases. An emerging question is whether the mutations associated with neurodegenerative diseases can independently lead to blood-brain barrier (BBB) dysfunction. Studies from patient-derived induced pluripotent stem cells suggest that mutations associated with neurodegenerative disease are non-cell autonomous, resulting in gain of toxic function in derived neurons and astrocytes. Here we assess whether selected mutations associated with neurodegenerative diseases can contribute to impairment of the blood-brain barrier. METHODS: We assessed barrier function of confluent monolayers of human brain microvascular endothelial cells (hBMECs) derived from induced pluripotent stem cells (iPSC) from three healthy individuals and eight individuals with neurodegenerative disease. We systematically assessed protein and gene expression of BBB biomarkers, transendothelial resistance (TEER), permeability of Lucifer yellow, permeability of D-glucose, permeability of rhodamine 123, the efflux ratio of rhodamine 123, and P-gp inhibition using Tariquidar for confluent monolayers of human brain microvascular endothelial cell (hBMECs). RESULTS: We provide evidence supporting the hypothesis that mutations associated with neurodegenerative disease can independently cause BBB dysfunction. These functional changes are not catastrophic since barrier breakdown would result in BBB impairment during development. Synergistic interactions between non-cell autonomous cerebrovascular dysfunction and the effects of gain-of-toxic function in neurons (e.g. toxic oligomers) are likely to increase disease burden through a positive feedback mechanism. CONCLUSIONS: These results suggest that the accumulation of defects in brain microvascular endothelial cells may ultimately lead to impairment of the BBB. Small changes in barrier function over time could lead to accumulated defects that result in positive feedback to unrelated central nervous system diseases.


Assuntos
Barreira Hematoencefálica/fisiologia , Células-Tronco Pluripotentes Induzidas/fisiologia , Mutação/fisiologia , Doenças Neurodegenerativas/genética , Doenças Neurodegenerativas/metabolismo , Adulto , Idoso , Barreira Hematoencefálica/patologia , Células Endoteliais/patologia , Células Endoteliais/fisiologia , Feminino , Humanos , Células-Tronco Pluripotentes Induzidas/patologia , Masculino , Pessoa de Meia-Idade , Doenças Neurodegenerativas/patologia
8.
Integr Comp Biol ; 59(4): 970-982, 2019 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-31168607

RESUMO

Longevity plays a key role in the fitness of organisms, so understanding the processes that underlie variance in senescence has long been a focus of ecologists and evolutionary biologists. For decades, the performance and ultimate decline of mitochondria have been implicated in the demise of somatic tissue, but exactly why mitochondrial function declines as individual's age has remained elusive. A possible source of decline that has been of intense debate is mutations to the mitochondrial DNA. There are two primary sources of such mutations: oxidative damage, which is widely discussed by ecologists interested in aging, and mitochondrial replication error, which is less familiar to most ecologists. The goal of this review is to introduce ecologists and evolutionary biologists to the concept of mitochondrial replication error and to review the current status of research on the relative importance of replication error in senescence. We conclude by detailing some of the gaps in our knowledge that currently make it difficult to deduce the relative importance of replication error in wild populations and encourage organismal biologists to consider this variable both when interpreting their results and as viable measure to include in their studies.


Assuntos
Envelhecimento/genética , DNA Mitocondrial/genética , Instabilidade de Microssatélites , Mitocôndrias/fisiologia , Mutação/fisiologia , Animais , Mitocôndrias/genética , Taxa de Mutação
9.
PLoS Comput Biol ; 15(6): e1006648, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31220071

RESUMO

Classically, phenotype is what is observed, and genotype is the genetic makeup. Statistical studies aim to project phenotypic likelihoods of genotypic patterns. The traditional genotype-to-phenotype theory embraces the view that the encoded protein shape together with gene expression level largely determines the resulting phenotypic trait. Here, we point out that the molecular biology revolution at the turn of the century explained that the gene encodes not one but ensembles of conformations, which in turn spell all possible gene-associated phenotypes. The significance of a dynamic ensemble view is in understanding the linkage between genetic change and the gained observable physical or biochemical characteristics. Thus, despite the transformative shift in our understanding of the basis of protein structure and function, the literature still commonly relates to the classical genotype-phenotype paradigm. This is important because an ensemble view clarifies how even seemingly small genetic alterations can lead to pleiotropic traits in adaptive evolution and in disease, why cellular pathways can be modified in monogenic and polygenic traits, and how the environment may tweak protein function.


Assuntos
Evolução Molecular , Genótipo , Fenótipo , Proteínas , Biologia Computacional , Modelos Genéticos , Modelos Moleculares , Mutação/genética , Mutação/fisiologia , Conformação Proteica , Proteínas/química , Proteínas/genética , Proteínas/metabolismo
10.
Medicina (Kaunas) ; 55(5)2019 May 07.
Artigo em Inglês | MEDLINE | ID: mdl-31067829

RESUMO

Background: Fabry disease (FD) is a rare X-linked inherited lysosomal storage disorder caused by α-galactosidase A deficiency leading to intracellular glycosphingolipid accumulation. FD manifestation is multisystem, and can differ depending on disease-related genetic variants. Currently, more than 700 different FD-causing mutations have been identified in the human GLA gene. We identified a novel mutation in a Lithuanian family with classical manifestations of Fabry disease, revealing severe effects to the cardiovascular systems of heterozygous women. Case presentation: A 49-year-old woman underwent echocardiography due to progressive dyspnea that lasted seven years, reduced physical activity, and periodic cardiac arrhythmia. Echocardiography revealed left ventricular hypertrophy with normal diastolic function. The patient had experienced acroparesthesia in her upper limbs and abdominal pain since childhood, and in the last decade had experienced mild proteinuria without renal failure. Her renal biopsy was typical for Fabry disease. The patient's brain magnetic resonance imaging (MRI) (T2 flair) showed white matter hyperintensities lesions. DNA sequencing of the proband, her mother and one of her sons showed a novel GLA gene exon 2 mutation, c.270C>G (p.Cys90Trp). All three patients had decreased α-galactosidase A activity and specific FD manifestations. Conclusion: A novel GLA mutation, c.270C>G (p.Cys90Trp), was found in a Lithuanian family with a classical form of Fabry disease in heterozygous women with predominant cardiac involvement. However, the exact manifestation of this mutation is still unclear as it is newly reported and further research must be done.


Assuntos
Doença de Fabry/genética , alfa-Galactosidase/análise , Dispneia/etiologia , Eletrocardiografia/métodos , Doença de Fabry/epidemiologia , Feminino , Glicolipídeos/análise , Glicolipídeos/sangue , Humanos , Lituânia , Pessoa de Meia-Idade , Mutação/fisiologia , Esfingolipídeos/análise , Esfingolipídeos/sangue , alfa-Galactosidase/sangue
12.
Neuroscience ; 410: 118-127, 2019 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-31055008

RESUMO

Alzheimer's disease (AD) is the neurodegenerative disorder with no cure. Recent studies suggest that dysregulated postsynaptic store-operated calcium entry (nSOCE) may underlie mushroom spine loss that is related to AD pathology. In the present study we observed that PSEN1ΔE9 familial AD (FAD) mutation causes mushroom spine loss in hippocampal neuronal cultures. We also demonstrated that amplitude of TRPC6-mediated nSOCE is increased in PSEN1ΔE9-expressing neurons and we suggested that inhibition of nSOCE may help to rescue synaptic defects in this model. We further established that nSOCE antagonist EVP4593 decreases PSEN1ΔE9-mediated nSOCE upregulation and rescues mushroom spines in PSEN1ΔE9-expressing neurons. Obtained results further highlight the connection between dysregulation of endoplasmic reticulum calcium signaling and synaptic loss in AD and suggest that calcium signaling modulators may have a therapeutic value for treatment of memory loss in AD.


Assuntos
Doença de Alzheimer/metabolismo , Proteínas de Ligação ao Cálcio/antagonistas & inibidores , Proteínas de Ligação ao Cálcio/metabolismo , Proteínas de Membrana/antagonistas & inibidores , Proteínas de Membrana/metabolismo , Neurônios/metabolismo , Éteres Fenílicos/farmacologia , Presenilina-1/biossíntese , Quinazolinas/farmacologia , Doença de Alzheimer/genética , Animais , Bloqueadores dos Canais de Cálcio/farmacologia , Proteínas de Ligação ao Cálcio/genética , Células Cultivadas , Expressão Gênica , Hipocampo/efeitos dos fármacos , Hipocampo/metabolismo , Proteínas de Membrana/genética , Camundongos , Camundongos Transgênicos , Mutação/fisiologia , Neurônios/efeitos dos fármacos , Presenilina-1/genética , Resultado do Tratamento
13.
Insect Biochem Mol Biol ; 109: 43-51, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-30970276

RESUMO

The spermatogenesis of animal is essential for the reproduction and a very large number of genes participate in this procession. The Maelstrom (Mael) is identified essential for spermatogenesis in both Drosophila and mouse, though the mechanisms appear to differ. It was initially found that Mael gene is necessary for axis specification of oocytes in Drosophila, and recent studies suggested that Mael participates in the piRNA pathway. In this study, we obtained Bombyx mori Mael mutants by using a binary transgenic CRISPR/Cas9 system and analyzed the function of Mael in B. mori, a model lepidopteran insect. The results showed that BmMael is not necessary for piRNA pathway in the ovary of silkworm, whereas it might be essential for transposon elements (TEs) repression in testis. The BmMael mutation resulted in male sterility, and further analysis established that BmMael was essential for spermatogenesis. The spermatogenesis defects occurred in the elongation stage and resulted in nuclei concentration arrest. RNA-seq and qRT-PCR analyses demonstrated that spermatogenesis defects were associated with tight junctions and apoptosis. We also found that BmMael was not involved in the silkworm sex determination pathway. Our data provide insights into the biological function of BmMael in male spermatogenesis and might be useful for developing novel methods to control lepidopteron pests.


Assuntos
Bombyx/fisiologia , Proteínas de Insetos/genética , Processos de Determinação Sexual/genética , Espermatogênese/genética , Animais , Apoptose/genética , Sequência de Bases , Bombyx/genética , Proteínas de Insetos/metabolismo , Masculino , Mutação/fisiologia , Reação em Cadeia da Polimerase em Tempo Real , Junções Íntimas/genética , Junções Íntimas/metabolismo
14.
Tuberculosis (Edinb) ; 115: 42-48, 2019 03.
Artigo em Inglês | MEDLINE | ID: mdl-30948175

RESUMO

Tuberculosis (TB) is the most prevalent infectious disease worldwide, with no fully effective vaccine yet available. Considering that BCG strains devoid of the BCG1416c or BCG1419c genes afforded protection in mice versus highly virulent M. tuberculosis challenge, or in chronic infection models compared to BCG, respectively, we hypothesized that a synergistic effect of these strains might occur and provide enhanced protection against TB. Herein, we evaluated this hypothesis throughout an experimental design approach, where different combinations of these strains were tested for their capacity to induce cytokines in vitro, compared to individual strains. Our results show that mixed-infection of murine macrophages using these strains significantly decreases induction of TNF-α, IL-1ß, IL-6 but increases IL-4 induction compared with individual strains. These results suggest the existence of interaction effects during infection, which reduce induction of pro-inflammatory cytokines, even though individual intracellular replication is not altered when strains are combined. This is the first report of the evaluation of a potential whole-live combined vaccine against tuberculosis, which paradoxically seems to reduce production of pro-inflammatory cytokines while induces IL-4, leading us to further hypothesize that this combination might contribute as a therapeutic vaccine to reduce inflammation in severe TB cases.


Assuntos
Interleucinas/metabolismo , Macrófagos/microbiologia , Mycobacterium bovis/fisiologia , Fator de Necrose Tumoral alfa/metabolismo , Animais , Vacina BCG , Interações Hospedeiro-Patógeno , Interleucina-1beta/metabolismo , Interleucina-4/metabolismo , Interleucina-6/metabolismo , Camundongos , Mutação/fisiologia , Mycobacterium bovis/genética , Mycobacterium tuberculosis/genética , Tuberculose/metabolismo , Tuberculose/prevenção & controle
15.
Med Sci (Paris) ; 35(3): 245-251, 2019 Mar.
Artigo em Francês | MEDLINE | ID: mdl-30931909

RESUMO

Alfred H. Sturtevant was the first to raise the question: why does the mutation rate not become reduced to zero? Indeed, most new mutations with a phenotypic effect are deleterious. Therefore, individuals who produce less mutants produce more viable and fertile offspring. Consequently, natural selection should increase the frequency of antimutator genotypes and progressively reduce the mutation rate to zero. However, no species has ever been found with a mutation rate equal to zero. Recent analyses suggest that setting the mutation rate above zero depends mainly on the effective size of the genome and the effective population size. The mutation rate is a trade-off between natural selection that operates to improve replication fidelity and the random genetic drift that sets the ultimate lower limit. This trade off illustrates the limitation of the power of natural selection in a world where natural populations have a finite size.


Assuntos
Evolução Molecular , Taxa de Mutação , Animais , Drosophila/genética , Genes Letais/fisiologia , Deriva Genética , Humanos , Relação entre Gerações , Modelos Genéticos , Mutação/fisiologia , Seleção Genética/genética
16.
PLoS Comput Biol ; 15(4): e1006981, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-31034466

RESUMO

Identifying driver mutations in cancer is notoriously difficult. To date, recurrence of a mutation in patients remains one of the most reliable markers of mutation driver status. However, some mutations are more likely to occur than others due to differences in background mutation rates arising from various forms of infidelity of DNA replication and repair machinery, endogenous, and exogenous mutagens. We calculated nucleotide and codon mutability to study the contribution of background processes in shaping the observed mutational spectrum in cancer. We developed and tested probabilistic pan-cancer and cancer-specific models that adjust the number of mutation recurrences in patients by background mutability in order to find mutations which may be under selection in cancer. We showed that mutations with higher mutability values had higher observed recurrence frequency, especially in tumor suppressor genes. This trend was prominent for nonsense and silent mutations or mutations with neutral functional impact. In oncogenes, however, highly recurring mutations were characterized by relatively low mutability, resulting in an inversed U-shaped trend. Mutations not yet observed in any tumor had relatively low mutability values, indicating that background mutability might limit mutation occurrence. We compiled a dataset of missense mutations from 58 genes with experimentally validated functional and transforming impacts from various studies. We found that mutability of driver mutations was lower than that of passengers and consequently adjusting mutation recurrence frequency by mutability significantly improved ranking of mutations and driver mutation prediction. Even though no training on existing data was involved, our approach performed similarly or better to the state-of-the-art methods.


Assuntos
Códon/genética , Replicação do DNA/genética , Mutação/genética , Mutação/fisiologia , Neoplasias/genética , Biologia Computacional , Humanos , Oncogenes/genética
17.
PLoS Comput Biol ; 15(2): e1006800, 2019 02.
Artigo em Inglês | MEDLINE | ID: mdl-30817762

RESUMO

Pollen provides an excellent system to study pattern formation at the single-cell level. Pollen surface is covered by the pollen wall exine, whose deposition is excluded from certain surface areas, the apertures, which vary between the species in their numbers, positions, and morphology. What determines aperture patterns is not understood. Arabidopsis thaliana normally develops three apertures, equally spaced along the pollen equator. However, Arabidopsis mutants whose pollen has higher ploidy and larger volume develop four or more apertures. To explore possible mechanisms responsible for aperture patterning, we developed a mathematical model based on the Gierer-Meinhardt system of equations. This model was able to recapitulate aperture patterns observed in the wild-type and higher-ploidy pollen. We then used this model to further explore geometric and kinetic factors that may influence aperture patterns and found that pollen size, as well as certain kinetic parameters, like diffusion and decay of morphogens, could play a role in formation of aperture patterns. In conjunction with mathematical modeling, we also performed a forward genetic screen in Arabidopsis and discovered two mutants with aperture patterns that had not been previously observed in this species but were predicted by our model. The macaron mutant develops a single ring-like aperture, matching the unusual ring-like pattern produced by the model. The doughnut mutant forms two pore-like apertures at the poles of the pollen grain. Further tests on these novel mutants, motivated by the modeling results, suggested the existence of an area of inhibition around apertures that prevents formation of additional apertures in their vicinity. This work demonstrates the ability of the theoretical model to help focus experimental efforts and to provide fundamental insights into an important biological process.


Assuntos
Arabidopsis , Modelos Biológicos , Morfogênese , Mutação , Pólen , Arabidopsis/genética , Arabidopsis/crescimento & desenvolvimento , Arabidopsis/fisiologia , Biologia Computacional , Simulação por Computador , Cinética , Morfogênese/genética , Morfogênese/fisiologia , Mutação/genética , Mutação/fisiologia , Pólen/genética , Pólen/crescimento & desenvolvimento , Pólen/fisiologia
18.
Neurochem Int ; 126: 19-26, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-30831216

RESUMO

Amyotrophic lateral sclerosis (ALS) is a lethal neurodegenerative disease caused by selective motor neuron death. Mutations in the gene encoding copper/zinc superoxide dismutase (SOD1) belong to one of the four major mutation clusters responsible for pathogenesis of ALS. Toxic gain-of-function (not loss-of-function) of SOD1 mutants causes motor neuron degeneration. Aberrant protein-protein interactions (PPI) between mutant SOD1 and other proteins are involved in this toxic gain-of-function. Therefore, PPI inhibitors of mutant SOD1 not only increase understanding of ALS pathogenesis, but can also be used as novel therapeutics for ALS. Although it is challenging to identify PPI inhibitors, prior knowledge of the binding site can increase success probability. We have previously reported that tubulin interacts with N-terminal residues 1-23 of mutant SOD1. In the present study, we performed virtual screening by docking simulation of 32,791 compounds using this N-terminal binding site as prior knowledge. An established assay system for interaction inhibition between mutant SOD1-tubulin was used as an in-house model system to identify mutant SOD1 PPI inhibitors, with the goal of developing novel therapeutics for ALS. Consequently, five of six assay-executable compounds among top-ranked compounds during docking simulation inhibited the mutant SOD1-tubulin interaction in vitro. Binding mode analysis predicted that some inhibitors might bind the tubulin binding site of G85R SOD1 by pi electron interaction with the aromatic ring of the Trp32 residue of G85R SOD1. Our screening methods may contribute to the identification of lead compounds for treating ALS.


Assuntos
Mutação/fisiologia , Superóxido Dismutase-1/química , Superóxido Dismutase-1/metabolismo , Tubulina (Proteína)/química , Tubulina (Proteína)/metabolismo , Animais , Células COS , Avaliação Pré-Clínica de Medicamentos/métodos , Inibidores Enzimáticos/química , Inibidores Enzimáticos/metabolismo , Inibidores Enzimáticos/farmacologia , Humanos , Mutação/efeitos dos fármacos , Ligação Proteica/fisiologia , Estrutura Secundária de Proteína , Superóxido Dismutase-1/antagonistas & inibidores , Superóxido Dismutase-1/genética , Tubulina (Proteína)/genética
19.
Zhonghua Er Ke Za Zhi ; 57(3): 211-216, 2019 Mar 02.
Artigo em Chinês | MEDLINE | ID: mdl-30818899

RESUMO

Objective: To explore the phenotype and genotype of mitochondrial DNA depletion syndromes (MDS) in Chinese children. Methods: The clinical and genetic data of 12 MDS patients (8 were boys and 4 were girls) diagnosed in the Department of Neurology in Beijing Children's Hospital, Capital Medical University from October 2010 to April 2018 were retrospectively collected and analyzed. Results: The developmental milestones were normal or mildly retardated before disease onset. The age of onset ranged from 0 to 2.9-year-old. Most cases developed postnatal or after infection. The most common initial symptoms were feeding difficulty, seizure, muscle weakness, psychomotor regression and hepatic dysfunction. At the last evaluation, all the patients had developmental retardation, failure to thrive, muscle weakness, and dysphagia. Other clinical features were weight loss (9 cases), hearing impairment (7 cases), ptosis (6 cases), seizure (5 cases), dyspnea (4 cases), visual impairment (1 case), hirsutism (1 case), lactic acidosis (7 cases), elevated hepatic enzymes (4 cases) and creatine kinase (2 cases), elevated protein in cerebrospinal fluid (3 cases), abnormalities on screening for inborn error of metabolism (10 cases) and brain magnetic resonance imaging (MRI) (10 cases), abnormal electromyogram (including neurogenic or myogenic injury) (5 cases). Five patients died of infection or multiple organ failure. A total of 18 novel mutations presented below were detected in these patients. Among the 6 cases of encephalomyopathy, there were 3 with SUCLG1 mutation (c. 916G>T, c. 619T>C, c. 980dupT were novel), 2 with SUCLA2 mutation (c. 851G>A, c.971G>A were novel), and one with RRM2B mutation (c.456-2A>G, c.212T>C were novel). All the cases of hepatic encephalopathy all had POLG mutations (c. 3151G>A, c. 2294C>T, c. 2858G>C, c. 680G>A and c. 150_158delGCAGCAGCA were novel). Two cases of infantile-onset spinocerebellar ataxia had TWNK mutations (c. 1163C>T, c. 1319T>C, c. 1388G>A and c. 257_258delAG were novel). One case of myopathy had TK2 mutations (c.557C>G and c.341A>T were novel). Conclusions: The clinical and genetic features of MDS were heterogeneous. Eighteen novel mutations in six MDS related genes were reported, which expanded the genetic spectrum of MDS in Chinese children.


Assuntos
DNA Mitocondrial/genética , Doenças Mitocondriais/genética , Doenças Mitocondriais/patologia , Succinato-CoA Ligases , Grupo com Ancestrais do Continente Asiático , Criança , Pré-Escolar , Feminino , Genótipo , Humanos , Lactente , Recém-Nascido , Masculino , Mutação/fisiologia , Fenótipo , Estudos Retrospectivos , Síndrome
20.
Biotechnol J ; 14(7): e1800643, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-30791213

RESUMO

α-l-Arabinofuranosidases are important in the degradation of plant polysaccharides and are used in several industrial processes. Although the use of filamentous fungi for the production of α-l-arabinofuranosidases is widely reported, there are few reports on strain engineering for enhanced production of these enzymes by fungi. In this study, the function of transcription factor AraR in l-arabinose release and catabolism by the fungus Penicillium oxalicum (P. oxalicum) is investigated. Also, a mutant of AraR, AraRA731V , is constructed to improve the production of α-l-arabinofuranosidases on the basis of the sequence homology between AraR and the xylanolytic gene activator XlnR. The AraRA731V -overexpressing strain can synthesize α-l-arabinofuranosidase in the absence of an inducer and shows a 54.1-fold increase in α-l-arabinofuranosidase production and a 7.4-fold increase in α-galactosidase production in the medium containing wheat bran. Determination of the transcript abundances of lignocellulolytic enzyme genes reveals significant upregulation of multiple α-l-arabinofuranosidase genes and downregulation of some cellulolytic and xylanolytic enzyme genes in the engineered strain relative to its parent. Taken together, the results suggest the conserved regulatory function of AraR in the family Trichocomaceae and provide a strategy for engineering fungal strains for enhanced α- l-arabinofuranosidase production.


Assuntos
Alanina/genética , Proteínas Fúngicas/genética , Glicosídeo Hidrolases , Penicillium , Fatores de Transcrição/genética , Arabinose/metabolismo , Proteínas Fúngicas/química , Proteínas Fúngicas/metabolismo , Engenharia Genética , Glicosídeo Hidrolases/análise , Glicosídeo Hidrolases/metabolismo , Mutação/genética , Mutação/fisiologia , Penicillium/genética , Penicillium/metabolismo , Fatores de Transcrição/química , Fatores de Transcrição/metabolismo
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