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1.
Proc Biol Sci ; 287(1934): 20200962, 2020 09 09.
Artigo em Inglês | MEDLINE | ID: mdl-32873209

RESUMO

Although polyploidy is widespread across the plant Tree of Life, its long-term evolutionary significance is still poorly understood. Here, we examine the effects of polyploidy in explaining the large-scale evolutionary patterns within angiosperms by focusing on a single family exhibiting extensive interspecific variation in chromosome numbers. We inferred ploidy from haploid chromosome numbers for 80% of species in the most comprehensive species-level chronogram for the Brassicaceae. After evaluating a total of 94 phylogenetic models of diversification, we found that ploidy influences diversification rates across the Brassicaceae. We also found that despite diversifying at a similar rate to diploids, polyploids have played a significant role in driving present-day differences in species richness among clades. Overall, in addition to highlighting the complexity in the evolutionary consequences of polyploidy, our results suggest that rare successful polyploids persist while significantly contributing to the long-term evolution of clades. Our findings further indicate that polyploidy has played a major role in driving the long-term evolution of the Brassicaceae and highlight the potential of polyploidy in shaping present-day diversity patterns across the plant Tree of Life.


Assuntos
Brassicaceae/genética , Diploide , Poliploidia , Evolução Biológica , Variação Genética , Genoma de Planta , Magnoliopsida , Filogenia , Ploidias
2.
Nat Commun ; 11(1): 4028, 2020 08 12.
Artigo em Inglês | MEDLINE | ID: mdl-32788591

RESUMO

Changes in atmospheric CO2 concentration have played a central role in algal and plant adaptation and evolution. The commercially important red algal genus, Pyropia (Bangiales) appears to have responded to inorganic carbon (Ci) availability by evolving alternating heteromorphic generations that occupy distinct habitats. The leafy gametophyte inhabits the intertidal zone that undergoes frequent emersion, whereas the sporophyte conchocelis bores into mollusk shells. Here, we analyze a high-quality genome assembly of Pyropia yezoensis to elucidate the interplay between Ci availability and life cycle evolution. We find horizontal gene transfers from bacteria and expansion of gene families (e.g. carbonic anhydrase, anti-oxidative related genes), many of which show gametophyte-specific expression or significant up-regulation in gametophyte in response to dehydration. In conchocelis, the release of HCO3- from shell promoted by carbonic anhydrase provides a source of Ci. This hypothesis is supported by the incorporation of 13C isotope by conchocelis when co-cultured with 13C-labeled CaCO3.


Assuntos
Carbono/metabolismo , Genoma , Rodófitas/genética , Rodófitas/metabolismo , Movimentos da Água , Exoesqueleto/química , Animais , Antioxidantes/farmacologia , Composição de Bases/genética , Evolução Biológica , Carbonato de Cálcio/metabolismo , Anidrases Carbônicas/genética , Anidrases Carbônicas/metabolismo , Núcleo Celular/genética , Dosagem de Genes , Perfilação da Expressão Gênica , Transferência Genética Horizontal/genética , Moluscos , Fotossíntese/efeitos dos fármacos , Ploidias , Rodófitas/efeitos dos fármacos , Superóxido Dismutase/genética , Transcrição Genética/efeitos dos fármacos
3.
PLoS Biol ; 18(8): e3000774, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32745097

RESUMO

The Scar/WAVE complex is the principal catalyst of pseudopod and lamellipod formation. Here we show that Scar/WAVE's proline-rich domain is polyphosphorylated after the complex is activated. Blocking Scar/WAVE activation stops phosphorylation in both Dictyostelium and mammalian cells, implying that phosphorylation modulates pseudopods after they have been formed, rather than controlling whether they are initiated. Unexpectedly, phosphorylation is not promoted by chemotactic signaling but is greatly stimulated by cell:substrate adhesion and diminished when cells deadhere. Phosphorylation-deficient or phosphomimetic Scar/WAVE mutants are both normally functional and rescue the phenotype of knockout cells, demonstrating that phosphorylation is dispensable for activation and actin regulation. However, pseudopods and patches of phosphorylation-deficient Scar/WAVE last substantially longer in mutants, altering the dynamics and size of pseudopods and lamellipods and thus changing migration speed. Scar/WAVE phosphorylation does not require ERK2 in Dictyostelium or mammalian cells. However, the MAPKKK homologue SepA contributes substantially-sepA mutants have less steady-state phosphorylation, which does not increase in response to adhesion. The mutants also behave similarly to cells expressing phosphorylation-deficient Scar, with longer-lived pseudopods and patches of Scar recruitment. We conclude that pseudopod engagement with substratum is more important than extracellular signals at regulating Scar/WAVE's activity and that phosphorylation acts as a pseudopod timer by promoting Scar/WAVE turnover.


Assuntos
Dictyostelium/genética , MAP Quinase Quinase Quinase 3/genética , Proteínas de Protozoários/genética , Pseudópodes/metabolismo , Família de Proteínas da Síndrome de Wiskott-Aldrich/genética , Animais , Sistemas CRISPR-Cas , Adesão Celular , Linhagem Celular Tumoral , Quimiotaxia/genética , Dictyostelium/metabolismo , Dictyostelium/ultraestrutura , Edição de Genes/métodos , Regulação da Expressão Gênica , MAP Quinase Quinase Quinase 3/metabolismo , Melanócitos/metabolismo , Melanócitos/ultraestrutura , Camundongos , Proteína Quinase 1 Ativada por Mitógeno/genética , Proteína Quinase 1 Ativada por Mitógeno/metabolismo , Mutação , Células NIH 3T3 , Fenótipo , Fosforilação , Ploidias , Proteínas de Protozoários/metabolismo , Pseudópodes/genética , Pseudópodes/ultraestrutura , Família de Proteínas da Síndrome de Wiskott-Aldrich/metabolismo
4.
Proc Natl Acad Sci U S A ; 117(31): 18880-18890, 2020 08 04.
Artigo em Inglês | MEDLINE | ID: mdl-32694208

RESUMO

Genomic instability contributes to tumorigenesis through the amplification and deletion of cancer driver genes. DNA copy number (CN) profiling of ensembles of tumors allows a thermodynamic analysis of the profile for each tumor. The free energy of the distribution of CNs is found to be a monotonically increasing function of the average chromosomal ploidy. The dependence is universal across several cancer types. Surprisal analysis distinguishes two main known subgroups: tumors with cells that have or have not undergone whole-genome duplication (WGD). The analysis uncovers that CN states having a narrower distribution are energetically more favorable toward the WGD transition. Surprisal analysis also determines the deviations from a fully stable-state distribution. These deviations reflect constraints imposed by tumor fitness selection pressures. The results point to CN changes that are more common in high-ploidy tumors and thus support altered selection pressures upon WGD.


Assuntos
Dosagem de Genes/genética , Instabilidade Genômica/genética , Neoplasias/genética , Variações do Número de Cópias de DNA/genética , Genoma/genética , Humanos , Ploidias , Termodinâmica
5.
Nat Commun ; 11(1): 3375, 2020 07 06.
Artigo em Inglês | MEDLINE | ID: mdl-32632155

RESUMO

Hybridization can drive speciation. We examine the hypothesis that Castanea henryi var. omeiensis is an evolutionary lineage that originated from hybridization between two near-sympatric diploid taxa, C. henryi var. henryi and C. mollissima. We produce a high-quality genome assembly for mollissima and characterize evolutionary relationships among related chestnut taxa. Our results show that C. henryi var. omeiensis has a mosaic genome but has accumulated divergence in all 12 chromosomes. We observe positive correlation between admixture proportions and recombination rates across the genome. Candidate barrier genomic regions, which isolate var. henryi and mollissima, are re-assorted in the hybrid lineage. We further find that the putative barrier segments concentrate in genomic regions with less recombination, suggesting that interaction between natural selection and recombination shapes the evolution of hybrid genomes during hybrid speciation. This study highlights that reassortment of parental barriers is an important mechanism in generating biodiversity.


Assuntos
Diploide , Fagaceae/genética , Genoma de Planta/genética , Hibridização Genética , Mosaicismo , Ploidias , Algoritmos , Evolução Molecular , Fagaceae/classificação , Especiação Genética , Modelos Genéticos , Recombinação Genética , Seleção Genética , Especificidade da Espécie , Sequenciamento Completo do Genoma/métodos
6.
Nat Commun ; 11(1): 3431, 2020 07 09.
Artigo em Inglês | MEDLINE | ID: mdl-32647202

RESUMO

Claudin-low breast cancers are aggressive tumors defined by the low expression of key components of cellular junctions, associated with mesenchymal and stemness features. Although they are generally considered as the most primitive breast malignancies, their histogenesis remains elusive. Here we show that this molecular subtype of breast cancers exhibits a significant diversity, comprising three main subgroups that emerge from unique evolutionary processes. Genetic, gene methylation and gene expression analyses reveal that two of the subgroups relate, respectively, to luminal breast cancers and basal-like breast cancers through the activation of an EMT process over the course of tumor progression. The third subgroup is closely related to normal human mammary stem cells. This unique subgroup of breast cancers shows a paucity of genomic aberrations and a low frequency of TP53 mutations, supporting the emerging notion that the intrinsic properties of the cell-of-origin constitute a major determinant of the genetic history of tumorigenesis.


Assuntos
Neoplasias da Mama/metabolismo , Claudinas/metabolismo , Neoplasias da Mama/genética , Neoplasias da Mama/patologia , Carcinogênese/genética , Carcinogênese/patologia , Diferenciação Celular , Linhagem Celular Tumoral , Variações do Número de Cópias de DNA/genética , Metilação de DNA/genética , Transição Epitelial-Mesenquimal/genética , Feminino , Regulação Neoplásica da Expressão Gênica , Heterogeneidade Genética , Genoma Humano , Humanos , Ploidias , Transdução de Sinais/genética
7.
PLoS Comput Biol ; 16(7): e1008012, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32658894

RESUMO

Single-cell DNA sequencing technologies are enabling the study of mutations and their evolutionary trajectories in cancer. Somatic copy number aberrations (CNAs) have been implicated in the development and progression of various types of cancer. A wide array of methods for CNA detection has been either developed specifically for or adapted to single-cell DNA sequencing data. Understanding the strengths and limitations that are unique to each of these methods is very important for obtaining accurate copy number profiles from single-cell DNA sequencing data. We benchmarked three widely used methods-Ginkgo, HMMcopy, and CopyNumber-on simulated as well as real datasets. To facilitate this, we developed a novel simulator of single-cell genome evolution in the presence of CNAs. Furthermore, to assess performance on empirical data where the ground truth is unknown, we introduce a phylogeny-based measure for identifying potentially erroneous inferences. While single-cell DNA sequencing is very promising for elucidating and understanding CNAs, our findings show that even the best existing method does not exceed 80% accuracy. New methods that significantly improve upon the accuracy of these three methods are needed. Furthermore, with the large datasets being generated, the methods must be computationally efficient.


Assuntos
Variações do Número de Cópias de DNA , Genoma Humano , Análise de Sequência de DNA/métodos , Análise de Célula Única/métodos , Algoritmos , Aberrações Cromossômicas , Biologia Computacional , Simulação por Computador , Dosagem de Genes , Humanos , Mutação , Neoplasias/genética , Ploidias , Distribuição de Poisson , Curva ROC , Reprodutibilidade dos Testes , Software
8.
Ann Bot ; 126(3): 363-376, 2020 08 13.
Artigo em Inglês | MEDLINE | ID: mdl-32504537

RESUMO

BACKGROUND AND AIMS: Whole-genome duplication is known to influence ecological interactions and plant physiology; however, despite abundant case studies, much is still unknown about the typical impact of genome duplication on plant secondary metabolites (PSMs). In this study, we assessed the impact of polyploidy events on PSM characteristics in non-cultivated plants. METHODS: We conducted a systematic review and meta-analysis to compare composition and concentration of PSMs among closely related plant species or species complexes differing in ploidy level. KEY RESULTS: We assessed 53 studies that focus on PSMs among multiple cytotypes, of which only 14 studies compared concentration quantitatively among cytotypes. We found that whole-genome duplication can have a significant effect on PSM concentration; however, these effects are highly inconsistent. CONCLUSION: Overall, there was no consistent effect of whole-genome duplication on PSM concentrations or profiles.


Assuntos
Duplicação Gênica , Genoma de Planta/genética , Humanos , Plantas/genética , Ploidias , Poliploidia
10.
PLoS One ; 15(5): e0233885, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32470029

RESUMO

In the Danio species, interspecific hybridization has been conducted in several combinations. Among them, only the hybrid between a zebrafish (D. rerio) female and a spotted danio (D. nigrofasciatus) male was reported to be fertile. However, beyond these investigations, by means of reproductive biology, gametes of the hybrid have also not been investigated genetically. For this study, we induced a hybrid of the D. rerio female and D. nigrofasciatus male in order to study its developmental capacity, reproductive performance and gametic characteristics. Its hybrid nature was genetically verified by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of the rhodopsin gene. Almost all the hybrids (36/37) were males, and only one was female. Developing oocytes were observed in the hybrid female, but ovulated eggs have not been obtained thus far. Microscopic observation revealed various head sizes of sperm in the hybrid males. Flow cytometry showed that the hybrid males generated aneuploid sperm with various ploidy levels up to diploidy. In backcrosses between D. rerio females and hybrid males, fertilization rates were significantly lower than the control D. rerio, and most resultant progeny with abnormal appearance exhibited various kinds of aneuploidies ranging from haploidy to triploidy, but only one viable progeny, which survived more than four months, was triploid. This suggested the contribution of fertile diploid sperm of the hybrid male to successful fertilization and development.


Assuntos
Aneuploidia , Fertilização/fisiologia , Hibridização Genética , Espermatozoides/fisiologia , Peixe-Zebra/genética , Peixe-Zebra/fisiologia , Animais , Cruzamentos Genéticos , DNA/genética , Feminino , Masculino , Ovário/citologia , Ploidias , Rodopsina/genética , Razão de Masculinidade , Espermatozoides/citologia
11.
Nat Commun ; 11(1): 2350, 2020 05 11.
Artigo em Inglês | MEDLINE | ID: mdl-32393766

RESUMO

BET inhibitors are promising therapeutic agents for the treatment of triple-negative breast cancer (TNBC), but the rapid emergence of resistance necessitates investigation of combination therapies and their effects on tumor evolution. Here, we show that palbociclib, a CDK4/6 inhibitor, and paclitaxel, a microtubule inhibitor, synergize with the BET inhibitor JQ1 in TNBC lines. High-complexity DNA barcoding and mathematical modeling indicate a high rate of de novo acquired resistance to these drugs relative to pre-existing resistance. We demonstrate that the combination of JQ1 and palbociclib induces cell division errors, which can increase the chance of developing aneuploidy. Characterizing acquired resistance to combination treatment at a single cell level shows heterogeneous mechanisms including activation of G1-S and senescence pathways. Our results establish a rationale for further investigation of combined BET and CDK4/6 inhibition in TNBC and suggest novel mechanisms of action for these drugs and new vulnerabilities in cells after emergence of resistance.


Assuntos
Quinase 4 Dependente de Ciclina/antagonistas & inibidores , Quinase 6 Dependente de Ciclina/antagonistas & inibidores , Resistencia a Medicamentos Antineoplásicos , Proteínas/antagonistas & inibidores , Neoplasias de Mama Triplo Negativas/tratamento farmacológico , Animais , Azepinas/farmacologia , Pontos de Checagem do Ciclo Celular/efeitos dos fármacos , Proliferação de Células/efeitos dos fármacos , Células Clonais , Quinase 4 Dependente de Ciclina/metabolismo , Quinase 6 Dependente de Ciclina/metabolismo , DNA de Neoplasias/metabolismo , Resistencia a Medicamentos Antineoplásicos/efeitos dos fármacos , Sinergismo Farmacológico , Feminino , Regulação Neoplásica da Expressão Gênica/efeitos dos fármacos , Camundongos , Modelos Biológicos , Mutação/genética , Paclitaxel/farmacologia , Piperazinas/farmacologia , Ploidias , Proteínas/metabolismo , Piridinas/farmacologia , Proteína do Retinoblastoma/genética , Proteína do Retinoblastoma/metabolismo , Resultado do Tratamento , Triazóis/farmacologia , Neoplasias de Mama Triplo Negativas/genética , Regulação para Cima/efeitos dos fármacos , Regulação para Cima/genética
12.
J Vis Exp ; (158)2020 04 19.
Artigo em Inglês | MEDLINE | ID: mdl-32364548

RESUMO

When the liver is injured, hepatocyte numbers decrease, while cell size, nuclear size and ploidy increase. The expansion of non-parenchymal cells such as cholangiocytes, myofibroblasts, progenitors and inflammatory cells also indicate chronic liver damage, tissue remodeling and disease progression. In this protocol, we describe a simple high-throughput approach for calculating changes in the cellular composition of the liver that are associated with injury, chronic disease and cancer. We show how information extracted from two-dimensional (2D) tissue sections can be used to quantify and calibrate hepatocyte nuclear ploidy within a sample and enable the user to locate specific ploidy subsets within the liver in situ. Our method requires access to fixed/frozen liver material, basic immunocytochemistry reagents and any standard high-content imaging platform. It serves as a powerful alternative to standard flow cytometry techniques, which require disruption of freshly collected tissue, loss of spatial information and potential disaggregation bias.


Assuntos
Núcleo Celular/metabolismo , Hepatócitos/metabolismo , Ensaios de Triagem em Larga Escala/métodos , Ploidias , Animais , Automação , Calibragem , Análise de Dados , Feminino , Citometria de Fluxo , Fluorescência , Processamento de Imagem Assistida por Computador , Fígado/metabolismo , Camundongos Endogâmicos C57BL
14.
Plant Biol (Stuttg) ; 22(4): 623-633, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32145146

RESUMO

Saccharum spontaneum L. is one of the most important germplasm resources for modern sugarcane breeding. Exploring the cold tolerance of S. spontaneum clones with different ploidy levels and screening for cold-tolerant material can be helpful in parent selection for breeding cold-tolerant sugarcane. Morphological indices, leaf ultrastructure and physiological indices were used to evaluate the cold tolerance of 36 S. spontaneum clones with different ploidy levels (2n = 40, 48, 54, 60, 64, 78, 80, 88, 92 and 96). The morphological indices of S. spontaneum clones with different ploidy levels were positively correlated with ploidy. Under low-temperature stress, the chloroplast and mitochondrial structures of the clones with high ploidy were more severely damaged than were those of clones with low ploidy. A comprehensive evaluation of the physiological indices showed that the 36 S. spontaneum clones could be divided into four categories: strongly cold tolerant, cold tolerant, moderately cold tolerant and cold sensitive. Correlation analysis of the morphological indices and cold tolerance revealed a significant negative correlation between cold tolerance and ploidy. On the basis of the morphological and physiological indices, optimal stepwise regression equations that can be used for the selection of cold-tolerant S. spontaneum resources were established. The S. spontaneum clones with low ploidy are more cold tolerant than those with high ploidy. Clones 12-37, 13-10 and 12-23 are strongly cold-tolerant germplasm resources, which suggests these germplasm sources have high potential for use in breeding cold-tolerant sugarcane.


Assuntos
Adaptação Fisiológica , Temperatura Baixa , Ploidias , Saccharum , Adaptação Fisiológica/genética , Cruzamento , Saccharum/anatomia & histologia , Saccharum/genética
15.
Cytogenet Genome Res ; 160(1): 47-56, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32172236

RESUMO

The chromosomal constitution of 9 dwarf (D) and 8 semidwarf (SD) lines derived by crossing hexaploid Triticale line NA-75 (AABBRR, 2n = 6x = 42) with Triticumaestivum (AABBDD, 2n = 6x = 42) cv. Chinese Spring was investigated using molecular cytogenetic techniques: fluorescence in situ hybridization and genomic in situ hybridization. A wheat-rye translocation (T4DS.7RL), 8 substitution lines, and a ditelosomic addition line (7RSdt) were identified. In the substitution lines, 1, 2, or 4 pairs of wheat chromosomes, belonging to the A, B, or D genome, were replaced by rye chromosomes. Substitutions between chromosomes belonging to different wheat genomes [5B(5A), 1D(1B)] also occurred. The lines were genetically stable, each carrying 42 chromosomes, except the wheat-rye ditelosomic addition line, which carried 21 pairs of wheat chromosomes and 1 pair of rye telocentric chromosomes (7RS). The chromosome pairing behavior of the lines was studied during metaphase I of meiosis. The chromosome pairing level and the number of ring bivalents were different for each line. Besides rod bivalents, univalent and multivalent associations (tri- and quadrivalents) were also detected. The main goal of the experiment was to develop genetically stable wheat/Triticale recombinant lines carrying chromosomes/chromatin fragments originating from the R genome of Triticale line NA-75. Introgression of rye genes into hexaploid wheat can broaden its genetic diversity, and the newly developed lines can be used in wheat breeding programs.


Assuntos
Meiose/genética , Triticale/genética , Triticum/genética , Cromatina/metabolismo , Pareamento Cromossômico , Cromossomos de Plantas , Cruzamentos Genéticos , Análise Citogenética , Genes de Plantas , Variação Genética , Hibridização In Situ , Hibridização in Situ Fluorescente , Metáfase , Ploidias , Secale/genética , Especificidade da Espécie , Translocação Genética
16.
PLoS Negl Trop Dis ; 14(1): e0007770, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-32004318

RESUMO

BACKGROUND: Genetic exchange in Trypanosoma cruzi is controversial not only in relation to its frequency, but also to its mechanism. Parasexual genetic exchange has been proposed based on laboratory hybrids, but population genomics strongly suggests meiosis in T. cruzi. In addition, mitochondrial introgression has been reported several times in natural isolates although its mechanism is not fully understood yet. Moreover, hybrid T. cruzi DTUs (TcV and TcVI) have inherited at least part of the kinetoplastic DNA (kDNA = mitochondrial DNA) from both parents. METHODOLOGY/PRINCIPAL FINDINGS: In order to address such topics, we sequenced and analyzed fourteen nuclear DNA fragments and three kDNA maxicircle genes in three TcI stocks which are natural clones potentially involved in events of genetic exchange. We also deep-sequenced (a total of 6,146,686 paired-end reads) the minicircle hypervariable region (mHVR) of the kDNA in such three strains. In addition, we analyzed the DNA content by flow cytometry to address cell ploidy. We observed that most polymorphic sites in nuclear loci showed a hybrid pattern in one cloned strain and the other two cloned strains were compatible as parental strains (or nearly related to the true parents). The three clones had almost the same ploidy and the DNA content was similar to the reference strain Sylvio (a nearly diploid strain). Despite maxicircle genes evolve faster than nuclear housekeeping ones, we detected no polymorphisms in the sequence of three maxicircle genes showing mito-nuclear discordance. Lastly, the hybrid stock shared 66% of its mHVR clusters with one putative parent and 47% with the other one; in contrast, the putative parental stocks shared less than 30% of the mHVR clusters between them. CONCLUSIONS/SIGNIFICANCE: The results suggest a reductive division, a natural hybridization, biparental inheritance of the minicircles in the hybrid and maxicircle introgression. The models including such phenomena and explaining the relationships between these three clones are discussed.


Assuntos
DNA de Protozoário/genética , Hibridização Genética , Trypanosoma cruzi/classificação , Trypanosoma cruzi/genética , DNA de Cinetoplasto/genética , Genes de Protozoários , Sequenciamento de Nucleotídeos em Larga Escala , Ploidias , Análise de Sequência de DNA
17.
Bioinformatics ; 36(9): 2938-2940, 2020 05 01.
Artigo em Inglês | MEDLINE | ID: mdl-31960894

RESUMO

SUMMARY: We present sismonr, an R package for an integral generation and simulation of in silico biological systems. The package generates gene regulatory networks, which include protein-coding and non-coding genes along with different transcriptional and post-transcriptional regulations. The effect of genetic mutations on the system behaviour is accounted for via the simulation of genetically different in silico individuals. The ploidy of the system is not restricted to the usual haploid or diploid situations but can be defined by the user to higher ploidies. A choice of stochastic simulation algorithms allows us to simulate the expression profiles of the genes in the in silico system. We illustrate the use of sismonr by simulating the anthocyanin biosynthesis regulation pathway for three genetically distinct in silico plants. AVAILABILITY AND IMPLEMENTATION: The sismonr package is implemented in R and Julia and is publicly available on the CRAN repository (https://CRAN.R-project.org/package=sismonr). A detailed tutorial is available from GitHub at https://oliviaab.github.io/sismonr/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
Algoritmos , Software , Simulação por Computador , Redes Reguladoras de Genes , Humanos , Ploidias
18.
BMC Plant Biol ; 20(1): 6, 2020 Jan 06.
Artigo em Inglês | MEDLINE | ID: mdl-31906864

RESUMO

BACKGROUND: Efficient organogenesis induction in eggplant (Solanum melongena L.) is required for multiple in vitro culture applications. In this work, we aimed at developing a universal protocol for efficient in vitro regeneration of eggplant mainly based on the use of zeatin riboside (ZR). We evaluated the effect of seven combinations of ZR with indoleacetic acid (IAA) for organogenic regeneration in five genetically diverse S. melongena and one S. insanum L. accessions using two photoperiod conditions. In addition, the effect of six different concentrations of indolebutyric acid (IBA) in order to promote rooting was assessed to facilitate subsequent acclimatization of plants. The ploidy level of regenerated plants was studied. RESULTS: In a first experiment with accessions MEL1 and MEL3, significant (p < 0.05) differences were observed for the four factors evaluated for organogenesis from cotyledon, hypocotyl and leaf explants, with the best results obtained (9 and 11 shoots for MEL1 and MEL3, respectively) using cotyledon tissue, 16 h light / 8 h dark photoperiod conditions, and medium E6 (2 mg/L of ZR and 0 mg/L of IAA). The best combination of conditions was tested in the other four accessions and confirmed its high regeneration efficiency per explant when using both cotyledon and hypocotyl tissues. The best rooting media was R2 (1 mg/L IBA). The analysis of ploidy level revealed that between 25 and 50% of the regenerated plantlets were tetraploid. CONCLUSIONS: An efficient protocol for organogenesis of both cultivated and wild accessions of eggplant, based on the use of ZR, is proposed. The universal protocol developed may be useful for fostering in vitro culture applications in eggplant requiring regeneration of plants and, in addition, allows developing tetraploid plants without the need of antimitotic chemicals.


Assuntos
Isopenteniladenosina/análogos & derivados , Organogênese Vegetal/fisiologia , Solanum melongena/crescimento & desenvolvimento , Cotilédone/efeitos dos fármacos , Cotilédone/crescimento & desenvolvimento , Hipocótilo/efeitos dos fármacos , Hipocótilo/crescimento & desenvolvimento , Técnicas In Vitro , Ácidos Indolacéticos/farmacologia , Isopenteniladenosina/farmacologia , Organogênese Vegetal/efeitos dos fármacos , Reguladores de Crescimento de Planta/farmacologia , Folhas de Planta/efeitos dos fármacos , Folhas de Planta/crescimento & desenvolvimento , Brotos de Planta/efeitos dos fármacos , Brotos de Planta/crescimento & desenvolvimento , Ploidias , Regeneração/efeitos dos fármacos , Solanum melongena/metabolismo
19.
Acta Cytol ; 64(3): 256-264, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31466063

RESUMO

BACKGROUND: Effusion cytology is a major diagnostic tool in medicine and has both therapeutic and prognostic implications. One of the dilemmas encountered is the differentiation between atypical cells and reactive mesothelial cells. The use of ancillary tools can reduce this grey zone and help to achieve a definitive diagnosis. OBJECTIVES: The main objective of this study was to evaluate the role of flow cytometry (FCM) and cell block with immunohistochemistry (IHC), along with the clinicoradiological investigations, to achieve a final diagnosis in effusion cytology to the maximum extent possible. METHOD: A prospective study was conducted. Effusion fluids, showing adequate amount and cellularity, were processed for conventional cytology, ploidy analysis by FCM, and cell block analysis, followed by IHC wherever required. Conventional cytological analysis was done by 2 independent pathologists, to look for interobserver variation, if any. The final result was achieved on the basis of integration of the results of the aforementioned studies, cytological details, clinicoradiological information, tissue biopsy findings, and follow-up. RESULT: A total of 90 samples were analyzed. On cytological examination, observer I categorized 60% samples as benign and 18.8% (n = 17) as malignant versus 58% categorized as benign and 23.3% (n = 21) as malignant by observer II. Observer I reported 19 (21.1%) equivocal cases and observer II reported 16 (17.7%). When both pathologists were considered together, the number of equivocal cases increased to 20. Sensitivity and specificity of FCM were 96.67 and 100%, respectively, and 100% for the cell block. On combining all techniques, the equivocal cases were resolved and a total of 33 cases were reported as malignant. However, 3 cases could still not be categorized and were labeled inconclusive. CONCLUSION: Conventional cytology combined with cell block IHC and FCM has the potential to minimize the requirement of tissue biopsy for confirmation. If the first sample is used judiciously for all the techniques, this may reduce the requirement for a second sample and possibly also the time required for a definite diagnosis and the initiation of therapy.


Assuntos
Líquido Ascítico/patologia , Citodiagnóstico/métodos , DNA de Neoplasias/análise , Neoplasias/diagnóstico , Ploidias , Citometria de Fluxo , Humanos , Imuno-Histoquímica/métodos , Neoplasias/genética , Derrame Pericárdico/diagnóstico , Derrame Pleural Maligno/diagnóstico , Sensibilidade e Especificidade
20.
Gut ; 69(1): 18-31, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31171626

RESUMO

OBJECTIVE: Peritoneal carcinomatosis (PC) occurs frequently in patients with gastric adenocarcinoma (GAC) and confers a poor prognosis. Multiplex profiling of primary GACs has been insightful but the underpinnings of PC's development/progression remain largely unknown. We characterised exome/transcriptome/immune landscapes of PC cells from patients with GAC aiming to identify novel therapeutic targets. DESIGN: We performed whole-exome sequencing (WES) and whole transcriptome sequencing (RNA-seq) on 44 PC specimens (43 patients with PC) including an integrative analysis of WES, RNA-seq, immune profile, clinical and pathological phenotypes to dissect the molecular pathogenesis, identifying actionable targets and/or biomarkers and comparison with TCGA primary GACs. RESULTS: We identified distinct alterations in PC versus primary GACs, such as more frequent CDH1 and TAF1 mutations, 6q loss and chr19 gain. Alterations associated with aggressive PC phenotypes emerged with increased mutations in TP53, CDH1, TAF1 and KMT2C, higher level of 'clock-like' mutational signature, increase in whole-genome doublings, chromosomal instability (particularly, copy number losses), reprogrammed microenvironment, enriched cell cycle pathways, MYC activation and impaired immune response. Integrated analysis identified two main molecular subtypes: 'mesenchymal-like' and 'epithelial-like' with discriminating response to chemotherapy (31% vs 71%). Patients with the less responsive 'mesenchymal-like' subtype had high expression of immune checkpoint T-Cell Immunoglobulin And Mucin Domain-Containing Protein 3 (TIM-3), its ligand galectin-9, V-domain Ig suppressor of T cell activation (VISTA) and transforming growth factor-ß as potential therapeutic immune targets. CONCLUSIONS: We have uncovered the unique mutational landscape, copy number alteration and gene expression profile of PC cells and defined PC molecular subtypes, which correlated with PC therapy resistance/response. Novel targets and immune checkpoint proteins have been identified with a potential to be translated into clinics.


Assuntos
Adenocarcinoma/secundário , Neoplasias Peritoneais/secundário , Neoplasias Gástricas/genética , Adenocarcinoma/tratamento farmacológico , Adenocarcinoma/genética , Adenocarcinoma/imunologia , Adulto , Idoso , Idoso de 80 Anos ou mais , Antineoplásicos/uso terapêutico , Instabilidade Cromossômica , Variações do Número de Cópias de DNA/genética , DNA de Neoplasias/genética , Feminino , Perfilação da Expressão Gênica/métodos , Humanos , Masculino , Pessoa de Meia-Idade , Terapia de Alvo Molecular/métodos , Mutação , Neoplasias Peritoneais/tratamento farmacológico , Neoplasias Peritoneais/genética , Neoplasias Peritoneais/imunologia , Ploidias , Neoplasias Gástricas/tratamento farmacológico , Neoplasias Gástricas/imunologia , Sequenciamento Completo do Exoma/métodos
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