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INTRODUCTION: Previous research on voice in Parkinson's disease (PD) has consistently demonstrated alterations in acoustic parameters, including fundamental frequency (F0), maximum phonation time, Shimmer, and Jitter. However, investigations into acoustic parameter alterations in individuals with PD are limited. METHODS: We conducted an experimental study involving 20 PD patients (six women and fourteen men). Subjective measures of voice (VHI-30 scale and GRBAS) and objective measures using the OnlineLAB App tool for analyzing biomechanical correlates of voice were recorded. The app analyzed a total of 22 biomechanical parameters of voice. RESULTS: The results of subjective measures were consistent with findings from previous studies. However, the results of objective measures did not align with studies that employed acoustic measures. CONCLUSIONS: The biomechanical analysis revealed alterations in various parameters according to gender. These findings open up a new avenue of research in voice analysis for patients with PD, whether through acoustic or biomechanical analysis, aiming to determine whether the observed changes in these patients' voices are attributable to age or disease progression. This line of investigation will help elucidate the relative contribution of these factors to vocal alterations in PD patients and provide a more comprehensive understanding of the underlying mechanisms.
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Doença de Parkinson , Distúrbios da Voz , Voz , Masculino , Humanos , Feminino , Doença de Parkinson/complicações , Qualidade da Voz , Fonação , Acústica da Fala , Distúrbios da Voz/etiologiaRESUMO
INTRODUCTION: The predominant alterations in voice of patients with multiple sclerosis (MS) are phonatory instability, vocal asthenia and roughness, shortness of breath, hypophonia, and hypernasality. However, research on alterations of acoustic parameters has few studies and disparate results. The objective of this study was to investigate voice disturbances in patients with MS, both with objective measures (analysis of biomechanical) and subjective measures (scales and questionnaires). METHODS: This is an experimental study with a total of 20 participants with MS. Voice samples were collected, and biomechanical correlates were analyzed through the Clinical Voice Systems program, Online Lab App. The VHI-30 (Voice Handicap Index) questionnaire, the GRBAS (grade, roughness, breathiness, asthenia, strain) scale, and the Hospital Anxiety and Depression Scale were used as subjective measures. RESULTS: Ninety-five percentages of participants feel and describe dysphonic difficulties. Self-perception of vocal disability correlated with auditory vocal perceptual analysis in the sample of women. CONCLUSION: The biomechanical parameters showed alterations in the strength of the glottic closure, the efficiency index, and the structural imbalance index.
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PREMISE: The inference of evolutionary relationships in the species-rich family Orchidaceae has hitherto relied heavily on plastid DNA sequences and limited taxon sampling. Previous studies have provided a robust plastid phylogenetic framework, which was used to classify orchids and investigate the drivers of orchid diversification. However, the extent to which phylogenetic inference based on the plastid genome is congruent with the nuclear genome has been only poorly assessed. METHODS: We inferred higher-level phylogenetic relationships of orchids based on likelihood and ASTRAL analyses of 294 low-copy nuclear genes sequenced using the Angiosperms353 universal probe set for 75 species (representing 69 genera, 16 tribes, 24 subtribes) and a concatenated analysis of 78 plastid genes for 264 species (117 genera, 18 tribes, 28 subtribes). We compared phylogenetic informativeness and support for the nuclear and plastid phylogenetic hypotheses. RESULTS: Phylogenetic inference using nuclear data sets provides well-supported orchid relationships that are highly congruent between analyses. Comparisons of nuclear gene trees and a plastid supermatrix tree showed that the trees are mostly congruent, but revealed instances of strongly supported phylogenetic incongruence in both shallow and deep time. The phylogenetic informativeness of individual Angiosperms353 genes is in general better than that of most plastid genes. CONCLUSIONS: Our study provides the first robust nuclear phylogenomic framework for Orchidaceae and an assessment of intragenomic nuclear discordance, plastid-nuclear tree incongruence, and phylogenetic informativeness across the family. Our results also demonstrate what has long been known but rarely thoroughly documented: nuclear and plastid phylogenetic trees can contain strongly supported discordances, and this incongruence must be reconciled prior to interpretation in evolutionary studies, such as taxonomy, biogeography, and character evolution.
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Genomas de Plastídeos , Orchidaceae , Núcleo Celular/genética , Orchidaceae/genética , Filogenia , Plastídeos/genéticaRESUMO
Polyploidy, or whole-genome duplication (WGD), is a recurrent mutation both in cell lineages and over evolutionary time. By globally changing the relationship between gene copy number and other cellular entities, it can induce dramatic changes at the cellular and phenotypic level. Perhaps surprisingly, then, the insights that these events can bring to understanding other cellular features are not as well appreciated as they could be. In this review, we draw on examples of polyploidy from animals, plants and yeast to explore how investigations of polyploid cells have improved our understanding of the cell cycle, biological network complexity, metabolic phenotypes and tumor biology. We argue that the study of polyploidy across organisms, cell types, and time scales serves not only as a window into basic cell biology, but also as a basis for a predictive biology with applications ranging from crop improvement to treating cancer.
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Evolução Biológica , Genoma , Poliploidia , Animais , Evolução Molecular , Humanos , Plantas/genéticaRESUMO
Our aim was to evaluate the morbidity and survival associated with combined cytoreductive surgery and hyperthermic intraperitoneal chemotherapy (HIPEC) in the treatment of recurrent ovarian cancer for patients aged 70 years and older. We conducted a monocentric study in a French university hospital and collected data on 15 women aged ≥ 70 years, treated by cytoreduction and HIPEC for ovarian cancer relapse. The median overall survival was 35 months, with a median disease-free survival of 15.6 months. When a Peritoneal Cancer Index subgroup analysis was performed, a statistically significant difference in the disease-free survival could be observed for a Peritoneal Cancer Index ≤ 13 (p = 0.036). A trend towards improvement of disease-free survival was observed when the Completeness of Cytoreductive Score was equal to 0 (p = 0.0915).
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Protocolos de Quimioterapia Combinada Antineoplásica/uso terapêutico , Hipertermia Induzida , Recidiva Local de Neoplasia/terapia , Neoplasias Ovarianas/terapia , Neoplasias Peritoneais/secundário , Neoplasias Peritoneais/terapia , Peritônio/cirurgia , Fatores Etários , Idoso , Antineoplásicos/administração & dosagem , Quimioterapia Adjuvante , Cisplatino/administração & dosagem , Terapia Combinada , Doxorrubicina/administração & dosagem , Feminino , Seguimentos , Humanos , Recidiva Local de Neoplasia/mortalidade , Neoplasias Ovarianas/mortalidade , Neoplasias Ovarianas/patologia , Neoplasias Peritoneais/mortalidade , Estudos Retrospectivos , Análise de Sobrevida , Resultado do TratamentoRESUMO
The biogeography, chromosome number evolution, pollination biology and evolutionary history of the plant family Araceae have recently become much clearer (Cabrera et al., 2008; Chartier et al., 2013; Cusimano et al., 2011, 2012; Nauheimer et al., 2012). However, phylogenetic ambiguity near the root of the tree precludes answering questions about the early evolution of the family. We use Illumina sequencing technology and reference based assembly to resolve the remaining questions in the deep phylogeny of Araceae. We sampled 32 genera and obtained 7 from GenBank (including an outgroup), representing 42 of 44 major clades described in Cusimano et al. (2011). A subsequent phylogenomic analysis based on mitochondrial data was performed to test congruence between plastid and mitochondrial data for phylogenetic inference. Plastid sequences produced strongly supported phylogenies. In contrast, mitochondrial phylogenies were weakly supported and incongruent with chloroplast data (Templeton test, p⩽0.0001), although several smaller clades were recovered. New strongly-supported clades seen here are: (1) Anubias and Montrichardia, excluding Calla, form a clade that is sister to the Zantedeschia clade; (2) the South African genus Zantedeschia is sister to the Old World Anchomanes clade; and (3) within the Zantedeschia clade, Philodendron is sister to the rest. Calla and Schismatoglottis form a clade at the base of one of two major clades in Aroideae based on complete chloroplast sequences. Although statistical support is weak, morphological and cytological features support this topology.
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Araceae/classificação , DNA de Cloroplastos/genética , DNA Mitocondrial/genética , Evolução Molecular , Filogenia , Araceae/genética , Teorema de Bayes , DNA de Plantas/genética , Funções Verossimilhança , Análise de Sequência de DNARESUMO
PREMISE OF THE STUDY: Cruciferous vegetables, many of which are in the genus Brassica (Brassicaceae), are prized for their nutritive value and have been cultivated for thousands of years. There are numerous wild northwestern Mediterranean species in the tribe Brassiceae, and it is therefore assumed this center of diversity is also the region of origin. Within the tribe, the Nigra and Oleracea clades contain the three diploid Brassica crops, B. oleracea, B. rapa, and B. nigra. These three species hybridized in the past to form the tetraploid crop species B. juncea, B. carinata, and B. napus. Collectively, these crop Brassicas have been thought to be closely related because they can still hybridize. METHODS: Using a combination of molecular phylogenetics, diversification analysis, and historical biogeography, we evaluated the relationships and origins of four nested clades: the tribe Brassiceae, the Nigra-Oleracea clade, the core Oleracea (includes B. oleracea + B. rapa and their respective wild relatives), and Brassica oleracea and relatives. KEY RESULTS: We found evidence that the tribe originated around the intersection forming between the Arabian Peninsula and Saharan Africa approximately 24 million years ago (Mya). Our data also suggest that the maternal genomes of the three diploid crop Brassicas are not closely related and that the Nigra-Oleracea clade diverged 20 Mya. Finally, our analyses indicate that the core Oleracea lineage giving rise to B. oleracea + B. rapa originated ≈3 Mya in the northeastern Mediterranean, from where ancestors of B. oleracea spread through Europe and B. rapa to Asia. CONCLUSIONS: These results challenge previous hypotheses about the biogeographic origins of the tribe Brassiceae and the crop Brassica species and appear to be correlated with major geological and climatic events in the Mediterranean basin.
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Brassica/genética , Produtos Agrícolas/genética , Variação Genética , Hibridização Genética , Filogenia , Filogeografia , Fatores de TempoRESUMO
A checklist of Orchidaceae from Caquetá, Colombia is presented here. We recorded 98 genera and 418 species, exceeding a previous inventory by 276 species. The checklist is conservative in the number of genera and species by including only taxa that were fully and reliably identified and that are either linked to a corresponding herbarium voucher, a living collection specimen or a photo taken in the field and published in iNaturalist by one of the authors or a collaborator. The documented species diversity in the region could dramatically increase in the next few years with additional collecting efforts in the eastern slopes of the Andes nested in Caquetá. About 9% (418/4600) of all Orchidaceae species recorded for Colombia are reported for this area, showing the important contribution to orchid diversity of Andean-Amazonian foothills of Caquetá.
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INTRODUCTION: Covid-19 is an infectious disease with a different symptomatic implication depending on each person. There are sequelae in the nervous, cardiovascular, and/or digestive system that involve the approach and multidisciplinary work of different health professionals where the speech therapist is included. In this way, we can speak of a direct relationship between speech therapy and Covid-19; especially in those patients with serious sequelae such as the inability to eat and/or speak and the loss of voice. The damage caused to the laryngeal mucosa triggers the loss of some of the qualities of the voice, limiting oral communication. That is why we can find dysphonias caused by a great weakness, by a continuous overexertion or because of a paralysis of the vocal cords. OBJECTIVES/HYPOTHESIS: The objective of this study was to identify the patterns of behavior in the biomechanical correlates of people who passed Covid-19 symptomatically with sequelae in voice. METHODS: An experimental study with a total of 21 participants (11 women and 10 men) with sequelae in voice post Covid-19 is presented. Voice samples were collected and biomechanical correlates were analyzed through the Voice Clinical Systems program. RESULTS AND CONCLUSIONS: The results show different altered biomechanical patterns between men and women that correlate with other infectious diseases.
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Genetic diversity and relatedness of accessions for coconut growing in Colombia was unknown until this study. Here we develop single nucleotide polymorphisms (SNPs) along the coconut genome based on Genotyping by Sequencing (GBS) with the goal of analyze the genetic diversity, population structure, and linkage disequilibrium (LD) of a diverse coconut panel consisting of 112 coconut accessions from the Atlantic and Pacific coasts of Colombia. A comprehensive catalog of approximately 40,000 SNPs with a minor allele frequency (MAF) of > 0.05 is presented. A total of 40,614 SNPs were found but only 19,414 anchored to chromosomes. Of these, 10,338 and 4606 were exclusive to the Atlantic and Pacific gene pools, respectively, and 3432 SNPs could differentiate both gene pools. A filtered subset of unlinked and anchored SNPs (1271) showed a population structure at K = 4, separating accessions from the Pacific and Atlantic coasts that can also be distinguished by palm height, as found in previous studies. The Pacific groups had a slow LD decay, low Fixation Index (Fst) and low nucleotide diversity (π), while the Atlantic group had slightly higher genetic diversity and faster LD decay. Genome-wide diversity analyses are of importance to promote germplasm conservation and breeding programs aimed at developing new cultivars better adapted to the region.
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Cocos/genética , Frequência do Gene , Genoma de Planta , Desequilíbrio de Ligação , Melhoramento Vegetal , Polimorfismo de Nucleotídeo Único , Colômbia , Estudo de Associação Genômica Ampla , Técnicas de GenotipagemRESUMO
Many fungal pathogens are carried and transmitted by seeds. These pathogens affect germination and seed quality. Their transmission from the germinating seed to seedling causes many diseases in crops. Seed defense mechanisms during germination are poorly documented. RNA-seq experiments were used to describe the molecular mechanisms involved in seed interaction with a necrotrophic fungus. Here the Arabidopsis thaliana/Alternaria brassicicola pathosystem was used to perform dual-transcriptomic approach. Arabidopsis thaliana seeds and necrotrophic fungus transcripts were identified at critical germination and seedling establishment stages. Total RNA was extracted from healthy and infected germinating seeds and seedlings at 3, 6 and 10 days after sowing. Transcript libraries were made and sequenced, then fungal and plant short reads were mapped and quantified respectively against Arabidopsis thaliana and Alternaria brassicicola reference transcriptomes. This dual-transcriptomic approach revealed that 3409, 7506 and 8589 Arabidopsis thaliana genes showed a differential expression at respectevely 3, 6 and 10 days after sowing between healthy and infected seeds, including 1192 genes differentially expressed at the three studied stages. Moreover, in this experiement, we also identified the dynamic of the transcript changes occurring at the same stages in the necrotrophic fungus concomitantly during germination and seedling establishment.
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The transmission of seed-borne pathogens by the germinating seed is responsible for major crop diseases. The immune responses of the seed facing biotic invaders are poorly documented so far. The Arabidopsis thaliana/Alternaria brassicicola patho-system was used to describe at the transcription level the responses of germinating seeds and young seedling stages to infection by the necrotrophic fungus. RNA-seq analyses of healthy versus inoculated seeds at 3 days after sowing (DAS), stage of radicle emergence, and at 6 and 10 DAS, two stages of seedling establishment, identified thousands of differentially expressed genes by Alternaria infection. Response to hypoxia, ethylene and indole pathways were found to be induced by Alternaria in the germinating seeds. However, surprisingly, the defense responses, namely the salicylic acid (SA) pathway, the response to reactive oxygen species (ROS), the endoplasmic reticulum-associated protein degradation (ERAD) and programmed cell death, were found to be strongly induced only during the latter post-germination stages. We propose that this non-canonical immune response in early germinating seeds compared to early seedling establishment was potentially due to the seed-to-seedling transition phase. Phenotypic analyses of about 14 mutants altered in the main defense pathways illustrated these specific defense responses. The unexpected germination deficiency and insensitivity to Alternaria in the glucosinolate deficient mutants allow hypothesis of a trade-off between seed germination, necrosis induction and Alternaria transmission to the seedling. The imbalance of the SA and jasmonic acid (JA) pathways to the detriment of the JA also illustrated a non-canonical immune response at the first stages of the seedling.
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PREMISE: Multiple transitions from insect to wind pollination are associated with polyploidy and unisexual flowers in Thalictrum (Ranunculaceae), yet the underlying genetics remains unknown. We generated a draft genome of Thalictrum thalictroides, a representative of a clade with ancestral floral traits (diploid, hermaphrodite, and insect pollinated) and a model for functional studies. Floral transcriptomes of T. thalictroides and of wind-pollinated, andromonoecious T. hernandezii are presented as a resource to facilitate candidate gene discovery in flowers with different sexual and pollination systems. METHODS: A draft genome of T. thalictroides and two floral transcriptomes of T. thalictroides and T. hernandezii were obtained from HiSeq 2000 Illumina sequencing and de novo assembly. RESULTS: The T. thalictroides de novo draft genome assembly consisted of 44,860 contigs (N50 = 12,761 bp, 243 Mbp total length) and contained 84.5% conserved embryophyte single-copy genes. Floral transcriptomes contained representatives of most eukaryotic core genes, and most of their genes formed orthogroups. DISCUSSION: To validate the utility of these resources, potential candidate genes were identified for the different floral morphologies using stepwise data set comparisons. Single-copy gene analysis and simple sequence repeat markers were also generated as a resource for population-level and phylogenetic studies.
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Morphotypes of Brassica oleracea are the result of a dynamic interaction between genes that regulate the transition between vegetative and reproductive stages and those that regulate leaf morphology and plant architecture. In kales, ornate leaves, extended vegetative phase, and nutritional quality are some of the characters potentially selected by humans during domestication. We used a combination of developmental studies and transcriptomics to understand the vegetative domestication syndrome of kale. To identify candidate genes that are responsible for the evolution of domestic kale, we searched for transcriptome-wide differences among three vegetative B. oleracea morphotypes. RNA-seq experiments were used to understand the global pattern of expressed genes during a mixture of stages at one time in kale, cabbage, and the rapid cycling kale line TO1000. We identified gene expression patterns that differ among morphotypes and estimate the contribution of morphotype-specific gene expression that sets kale apart (3958 differentially expressed genes). Differentially expressed genes that regulate the vegetative to reproductive transition were abundant in all morphotypes. Genes involved in leaf morphology, plant architecture, defense, and nutrition were differentially expressed in kale. This allowed us to identify a set of candidate genes we suggest may be important in the kale domestication syndrome. Understanding candidate genes responsible for kale domestication is of importance to ultimately improve Cole crop production.
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Mycosphaerellaceae is a highly diverse fungal family containing a variety of pathogens affecting many economically important crops. Mitochondria play a crucial role in fungal metabolism and in the study of fungal evolution. This study aims to: (i) describe the mitochondrial genome of Pseudocercospora fijiensis, and (ii) compare it with closely related species (Sphaerulina musiva, S. populicola, P. musae and P. eumusae) available online, paying particular attention to the Sigatoka disease's complex causal agents. The mitochondrial genome of P. fijiensis is a circular molecule of 74,089 bp containing typical genes coding for the 14 proteins related to oxidative phosphorylation, 2 rRNA genes and a set of 38 tRNAs. P. fijiensis mitogenome has two truncated cox1 copies, and bicistronic transcription of nad2-nad3 and atp6-atp8 confirmed experimentally. Comparative analysis revealed high variability in size and gene order among selected Mycosphaerellaceae mitogenomes likely to be due to rearrangements caused by mobile intron invasion. Using fossil calibrated Bayesian phylogenies, we found later diversification times for Mycosphaerellaceae (66.6 MYA) and the Sigatoka disease complex causal agents, compared to previous strict molecular clock studies. An early divergent Pseudocercospora fijiensis split from the sister species P. musae + P. eumusae 13.31 MYA while their sister group, the sister species P. eumusae and P. musae, split from their shared common ancestor in the late Miocene 8.22 MYA. This newly dated phylogeny suggests that species belonging to the Sigatoka disease complex originated after wild relatives of domesticated bananas (section Eumusae; 27.9 MYA). During this time frame, mitochondrial genomes expanded significantly, possibly due to invasions of introns into different electron transport chain genes.
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Recent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes. However, uncertainty remains within several subtribes and genera for which phylogenetic relationships have not ever been tested in a phylogenomic context. To address these knowledge-gaps, we here provide the most extensively sampled analysis of the orchid family to date, based on 78 plastid coding genes representing 264 species, 117 genera, 18 tribes and 28 subtribes. Divergence times are also provided as inferred from strict and relaxed molecular clocks and birth-death tree models. Our taxon sampling includes 51 newly sequenced plastid genomes produced by a genome skimming approach. We focus our sampling efforts on previously unplaced clades within tribes Cymbidieae and Epidendreae. Our results confirmed phylogenetic relationships in Orchidaceae as recovered in previous studies, most of which were recovered with maximum support (209 of the 262 tree branches). We provide for the first time a clear phylogenetic placement for Codonorchideae within subfamily Orchidoideae, and Podochilieae and Collabieae within subfamily Epidendroideae. We also identify relationships that have been persistently problematic across multiple studies, regardless of the different details of sampling and genomic datasets used for phylogenetic reconstructions. Our study provides an expanded, robust temporal phylogenomic framework of the Orchidaceae that paves the way for biogeographical and macroevolutionary studies.
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Biodiversidade , Evolução Molecular , Genomas de Plastídeos , Orchidaceae/genética , Filogenia , Plastídeos/genética , Orchidaceae/classificaçãoRESUMO
Background: Although most thyroid nodules with indeterminate cytology are benign, in most of the world, surgery remains as the most frequent diagnostic approach. We have previously reported a 10-gene thyroid genetic classifier, which accurately predicts benign thyroid nodules. The assay is a prototype diagnostic kit suitable for reference laboratory testing and could potentially avoid unnecessary diagnostic surgery in patients with indeterminate thyroid cytology. Methods: Classifier performance was tested in two independent, ethnically diverse, prospective multicenter trials (TGCT-1/Chile and TGCT-2/USA). A total of 4061 fine-needle aspirations were collected from 15 institutions, of which 897 (22%) were called indeterminate. The clinical site was blind to the classifier score and the clinical laboratory blind to the pathology report. A matched surgical pathology and valid classifier score was available for 270 samples. Results: Cohorts showed significant differences, including (i) clinical site patient source (academic, 43% and 97% for TGCT-1 and -2, respectively); (ii) ethnic diversity, with a greater proportion of the Hispanic population (40% vs. 3%) for TGCT-1 and a greater proportion of African American (11% vs. 0%) and Asian (10% vs. 1%) populations for TGCT-2; and (iii) tumor size (mean of 1.7 and 2.5 cm for TGCT-1 and -2, respectively). Overall, there were no differences in the histopathological profile between cohorts. Forty-one of 155 and 45 of 115 nodules were malignant (cancer prevalence of 26% and 39% for TGCT-1 and -2, respectively). The classifier predicted 37 of 41 and 41 of 45 malignant nodules, yielding a sensitivity of 90% [95% confidence interval; CI 77-97] and 91% [95% CI 79-98] for TGCT-1 and -2, respectively. One hundred one of 114 and 61 of 70 nodules were correctly predicted as benign, yielding a specificity of 89% [95% CI 82-94] and 87% [95% CI 77-94], respectively. The negative predictive values for TGCT-1 and TGCT-2 were 96% and 94%, respectively, whereas the positive predictive values were 74% and 82%, respectively. The overall accuracy for both cohorts was 89%. Conclusions: Clinical validation of the classifier demonstrates equivalent performance in two independent and ethnically diverse cohorts, accurately predicting benign thyroid nodules that can undergo surveillance as an alternative to diagnostic surgery.
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Glândula Tireoide/patologia , Neoplasias da Glândula Tireoide/genética , Nódulo da Glândula Tireoide/genética , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Biópsia por Agulha Fina , Citodiagnóstico , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Estudos Prospectivos , Sensibilidade e Especificidade , Neoplasias da Glândula Tireoide/patologia , Nódulo da Glândula Tireoide/patologia , Adulto JovemRESUMO
PREMISE: Chloroplast primers were developed for phylogenetic and comparative studies in Thalictrum (Ranunculaceae). METHODS AND RESULTS: We assembled and annotated the complete plastome sequence of T. thalictroides by combining multiple whole genome sequencing libraries. Using transcriptome-sequencing libraries, we also assembled a partial plastome of the related species T. hernandezii. From the newly assembled plastomes and one previously sequenced plastome, we designed and validated 28 primer pairs to target variable portions of the chloroplast genome in Thalictrum. Furthermore, we tested the validated primers in 62 species of Thalictrum. The total alignment length of the 28 regions was 15,268 bp with 2443 variable sites and 92% character occupancy. CONCLUSIONS: The newly developed chloroplast primer pairs improve the phylogenetic resolution (bootstrap support and tree certainty) in Thalictum and will be a useful resource for future phylogenetic and evolutionary studies for species in the genus and in close relatives in Thalictroideae.
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BACKGROUND: In most of the world, diagnostic surgery remains the most frequent approach for indeterminate thyroid cytology. Although several molecular tests are available for testing in centralized commercial laboratories in the United States, there are no available kits for local laboratory testing. The aim of this study was to develop a prototype in vitro diagnostic (IVD) gene classifier for the further characterization of nodules with an indeterminate thyroid cytology. METHODS: In a first stage, the expression of 18 genes was determined by quantitative polymerase chain reaction (qPCR) in a broad histopathological spectrum of 114 fresh-tissue biopsies. Expression data were used to train several classifiers by supervised machine learning approaches. Classifiers were tested in an independent set of 139 samples. In a second stage, the best classifier was chosen as a model to develop a multiplexed-qPCR IVD prototype assay, which was tested in a prospective multicenter cohort of fine-needle aspiration biopsies. RESULTS: In tissue biopsies, the best classifier, using only 10 genes, reached an optimal and consistent performance in the ninefold cross-validated testing set (sensitivity 93% and specificity 81%). In the multicenter cohort of fine-needle aspiration biopsy samples, the 10-gene signature, built into a multiplexed-qPCR IVD prototype, showed an area under the curve of 0.97, a positive predictive value of 78%, and a negative predictive value of 98%. By Bayes' theorem, the IVD prototype is expected to achieve a positive predictive value of 64-82% and a negative predictive value of 97-99% in patients with a cancer prevalence range of 20-40%. CONCLUSIONS: A new multiplexed-qPCR IVD prototype is reported that accurately classifies thyroid nodules and may provide a future solution suitable for local reference laboratory testing.
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Regulação Neoplásica da Expressão Gênica , Proteínas de Neoplasias/metabolismo , Glândula Tireoide/metabolismo , Neoplasias da Glândula Tireoide/diagnóstico , Nódulo da Glândula Tireoide/diagnóstico , Biomarcadores Tumorais/metabolismo , Biópsia por Agulha Fina , Chile/epidemiologia , Estudos de Coortes , Biologia Computacional , Diagnóstico Diferencial , Sistemas Inteligentes , Seguimentos , Humanos , Aprendizado de Máquina , Proteínas de Neoplasias/genética , Estadiamento de Neoplasias , Guias de Prática Clínica como Assunto , Valor Preditivo dos Testes , Prevalência , Estudos Prospectivos , Reprodutibilidade dos Testes , Sensibilidade e Especificidade , Glândula Tireoide/patologia , Neoplasias da Glândula Tireoide/epidemiologia , Neoplasias da Glândula Tireoide/metabolismo , Neoplasias da Glândula Tireoide/patologia , Nódulo da Glândula Tireoide/epidemiologia , Nódulo da Glândula Tireoide/metabolismo , Nódulo da Glândula Tireoide/patologiaRESUMO
Acyl-CoA-binding protein (ACBP) was first identified in mammals as a neuropeptide, and was demonstrated to belong to an important house-keeping protein family that extends across eukaryotes and some prokaryotes. In plants, the Arabidopsis ACBP family consists of six AtACBPs (AtACBP1 to AtACBP6), and has been investigated using gene knock-out mutants and overexpression lines. Herein, recent findings on the AtACBPs are examined to provide an insight on their functions in various plant developmental processes, such as embryo and seed development, seed dormancy and germination, seedling development and cuticle formation, as well as their roles under various environmental stresses. The significance of the AtACBPs in acyl-CoA/lipid metabolism, with focus on their interaction with long to very-long-chain (VLC) acyl-CoA esters and their potential role in the formation of lipid droplets in seeds and vegetative tissues are discussed. In addition, recent findings on the rice ACBP family are presented. The similarities and differences between ACBPs from Arabidopsis and rice, that represent eudicot and monocot model plants, respectively, are analyzed and the evolution of plant ACBPs by phylogenetic analysis reviewed. Finally, we propose potential uses of plant ACBPs in phytoremediation and in agriculture related to the improvement of environmental stress tolerance and seed oil production.