ABSTRACT
An 83-year-old man presented an elevated skin lesion in the left temporal area. The resected specimen was identified between a basal cell carcinoma and an atypical fibroxanthoma. A final diagnosis of basal cell carcinoma and atypical fibroxanthoma was made. This study reports a rare case of a cutaneous collision.
ABSTRACT
Despite effective vaccines, measles virus (MeV) outbreaks occur sporadically. Therefore, developing anti-MeV agents remains important for suppressing MeV infections. We previously designed peptide-based MeV fusion inhibitors, M1 and M2, that target MeV class I fusion protein (F protein). Here, we developed a novel fusion inhibitor, MEK35, that exerts potent activity against M1/M2-resistant MeV variants. Comparing MEK35 to M1 derivatives revealed that combining disordered and helical elements was essential for overcoming M1/M2 resistance. Moreover, we propose a three-step antiviral process for peptide-based fusion inhibitors: (i) disordered peptides interact with F protein; (ii) the peptides adopt a partial helical conformation and bind to F protein through hydrophobic interactions; and (iii) subsequent interactions involving the disordered region of the peptides afford a peptide-F protein with a high-affinity peptide-F protein interaction. An M1-resistant substitution blocks the second step. These results should aid the development of novel viral fusion inhibitors targeting class I F protein.
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Common buckwheat, Fagopyrum esculentum, is an orphan crop domesticated in southwest China that exhibits heterostylous self-incompatibility. Here we present chromosome-scale assemblies of a self-compatible F. esculentum accession and a self-compatible wild relative, Fagopyrum homotropicum, together with the resequencing of 104 wild and cultivated F. esculentum accessions. Using these genomic data, we report the roles of transposable elements and whole-genome duplications in the evolution of Fagopyrum. In addition, we show that (1) the breakdown of heterostyly occurs through the disruption of a hemizygous gene jointly regulating the style length and female compatibility and (2) southeast Tibet was involved in common buckwheat domestication. Moreover, we obtained mutants conferring the waxy phenotype for the first time in buckwheat. These findings demonstrate the utility of our F. esculentum assembly as a reference genome and promise to accelerate buckwheat research and breeding.
Subject(s)
Fagopyrum , Fagopyrum/genetics , Domestication , Plant Breeding , Chromosome Mapping , Base SequenceABSTRACT
BACKGROUND: The onset of schizophrenia is associated with both genetic and environmental risks during brain development. Environmental factors during pregnancy can represent risk factors for schizophrenia, and we have previously reported that several microRNA and mRNA expression changes in fetal brains exposed to haloperidol during pregnancy may be related to the onset of this disease. This study aimed to replicate that research and focused on apoptotic-related gene expression changes. METHODS: Haloperidol (1 mg/kg) or aripiprazole (1 mg/kg) was injected into pregnant mice. Using RNA sequencing for the hippocampus of each offspring born from pregnant mice exposed to haloperidol, we analyzed genes identified as changed in our previous report and validated two apoptosis-related genes (Cdkn1a and Apaf1) using quantitative polymerase chain reaction (qPCR) methods. Furthermore, we attempted to elucidate the direct effects of haloperidol and aripiprazole on those mRNA expressions in in vitro experiments. RESULTS: RNA sequencing successfully replicated 16 up-regulated and 5 down-regulated genes in this study. Of those, up-regulations of Cdkn1a and Apaf1 mRNA expression were successfully validated by direct quantification. Moreover, haloperidol and aripiprazole dose-dependent upregulation of both mRNA expressions were confirmed in a Neuro2a cell line. CONCLUSIONS: In the hippocampus of offspring, intraperitoneal injection of haloperidol to pregnant mice induced up-regulation of apoptotic genes that representing the phenotypic change without apoptosis. These findings will be useful for understanding the molecular biological mechanisms underlying the effects of antipsychotics on the fetal brain.
Subject(s)
Antipsychotic Agents , Quinolones , Mice , Animals , Haloperidol/pharmacology , Aripiprazole/pharmacology , Piperazines/pharmacology , Quinolones/pharmacology , Antipsychotic Agents/pharmacology , Hippocampus/metabolism , RNA, Messenger/metabolismABSTRACT
Serine hydroxymethyltransferase (SHMT) produces 5,10-methylenetetrahydrofolate (CH2-THF) from tetrahydrofolate with serine to glycine conversion. SHMT is a potential drug target in parasites, viruses and cancer. (+)-SHIN-1 was developed as a human SHMT inhibitor for cancer therapy. However, the potential of SHMT as an antibacterial target is unknown. Here, we show that (+)-SHIN-1 bacteriostatically inhibits the growth of Enterococcus faecium at a 50% effective concentration of 10-11 M and synergistically enhances the antibacterial activities of several nucleoside analogues. Our results, including crystal structure analysis, indicate that (+)-SHIN-1 binds tightly to E. faecium SHMT (efmSHMT). Two variable loops in SHMT are crucial for inhibitor binding, and serine binding to efmSHMT enhances the affinity of (+)-SHIN-1 by stabilising the loop structure of efmSHMT. The findings highlight the potency of SHMT as an antibacterial target and the possibility of developing SHMT inhibitors for treating bacterial, viral and parasitic infections and cancer.
Subject(s)
Glycine Hydroxymethyltransferase , Neoplasms , Anti-Bacterial Agents/pharmacology , Carbon , Glycine Hydroxymethyltransferase/chemistry , Glycine Hydroxymethyltransferase/metabolism , Humans , Serine/metabolismABSTRACT
BACKGROUND: Late-onset Alzheimer's disease (LOAD) is a complex disease in which neuroinflammation plays an important pathophysiological role, and exposure to neurotoxic substrates such as aldehydes may contribute. Blood mRNA expression levels of neuroinflammation-related genes appear to be potential biological markers of LOAD. A relationship between ALDH2 and LOAD has been suggested. OBJECTIVE: Our objective was to examine blood ALDH2 expression in Japanese LOAD patients, conduct a genetic association study, and add new studies to an extended meta-analysis of the Asian population. METHODS: A blood expression study (45 AD subjects, 54 controls) in which total RNA was isolated from whole peripheral blood samples and ALDH2 expression measured was conducted. In addition, a genetic association study (271 AD subjects, 492 controls) using genomic DNA from whole peripheral blood samples was conducted. Finally, a meta-analysis examined the relationship between ALDH2*2 frequency and the risk of LOAD. RESULTS: ALDH2 mRNA expression was significantly higher in LOAD than in controls, and also higher in men with LOAD than in women with LOAD (pâ=â0.043). The genotypes in the two classified groups and the allele frequency were significantly different between AD and control subjects. The meta-analysis showed a significant difference in the ALDH2*2 allele, with an increased AD risk (ORâ=â1.38; 95% CIâ=â1.02-1.85; pâ=â0.0348, I2â=â81.1%). CONCLUSION: There was a significant increase in blood ALDH2 expression, and a genetic association with ALDH2*2 in LOAD. ALDH2 may have significant roles in the pathogenesis of LOAD in the Asian population.
Subject(s)
Alzheimer Disease , Aldehyde Dehydrogenase/genetics , Aldehyde Dehydrogenase, Mitochondrial/genetics , Alzheimer Disease/genetics , Female , Genetic Predisposition to Disease/genetics , Humans , Male , Polymorphism, Genetic , Polymorphism, Single Nucleotide/genetics , RNA, MessengerABSTRACT
Aim: This study aimed to investigate the expression levels and methylation status of microtubule-associated protein tau (MAPT) in the blood of Alzheimer's disease (AD) patients and age- and sex-matched healthy controls. Methods: Fifty AD outpatients and 50 healthy contorls were enrolled. Blood samples were collected for processing of complementary DNA and genomic DNA. MAPT messenger ribonucleic acid (mRNA) expression was analyzed by real-time quantitative polymerase chain reaction. The methylation rates of four cytosine-phosphate-guanine (CpG) sites in the upstream region of MAPT exon1 were evaluated by the pyrosequencing method. Results: No significant differences in MAPT mRNA expression levels were found between AD and control subjects (AD 0.97 ± 0.49 vs. control 1.0 ± 0.64, p = 0.62). MAPT mRNA expression levels were not correlated with any other clinical characteristics or results of psychological tests. MAPT mRNA expression levels were significantly higher in AD subjects treated with acetylcholinesterase inhibitors (AchEIs) (n = 25) than in subjects not treated with AChEIs (n = 25) (unmedicated 0.83 ± 0.33 vs. medicated 1.12 ± 0.59, p = 0.049). The AD subjects did not differ from the control subjects in methylation rates at selected CpG sites. MAPT methylation status were not correlated with clinical characteristics, the results of psychological tests, or MAPT mRNA expression. Conclusion: MAPT mRNA expression levels and methylation status in blood do not appear useful as biomarkers for AD or the examined CpG sites were not genetically significant for MAPT gene expression or AD pathology. However, AChEIs may alter MAPT mRNA expression. Further studies are needed to explore blood biomarkers that can discriminate AD patients from controls.
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BACKGROUND: Phosphatidylinositol-binding clathrin assembly protein (PICALM) is a validated genetic risk factor for late-onset Alzheimer's disease (AD) and is associated with other neurodegenerative diseases. However, PICALM expression in the blood of neurodegenerative diseases remains elusive. OBJECTIVE: This study aimed to assess the usefulness of PICALM expression levels in the blood of patients with AD, Parkinson's disease (PD), dementia with Lewy bodies (DLB), and geriatric major depressive disorder (MDD) as a diagnostic biomarker. METHODS: In total, 45, 20, 21, and 19 patients with AD, PD, DLB, and geriatric MDD, respectively, and 54 healthy controls (HCs) were enrolled in the study. Expression data from Gene Expression Omnibus database (GSE97760), (GSE133347) and (GSE98793), (GSE48350), and (GSE144459) were used to validate the ability of biomarkers in the blood of patients with AD, PD, geriatric MDD, and a postmortem human AD brain and animal model of AD (3xTg-AD mouse), respectively. RESULTS: PICALM mRNA expression in human blood was significantly increased in patients with AD compared with that in HCs. PICALM mRNA expression and age were negatively correlated only in patients with AD. PICALM mRNA expression in human blood was significantly lower in patients with PD than in HCs. No changes in PICALM mRNA expression were found in patients with DLB and geriatric MDD. CONCLUSION: PICALM mRNA expression in blood was higher in patients with AD, but lower in patients with PD, which suggests that PICALM mRNA expression in human blood may be a useful biomarker for differentiating neurodegenerative diseases and geriatric MDD.
Subject(s)
Depression/blood , Monomeric Clathrin Assembly Proteins/blood , Neurodegenerative Diseases/blood , Aged , Alzheimer Disease/blood , Case-Control Studies , Depressive Disorder, Major/blood , Female , Humans , Lewy Body Disease/blood , Male , Monomeric Clathrin Assembly Proteins/metabolism , Parkinson Disease/blood , RNA, Messenger/blood , RNA, Messenger/metabolismABSTRACT
Cultivation of quinoa (Chenopodium quinoa), an annual pseudocereal crop that originated in the Andes, is spreading globally. Because quinoa is highly nutritious and resistant to multiple abiotic stresses, it is emerging as a valuable crop to provide food and nutrition security worldwide. However, molecular analyses have been hindered by the genetic heterogeneity resulting from partial outcrossing. In this study, we generated 136 inbred quinoa lines as a basis for the molecular identification and characterization of gene functions in quinoa through genotyping and phenotyping. Following genotyping-by-sequencing analysis of the inbred lines, we selected 5,753 single-nucleotide polymorphisms (SNPs) in the quinoa genome. Based on these SNPs, we show that our quinoa inbred lines fall into three genetic sub-populations. Moreover, we measured phenotypes, such as salt tolerance and key growth traits in the inbred quinoa lines and generated a heatmap that provides a succinct overview of the genotype-phenotype relationship between inbred quinoa lines. We also demonstrate that, in contrast to northern highland lines, most lowland and southern highland lines can germinate even under high salinity conditions. These findings provide a basis for the molecular elucidation and genetic improvement of quinoa and improve our understanding of the evolutionary process underlying quinoa domestication.
Subject(s)
Chenopodium quinoa/genetics , Polymorphism, Single Nucleotide , Salt Tolerance/genetics , Chenopodium quinoa/physiology , Genome-Wide Association Study , PhenotypeABSTRACT
The epigenetic impact of malnutrition in mothers with hyperemesis gravidarum (HG) on their offspring has not been fully elucidated. Recently, several reports have demonstrated that children born to mothers with HG were small for gestational age and had low birth weight, reduced insulin sensitivity, and neurodevelopmental delays during childhood. Therefore, we examined the relationship between fetal growth and changes in the maternal body weight in HG cases. A total of 34 patients with HG were hospitalized and delivered at term between 2009 and 2012. The records of 69 cases of pregnant women without a history of HG were extracted after matching their maternal age, parity, pregestational body mass index (BMI), gestational age, and fetal sex ratio with those of the HG group for comparison. The maternal weight gain at term was less in the HG than in the control group. There was no statistical difference in birth weight, placental weight, and ultrasonic fetometric parameters expressed in standard deviation (SD) scores, including biparietal diameter, abdominal circumference, and femur length, between the HG and the control group. Whereas fetal head growth in the HG group was positively associated with maternal weight gain at 20 weeks of gestation only, this association was not observed in the control group. We herein demonstrate that maternal weight gain from the nadir is associated with fetal head growth at mid-gestation. Thus, maternal undernutrition in the first trimester of pregnancy could affect fetal brain growth and development, leading to an increased risk of neurodevelopmental delays in later life.
Subject(s)
Fetal Development/physiology , Fetal Nutrition Disorders/etiology , Fetal Nutrition Disorders/physiopathology , Gestational Weight Gain , Head/embryology , Head/growth & development , Hyperemesis Gravidarum/complications , Malnutrition/etiology , Maternal Nutritional Physiological Phenomena/physiology , Pregnancy Complications/etiology , Adult , Female , Gestational Age , Humans , Hyperemesis Gravidarum/physiopathology , Male , Pregnancy , Pregnancy Trimester, First , Retrospective Studies , Young AdultABSTRACT
Common buckwheat (Fagopyrum esculentum) is a heterostylous self-incompatible (SI) species with two different flower morphologies, pin and thrum. The SI trait is controlled by a single gene complex locus, S. Self-compatible (SC) lines were developed by crossing F. esculentum and F. homotropicum; these lines have an SC gene, Sh , which is dominant over the s allele and recessive to the S allele. S-ELF3 has been identified as a candidate gene in the S locus and is present in the S and Sh but not s alleles. A single-nucleotide deletion in the S-ELF3 gene of the Sh allele results in a frame shift. To develop co-dominant markers to distinguish between ShSh and Shs plants, we performed a next-generation sequencing analysis in combination with bulked-segregant analysis. We developed four co-dominant markers linked to the S locus. We investigated the polymorphism frequency between a self-compatible line and leading Japanese buckwheat cultivars. Linkage between a developed sequence-tagged-site marker and flower morphology was confirmed using more than 1000 segregating plants and showed no recombination. The developed markers would be useful for buckwheat breeding and also to produce lines for genetic analysis such as recombinant inbred lines.
ABSTRACT
AIMS: The aim of our study was to examine the feasibility of the use of a pedometer to quantify the amount of exercise and the relationship between the amount of exercise and carbohydrate metabolism in pregnant women with impaired glucose tolerance. METHODS: Seven pregnant women with impaired glucose tolerance (gestational diabetes: three, overt diabetes in pregnancy: one, pregestational diabetes type 2: three) were provided with pedometers. The relationship between pedometer data with blood glucose levels, maternal body weight, amount of insulin administered, blood hemoglobin A1c (HbA1c) levels, blood glycoalbumin levels and infant birth weight was investigated. RESULTS: When the 24-h-based data were examined, there was no correlation between the number of steps walked and blood glucose level immediately after walking, nor the average number of steps per day and the fasting blood glucose level in the next day. However, 4-week-based data showed that there was a negative correlation between the number of steps per day and the change in HbA1c level. Moreover, there was a negative correlation between the average number of steps per day and change in the maternal body weight. A 1-week-based data from five participants who were being administered insulin indicated that there was a negative correlation between the average number of steps per day and the total amount of insulin administered per day. CONCLUSION: Active application of pedometers is suggested to be feasible to improve metabolic control in pregnant women with glucose intolerance through the quantification of their exercise.
Subject(s)
Blood Glucose , Exercise/physiology , Glucose Intolerance/blood , Pregnancy Complications/blood , Pregnant Women , Actigraphy , Adult , Female , Glucose Intolerance/physiopathology , Glucose Tolerance Test , Glycated Hemoglobin , Humans , Insulin/blood , Pregnancy , Pregnancy Complications/physiopathologyABSTRACT
O acondicionamento de bebidas carbonatadas em embalagens de alumínio e o aumento do consumo, intensifica a preocupação com relação à contaminação da superfície a ter contato com a boca e à necessidade da higienização das embalagens. O objetivo deste trabalho foi avaliar a contaminação microbiológica, por meio da pesquisa de coliformes totais, coliformes termotolerante, Escherichia coli, contagem total de bactérias aeróbias mesófilas e contagem total de bolores e leveduras, na superfície superior externa de latas de cervejas e de refrigerantes, refrigerados comercializadas em bares, restaurantes, ambulantes e quiosques; bem como avaliar a influência do selo de alumínio na proteção contra a contaminação em latas de cerveja. Foram avaliadas 90 latas de alumínio, sendo 30 seladas e 30 não seladas contendo cerveja e 30 latas não seladas contendo refrigerante. Os resultados mostraram que 34% das amostras estavam contaminadas por coliformes totais, sendo observado valor igual ou superior a 2400 NMP/cm² em uma amostra de cerveja selada e cerveja não selada, adquiridas de ambulante, e uma amostra não selada adquirida de bar. Quanto a coliformes termotolerante 2,2% das embalagens estavam contaminadas, sendo este detectado em duas amostras de cerveja não selada (4 e 7 NMP/cm²) proveniente de bar. Não foi detectada Escherichia coli nas amostras analisadas. Bactérias aeróbias mesófilas foram detectadas em 84 (93,3%) amostras, sendo a maior contagem observada em uma amostra de refrigerante adquirida de quiosque, com o valor de 2,8x10³ UFC/cm². A contaminação por bolores e leveduras foi observada em 59 (65,5%) amostras, sendo a maior contagem com o valor de 2,7x10³ UFC/cm², observada em uma embalagem de cerveja não selada. Concluiu-se que latas seladas ou sem selo apresentaram níveis de contaminação semelhante, indicando que o selo não promove proteção contra contaminação e as amostras que apresentaram maior contaminação foram aquelas refrigeradas em caixas de isopor com água e gelo.
The packaging of carbonated beverages in aluminum packaging and the increase in consumption increases the concern with regard to contamination of the surface to have contact with the mouth and the need for hygiene of the packages. The objective of this study was to evaluate the microbiological contamination of the external surface of beers and refrigerated cans, commercialized in bars, restaurants, street vendors and kiosks; as well as to evaluate the influence of the aluminum seal in the protection against contamination in beer cans. the following analyzes were performed: total coliforms, thermotolerant coliforms, Escherichia coli, count of mesophilic aerobic bacteria and counts of molds and yeasts. Ninety aluminum cans were evaluated, of which 30 were sealed and 30 unsealed containing beer and 30 unsealed cans containing refrigerant. The results showed that 34% of samples were contaminated by total coliforms, with a value of 2400 NMP / cm² being observed in a sample of sealed beer and unsealed beer, purchased on the street, and an unsealed sample purchased from the bar. Regarding thermotolerant coliforms, 2.2% of the packages were contaminated, being detected in two samples of unsealed beer (4 and 7 NMP / cm²) from the bar. No Escherichia coli was detected in the analyzed samples. Mesophilic aerobic bacteria were detected in 84 (93.3%) samples, the highest observed in a sample of kiosk purchased refrigerant, with a value of 2.8x10³ CFU / cm². Contamination by molds and yeasts was observed in 59 (65.5%) samples, the highest count being 2.7x10³ CFU / cm², observed in an unsealed beer package. It was concluded that sealed or unsealed cans had levels of similar contamination, indicating that the seal does not promote protection against contamination and the samples that presented the highest contamination were those refrigerated in styrofoam boxes with water and ice.
Subject(s)
Microbiological Techniques , Environmental Pollution , Food Packaging , Foodborne Diseases , Carbonated Beverages , Product Packaging , Food Storage , Food SupplyABSTRACT
O objetivo do presente estudo foi avaliar a presença de fungos, bactérias e partes de insetos de 30 barras de cerais, sendo 10 tradicionais, 10 lights e 10 diets, de diferentes marcas, comercializadas no município de Taubaté, São Paulo. As amostras foram avaliadas quanto à contagem total de bactérias aeróbias mesófilas e fungos e contagem de larvas, ovos e demais sujidades. Os resultados apontaram que todas as amostras estavam contaminadas com bactérias e fungos, sendo que algumas amostras apresentaram elevadas contagens de bactérias aeróbias mesófilas. Todas as amostras apresentaram fragmentos de insetos.
The aim of the present study was to evaluate the presence of fungi, bacteria and parts of insects of 30 cereal bars, 10 of which were traditional, 10 lights and 10 diets of different brands marketed in the city of Taubaté, São Paulo. Samples were evaluated for total counts of aerobic mesophilic bacteria, fungi and counts of larvae, eggs and other contaminants. The results indicated that all samples were contaminated with bacteria, fungi, and some samples showed high counts of aerobic mesophilic bacteria. All samples showed fragments of insects.
Subject(s)
Industrialized Foods , Fungi , Insecta , Mites , Food Samples , Edible GrainABSTRACT
To evaluate the potential of genomic selection (GS), a selection experiment with GS and phenotypic selection (PS) was performed in an allogamous crop, common buckwheat (Fagopyrum esculentum Moench). To indirectly select for seed yield per unit area, which cannot be measured on a single-plant basis, a selection index was constructed from seven agro-morphological traits measurable on a single plant basis. Over 3 years, we performed two GS and one PS cycles per year for improvement in the selection index. In GS, a prediction model was updated every year on the basis of genotypes of 14,598-50,000 markers and phenotypes. Plants grown from seeds derived from a series of generations of GS and PS populations were evaluated for the traits in the selection index and other yield-related traits. GS resulted in a 20.9% increase and PS in a 15.0% increase in the selection index in comparison with the initial population. Although the level of linkage disequilibrium in the breeding population was low, the target trait was improved with GS. Traits with higher weights in the selection index were improved more than those with lower weights, especially when prediction accuracy was high. No trait changed in an unintended direction in either GS or PS. The accuracy of genomic prediction models built in the first cycle decreased in the later cycles because the genetic bottleneck through the selection cycles changed linkage disequilibrium patterns in the breeding population. The present study emphasizes the importance of updating models in GS and demonstrates the potential of GS in mass selection of allogamous crop species, and provided a pilot example of successful application of GS to plant breeding.
ABSTRACT
BACKGROUND: In patients with chronic kidney disease (CKD), many metabolites of gut microbiota retain in the body as uremic toxins (UTs). However, the kinds of bacteria producing UTs are rarely discussed. METHODS: We analyzed UT production and the composition of gut microbiota in CKD rats and cecectomized rats. AST-120, a spherical carbon adsorbent, was administrated to evaluate how the precursors of UT affect gut microbiota. Serum and urine levels of UTs were quantified by liquid chromatography/electrospray ionization-tandem mass spectrometry. Gut microbiota were analyzed using 454-pyrosequencing of the 16S rRNA gene. Operational taxonomic unit (OTU) clustering and UniFrac analysis were performed to compare gut microbiota among the groups. RESULTS: Serum and urine levels of indoxyl sulfate and phenyl sulfate were higher in CKD versus control rats (p < 0.05). AST-120 administration decreased UT production (p < 0.01) and changed overall gut microbiota composition in CKD rats. UT urinary excretion and gut microbiota composition changed in cecectomized rats, with the relative abundance of Clostridia- and Bacteroidia-affiliated species being significantly reduced (p < 0.01). We identified candidate indole- and phenol-producing intestinal microbiota, 3 Clostridia, and 2 Bacteroidia. These OTUs have a tryptophanase/tyrosine phenol-lyase gene in the closest sequenced genome out of the OTUs declined following cecectomy. CONCLUSION: Our data suggest that UT production is correlated with a subset of indigenous gut microbiota. However, UT may be induced by other non-symbiotic microbiota that are influenced by factors other than microbiota populations. The relationship between specific microbiota and UTs in patients requires further clarification.
Subject(s)
Gastrointestinal Microbiome/physiology , Renal Insufficiency, Chronic/microbiology , Toxins, Biological/biosynthesis , Animals , Bacteroidetes/genetics , Bacteroidetes/isolation & purification , Clostridium/genetics , Clostridium/isolation & purification , Disease Models, Animal , Gastrointestinal Microbiome/genetics , Humans , Indican/biosynthesis , Male , RNA, Bacterial/genetics , RNA, Ribosomal, 16S/genetics , Rats , Rats, Sprague-Dawley , Sulfuric Acid Esters/metabolism , Toxins, Biological/urineABSTRACT
Chenopodium quinoa Willd. (quinoa) originated from the Andean region of South America, and is a pseudocereal crop of the Amaranthaceae family. Quinoa is emerging as an important crop with the potential to contribute to food security worldwide and is considered to be an optimal food source for astronauts, due to its outstanding nutritional profile and ability to tolerate stressful environments. Furthermore, plant pathologists use quinoa as a representative diagnostic host to identify virus species. However, molecular analysis of quinoa is limited by its genetic heterogeneity due to outcrossing and its genome complexity derived from allotetraploidy. To overcome these obstacles, we established the inbred and standard quinoa accession Kd that enables rigorous molecular analysis, and presented the draft genome sequence of Kd, using an optimized combination of high-throughput next generation sequencing on the Illumina Hiseq 2500 and PacBio RS II sequencers. The de novo genome assembly contained 25 k scaffolds consisting of 1 Gbp with N50 length of 86 kbp. Based on these data, we constructed the free-access Quinoa Genome DataBase (QGDB). Thus, these findings provide insights into the mechanisms underlying agronomically important traits of quinoa and the effect of allotetraploidy on genome evolution.
Subject(s)
Adaptation, Physiological , Chenopodium quinoa/genetics , Genome, Plant , Tetraploidy , Chenopodium quinoa/chemistry , DNA, Plant/chemistry , DNA, Plant/genetics , Inbreeding , Nutritive Value , Plant BreedingABSTRACT
Buckwheat (Fagopyrum esculentum Moench; 2n = 2x = 16) is a nutritionally dense annual crop widely grown in temperate zones. To accelerate molecular breeding programmes of this important crop, we generated a draft assembly of the buckwheat genome using short reads obtained by next-generation sequencing (NGS), and constructed the Buckwheat Genome DataBase. After assembling short reads, we determined 387,594 scaffolds as the draft genome sequence (FES_r1.0). The total length of FES_r1.0 was 1,177,687,305 bp, and the N50 of the scaffolds was 25,109 bp. Gene prediction analysis revealed 286,768 coding sequences (CDSs; FES_r1.0_cds) including those related to transposable elements. The total length of FES_r1.0_cds was 212,917,911 bp, and the N50 was 1,101 bp. Of these, the functions of 35,816 CDSs excluding those for transposable elements were annotated by BLAST analysis. To demonstrate the utility of the database, we conducted several test analyses using BLAST and keyword searches. Furthermore, we used the draft genome as a reference sequence for NGS-based markers, and successfully identified novel candidate genes controlling heteromorphic self-incompatibility of buckwheat. The database and draft genome sequence provide a valuable resource that can be used in efforts to develop buckwheat cultivars with superior agronomic traits.
Subject(s)
Fagopyrum/genetics , Genome, Plant , Plant Breeding , Adaptation, Physiological/genetics , Contig Mapping , DNA, Plant/chemistry , DNA, Plant/genetics , High-Throughput Nucleotide Sequencing , Quantitative Trait, Heritable , Sequence Analysis, DNAABSTRACT
INTRODUCTION: The concept of maintenance therapy is one of the highly relevant approaches in the management of advanced ovarian cancer. The fundamental goal of maintenance therapy is to improve survival outcomes. We attempted to reinforce maintenance chemotherapy by adding oral etoposide following taxane administration. CASES: We retrospectively evaluated 14 patients with advanced ovarian cancer who had achieved clinically defined complete response to a primary platinum/taxane chemotherapy regimen and who were administered oral etoposide (50 mg/day × 21 days per cycle monthly for 3-5 cycles) following paclitaxel or docetaxel administration as maintenance chemotherapy. With regard to oral etoposide toxicity, grade 2 oral mucositis and grade 3 anemia were observed in 1 patient each. Three to five cycles of etoposide were administered to all patients, though daily dosage was reduced to 25 mg in 2 patients due to toxicity. The median progression-free survival was 43.5 months, the median overall survival was 86 months, and 5-year overall survival was 77.1%. CONCLUSION: The results from this ovarian cancer treatment evaluation suggest that oral etoposide may be administered safely following paclitaxel or docetaxel as maintenance chemotherapy. We expect this regimen to contribute to the improvement in the survival outcomes of patients with advanced ovarian cancer.