The Amaranth Genome: Genome, Transcriptome, and Physical Map Assembly.

Amaranth ( L.) is an emerging pseudocereal native to the New World that has garnered increased attention in recent years because of its nutritional quality, in particular its seed protein and more specifically its high levels of the essential amino acid lysine. It belongs to the Amaranthaceae family, is an ancient paleopolyploid that shows disomic inheritance (2 = 32), and has an estimated genome size of 466 Mb. Here we present a high-quality draft genome sequence of the grain amaranth. The genome assembly consisted of 377 Mb in 3518 scaffolds with an N of 371 kb. Repetitive element analysis predicted that 48% of the genome is comprised of repeat sequences, of which -like elements were the most commonly classified retrotransposon. A de novo transcriptome consisting of 66,370 contigs was assembled from eight different amaranth tissue and abiotic stress libraries. Annotation of the genome identified 23,059 protein-coding genes. Seven grain amaranths (, , and ) and their putative progenitor () were resequenced. A single nucleotide polymorphism (SNP) phylogeny supported the classification of as the progenitor species of the grain amaranths. Lastly, we generated a de novo physical map for using the BioNano Genomics' Genome Mapping platform. The physical map spanned 340 Mb and a hybrid assembly using the BioNano physical maps nearly doubled the N of the assembly to 697 kb. Moreover, we analyzed synteny between amaranth and sugar beet ( L.) and estimated, using analysis, the age of the most recent polyploidization event in amaranth.

Chromosomal localization of two novel repetitive sequences isolated from the Chenopodium quinoa Willd. genome.

The chromosomal organization of two novel repetitive DNA sequences isolated from the Chenopodium quinoa Willd. genome was analyzed across the genomes of selected Chenopodium species. Fluorescence in situ hybridization (FISH) analysis with the repetitive DNA clone 18-24J in the closely related allotetraploids C. quinoa and Chenopodium berlandieri Moq. (2n = 4x = 36) evidenced hybridization signals that were mainly present on 18 chromosomes; however, in the allohexaploid Chenopodium album L. (2n = 6x = 54), cross-hybridization was observed on all of the chromosomes. In situ hybridization with rRNA gene probes indicated that during the evolution of polyploidy, the chenopods lost some of their rDNA loci. Reprobing with rDNA indicated that in the subgenome labeled with 18-24J, one 35S rRNA locus and at least half of the 5S rDNA loci were present. A second analyzed sequence, 12-13P, localized exclusively in pericentromeric regions of each chromosome of C. quinoa and related species. The intensity of the FISH signals differed considerably among chromosomes. The pattern observed on C. quinoa chromosomes after FISH with 12-13P was very similar to GISH results, suggesting that the 12-13P sequence constitutes a major part of the repetitive DNA of C. quinoa.

Characterization of Salt Overly Sensitive 1 (SOS1) gene homoeologs in quinoa (Chenopodium quinoa Willd.).

Salt tolerance is an agronomically important trait that affects plant species around the globe. The Salt Overly Sensitive 1 (SOS1) gene encodes a plasma membrane Na+/H+ antiporter that plays an important role in germination and growth of plants in saline environments. Quinoa (Chenopodium quinoa Willd.) is a halophytic, allotetraploid grain crop of the family Amaranthaceae with impressive nutritional content and an increasing worldwide market. Many quinoa varieties have considerable salt tolerance, and research suggests quinoa may utilize novel mechanisms to confer salt tolerance. Here we report the cloning and characterization of two homoeologous SOS1 loci (cqSOS1A and cqSOS1B) from C. quinoa, including full-length cDNA sequences, genomic sequences, relative expression levels, fluorescent in situ hybridization (FISH) analysis, and a phylogenetic analysis of SOS1 genes from 13 plant taxa. The cqSOS1A and cqSOS1B genes each span 23 exons spread over 3477 bp and 3486 bp of coding sequence, respectively. These sequences share a high level of similarity with SOS1 homologs of other species and contain two conserved domains, a Nhap cation-antiporter domain and a cyclic-nucleotide binding domain. Genomic sequence analysis of two BAC clones (98 357 bp and 132 770 bp) containing the homoeologous SOS1 genes suggests possible conservation of synteny across the C. quinoa sub-genomes. This report represents the first molecular characterization of salt-tolerance genes in a halophytic species in the Amaranthaceae as well as the first comparative analysis of coding and non-coding DNA sequences of the two homoeologous genomes of C. quinoa.

Simple sequence repeat marker development and genetic mapping in quinoa (Chenopodium quinoa Willd.).

Quinoa is a regionally important grain crop in the Andean region of South America. Recently quinoa has gained international attention for its high nutritional value and tolerances of extreme abiotic stresses. DNA markers and linkage maps are important tools for germplasm conservation and crop improvement programmes. Here we report the development of 216 new polymorphic SSR (simple sequence repeats) markers from libraries enriched for GA, CAA and AAT repeats, as well as 6 SSR markers developed from bacterial artificial chromosome-end sequences (BES-SSRs). Heterozygosity (H) values of the SSR markers ranges from 0.12 to 0.90, with an average value of 0.57. A linkage map was constructed for a newly developed recombinant inbred lines (RIL) population using these SSR markers. Additional markers, including amplified fragment length polymorphisms (AFLPs), two 11S seed storage protein loci, and the nucleolar organizing region (NOR), were also placed on the linkage map. The linkage map presented here is the first SSR-based map in quinoa and contains 275 markers, including 200 SSR. The map consists of 38 linkage groups (LGs) covering 913 cM. Segregation distortion was observed in the mapping population for several marker loci, indicating possible chromosomal regions associated with selection or gametophytic lethality. As this map is based primarily on simple and easily-transferable SSR markers, it will be particularly valuable for research in laboratories in Andean regions of South America.

Molecular and cytological characterization of ribosomal RNA genes in Chenopodium quinoa and Chenopodium berlandieri.

The nucleolus organizer region (NOR) and 5S ribosomal RNA (rRNA) genes are valuable as chromosome landmarks and in evolutionary studies. The NOR intergenic spacers (IGS) and 5S rRNA nontranscribed spacers (NTS) were PCR-amplified and sequenced from 5 cultivars of the Andean grain crop quinoa (Chenopodium quinoa Willd., 2n = 4x = 36) and a related wild ancestor (C. berlandieri Moq. subsp. zschackei (Murr) A. Zobel, 2n = 4x = 36). Length heterogeneity observed in the IGS resulted from copy number difference in subrepeat elements, small re arrangements, and species-specific indels, though the general sequence composition of the 2 species was highly similar. Fifteen of the 41 sequence polymorphisms identified among the C. quinoa lines were synapomorphic and clearly differentiated the highland and lowland ecotypes. Analysis of the NTS sequences revealed 2 basic NTS sequence classes that likely originated from the 2 allopolyploid subgenomes of C. quinoa. Fluorescence in situ hybridization (FISH) analysis showed that C. quinoa possesses an interstitial and a terminal pair of 5S rRNA loci and only 1 pair of NOR, suggesting a reduction in the number of rRNA loci during the evolution of this species. C. berlandieri exhibited variation in both NOR and 5S rRNA loci without changes in ploidy.

Construction of a quinoa (Chenopodium quinoa Willd.) BAC library and its use in identifying genes encoding seed storage proteins.

Quinoa (Chenopodium quinoa Willd.) is adapted to the harsh environments of the Andean Altiplano region. Its seeds have a well-balanced amino acid composition and exceptionally high protein content with respect to human nutrition. Quinoa grain is a staple in the diet of some of the most impoverished people in the world. The plant is an allotetraploid displaying disomic inheritance (2n=4x=36) with a di-haploid genome of 967 Mbp (megabase pair), or 2C=2.01 pg. We constructed two quinoa BAC libraries using BamHI (26,880 clones) and EcoRI (48,000 clones) restriction endonucleases. Cloned inserts in the BamHI library average 113 kb (kilobase) with approximately 2% of the clones lacking inserts, whereas cloned inserts in the EcoRI library average 130 kb and approximately 1% lack inserts. Three plastid genes used as probes of high-density arrayed blots of 73,728 BACs identified approximately 2.8% of the clones as containing plastid DNA inserts. We estimate that the combined quinoa libraries represent at least 9.0 di-haploid nuclear genome equivalents. An average of 12.2 positive clones per probe were identified with 13 quinoa single-copy ESTs as probes of the high-density arrayed blots, suggesting that the estimate of 9.0x coverage of the genome is conservative. Utility of the BAC libraries for gene identification was demonstrated by probing the library with a partial sequence of the 11S globulin seed storage protein gene and identifying multiple positive clones. The presence of the 11S globulin gene in four of the clones was verified by direct comparison with quinoa genomic DNA on a Southern blot. Besides serving as a useful tool for gene identification, the quinoa BAC libraries will be an important resource for physical mapping of the quinoa genome.

A genetic linkage map of quinoa ( Chenopodium quinoa) based on AFLP, RAPD, and SSR markers.

Quinoa ( Chenopodium quinoa Willd.) is an important seed crop for human consumption in the Andean region of South America. It is the primary staple in areas too arid or saline for the major cereal crops. The objective of this project was to build the first genetic linkage map of quinoa. Selection of the mapping population was based on a preliminary genetic similarity analysis of four potential mapping parents. Breeding lines 'Ku-2' and '0654', a Chilean lowland type and a Peruvian Altiplano type, respectively, showed a low similarity coefficient of 0.31 and were selected to form an F(2) mapping population. The genetic map is based on 80 F(2) individuals from this population and consists of 230 amplified length polymorphism (AFLP), 19 simple-sequence repeat (SSR), and six randomly amplified polymorphic DNA markers. The map spans 1,020 cM and contains 35 linkage groups with an average marker density of 4.0 cM per marker. Clustering of AFLP markers was not observed. Additionally, we report the primer sequences and map locations for 19 SSR markers that will be valuable tools for future quinoa genome analysis. This map provides a key starting point for genetic dissection of agronomically important characteristics of quinoa, including seed saponin content, grain yield, maturity, and resistance to disease, frost, and drought. Current efforts are geared towards the generation of more than 200 mapped SSR markers and the development of several recombinant-inbred mapping populations.

Mendelian controversies: a botanical and historical review.

Gregor Mendel was a 19(th) century priest and botanist who developed the fundamental laws of inheritance. The year 2000 marked a century since the rediscovery of those laws and the beginning of genetics. Although Mendel is now recognized as the founder of genetics, significant controversy ensued about his work throughout the 20(th) century. In this paper, we review five of the most contentious issues by looking at the historical record through the lens of current botanical science: (1) Are Mendel's data too good to be true? (2) Is Mendel's description of his experiments fictitious? (3) Did Mendel articulate the laws of inheritance attributed to him? (4) Did Mendel detect but not mention linkage? (5) Did Mendel support or oppose Darwin?A synthesis of botanical and historical evidence supports our conclusions: Mendel did not fabricate his data, his description of his experiments is literal, he articulated the laws of inheritance attributed to him insofar as was possible given the information he had, he did not detect linkage, and he neither strongly supported nor opposed Darwin.

Operative techniques of uvulopalatopharyngoplasty.

Uvulopalatopharyngoplasty is, for the most part, both safe and effective as a surgical treatment for obstructive sleep apnea and severe snoring. Most complications can be avoided with proper surgical technique. Palatal dysfunction can be avoided if the shortening of the soft palate in the midline (uvula) area is minimized. Nasopharyngeal stenosis can be avoided with minimization of the posterior pillar resection and by avoidance of pharyngeal undermining. The effectiveness of surgery can be improved by placing emphasis 1) on opening the nasopharynx widely in the lateral port areas and 2) on tissue removal deep in the inferior tonsillar poles (and hypopharynx) with mucosal advancement and suturing.

Male-specific DNA in the dioecious species Atriplex garrettii (Chenopodiaceae).

The mechanism of sex determination in dioecious species of the genus Atriplex (Chenopodiaceae) has not been determined. This paper reports the discovery of a male-specific DNA fragment in the diploid dioecious species A. garrettii. DNA samples extracted individually from ten male and ten female plants were bulked by sex. Random amplified polymorphic DNA (RAPD) fragments were generated in the two bulks in order to identify markers that were polymorphic between male and female plants. A total of 158 decamer primers were tested. A 2075 base-pair (bp) male-specific DNA fragment generated with the OPAF-14 primer was identified. The fragment was cloned and partially sequenced and 24-mer primers that exclusively amplified this fragment were constructed. When 124 male plants, 126 female plants, and one hermaphroditic plant were tested individually, the male-specific 2075-bp DNA fragment was present in the hermaphrodite and all but one of the male plants, and was absent in all female plants. A smaller DNA fragment (~1800 bp) that was homologous to the 2075-bp fragment was amplified from the single male plant that lacked the 2075-bp fragment. Cytogenetic analysis revealed no apparent heteromorphic sex chromosomes. These observations suggest that sex determination in A. garrettii is genetic, with no evidence of heteromorphic sex chromosomes.

Avaliaçäo da açäo de três soluçöes auxiliares quelantes na microdureza da dentina radicular / The evaluation of three solutions auxiliaries chelanting solution in a radicular dentine microhardness

Estudou-se a açäo das soluçöes de EDTA, EDTAC e EDTAT sobre a microdureza da dentina radicular do terço cervical após suas aplicaçöes durante cinco minutos sobre a superfície dentinária. Utilizaram-se cinco incisivos centrais superiores, os quais tiveram suas coroas seccionadas na junçäo esmalte/cemento. As raízes foram incluídas em blocos de acrílico de rápida polimerizaçäo e seccionadas em cortes transversais com 1 mm de espessura. Dividiu-se cada corte em quatro partes, sendo que cada uma delas foi colocada sobre um disco de acrílico de modo a formar um corpo de prova. Sobre cada superfície de dentina, aplicou-se a soluçäo a ser testada e, após cinco minutos, mediu-se a microdureza Vickers da superfície. Os autores concluíram que as soluçöes quelantes testadas reduziram a microdureza da dentina e que as soluçöes de EDTA e EDTA-T agiram de modo semelhante. A soluçäo de EDTAC promoveu a maior reduçäo da microdureza da dentina, no tempo pesquisado

Preparing nurses for tomorrow's reality. Strategies from an honors program.

The healthcare environment is changing at an unprecedented pace. To be prepared adequately to respond to these demands in healthcare, nurses must exhibit flexibility, creativity, independence, critical thinking, leadership, and collaboration. The authors describe an honors program and the teaching strategies used to enhance several of these characteristics. These strategies can be tailored for students in non-honors programs to develop the attributes required of baccalaureate nursing graduates.

Cisto nasolabial / Nasolabial cyst

Os autores relatam um caso cirúrgico de um cisto nasolabial apresentando seus aspectos radiográficos e clínicos em uma paciente branca de 65 anos de idade. A remoçäo completa da lesäo foi muito facilitada após o preenchimento da loja cística com hidrocolóide irreversível (alginato)

Inflammatory diseases of the sinuses: bacteriology and antibiotics.

This article provides an overview of the antimicrobial agents most commonly employed against the bacteria that cause infections in the ear, nose, throat, head, and neck. Because new bacterial resistances appear so regularly, as do new antibiotics, the reader is encouraged to supplement the information provided within this article with current information from the available literature. Specific treatment strategies for both acute and chronic sinusitis also are reviewed.

Uvulopalatopharyngoplasty: strategies for success and safety.

Management of snoring and/or obstructive sleep apnea patients may include uvulopalatopharyngoplasty, a surgical operation that occasionally generates complications. The most serious are perioperative airway problems and palatal dysfunction. Strategies to minimize risks and maximize efficacy are discussed.

Neurostimulation for obstructive sleep apnea: investigations.

Neurostimulation of the upper airway muscles (accessory muscles of respiration) was accomplished in anesthetized dogs and sleeping humans by electrical stimulation of the hypoglossal nerves. Such stimulations relieved partial airway obstructions in dogs. They also aborted (shortened) obstructive sleep apnea events in humans who suffer with obstructive sleep apnea syndrome. In one subject, stimulations delivered in advance of apneic events (by automatic cycling) prevented apneas. Neurostimulation for obstructive sleep apnea may be an important concept for future research and development.

Predicting the effect of nasal surgery on snoring: a simple test.

The Nasal Spray Test, as herein described, is a simple, reliable, no-cost, self-administered test for assessment of the nasal component in several combined etiologies of snoring and obstructive sleep apnea. A topical decongestant is sprayed into the nose on alternate nights for one week. Spray-nights are compared to non-spray nights for the severity of snoring and apnea. Improvement on the spray-nights implies that nasal obstruction is a causative factor in snoring and that relief of that obstruction will also improve the snoring problem. The test helps the physician decide when nasal surgery should or should not be performed for the complaint of snoring.

Uvulopalatopharyngoplasty complications and avoidance strategies.

Reports of uvulopalatopharyngoplasty complications were elicited from 72 locations in the United States. We asked physicians to report all complications that had occurred in the 9 years since the operation was introduced. Sixteen fatalities were reported; respiratory distress was the most common cause. Forty-six cases of nasopharyngeal stenosis were reported and 42 cases of palatal incompetence were reported. Hemorrhages and wound dehiscences were also reported. A retrospective analysis of the complications was made and diagnostic-therapeutic strategies are discussed with respect to prevention of complications.