Phylogenetics of Cucumis (Cucurbitaceae)

Background: Melon, Cucumis melo, and cucumber, C. sativus, are among the most widely cultivated crops worldwide. Cucumis, as traditionally conceived, is geographically centered in Africa, with C. sativus and C. hystrix thought to be the only Cucumis species in Asia. This taxonomy forms the basis for all ongoing Cucumis breeding and genomics efforts. We tested relationships among Cucumis and related genera based on DNA sequences from chloroplast gene, intron, and spacer regions (rbcL, matK, rpl20-rps12, trnL, and trnL-F), adding nuclear internal transcribed spacer sequences to resolve relationships within Cucumis. Results: Analyses of combined chloroplast sequences (4,375 aligned nucleotides) for 123 of the 130 genera of Cucurbitaceae indicate that the genera Cucumella, Dicaelospermum, Mukia, Myrmecosicyos, and Oreosyce are embedded within Cucumis. Phylogenetic trees from nuclear sequences for these taxa are congruent, and the combined data yield a well-supported phylogeny. The nesting of the five genera in Cucumis greatly changes the natural geographic range of the genus, extending it throughout the Malesian region and into Australia. The closest relative of Cucumis is Muellerargia, with one species in Australia and Indonesia, the other in Madagascar. Cucumber and its sister species, C. hystrix, are nested among Australian, Malaysian, and Western Indian species placed in Mukia or Dicaelospermum and in one case not yet formally described. Cucumis melo is sister to this Australian/Asian clade, rather than being close to African species as previously thought. Molecular clocks indicate that the deepest divergences in Cucumis, including the split between C. melo and its Australian/Asian sister clade, go back to the mid-Eocene. Conclusion: Based on congruent nuclear and chloroplast phylogenies we conclude that Cucumis comprises an old Australian/Asian component that was heretofore unsuspected. Cucumis sativus evolved within this Australian/Asian clade and is phylogenetically far more distant from C. melo than implied by the current morphological classification

Charles Berg Senior Piano Recital

This is the recording and final documentation of my senior piano recital, which took place on November 21, 2020. Due to the COVID shutdown, this recital was performed at a private venue, removed from the audience and recital hall of Loyola Marymount University. It consists of over an hour of music from Bach, Beethoven, Mozart, Debussy, Chopin, Schubert, and a final medley of assorted tunes which I arranged by ear. The entire program is performed by memory, and features a wide range of keys, periods, and styles

Evaluation of the operation of WWTP Jablunkov after reconstruction

Cílem bakalářské práce je vyhodnocení rekonstrukce mechanicko-biologické čistírny odpadních vod Jablunkov realizované v roce 2019. Předmětem této rekonstrukce bylo navýšení projektované kapacity ČOV ze stávajících 8000 EO na 9980 EO, navýšení množství vzduchu dodávaného do aktivačních nádrží, za účelem zvýšení účinnosti nitrifikace, a instalace nové jednotky odvodňování kalů. V rámci úpravy technologie došlo k vybudování nového lapáku štěrku vč. zdvihacího zařízení, k úpravě lapáku tuku a písku, k přidání provzdušňovacích elementů aktivačních nádrží, k úpravě stávajících dmýchadel, vč. dmýcharny, a v neposlední řadě položení nového potrubí přívodu vzduchu do aktivačních nádrží. Součástí práce je vyhodnocení sledovaných parametrů kvality vypouštěných čištěných odpadních vod, koncentrace kyslíku dodaného do procesu nitrifikace a výsledky odvodňování kalů před a po rekonstrukci, včetně vyhodnocení spotřeby elektrické energie. V rámci práce byl rovněž hodnocen vliv rekonstrukce hrubého předčištění na množství těženého odpadu a snížení náročnosti manipulace pro obsluhu ČOV.The aim of the bachelor thesis is to evaluate the reconstruction of mechanical-biological wastewater treatment plant Jablunkov carried out in 2019. The subject of this reconstruction was to increase the projected WWTP capacity from the existing 8000 PE to 9980 PE, increase the amount of air supplied to activation tanks to increase nitrification efficiency and installation a new sludge dewatering units. As part of the modification of the technology, a new gravel trap was built, incl. lifting equipment, to modify the grease and sand trap, to add aeration elements to the activation tanks, to modify existing blowers, incl. blowers, and last but not least the laying of new air supply pipes to the activation tanks. Part of the bachelor thesis is the evaluation of the monitored parameters of the quality of discharged treated wastewater, the amount of oxygen supplied to the nitrification process and the results of sludge dewatering before and after reconstructionincluding evaluation of electrical consumption. The diploma work also evaluated the impact of the reconstruction of rough pre-treatment on the amount of mined waste and reducing the complexity of handling for COV operator.546 - Katedra environmentálního inženýrstvívelmi dobř

A phylogenetic analysis of Apostasioideae (Orchidaceae) based on ITS, trn L-F and mat K sequences

Abstract.: The orchid subfamily Apostasioideae consists of two genera, Apostasia and Neuwiedia. To study the position of Apostasioideae within Orchidaceae and their intra- and intergeneric relationships, a molecular phylogenetic analysis has been conducted on the nuclear ITS region and the two plastid DNA regions trnL-F intron and matK. The two genera traditionally ascribed to Apostasioideae are each monophyletic. In Apostasia, A. nuda, with two stamens and no staminode, is sister to a clade comprising three species characterised by two stamens and one staminode. Within Neuwiedia, maximum parsimony analyses place N. zollingeri as sister to the clade formed by N. borneensis and N. veratrifolia. A family-wide phylogenetic analysis of matK sequences representing all proposed subfamilies of Orchidaceae produced five moderately to well-supported clades. One of these clades, Apostasioideae, is sister to the clade formed by Vanilloideae, Cypripedioideae, Orchidoideae and Epidendroideae. High transition-transversion ratio and the absence of stop codons in the individual sequences suggest that matK is at the transition from a possibly functional gene to a pseudogene in Apostasioideae, contrary to what is found in some other groups of Orchidacea

Structure and Development of Flowers and Inflorescences in Burmannia (Burmanniaceae, Dioscoreales)

Species of the genus Burmannia possess distinctive and highly elaborated flowers with prominent floral tubes that often bear large longitudinal wings. Complicated floral structure of Burmannia hampers understanding its floral evolutionary morphology and biology of the genus. In addition, information on structural features believed to be taxonomically important is lacking for some species. Here we provide an investigation of flowers and inflorescences of Burmannia based on a comprehensive sampling that included eight species with various lifestyles (autotrophic, partially mycoheterotrophic and mycoheterotrophic). We describe the diversity of inflorescence architecture in the genus: a basic (most likely, ancestral) inflorescence type is a thyrsoid comprising two cincinni, which is transformed into a botryoid in some species via reduction of the lateral cymes to single flowers. Burmannia oblonga differs from all the other studied species in having an adaxial (vs. transversal) floral prophyll. For the first time, we describe in detail early floral development in Burmannia. We report presence of the inner tepal lobes in B. oblonga, a species with reportedly absent inner tepals; the growth of the inner tepal lobes is arrested after the middle stage of floral development of this species, and therefore they are undetectable in a mature flower. Floral vasculature in Burmannia varies to reflect the variation of the size of the inner tepal lobes; in B. oblonga with the most reduced inner tepals their vascular supply is completely lost. The gynoecium consists of synascidiate, symplicate, and asymplicate zones. The symplicate zone is secondarily trilocular (except for its distal portion in some of the species) without visible traces of postgenital fusion, which prevented earlier researchers to correctly identify the zones within a definitive ovary. The placentas occupy the entire symplicate zone and a short distal portion of the synascidiate zone. Finally, we revealed an unexpected diversity of stamen-style interactions in Burmannia. In all species studied, the stamens are tightly arranged around the common style to occlude the flower entrance. However, in some species the stamens are free from the common style, whereas in the others the stamen connectives are postgenitally fused with the common style, which results in formation of a gynostegium

A phylogenetic analysis of Apostasioideae (Orchidaceae) based on ITS, trn L-F and mat K sequences

The orchid subfamily Apostasioideae consists of two genera, Apostasia and Neuwiedia . To study the position of Apostasioideae within Orchidaceae and their intra- and intergeneric relationships, a molecular phylogenetic analysis has been conducted on the nuclear ITS region and the two plastid DNA regions trn L-F intron and mat K. The two genera traditionally ascribed to Apostasioideae are each monophyletic. In Apostasia , A. nuda , with two stamens and no staminode, is sister to a clade comprising three species characterised by two stamens and one staminode. Within Neuwiedia , maximum parsimony analyses place N. zollingeri as sister to the clade formed by N. borneensis and N. veratrifolia . A family-wide phylogenetic analysis of mat K sequences representing all proposed subfamilies of Orchidaceae produced five moderately to well-supported clades. One of these clades, Apostasioideae, is sister to the clade formed by Vanilloideae, Cypripedioideae, Orchidoideae and Epidendroideae. High transition-transversion ratio and the absence of stop codons in the individual sequences suggest that mat K is at the transition from a possibly functional gene to a pseudogene in Apostasioideae, contrary to what is found in some other groups of Orchidaceae.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/41641/1/606_2004_Article_133.pd

Evolution and development of fruits of Erycina pusilla and other orchid species

Fruits play a crucial role in seed dispersal. They open along dehiscence zones. Fruit dehiscence zone formation has been intensively studied in Arabidopsis thaliana. However, little is known about the mechanisms and genes involved in the formation of fruit dehiscence zones in species outside the Brassicaceae. The dehiscence zone of A. thaliana contains a lignified layer, while dehiscence zone tissues of the emerging orchid model Erycina pusilla include a lipid layer. Here we present an analysis of evolution and development of fruit dehiscence zones in orchids. We performed ancestral state reconstructions across the five orchid subfamilies to study the evolution of selected fruit traits and explored dehiscence zone developmental genes using RNA-seq and qPCR. We found that erect dehiscent fruits with non-lignified dehiscence zones and a short ripening period are ancestral characters in orchids. Lignified dehiscence zones in orchid fruits evolved multiple times from non-lignified zones. Furthermore, we carried out gene expression analysis of tissues from different developmental stages of E. pusilla fruits. We found that fruit dehiscence genes from the MADS-box gene family and other important regulators in E. pusilla differed in their expression pattern from their homologs in A. thaliana. This suggests that the current A. thaliana fruit dehiscence model requires adjustment for orchids. Additionally, we discovered that homologs of A. thaliana genes involved in the development of carpel, gynoecium and ovules, and genes involved in lipid biosynthesis were expressed in the fruit valves of E. pusilla, implying that these genes may play a novel role in formation of dehiscence zone tissues in orchids. Future functional analysis of developmental regulators, lipid identification and quantification can shed more light on lipid-layer based dehiscence of orchid fruits

Cost-effectiveness of active monitoring versus antidepressants for major depression in primary health care: a 12-month non-randomized controlled trial (INFAP study)

Background Clinical practice guidelines for the treatment of major depressive disorder (MDD) recommend antidepressants for patients with moderate-severe depression and active monitoring for patients with mild-moderate symptoms. The feasibility and efficiency of active monitoring has not been proven conclusively. The aim of this study is to evaluate the cost-effectiveness of active monitoring in comparison to antidepressants for primary care patients with mild-moderate MDD. Methods/Design This is a 12-month follow-up multicenter observational prospective controlled trial. Patients are enrolled in 12 primary care centers in Barcelona (Spain). Eligible patients are adults (≥18 years-old) with a new episode of MDD that sign a written consent to participate. This is a naturalistic study in which general practitioners (GPs) use their professional judgment to allocate patients into active monitoring or antidepressants groups. GPs treat the patients following their clinical criteria. At baseline, GPs complete a questionnaire (sociodemographic/job characteristics, training, attitude towards depression, interest on mental health and participation in communication groups). Patients’ measurements take place at baseline and after six and 12 months. Main outcome measures include severity of depression (PHQ-9), health-related quality of life (EuroQol-5D) and use of healthcare and social care services (Client Service Receipt Inventory). Secondary outcomes include diagnosis of MDD according to DSM-IV diagnostic criteria (SCID-I), disability (WHO-DAS), anxiety (BAI), comorbidities, medication side-effects and beliefs about medicines (BMQ). The analysis will be done according to the intention to treat analysis. Missing data will be imputed using multiple imputation by chained equations. To minimize the bias resulting from the lack of randomization, a propensity score will be used. Incremental effects and costs between groups will be modelled in each of the imputed databases using multivariate generalized linear models and then combined as per Rubin’s rules. Propensity scores will be used to adjust the models. Incremental cost-effectiveness ratios will be calculated by dividing the difference in costs between groups by the difference in effects. To deal with the uncertainty, resampling techniques with bootstrapping will be used and cost-effectiveness planes and cost-effectiveness acceptability curves will be constructed. A series of sensitivity analyses will be performed. Discussion Given the high burden and costs generated by depressive disorder, it is important that general practitioners treat major depression efficiently. Recent evidence has suggested that antidepressants have low benefits for patients with mild to moderate major depression. For such cases of depression, active monitoring exists as a treatment option, but it is not without difficulties for implementation and its effectiveness and efficiency have not been demonstrated conclusively. The results of the study will provide information on which is the most efficient approach to treat patients with mild to moderate major depression in primary care

De novo assembly of the zucchini genome reveals a whole‐genome duplication associated with the origin of the Cucurbita genus

The Cucurbita genus (squashes, pumpkins and gourds) includes important domesticated species such as C. pepo, C. maxima and C. moschata. In this study, we present a high-quality draft of the zucchini (C. pepo) genome. The assembly has a size of 263 Mb, a scaffold N50 of 1.8 Mb and 34 240 gene models. It includes 92% of the conserved BUSCO core gene set, and it is estimated to cover 93.0% of the genome. The genome is organized in 20 pseudomolecules that represent 81.4% of the assembly, and it is integrated with a genetic map of 7718 SNPs. Despite the small genome size, three independent lines of evidence support that the C. pepo genome is the result of a whole-genome duplication: the topology of the gene family phylogenies, the karyotype organization and the distribution of 4DTv distances. Additionally, 40 transcriptomes of 12 species of the genus were assembled and analysed together with all the other published genomes of the Cucurbitaceae family. The duplication was detected in all the Cucurbita species analysed, including C. maxima and C. moschata, but not in the more distant cucurbits belonging to the Cucumis and Citrullus genera, and it is likely to have occurred 30 ± 4 Mya in the ancestral species that gave rise to the genus

Sinocurculigo, a New Genus of Hypoxidaceae from China Based on Molecular and Morphological Evidence

, with eight species are distributed in China. Recently, we have found a hypoxid-like plant in China that is quite different in floral structure from any of the three genera and even of the known taxa in Hypoxidaceae. regions of 59 taxa in Hypoxidaceae and its alliance. Findings of the molecular investigation is consistent with those of the morphological analysis.