Tribal Relationships in the Gesneriaceae: Evidence from DNA Sequences of the Chloroplast Gene \u3cem\u3endh\u3c/em\u3eF

The tribal relationships of the Gesneriaceae are investigated using ndhF sequences. A full analysis of 70 taxa including 16 species from the Scrophulariaceae, Bigoniaceae, and Acanthaceae as outgroups, resulted in two most-parsimonious trees of 5610 steps each. In all trees the Gesneriaceae were a monophyletic group and Paulownia was the closest single-species outgroup for the analysis. Further analyses eliminated all but the members of the Gesneriaceae and Paulownia in order to better asses relationships within the family. The smaller analysis resulted in a single most-parsimonious tree of 4613 steps. The Klugieae are identified as the sister to the remainder of the family and could potentially be separated as a distinct subfamily. The subfamilies Cyrtandroideae (excluding Klugieae) and Gesnerioideae are monophyletic. The placement of Coronallthereae in Cyrtandroideae does not have support from this analysis, whereas its placement in Gesnerioideae is supported. Alternatively Coronanthereae could be segregated as a seperate subfamily but in order to avoid a paraphyletic Gesnerioideae would either include the Napeantheae and Beslerieae or elevate these two tribes to an additional subfamily. Within Gesnerioideae the genus Sinningia is removed from the tribe Gloxinieae into the Sinningieae, which also contains the recently combined species Sinningia brasiliensis (Lietzia), as well as Paliavana and Vanhouttea. The Episcieae, Gesnerieae, Napeantheae, and Beslerieae are identified as monophyletic groups, as are the remainder of the Gloxineae with Sinningia sensu lato removed. Within Cyrtandroideae, several well-supported, monophyletic lineages within the large, heterogeneous tribe Didymocarpeae are identified, and with the current data the tribe Trichosporeae appears to be polyphyletic. The distribution of chromosome numbers, nodal anatomy, placental structure, and stem modification are examined based on these molecular trees

Extensive error in the number of genes inferred from draft genome assemblies

Current sequencing methods produce large amounts of data, but genome assemblies based on these data are often woefully incomplete. These incomplete and error-filled assemblies result in many annotation errors, especially in the number of genes present in a genome. In this paper we investigate the magnitude of the problem, both in terms of total gene number and the number of copies of genes in specific families. To do this, we compare multiple draft assemblies against higher-quality versions of the same genomes, using several new assemblies of the chicken genome based on both traditional and next-generation sequencing technologies, as well as published draft assemblies of chimpanzee. We find that upwards of 40% of all gene families are inferred to have the wrong number of genes in draft assemblies, and that these incorrect assemblies both add and subtract genes. Using simulated genome assemblies of Drosophila melanogaster, we find that the major cause of increased gene numbers in draft genomes is the fragmentation of genes onto multiple individual contigs. Finally, we demonstrate the usefulness of RNA-Seq in improving the gene annotation of draft assemblies, largely by connecting genes that have been fragmented in the assembly process

Redox-neutral organocatalytic Mitsunobu reactions

Nucleophilic substitution reactions of alcohols are amongst the most fundamental and strategically important transformations in organic chemistry. For over half a century these reactions have been achieved using stoichiometric, and often hazardous, reagents to activate the otherwise unreactive alcohols. Here we demonstrate that a specially designed phosphine oxide promotes nucleophilic substitution reactions of primary and secondary alcohols within a redoxneutral catalysis manifold that produces water as the sole by-product. The scope of the catalytic coupling process encompasses a range of acidic pronucleophiles that allow stereospecific construction of carbon-oxygen and carbon-nitrogen bonds

Religious Identity, Religious Attendance, and Parental Control

Using a national sample of adolescents aged 10–18 years and their parents (N = 5,117), this article examines whether parental religious identity and religious participation are associated with the ways in which parents control their children. We hypothesize that both religious orthodoxy and weekly religious attendance are related to heightened levels of three elements of parental control: monitoring activities, normative regulations, and network closure. Results indicate that an orthodox religious identity for Catholic and Protestant parents and higher levels of religious attendance for parents as a whole are associated with increases in monitoring activities and normative regulations of American adolescents

Propulsion in a viscoelastic fluid

Flagella beating in complex fluids are significantly influenced by viscoelastic stresses. Relevant examples include the ciliary transport of respiratory airway mucus and the motion of spermatozoa in the mucus-filled female reproductive tract. We consider the simplest model of such propulsion and transport in a complex fluid, a waving sheet of small amplitude free to move in a polymeric fluid with a single relaxation time. We show that, compared to self-propulsion in a Newtonian fluid occurring at a velocity U_N, the sheet swims (or transports fluid) with velocity U / U_N = [1+De^2 (eta_s)/(eta) ]/[1+De^2], where eta_s is the viscosity of the Newtonian solvent, eta is the zero-shear-rate viscosity of the polymeric fluid, and De is the Deborah number for the wave motion, product of the wave frequency by the fluid relaxation time. Similar expressions are derived for the rate of work of the sheet and the mechanical efficiency of the motion. These results are shown to be independent of the particular nonlinear constitutive equations chosen for the fluid, and are valid for both waves of tangential and normal motion. The generalization to more than one relaxation time is also provided. In stark contrast with the Newtonian case, these calculations suggest that transport and locomotion in a non-Newtonian fluid can be conveniently tuned without having to modify the waving gait of the sheet but instead by passively modulating the material properties of the liquid.Comment: 21 pages, 1 figur

Pharmacology of DB844, an Orally Active aza Analogue of Pafuramidine, in a Monkey Model of Second Stage Human African Trypanosomiasis

Novel drugs to treat human African trypanosomiasis (HAT) are still urgently needed despite the recent addition of nifurtimox-eflornithine combination therapy (NECT) to WHO Model Lists of Essential Medicines against second stage HAT, where parasites have invaded the central nervous system (CNS). The pharmacology of a potential orally available lead compound, N-methoxy-6-{5-[4-(N-methoxyamidino) phenyl]-furan-2-yl}-nicotinamidine (DB844), was evaluated in a vervet monkey model of second stage HAT, following promising results in mice. DB844 was administered orally to vervet monkeys, beginning 28 days post infection (DPI) with Trypanosoma brucei rhodesiense KETRI 2537. DB844 was absorbed and converted to the active metabolite 6-[5-(4-phenylamidinophenyl)-furanyl-2-y​l]-nicotinamide(DB820), exhibiting plasma Cmax values of 430 and 190 nM for DB844 and DB820, respectively, after the 14th dose at 6 mg/kg qd. A 100-fold reduction in blood trypanosome counts was observed within 24 h of the third dose and, at the end of treatment evaluation performed four days post the last drug dose, trypanosomes were not detected in the blood or cerebrospinal fluid of any monkey. However, some animals relapsed during the 300 days of post treatment monitoring, resulting in a cure rate of 3/8 (37.5%) and 3/7 (42.9%) for the 5 mg/kg×10 days and the 6 mg/kg×14 days dose regimens respectively. These DB844 efficacy data were an improvement compared with pentamidine and pafuramidine both of which were previously shown to be non-curative in this model of CNS stage HAT. These data show that synthesis of novel diamidines with improved activity against CNS-stage HAT was possible.This investigation received financial support from the Bill and Melinda Gates Foundation through the Consortium for Parasitic Drug Development

Systemic sclerosis-associated pulmonary hypertension: why disease-specific composite endpoints are needed

Pulmonary arterial hypertension (PAH) is a serious complication of systemic sclerosis (SSc). In clinical trials PAH-SSc has been grouped with other forms, including idiopathic PAH. The primary endpoint for most pivotal studies was improvement in exercise capacity. However, composite clinical endpoints that better reflect long-term outcome may be more meaningful. We discuss potential endpoints and consider why the same measures may not be appropriate for both idiopathic PAH and PAH-SSc due to inherent differences in clinical outcome and management strategies of these two forms of PAH. Failure to take this into account may compromise progress in managing PAH in SSc

Electron inflow velocities and reconnection rates at earth's magnetopause and magnetosheath

Electron inflow and outflow velocities during magnetic reconnection at and near the dayside magnetopause are measured using satellites from NASA's Magnetospheric Multiscale (MMS) mission. A case study is examined in detail, and three other events with similar behavior are shown, with one of them being a recently published electron-only reconnection event in the magnetosheath. The measured inflow speeds of 200–400 km/s imply dimensionless reconnection rates of 0.05–0.25 when normalized to the relevant electron Alfvén speed, which are within the range of expectations. The outflow speeds are about 1.5–3 times the inflow speeds, which is consistent with theoretical predictions of the aspect ratio of the inner electron diffusion region. A reconnection rate of 0.04 ± 25% was obtained for the case study event using the reconnection electric field as compared to the 0.12 ± 20% rate determined from the inflow velocity.publishedVersio