The chloroplast trnH-psbA spacer region has been proposed as a prime candidate for use in DNA barcoding of plants because of its high substitution rate. However, frequent inversions associated with ...palindromic sequences within this region have been found in multiple lineages of Angiosperms and may complicate its use as a barcode, especially if they occur within species.
Here, we evaluate the implications of intraspecific inversions in the trnH-psbA region for DNA barcoding efforts. We report polymorphic inversions within six species of Gentianaceae, all narrowly circumscribed morphologically: Gentiana algida, Gentiana fremontii, Gentianopsis crinita, Gentianopsis thermalis, Gentianopsis macrantha and Frasera speciosa. We analyze these sequences together with those from 15 other species of Gentianaceae and show that typical simple methods of sequence alignment can lead to misassignment of conspecifics and incorrect assessment of relationships.
Frequent inversions in the trnH-psbA region, if not recognized and aligned appropriately, may lead to large overestimates of the number of substitution events separating closely related lineages and to uniting more distantly related taxa that share the same form of the inversion. Thus, alignment of the trnH-psbA spacer region will need careful attention if it is used as a marker for DNA barcoding.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Scheme illustrating the lower density of deep energy states in NTs grown in 12wt.% H2O. As a result, such NTs exhibit efficient electron transport properties. In contrast electron transport is ...difficult in the case of 2wt.% H2O NTs as the density of deep states, acting as recombination center, is larger.
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The microstructural and photoelectrochemical properties of anodized TiO2 Nanotubes (NTs) grown in ethylene glycol containing 0.1M NH4F and a variable amount of H2O, either 2wt.% (low water content) or 12wt.% (high water content) have been investigated. The study has been conducted at a fixed anodizing potential, as it is known that also the applied potential can affect the electron transport properties of the NTs. The amount of water also has an impact on the microstructure of the NTs; those prepared in 12wt.% H2O have a rough wall, whereas those made at 2wt.% are mostly smooth. In addition the water content affects the dissolution of the forming oxide and consequently has an impact also on the diameter and the length of the NTs. For a fixed potential (30V), when working at 12wt.% H2O content, it is necessary to extend the anodizing time to 60min to obtain ∼1.4μm long NTs. A similar length is achieved at 2wt.% H2O content after 20min.
The photocurrent density measurements reveal an improved photoactivity for NTs grown in high water content electrolytes (1.1mA/cm2 in 12wt.% H2O vs 0.75mA/cm2 in 2wt.% H2O at 1V vs RHE). Similarly the Incident Photon to Current Efficiency (IPCE) of NTs obtained in 12wt.% H2O is consistently higher than for 2wt.% H2O over the range 350-300nm (with values > 40% at 320-300nm). Electrochemical Impedance Spectroscopy (EIS) analysis shows similar electron transport and charge transfer properties for NTs grown in low and high water contents. EIS is mainly sensitive to the bottom of the NTs, whereas the NTs wall is not active at potentials more positive than the flat band potential. EIS also reveals that the poorer photoelectrochemical properties of NTs grown in 2wt.% H2O are due to a larger density of deep intra band-gap energy states in comparison with 12wt.% H2O.
This article introduces a large new cross‐country database, the Database of Political Institutions. It covers 177 countries over 21 years, 1975–95. The article presents the intuition, construction, ...and definitions of the different variables. Among the novel variables introduced are several measures of checks and balances, tenure and stability, identification of party affiliation with government or opposition, and fragmentation of opposition and government parties in the legislature.
1 Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, Boston, 02114
2 Department of Otology and Laryngology, Harvard Medical School, Boston, 02114
3 Program in Speech and Hearing ...Bioscience and Technology, Division of Health Science and Technology, Harvard/Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
Submitted 3 July 2003;
accepted in final form 12 August 2003
The olivocochlear (OC) efferent innervation of the mammalian inner ear consists of two subdivisions, medial (MOC) and lateral (LOC), with different peripheral terminations on outer hair cells and cochlear afferent terminals, respectively. The cochlear effects of electrically activating MOC efferents are well known, i.e., response suppression effected by reducing outer hair cells' contribution to cochlear amplification. LOC peripheral effects are unknown, because their unmyelinated axons are difficult to electrically stimulate. Here, stimulating electrodes are placed in the inferior colliculus (IC) to indirectly activate the LOC system, while recording cochlear responses bilaterally from anesthetized guinea pigs. Shocks at some IC sites produced novel cochlear effects attributable to activation of the LOC system: long-lasting (520 min) enhancement or suppression of cochlear neural responses (compound action potentials and round window noise), without changes in cochlear responses dominated by outer hair cells (otoacoustic emissions and cochlear microphonics). These novel effects also differed from classic MOC effects in their lack of dependence on the level and frequency of the acoustic stimulus. These effects disappeared on sectioning the entire OC bundle, but not after selective lesioning of the MOC tracts or the cochlea's autonomic innervation. We conclude that the LOC pathway comprises two functional subdivisions, capable of inducing slow increases or decreases in response magnitudes in the auditory nerve. Such a system may be useful in maintaining accurate binaural comparisons necessary for sound localization in the face of slow changes in interaural sensitivity.
Address for reprint requests and other correspondence: M. C. Liberman, Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, 243 Charles St., Boston, MA 02114 (E-mail: mcl{at}epl.meei.harvard.edu ).
To examine women’s emotional responses to learning the diagnosis of premature ovarian failure (POF) and identify the sources of support used for coping.
Observational study.
National Institutes of ...Health Clinical Center.
One hundred women previously diagnosed with POF of median age 28 years at diagnosis.
Structured telephone interviews based on focus group findings.
Manner informed of POF diagnosis, emotional response, and areas of emotional support.
Overall, 71% were unsatisfied with the manner in which they were informed by their clinician, and 89% reported experiencing moderate to severe emotional distress at the time. The degree of emotional distress was positively correlated with the degree of dissatisfaction with the manner in which the women had been informed of the diagnosis. Thorough and accurate medical information on POF, support of others, and spirituality were perceived as helpful in coping.
Learning the diagnosis of POF can be emotionally traumatic and difficult for women. The findings suggest that the manner in which patients are informed of this diagnosis can significantly impact their level of distress. Patients perceive a need for clinicians to spend more time with them and provide more information about POF.
Correction for A generalized method for alignment of block copolymer films: solvent vapor annealing with soft shear by Zhe Qiang
et al.
,
Soft Matter
, 2014,
10
, 60686076,
...https://doi.org/10.1039/C4SM00875H
.
One of the key issues associated with the utilization of block copolymer (BCP) thin films in nanoscience and nanotechnology is control of their alignment and orientation over macroscopic dimensions. ...We have recently reported a method, solvent vapor annealing with soft shear (SVA-SS), for fabricating unidirectional alignment of cylindrical nanostructures. This method is a simple extension of the common SVA process by adhering a flat, crosslinked poly(dimethylsiloxane) (PDMS) pad to the BCP thin film. The impact of processing parameters, including annealing time, solvent removal rate and the physical properties of the PDMS pad, on the quality of alignment quantified by the Herman's orientational factor (S) is systematically examined for a model system of polystyrene-block-polyisoprene-block-polystyrene (SIS). As annealing time increases, the SIS morphology transitions from isotropic rods to highly aligned cylinders. Decreasing the rate of solvent removal, which impacts the shear rate imposed by the contraction of the PDMS, improves the orientation factor of the cylindrical domains; this suggests the nanostructure alignment is primarily induced by contraction of PDMS during solvent removal. Moreover, the physical properties of the PDMS controlled by the crosslink density impact the orientation factor by tuning its swelling extent during SVA-SS and elastic modulus. Decreasing the PDMS crosslink density increases S; this effect appears to be primarily driven by the changes in the solubility of the SVA-SS solvent in the PDMS. With this understanding of the critical processing parameters, SVA-SS has been successfully applied to align a wide variety of BCPs including polystyrene-block-polybutadiene-block-polystyrene (SBS), polystyrene-block-poly(N,N-dimethyl-n-octadecylammonium p-styrenesulfonate) (PS-b-PSS-DMODA), polystyrene-block-polydimethylsiloxane (PS-b-PDMS) and polystyrene-block-poly(2-vinlypyridine) (PS-b-P2VP). These results suggest that SVA-SS is a generalizable method for the alignment of BCP thin films.
Many companies and global regulatory programs have expressed the intent to move away from in vivo animal testing to new approach methods (NAMs) as part of product safety assessments. NAMs, which ...include non-animal approaches for testing and assessment – from computer-based modeling to in chemico or in vitro models – allow faster data generation with potentially greater relevance to humans while avoiding animal use. To monitor progress implementing NAMs, each organization first must define what is in scope, starting with the definition of “animal” (e.g., mammals, vertebrates) and applicable studies (e.g., animals used for “in-house” experiments, at contract research organizations, as part of environmental monitoring). Next, organizations must establish baseline animal use, including defined rules for inclusion/ exclusion of animals that ensure consistency in future assessments. Lastly, organizations must establish metrics for animal savings based on the utility of NAM data. This paper presents one approach to establish “animal use” metrics in a toxicology program at The Dow Chemical Company. The premise of our program is that most NAM information has value for animal savings, but the value depends on how data are used (e.g., research and development, screening, or regulatory requirements) and the level of certainty for internal decision-making. This manuscript provides metrics on the impact of NAMs, allowing a quantitative assessment of animal use numbers over time, accountability for resources spent on NAM development, and identification of areas where NAM development is still needed. This approach can be refined for use at other organizations.
Identification of essential habitat is a fundamental component of amphibian conservation; however, species with complex life histories frequently move among habitats. To better understand dynamic ...habitat use, we evaluated Wood Frog (Lithobates sylvaticus (LeConte, 1825)) habitat selection and movement patterns during the spring migration and foraging periods and described the spatiotemporal variability of habitats used during all annual life-history periods. We radio-tracked 71 frogs in Maine during 2011–2013 and evaluated spring migration, foraging activity center (FAC), and within-FAC habitat selection. Telemetered frogs spent the greatest percentage of each field season in hibernacula (≥54.4%), followed by FACs (≥25.5%), migration habitat (≥16.9%), and breeding sites (≥4.5%). FACs ranged 49 – 1 335 m
2
(568.0 ± 493.4 m
2
) and annual home ranges spanned 1 413 – 32 165 m
2
(11 780.6 ± 12 506.1 m
2
). During spring migration, Wood Frogs exhibited different movement patterns (e.g., turn angles), selected different habitat features, and selected habitat features less consistently than while occupying FACs, indicating that the migration and foraging periods are ecologically distinct. Habitat-use studies that do not discriminate among annual life-history periods may obscure true ecological relationships and fail to identify essential habitat necessary for sustaining amphibian populations.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Abstract
Study question
What role does the X chromosome play in early embryo metabolism? Does X chromosome copy number contribute to sex differences in early embryonic metabolism?
Summary answer
...Chromosome X contains several metabolism-related genes that are expressed prior to X-inactivation, suggesting that their dosage plays a role in sex-biased regulation of embryo metabolism.
What is known already
Published reports indicate that sex differences in preimplantation embryo metabolism exist across mammalian species, including humans. Two observations supporting this are that male embryos reach blastocyst stage earlier than their female counterparts, and that glucose uptake and processing is thought to be higher in female compared to male embryos. It has been hypothesized that these differences reflect the location of the metabolism gene G6PD, the rate limiting enzyme in the Pentose Phosphate Pathway, on Chromosome X.
Study design, size, duration
This study is a reanalysis of publicly available RNA-seq data, including 1176 single cells from 59 blastocysts (24 E5, 18 E6, 17 E7) published in one study (Petropoulos et al 2016).
Participants/materials, setting, methods
Cells were subjected to a digital karyotype inference algorithm and aneuploid samples were removed from the dataset. Sex differential gene expression analyses (DE) were then performed in euploid trophectoderm cells (TE; 233 XY from 16 embryos and 180 XX cells from 12 embryos). Cell numbers from ICM were too sparse to compare.
Main results and the role of chance
Analysis of XX and XY TE revealed 618 significantly differentially expressed genes (DEGs; 507 upregulated in XX cells, and 111 upregulated in XY cells). These genes are spread across autosomes and sex chromosomes. Interestingly, G6PD is not significantly more highly expressed in XX cells.
Gene Ontology (GO) analysis of the XX-biased DEGs revealed a transcriptional sex bias in metabolism-related GO categories, including “mitochondrial ATP synthesis coupled electron transport”, and “respiratory chain complex I”.
Gene-level assessment revealed that the drivers of these enrichments are spread across the genome, but 28/64 reside on Chromosome X (hypergeometric p-value = 5.984473e–27), including NDUFA1, NDUFB11, and COX7B (components of the electron transport chain), and SLC25A5 (an ATP/ADP transporter involved in maintaining mitochondrial membrane potential). This indicates a direct role for multiple X-linked genes in sex-biased regulation of embryo metabolism.
Metabolic genes that are not sex-biased are distributed across the genome, with no significant enrichment on Chromosome X (76/266, hypergeometric p-value=0.607). Together, these data indicate that GO metabolic term X enrichment is a feature of sex-biased expression and not due to an accumulation of metabolism-related genes on the X.
Limitations, reasons for caution
This analysis draws on publicly available data, and thus we are unable to perform orthogonal validation of karyotype calls. Additionally, while the initial dataset is large, the quality-filtered dataset (euploid XX and XY TE) is small, and single cell data is infamously variable. Further data collection is required.
Wider implications of the findings: Our analysis of sex-biased gene expression in early human embryos suggests a more important role for the X chromosome in modulating sex biases in early embryo metabolism than previously recognized. This study provides insight into the mechanisms underlying the development of metabolic sex differences throughout the lifespan.
Trial registration number
NA
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