rDolphin: a GUI R package for proficient automatic profiling of 1D <Superscript>1</Superscript>H-NMR spectra of study datasets

Introduction

Adoption of automatic profiling tools for ¹H-NMR-based metabolomic studies still lags behind other approaches in the absence of the flexibility and interactivity necessary to adapt to the properties of study data sets of complex matrices.

Objectives

To provide an open source tool that fully integrates these needs and enables the reproducibility of the profiling process.

Methods

rDolphin incorporates novel techniques to optimize exploratory analysis, metabolite identification, and validation of profiling output quality.

Results

The information and quality achieved in two public datasets of complex matrices are maximized.

Conclusion

rDolphin is an open-source R package (http://github.com/danielcanueto/rDolphin) able to provide the best balance between accuracy, reproducibility and ease of use.

     

Effect of Fluorination on Skin Sensitization Potential and Fragrant Properties of Cinnamyl Compounds

A series of three α‐ and three β‐fluorinated representatives of the family of cinnamate‐derived odorants (cinnamaldehyde ( 1 ), cinnamyl alcohol ( 2 ), and ethyl cinnamate ( 3 )) as used as fragrance ingredients is described. Olfactive evaluation shows that the fluorinated compounds exhibit a similar odor profile to their parent compounds, but the olfactive detection thresholds are clearly higher. In vitro evaluation of the skin sensitizing properties with three different assays indicates that α‐fluorination of Michael acceptor systems 1 and 3 slightly improves the skin sensitization profile. α‐Fluorocinnamyl alcohol 2b is a weaker skin sensitizer than cinnamyl alcohol 2a by in vitro tests and the fluorinated product drops below the sensitization threshold of the KeratinoSens^® assay. On the other hand, β‐fluorination of compounds 1  –  3 results in highly reactive products which display a worsened in vitro skin sensitization profile.     

Could White Coat Ocular Hypertension Affect to the Accuracy of the Diagnosis of Glaucoma? Relationships Between Anxiety and Intraocular Pressure in a Simulated Clinical Setting

Sixty-one healthy subjects participated in a laboratory study carried out in a simulated clinical setting. Anticipatory anxiety-state was assessed at the arrival and immediately after, with no brief phase of adaptation, measurements of intraocular pressure, heart rate, systolic and diastolic blood pressure were collected. At the end of the procedure, anxiety-trait was also assessed. Results suggest that high levels of both anxiety-state and anxiety-trait significantly predicted a clinically relevant increase of intraocular pressure. Anxiety-state mediated the relationship between anxiety-trait and intraocular pressure, which also was found to be related with heart rate but not related to both systolic and diastolic blood pressure. These results suggest a common mechanism of regulation underlying anxiogenic variability found on both intraocular pressure and heart rate. A reduction in parasympathetic activity appears as a possible mechanism underlying to this phenomenon. This anxiety-enhanced intraocular pressure could be considered a phenomenon analogous to white coat hypertension found in the measurement of blood pressure; therefore, it probably should be taken into account in the clinical context to prevent errors in the diagnosis of glaucoma. Further research on cognitive and emotional regulation of intraocular pressure is needed to best characterize this hypothetical phenomenon.     

Elusive data underlying debate at the prokaryote-eukaryote divide

Background

The origin of eukaryotic cells was an important transition in evolution. The factors underlying the origin and evolutionary success of the eukaryote lineage are still discussed. One camp argues that mitochondria were essential for eukaryote origin because of the unique configuration of internalized bioenergetic membranes that they conferred to the common ancestor of all known eukaryotic lineages. A recent paper by Lynch and Marinov concluded that mitochondria were energetically irrelevant to eukaryote origin, a conclusion based on analyses of previously published numbers of various molecules and ribosomes per cell and cell volumes as a presumed proxy for the role of mitochondria in evolution. Their numbers were purportedly extracted from the literature.

Results

We have examined the numbers upon which the recent study was based. We report that for a sample of 80 numbers that were purportedly extracted from the literature and that underlie key inferences of the recent study, more than 50% of the values do not exist in the cited papers to which the numbers are attributed. The published result cannot be independently reproduced. Other numbers that the recent study reports differ inexplicably from those in the literature to which they are ascribed. We list the discrepancies between the recently published numbers and the purported literature sources of those numbers in a head to head manner so that the discrepancies are readily evident, although the source of error underlying the discrepancies remains obscure.

Conclusion

The data purportedly supporting the view that mitochondria had no impact upon eukaryotic evolution data exhibits notable irregularities. The paper in question evokes the impression that the published numbers are of up to seven significant digit accuracy, when in fact more than half the numbers are nowhere to be found in the literature to which they are attributed. Though the reasons for the discrepancies are unknown, it is important to air these issues, lest the prominent paper in question become a point source of a snowballing error through the literature or become interpreted as a form of evidence that mitochondria were irrelevant to eukaryote evolution.

Reviewers

This article was reviewed by Eric Bapteste, Jianzhi Zhang and Martin Lercher.

     

Where did Mikrotia magna originate? Drawing ecogeographical inferences from body mass reconstructions

Terre Rosse deposits (upper Miocene; Gargano, Italy) have provided fossil remains of an insular fauna among which the genus Mikrotia (Rodentia) stands out. Several paleobiological studies have already been conducted on this genus, but its body mass has not yet been calculated accurately. The aim of the present work is to reconstruct Mikrotia magna's weight, a paramount aspect of organismal biology, especially on islands where mammals modify their size, becoming giants or dwarfs (‘island rule’). Our analysis using postcranial elements (femora and humeri) predicts weights ranging from 1300 g to 1900 g (old and young populations, respectively). The presence of a large number of micromammals on the Gargano paleo-island suggests a high interspecific competition for species of the same ecological guild (Prolagus or cricetids were direct competitors of Mikrotia), which may lead to only moderate gigantism, or even body mass reductions in small mammals, following Palkovacs's model. This contrasts with the huge weight of M. magna inferred in this study. In this regard, stratigraphic and taxonomic studies suggest that M. magna was an immigrant from a neighboring island, indicating that this species originated and achieved its enormous size under other selective pressures. A native island with a lower number of competitors, and therefore with less resource limitation than Terre Rosse, might be the principal explanation for such a degree of gigantism.     

Expression profiling of microRNAs in human bone tissue from postmenopausal women

Bone tissue is composed of several cell types, which express their own microRNAs (miRNAs) that will play a role in cell function. The set of total miRNAs expressed in all cell types configures the specific signature of the bone tissue in one physiological condition. The aim of this study was to explore the miRNA expression profile of bone tissue from postmenopausal women. Tissue was obtained from trabecular bone and was analyzed in fresh conditions (n = 6). Primary osteoblasts were also obtained from trabecular bone (n = 4) and human osteoclasts were obtained from monocyte precursors after in vitro differentiation (n = 5). MicroRNA expression profiling was obtained for each sample by microarray and a global miRNA analysis was performed combining the data acquired in all the microarray experiments. From the 641 miRNAs detected in bone tissue samples, 346 (54%) were present in osteoblasts and/or osteoclasts. The other 46% were not identified in any of the bone cells analyzed. Intersection of osteoblast and osteoclast arrays identified 101 miRNAs shared by both cell types, which accounts for 30–40% of miRNAs detected in these cells. In osteoblasts, 266 miRNAs were detected, of which 243 (91%) were also present in the total bone array, representing 38% of all bone miRNAs. In osteoclasts, 340 miRNAs were detected, of which 196 (58%) were also present in the bone tissue array, representing 31% of all miRNAs detected in total bone. These analyses provide an overview of miRNAs expressed in bone tissue, broadening our knowledge in the microRNA field.     

Antimitotic and hormone effects on green double haploid plant production through anther culture of Mediterranean japonica rice

Rice double haploid (DH) plants are produced mainly through anther culture. In order to improve the anther culture protocol, microspores of two japonica rice genotypes (NRVC980385 and H28) were subjected to three growth regulator combinations and four colchicine treatments on induction medium. In addition, a post anther culture procedure using colchicine or oryzalin was tested to induce double haploid plantlets from haploid plantlets. A cold pre-treatment of microspores for 9 days at 10 °C increased callus induction 50-fold in the NRCV980385 genotype. For both genotypes, 2 mg L^?1 2,4-D and 1 mg L^?1 kinetin on colchicine-free induction medium gave the best culture responses. The culturability of both genotypes changed on colchicine-supplemented induction media. A high genotype dependency was recorded for callus induction, callus regenerating green plantlets and regeneration of green double haploid plantlets. Colchicine at 300 mg L^?1 for 48 h enhanced callus induction 100-fold in H28. Colchicine-supplemented media clearly improved green double haploid plantlet regeneration. We showed that the post-anther culture treatment of haploid plantlets at 500 mg L^?1 of colchicine permitted fertile double haploid plantlets to be generated. Finally, an enhanced medium-throughput flow cytometry protocol for rice was tested to analyse all the plantlets from anther and post anther culture.     

A net ecosystem carbon budget for snow dominated forested headwater catchments: linking water and carbon fluxes to critical zone carbon storage

Climate-driven changes in carbon (C) cycling of forested ecosystems have the potential to alter long-term C sequestration and the global C balance. Prior studies have shown that C uptake and partitioning in response to hydrologic variation are system specific, suggesting that a comprehensive assessment is required for distinct ecosystems. Many sub-humid montane forest ecosystems in the US are projected to experience increased water limitation over the next decades and existing water-limited forests can be used as a model for how changes in the hydrologic cycle will impact such ecosystems more broadly. Toward that goal we monitored precipitation, net ecosystem exchange and lateral soil and stream C fluxes in three semi-arid to sub-humid montane forest catchments for several years (WY 2009–2013) to investigate how the amount and timing of water delivery affect C stores and fluxes. The key control on aqueous and gaseous C fluxes was the distribution of water between winter and summer precipitation, affecting ecosystem C uptake versus heterotrophic respiration. We furthermore assessed C stores in soil and above- and below-ground biomass to assess how spatial patterns in water availability influence C stores. Topographically-driven patterns in catchment wetness correlated with modeled soil C stores, reflecting both long-term trends in local C uptake as well as lateral redistribution of C leached from upslope organic soil horizons to convergent landscape positions. The results suggest that changes in the seasonality of precipitation from winter snow to summer rain will influence both the amount and the spatial distribution of soil C stores.     

Regulation of Androgen Receptor Activity by Transient Interactions of Its Transactivation Domain with General Transcription Regulators

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The Xerobranching Response Represses Lateral Root Formation When Roots Are Not in Contact with Water

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