Miracle-dz/UniFAR-FTUs huggingface dataset:
Applications in Stimulated Emission Depletion Microscopy: Localization of a Protein Toxin in the Endoplasmic Reticulum Following Retrograde Transport

Abstract Retrograde transport is a process in which proteins are trafficked from the plasma membrane and endosomes to biosynthetic and secretory organelles, namely the Golgi apparatus and endoplasmic reticulum (ER). A number of plant and bacterial toxins, including cholera toxin and ricin toxin, exploit retrograde transport to gain entry into host cells, although the specifics of this process have remained difficult to probe by laser scanning confocal microscopy (LSCM). Here we demonstrate the use of super-resolution and live-cell imaging [stimulated emission depletion (STED)] to visualize exogenously applied ricin toxin within the ER. The improved resolution obtained by STED, as compared with LSCM (0.09 versus 0.19 μm), provides a more accurate determination of the amount of ricin that had trafficked to the ER.
REVIEW: PART OF A SPECIAL ISSUE ON POPULATION BIOLOGY Pollination patterns and plant breeding systems in the Galapagos: a review

† Background Despite the importance of the Galapagos Islands for the development of central concepts in ecology and evolution, the understanding of many ecological processes in this archipelago is still very basic. One such process is pollination, which provides an important service to both plants and their pollinators. The rather modest level of knowledge on this subject has so far limited our predictive power on the consequences of the increasing threat of introduced plants and pollinators to this unique archipelago. † Scope As a first step toward building a unified view of the state of pollination in the Galapagos, a thorough literature search was conducted on the breeding systems of the archipelago's flora and compiled all documented flower -visitor interactions. Based on 38 studies from the last 100 years, we retrieved 329 unique interactions between 123 flowering plant species (50 endemics, 39 non-endemic natives, 26 introduced and eight of unknown origin) from 41 families and 120 animal species from 13 orders. We discuss the emergent patterns and identify promising research avenues in the field. † Conclusions Although breeding systems are known for ,20 % of the flora, most species in our database were self-compatible. Moreover, the incidence of autogamy among endemics, non-endemic natives and alien species did not differ significantly, being high in all groups, which suggests that a poor pollinator fauna does not represent a constraint to the integration of new plant species into the native communities. Most interactions detected (approx. 90 %) come from a single island (most of them from Santa Cruz). Hymenopterans (mainly the endemic carpenter bee Xylocopa darwinii and ants), followed by lepidopterans, were the most important flower visitors. Dipterans were much more important flower visitors in the humid zone than in the dry zone. Bird and lizard pollination has been occasionally reported in the dry zone. Strong biases were detected in the sampling effort dedicated to different islands, time of day, focal plants and functional groups of visitors. Thus, the existing patterns need to be confronted with new and less biased data. The implementation of a com- munity-level approach could greatly increase our understanding of pollination on the islands and our ability to predict the consequences of plant invasions for the natural ecosystems of the Galapagos.
Prader-Willi syndrome: development and manifestations

Edited by Ivan Nicoletti, Lodovico Benso, Giulio Gilli. Florence: Nicompe, 2004, €130.00, pp 653. ISBN 88-87814-22-8 Auxology, for the uninitiated, is the study of growth. This large book aims to cover exactly what it says in the title: normal growth and how to measure it, and abnormal growth secondary to illness. It is a multi-author text (n = 67), mainly with European contributors, and is edited by a well respected Italian team. The nearest book in scope would be the classic Faulkner and Tanner three volume treatise Human …
Use of genotype x environment interactions to understand rooting depth and the ability of wheat to penetrate hard soils.

BACKGROUND Root systems are well-recognized as complex and a variety of traits have been identified as contributing to plant adaptation to the environment. A significant proportion of soil in south-western Australia is prone to the formation of hardpans of compacted soil that limit root exploration and thus access to nutrients and water for plant growth. Genotypic variation has been reported for root-penetration ability of wheat in controlled conditions, which has been related to field performance in these environments. However, research on root traits in field soil is recognized as difficult and labour intensive. Pattern analysis of genotype × environment (G × E) interactions is one approach that enables interpretation of these complex relationships, particularly when undertaken with probe genotypes with well-documented traits, in this case, for the ability to penetrate a wax layer. While the analytical approach is well-established in the scientific literature, there are very few examples of pattern analysis for G × E interactions applied to root traits of cereal crops. SCOPE In this viewpoint, we aim to review the approach of pattern analysis for G × E interaction and the importance of environment and genotype characterization, with a focus on root traits. We draw on our research on G × E interaction for root depth and related studies on genotypic evaluation for root-penetration ability. In doing so, we wish to explore how pattern analysis can aid in the interpretation of complex root traits and their interaction with the environment and how this may explain patterns of adaptation and inform future research. CONCLUSIONS With appropriate characterization of environments and genotypes, the G × E approach can be used to aid in the interpretation of the complex interactions of root systems with the environment, inform future research and therefore provide supporting evidence for selecting specific root traits for target environments in a crop breeding programme.
Evaluation of anti-nociceptive activity of Cissus quadrangularis on albino mice

Th roughout the history, man has used several forms of therapy for relief of pain; among them, medicinal herbs have gained popularity because of its wide use and less side eff ects. Cissus quadrangularis, for example, is a commonly used folklore medicine in India to hasten the fracture healing process; in Cameroon, the whole plant is used for the treatment of oral dehydration, while in Africa and Asia, the leaves, stems and roots are utilized for the treatment of various ailments. Th e plant extract were prepared by using chloroform and distilled water in proportion (20:80), macerated for 72 h with occasional stirring and concentrated under dry vacuum. Th e extract of Cissus quadrangularis was examined for centrally acting analgesics by using the hot plate method, formalin test and acetic acidinduced writhing method for peripherally acting analgesics. Th e doses administered were 250 mg/kg and 350 mg/kg. Th e animal that administered both the doses showed signifi cant analgesic activity. Th e animal that administered a dose of 350 mg/kg has shown the maximum analgesic activity which is comparable to the standard. Key words: Analgesic, Cissus quadrangularis, formalin, writhing
Whole-exome targeted sequencing of the uncharacterized pine genome.

The large genome size of many species hinders the development and application of genomic tools to study them. For instance, loblolly pine (Pinus taeda L.), an ecologically and economically important conifer, has a large and yet uncharacterized genome of 21.7 Gbp. To characterize the pine genome, we performed exome capture and sequencing of 14 729 genes derived from an assembly of expressed sequence tags. Efficiency of sequence capture was evaluated and shown to be similar across samples with increasing levels of complexity, including haploid cDNA, haploid genomic DNA and diploid genomic DNA. However, this efficiency was severely reduced for probes that overlapped multiple exons, presumably because intron sequences hindered probe:exon hybridizations. Such regions could not be entirely avoided during probe design, because of the lack of a reference sequence. To improve the throughput and reduce the cost of sequence capture, a method to multiplex the analysis of up to eight samples was developed. Sequence data showed that multiplexed capture was reproducible among 24 haploid samples, and can be applied for high-throughput analysis of targeted genes in large populations. Captured sequences were de novo assembled, resulting in 11 396 expanded and annotated gene models, significantly improving the knowledge about the pine gene space. Interspecific capture was also evaluated with over 98% of all probes designed from P. taeda that were efficient in sequence capture, were also suitable for analysis of the related species Pinus elliottii Engelm.
Potential of advanced photoplethysmography sensing for noninvasive vascular diagnostics and early screening

Advanced sensor device for shape analysis of the tissue- reflected mean single period photoplethysmography (SPPPG) signals has been designed and clinically tested. The SPPPG signal shape reveals individual features of the patient's cardio-vascular state. Clinical studies of several patient groups (e.g. diabetes mellitus, atherosclerosis obliterans, Raynaud's syndrome) made possible to specify components of the SPPPG signal that are sensitive to the corresponding organic or functional pathologies. Comparison of the right and left arm finger SPPPG signal shapes, for instance, appears to be efficient tool for early screening of unilateral atherosclerosis obliterans.
Sesquiterpene lactone stereochemistry influences herbivore resistance and plant fitness in the field.

BACKGROUND AND AIMS Stereochemical variation is widely known to influence the bioactivity of compounds in the context of pharmacology and pesticide science, but our understanding of its importance in mediating plant-herbivore interactions is limited, particularly in field settings. Similarly, sesquiterpene lactones are a broadly distributed class of putative defensive compounds, but little is known about their activities in the field. METHODS Natural variation in sesquiterpene lactones of the common cocklebur, Xanthium strumarium (Asteraceae), was used in conjunction with a series of common garden experiments to examine relationships between stereochemical variation, herbivore damage and plant fitness. KEY RESULTS The stereochemistry of sesquiterpene lactone ring junctions helped to explain variation in plant herbivore resistance. Plants producing cis-fused sesquiterpene lactones experienced significantly higher damage than plants producing trans-fused sesquiterpene lactones. Experiments manipulating herbivore damage above and below ambient levels found that herbivore damage was negatively correlated with plant fitness. This pattern translated into significant fitness differences between chemotypes under ambient levels of herbivore attack, but not when attack was experimentally reduced via pesticide. CONCLUSIONS To our knowledge, this work represents only the second study to examine sesquiterpene lactones as defensive compounds in the field, the first to document herbivore-mediated natural selection on sesquiterpene lactone variation and the first to investigate the ecological significance of the stereochemistry of the lactone ring junction. The results indicate that subtle differences in stereochemistry may be a major determinant of the protective role of secondary metabolites and thus of plant fitness. As stereochemical variation is widespread in many groups of secondary metabolites, these findings suggest the possibility of dynamic evolutionary histories within the Asteraceae and other plant families showing extensive stereochemical variation.
An in vitro system for the rapid functional characterization of genes involved in carotenoid biosynthesis and accumulation.

We have developed an assay based on rice embryogenic callus for rapid functional characterization of metabolic genes. We validated the assay using a selection of well-characterized genes with known functions in the carotenoid biosynthesis pathway, allowing rapid visual screening of callus phenotypes based on tissue color. We then used the system to identify the functions of two uncharacterized genes: a chemically synthesized β-carotene ketolase gene optimized for maize codon usage, and a wild-type Arabidopsis thaliana ortholog of the cauliflower Orange gene. In contrast to previous reports (Lopez, A.B., Van Eck, J., Conlin, B.J., Paolillo, D.J., O'Neill, J. and Li, L. () J. Exp. Bot. 59, 213-223; Lu, S. , Van Eck, J., Zhou, X. , Lopez, A.B. , O'Halloran, D.M. , Cosman, K.M. , Conlin, B.J., Paolillo, D.J., Garvin, D.F. , Vrebalov, J., Kochian, L.V. , Küpper, H. , Earle, E.D. , Cao, J. and Li, L. () Plant Cell 18, 3594-3605), we found that the wild-type Orange allele was sufficient to induce chromoplast differentiation. We also found that chromoplast differentiation was induced by increasing the availability of precursors and thus driving flux through the pathway, even in the absence of Orange. Remarkably, we found that diverse endosperm-specific promoters were highly active in rice callus despite their restricted activity in mature plants. Our callus system provides a unique opportunity to predict the effect of metabolic engineering in complex pathways, and provides a starting point for quantitative modeling and the rational design of engineering strategies using synthetic biology. We discuss the impact of our data on analysis and engineering of the carotenoid biosynthesis pathway.
Concurrent Training with Different Aerobic Exercises

Abstract The aim of the present study was to compare the effects of using different intensities and types of aerobic exercise (i. e., cycle ergometer or running) during concurrent training on neuromuscular adaptations. A total of 44 young women were randomly assigned to 1 of 4 groups: concurrent strength and continuous running training (SCR, n=10), concurrent strength and interval running training (SIR, n=11), concurrent strength and continuous cycle ergometer training (SCE, n=11), or strength training only (STO, n=12). Each group trained twice a week during 11 weeks. The following strength measurements were made on all subjects before and after training period: maximal strength (1RM) in knee extension, bench press and leg press exercises; local muscular endurance (number of repetitions at 70% of 1 RM) in knee extension and bench press exercises; and isometric and isokinetic peak torque of knee extension. There were significant increases in the upper and lower-body 1 RM, isometric and isokinetic peak torque in all training groups (p<0.001), with no differences between groups. The present results suggest that in young women, concurrent training performed twice a week promotes similar neuromuscular adaptations to strength training alone, regardless of the type and the intensity in which the aerobic training is performed.
Estrogen Receptor α Polymorphism and Risk of Cardiovascular Disease, Cancer, and Hip Fracture: Cross-Sectional, Cohort, and Case–Control Studies and a Meta-Analysis

Background— We hypothesized that the estrogen receptor α (ESR1) IVS1-397T/C polymorphism affects high-density lipoprotein cholesterol response to hormone replacement therapy and risk of cardiovascular disease (CVD), cancer of reproductive organs, and hip fracture. Methods and Results— We studied cross-sectionally 9244 individuals from the Danish general population and followed them up for 23 to 25 years. End points were CVD (ischemic heart disease, myocardial infarction, angina pectoris, ischemic cerebrovascular disease, ischemic stroke, other ischemic cerebrovascular disease, venous thromboembolism, deep vein thrombosis, and pulmonary embolism), cancer of reproductive organs (breasts, ovaries, uterus, and prostate), and hip fracture. We also studied patients with ischemic heart disease (n=2495), ischemic cerebrovascular disease (n=856), and breast cancer (n=1256) versus general population controls. The CC, CT, and TT genotypes had general population frequencies of 21%, 50%, and 29%, respectively. Cross-sectionally, genotype did not influence high-density lipoprotein cholesterol response to hormone replacement therapy. In the cohort study, there were no differences in risks of CVD, cancer of reproductive organs, or hip fracture between genotypes. In case–control studies, risk of CVD did not differ between genotypes; however, the odds ratio for breast cancer in women with TT versus CC genotypes was 1.4 (95% CI, 1.1 to 1.7). Meta-analysis in men of 6 previous and the present 2 studies, including 4799 cases and 12 190 controls, showed odds ratios in CC versus CT and TT genotypes for fatal and nonfatal myocardial infarction of 0.81 (95% CI, 0.59 to 1.12) and 1.08 (95% CI, 0.97 to 1.21). Conclusions— ESR1 IVS1-397T/C polymorphism does not influence high-density lipoprotein cholesterol response to hormone replacement therapy or risk of CVD, most cancers of reproductive organs, or hip fracture.
Transcription factors in the pathogenesis of diabetic nephropathy

Approximately a third of patients with diabetes develop diabetic kidney disease, and diabetes is the leading cause of end-stage renal disease in most developed countries. Hyperglycaemia is known to activate genes that ultimately lead to extracellular matrix accumulation, the hallmark of diabetic nephropathy. Several transcription factors have been implicated in glucose-mediated expression of genes involved in diabetic nephropathy. This review focuses on the transcription factors upstream stimulatory factors 1 and 2 (USF1 and 2), activator protein 1 (AP-1), nuclear factor (NF)-κB, cAMP-response-element-binding protein (CREB), nuclear factor of activated T cells (NFAT), and stimulating protein 1 (Sp1). In response to high glucose, several of these transcription factors regulate the gene encoding the profibrotic cytokine transforming growth factor β, as well as genes for a range of other proteins implicated in inflammation and extracellular matrix turnover, including thrombospondin 1, the chemokine CCL2, osteopontin, fibronectin, decorin, plasminogen activator inhibitor 1 and aldose reductase. Identifying the molecular mechanisms by which diabetic nephropathy occurs has important clinical implications as therapies can then be tailored to target those at risk. Strategies to specifically target transcription factor activation and function may be employed to halt the progression of diabetic nephropathy.
Molecular pathophysiology of psoriasis and molecular targets of antipsoriatic therapy

Psoriasis is a chronic inflammatory skin disease characterised by elevated red scaly plaques on specific body sites. Histologically, the plaques are defined by epidermal hyperplasia, epidermal and dermal infiltration by leukocytes, and changes in the dermal microvasculature. Differentiation and activation are disturbed in lesional psoriatic keratinocytes, and the pool of proliferating keratinocytes is increased, which is accompanied by enhanced production of proinflammatory cytokines, adhesion molecules and antimicrobial peptides. These changes in psoriatic keratinocytes are caused by altered expression of genes associated with epidermal differentiation, and by activation of signalling pathways involving signal transducer and activator of transcription 3 (STAT3), type I interferon (IFN) and mitogen-activated protein kinase (MAPK). The number of T cells, and myeloid and plasmacytoid dendritic cells (DCs) is markedly increased in psoriatic lesions. Myeloid DCs produce interleukin (IL)-23, tumour necrosis factor (TNF)-α and inducible nitric oxide synthase (iNOS), which are crucial cytokines in the pathogenesis of psoriasis. IL-23 stimulates the secretion of IL-22 by T helper 17 cells, and IL-22 induces epidermal hyperplasia. The crosstalk between keratinocytes and leukocytes via their proinflammatory cytokines creates the vicious circle of chronic skin inflammation seen in psoriasis. This suggests that optimal treatment of psoriasis needs to target pathogenic pathways in both leukocytes and keratinocytes.
Asymmetrical natural hybridization varies among hybrid swarms between two diploid Rhododendron species

Background and Aims The extent to which hybridization leads to gene flow between plant species depends on the structure of hybrid populations. However, if this varies between locations, species barriers might prove permeable in some locations but not in others. To assess possible variation in hybrid population structure, the magnitude and direction of natural hybridization between two Chinese endemic species, Rhododendron spiciferum and Rhododendron spinuliferum , were evaluated. Methods Thirteen nuclear microsatellite markers were employed to characterize 566 individuals collected from 15 non-allopatric populations and nine allopatric parental populations. Chloroplast DNA (cpDNA) sequences were obtained from a subset of samples. Genetic structure and direction of gene flow was determined using a combination of STRUCTURE and NEWHYBRIDS analysis. Key Results Nuclear analysis revealed that parental taxa formed two genetically distinct clusters and hybrids shared the genetic background of both parents and did not form a separate genetic lineage. Overall, hybrid swarms were dominated by early- and later-generation hybrids, with a significantly higher proportion of hybrids (59·6 %) possessing >50 % R. spiciferum-like nuclear germplasm. The cpDNA analysis further indicated that a significantly greater proportion of hybrids (61·1 %) possessed the R. spiciferum cpDNA haplotype. Conclusions Gene flow between R. spiciferum and R. spinuliferum was found to be bidirectional in 14 of the 15 hybrid swarms and asymmetrical in six hybrid swarms. Asymmetrical gene flow was evident for only nuclear DNA (nDNA) in two populations, for only cpDNA in three populations, and for both nDNA and cpDNA in one population. Collectively, the variation in genetic structure found among the 15 hybrid swarms suggests that introgression rather than hybrid speciation is a more likely outcome of hybridization between these hybridizing taxa.
Analysis of ototoxicity in young children receiving carboplatin in the context of conservative management of unilateral or bilateral retinoblastoma

Carboplatin plays an important role in the conservative management of retinoblastoma, but is associated with risk of ototoxicity in these young children whose sensory prognosis may be also compromised by their loss of vision. This retrospective study analyzed the impact of carboplatin on hearing in the context of conservative management of children with retinoblastoma.