Universal markers for comparative mapping and phylogenetic analysis in the Asteraceae (Compositae)

The development of universal markers that can be assayed across taxa, but which are polymorphic within taxa, can facilitate both comparative map-based studies and phylogenetic analyses. Here we describe the development of such markers for use in the Asteraceae, which includes the crops lettuce, sunflower, and safflower as well as dozens of locally important crop and weed species. Using alignments of a conserved orthologous set (COS) of ESTs from lettuce and sunflower and genomic sequences of Arabidopsis, we designed a suite of primer pairs that are conserved across species, but which are predicted to flank introns. We then tested 192 such primer pairs in 8 species from across the family. Of these, 163 produced an amplicon in at least 1 taxon, and 125 amplified in at least half of the taxa surveyed. Thirty-nine amplified in all 8 species. Comparisons amongst sequences within the lettuce and sunflower EST databases indicate that the vast majority of these loci will be polymorphic. As a direct test of the utility of these markers outside the lettuce and sunflower subfamilies, we sequenced a subset of ten loci from a panel of cultivated safflower individuals. All 10 loci proved to be single-locus, and nine of the 10 loci were polymorphic with an average of 12.8 SNPs per kb. Taken together, these loci will provide an initial backbone for comparative genetic analyses within the Asteraceae. Moreover, our results indicate that these loci are phylogenetically informative, and hence can be used to resolve evolutionary relationships between taxa within the family as well as within species. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Mark A. Chapman and JianCheng Chang have contributed equally to this work.     

Stimulation of fecal fat excretion and the disposal of protoporphyrin in a murine model for erythropoietic protoporphyria

Erythropoietic protoporphyria (EPP) is characterized by toxic accumulation of the hydrophobic compound protoporphyrin (PP). Ferrochelatase-deficient (fch/fch) mice are an animal model for human EPP. Recently, we have demonstrated that the accumulation of another hydrophobic compound, unconjugated bilirubin, could effectively be treated by stimulation of fecal fat excretion. We investigated whether stimulation of fecal fat excretion enhanced the disposal of PP in fch/fch mice. Fch/fch mice were fed for 8 wk with a high-fat diet (16 wt% fat; control) or with the high-fat diet mixed with either a nonabsorbable fat (sucrose polyester) or the intestinal lipase inhibitor orlistat. The effects of the treatments on fecal excretion of fat and PP and on hepatic PP concentrations were compared with control diets. Fecal fat excretion in fch/fch mice on a high-fat diet was higher than in mice on a low-fat diet (+149%, P < 0.05). Sucrose polyesters and orlistat increased fecal fat excretion even more, up to sixfold of control values. However, none of the different treatments affected fecal PP excretion or hepatic PP concentration. Treatment of fch/fch mice with a high-fat diet, a nonabsorbable fat diet, or with orlistat increased the fecal excretion of fat but did not increase fecal PP excretion or decrease hepatic PP concentration. The present data indicate that accumulation of PP is not amenable to stimulation of fecal fat excretion.     

Field patterns of leaf plasticity in adults of the long-lived evergreen Quercus coccifera

BACKGROUND AND AIMS: Quercus coccifera, as a long-lived sprouter, responds plastically to environmental variation. In this study, the role of foliar plasticity as a mechanism of habitat selection and modification within the canopy and across contrasted habitats was characterized. An examination was made of the differential contribution of inner and outer canopy layers to the crown plasticity expressed in the field by adult individuals and its dependence on environmental and genetic factors. METHODS: Within-crown variation in eight foliar traits was examined in nine populations dominated by Q. coccifera. The difference between mean trait values at the inner and outer canopy layers was used as a proxy for crown plasticity to light. Correlations between geographic distances, environmental differences (climatic and edaphic) and phenotypic divergence (means and plasticities) were assessed by partial Mantel tests. A subset of field measurements was compared with data from a previous common garden experiment. KEY RESULTS: Phenotypic adjustment of sun leaves contributed significantly to the field variation in crown plasticity. Plasticity in leaf angle, lobation, xanthophyll cycle pigments and beta-carotene content was expressed in sun and shade leaves concurrently and in opposite directions. Phenotypic plasticity was more strongly correlated with environmental variation than mean trait values. Populations of taller plants with larger, thinner (higher specific leaf area) and less spiny leaves exhibited greater plasticity. In these populations, the midday light environment was more uniform at the inner than at the outer canopy layers. Field and common garden data ranked populations in the same order of plasticity. CONCLUSIONS: The expression of leaf plasticity resulted in a phenotypic differentiation that suggests a mechanism of habitat selection through division of labour across canopy layers. Signs of plasticity-mediated habitat modification were found only in the most plastic populations. Intracanopy plasticity was sensitive to environmental variation but also exhibited a strong genetic component.     

Los mamíferos insulares del Mioceno medio y superior de Menorca (islas Baleares, Mediterráneo occidental)

The insular mammals from the karstic deposits of Punta Nati-2 and the marine beds of es Cul de sa Ferrada, placed in the northwest coast of Minorca (Balearic islands, Spain, western Mediterranean) are described in this work. One of the mammals (only present in Punta Nati-2) is a new glirid species, Margaritamys adroveri, closely related with Margaritamys llulli Mein and Adrover, 1982 and Pseudodryomys granatensis Agustí, 1993, from the middle Miocene of Santa Margalida and Sant Llorenç (Mallorca) and Murchas (Granada), respectively. M. adroveri shows more derived characters than P. granatensis and is more archaic than M. llulli, the size being similar to P. granatensis. The ochotonid present in Minorca is very similar to Gymnesicolagus gelaberti Mein and Adrover, 1982 from Mallorca. In the two minorcan deposits were recovered the first mandibles of this ochotonid, characterized by their big size. The medium weight (estimated from the length of the lower row) for G. aff. gelaberti is 5.4 kg, very similar to that some extant leporids like Lepus alleni Mearns, 1890 or Lepus arcticus Ross, 1819 and higher than any other living ochotonid. Doubtless, the big size of G. aff. gelaberti is a consequence of insular evolution, but not the short diastema, a primitive character shared with continental ochotonids and insular leporids. The discovery of a mandible in the marine beds of es Cul de sa Ferrada permits to place G. aff. gelaberti in the lower Tortonian, which represents the youngest record for this species with respect the faunal associations of Mallorca and Granada, Langhian-Serravalian in age (middle-upper Miocene). The fauna from Punta Nati-2 may represent an endemic association or a faunal group closely related to the fauna of Mallorca and Granada, but in an older context. The age of Gymnesicolagus and the presence of a similar fauna in Mallorca and Minorca suggest a connection between both islands during the Serravalian and the existence of an emerged area in Minorca after the Tortonian transgression.     

Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors

We describe a chemical proteomics approach to profile the interaction of small molecules with hundreds of endogenously expressed protein kinases and purine-binding proteins. This subproteome is captured by immobilized nonselective kinase inhibitors (kinobeads), and the bound proteins are quantified in parallel by mass spectrometry using isobaric tags for relative and absolute quantification (iTRAQ). By measuring the competition with the affinity matrix, we assess the binding of drugs to their targets in cell lysates and in cells. By mapping drug-induced changes in the phosphorylation state of the captured proteome, we also analyze signaling pathways downstream of target kinases. Quantitative profiling of the drugs imatinib (Gleevec), dasatinib (Sprycel) and bosutinib in K562 cells confirms known targets including ABL and SRC family kinases and identifies the receptor tyrosine kinase DDR1 and the oxidoreductase NQO2 as novel targets of imatinib. The data suggest that our approach is a valuable tool for drug discovery.     

Antibody microarray analysis of inflammatory mediator release by human leukemia T-cells and human non small cell lung cancer cells.

Cytokines and chemokines are responsible for regulating inflammation and the immune response. Cytokine and chemokine release is typically measured by quantitative enzyme-linked immunosorbant assay (ELISA) or Western blot analysis. To expedite the analysis of samples for multiple cytokines/chemokines, we have developed slide-based Thermo Scientific ExcelArray Antibody Sandwich Microarrays. Each slide consists of 16 subarrays (wells), each printed with 12 specific antibodies in triplicate and positive and negative control elements. This 16-well format allows for the analysis of 10 test samples using a six-point standard curve. The array architecture is based on the "sandwich" ELISA, in which an analyte protein is sandwiched between an immobilized capture antibody and a biotinylated detection antibody, using streptavidin-linked Thermo Scientific DyLight 649 Dye for quantitation. The observed sensitivity of this assay was <10 pg/mL. In our experiments, the Jurkat cell line was used as a model for human T-cell leukemia, and the A549 cell line was used as a model for human non-small cell lung cancer. To evoke a cytokine/chemokine response, cells were stimulated with tumor necrosis factor alpha (TNFalpha), phorbol-12-myristate-13-acetate (PMA, TPA), and phytohemagglutinin (PHA). Cell supernatants derived from both untreated and stimulated cells were analyzed on four different arrays (Inflammation I, Inflammation II, Angiogenesis, and Chemotaxis), enabling the quantitation of 41 unique analytes. Stimulated cells showed an increase in the expression level of many of the test analytes, including IL-8, TNF-alpha, and MIP-1alpha, compared to the non-treated controls. Our experiments clearly demonstrate the utility of antibody microarray analysis of cell-culture supernatants for the profiling of cellular inflammatory mediator release.     

An assessment of Putative Sexually Antagonistic Traits in a Freshwater Amphipod Species

Sexual conflict can result in an ‘evolutionary arms race’ between males and females, with the evolution of sexual antagonistic traits used to resolve the conflict in favor of one sex over the other. We assessed the resolution of sexual conflict in a Hyalella amphipod species by manipulating putative sexually antagonistic traits in males and females and used mate‐guarding duration as our metric of conflict resolution. We discovered that large male posterior gnathopod size increased mate‐guarding duration, which suggests that it is a sexually antagonistic trait in this species. In contrast, female and male body size did not significantly affect mate‐guarding duration. Given that male posterior gnathopods show heightened condition dependence, future investigations should explore the interactive effects of sexual conflict and ecological context on trait evolution, phenotypic divergence, and speciation to elucidate the complex mechanisms involved in the evolution of biological diversity.     

Effect of older age on treatment decisions and outcomes among patients with traumatic spinal cord injury

Background:

Older people are at increased risk of traumatic spinal cord injury from falls. We evaluated the impact of older age (≥ 70 yr) on treatment decisions and outcomes.

Methods:

We identified patients with traumatic spinal cord injury for whom consent and detailed data were available from among patients recruited (2004–2013) at any of the 31 acute care and rehabilitation hospitals participating in the Rick Hansen Spinal Cord Injury Registry. Patients were assessed by age group (< 70 v. ≥ 70 yr). The primary outcome was the rate of acute surgical treatment. We used bivariate and multivariate regression models to assess patient and injury-related factors associated with receiving surgical treatment and with the timing of surgery after arrival to a participating centre.

Results:

Of the 1440 patients included in our study cohort, 167 (11.6%) were 70 years or older at the time of injury. Older patients were more likely than younger patients to be injured by falling (83.1% v. 37.4%; p < 0.001), to have a cervical injury (78.0% v. 61.6%; p = 0.001), to have less severe injuries on admission (American Spinal Injury Association Impairment Scale grade C or D: 70.5% v. 46.9%; p < 0.001), to have a longer stay in an acute care hospital (median 35 v. 28 d; p < 0.005) and to have a higher in-hospital mortality (4.2% v. 0.6%; p < 0.001). Multivariate analysis did not show that age of 70 years or more at injury was associated with a decreased likelihood of surgical treatment (adjusted odds ratio [OR] 0.48, 95% confidence interval [CI] 0.22–1.07). An unplanned sensitivity analysis with different age thresholds showed that a threshold of 65 years was associated with a decreased chance of surgical treatment (OR 0.39, 95% CI 0.19–0.80). Older patients who underwent surgical treatment had a significantly longer wait time from admission to surgery than younger patients (37 v. 19 h; p < 0.001).

Interpretation:

We found chronological age to be a factor influencing treatment decisions but not at the 70-year age threshold that we had hypothesized. Older patients waited longer for surgery and had a substantially higher in-hospital mortality despite having less severe injuries than younger patients. Further research into the link between treatment delays and outcomes among older patients could inform surgical guideline development.Globally there has been an epidemiologic shift in the age of patients who sustain a traumatic spinal cord injury.^1–3 Although most people who have traumatic spinal cord injuries are 16–30 years old, there has been a progressive increase in the number who are over 70. The average age at injury has increased from 29 to 40 years.⁴ By 2032, patients over 70 are predicted to account for most patients with new traumatic spinal cord injuries.⁵ This change is attributed in part to aging baby boomers. It is unknown whether the management and outcomes of these older patients differ compared with younger patients.Older patients typically have more comorbid conditions, including cardiovascular disease, respiratory disorders, cerebrovascular disease and dementia, which are thought to increase their risk of perioperative adverse events.⁶ The use of anticoagulants for cardiac and cerebrovascular indications can delay timely surgical interventions. Older patients are also at increased risk of postoperative and medication-related adverse events, such as delirium.⁷ As a direct consequence of this perceived risk of perioperative adverse events and ambiguity about the optimal treatment for spinal cord injury in older patients, surgeons may deliberate for some time before making a clear therapeutic decision, they may choose nonoperative treatment,⁸ or they may delay the surgical treatment in an effort to optimize the patient’s condition medically.Given the increasing incidence of traumatic spinal cord injury in older adults, and the potential for differences in treatment among older and younger patients, we evaluated the impact of age on treatment decisions and outcomes among patients with traumatic spinal cord injury. We hypothesized that surgical management would differ at an age threshold of 70 years.