Laser desorption 7.87 eV postionization mass spectrometry of antibiotics in Staphylococcus epidermidis bacterial biofilms

This paper describes the development of laser desorption 7.87 eV vacuum UV (VUV) postionization MS to detect antibiotics within intact bacterial colony biofilms. As >99% of the molecules ejected by laser desorption are neutrals, VUV photoionization of these neutrals can provide significantly increased signal as compared to the detection of directly emitted ions. Postionization with VUV radiation from the molecular fluorine laser single photon ionizes laser desorbed neutrals with ionization potentials below the 7.87 eV photon energy. Antibiotics with structures indicative of sub-7.87 eV ionization potentials were examined for their ability to be detected by 7.87 eV laser desorption postionization MS. Tetracycline, sulfadiazine, and novobiocin were successfully detected neat as dried films physisorbed on porous silicon oxide substrates. Tetracycline and sulfadiazine were then detected within intact Staphylococcus epidermidis colony biofilms, the former with LOD in the micromolar concentration range.     

Control of eIF4E cellular localization by eIF4E-binding proteins, 4E-BPs

Eukaryotic initiation factor (eIF) 4E, the mRNA 5'-cap-binding protein, mediates the association of eIF4F with the mRNA 5'-cap structure to stimulate cap-dependent translation initiation in the cytoplasm. The assembly of eIF4E into the eIF4F complex is negatively regulated through a family of repressor proteins, called the eIF4E-binding proteins (4E-BPs). eIF4E is also present in the nucleus, where it is thought to stimulate nuclear-cytoplasmic transport of certain mRNAs. eIF4E is transported to the nucleus via its interaction with 4E-T (4E-transporter), but it is unclear how it is retained in the nucleus. Here we show that a sizable fraction (approximately 30%) of 4E-BP1 is localized to the nucleus, where it binds eIF4E. In mouse embryo fibroblasts (MEFs) subjected to serum starvation and/or rapamycin treatment, nuclear 4E-BPs sequester eIF4E in the nucleus. A dramatic loss of nuclear 4E-BP1 occurs in c-Ha-Ras-expressing MEFs, which fail to show starvation-induced nuclear accumulation of eIF4E. Therefore, 4E-BP1 is a regulator of eIF4E cellular localization.     

A Survey of Honey Bee Colony Losses in the U.S., Fall 2007 to Spring 2008

Background

Honey bees are an essential component of modern agriculture. A recently recognized ailment, Colony Collapse Disorder (CCD), devastates colonies, leaving hives with a complete lack of bees, dead or alive. Up to now, estimates of honey bee population decline have not included losses occurring during the wintering period, thus underestimating actual colony mortality. Our survey quantifies the extent of colony losses in the United States over the winter of 2007–2008.

Methodology/Principal Findings

Surveys were conducted to quantify and identify management factors (e.g. operation size, hive migration) that contribute to high colony losses in general and CCD symptoms in particular. Over 19% of the country''s estimated 2.44 million colonies were surveyed. A total loss of 35.8% of colonies was recorded; an increase of 11.4% compared to last year. Operations that pollinated almonds lost, on average, the same number of colonies as those that did not. The 37.9% of operations that reported having at least some of their colonies die with a complete lack of bees had a total loss of 40.8% of colonies compared to the 17.1% loss reported by beekeepers without this symptom. Large operations were more likely to have this symptom suggesting that a contagious condition may be a causal factor. Sixty percent of all colonies that were reported dead in this survey died without dead bees, and thus possibly suffered from CCD. In PA, losses varied with region, indicating that ambient temperature over winter may be an important factor.

Conclusions/Significance

Of utmost importance to understanding the recent losses and CCD is keeping track of losses over time and on a large geographic scale. Given that our surveys are representative of the losses across all beekeeping operations, between 0.75 and 1.00 million honey bee colonies are estimated to have died in the United States over the winter of 2007–2008. This article is an extensive survey of U.S. beekeepers across the continent, serving as a reference for comparison with future losses as well as providing guidance to future hypothesis-driven research on the causes of colony mortality.     

Individual‐specific variation in the respiratory activities of HMECs and their bioenergetic response to IGF1 and TNFα

Metabolic reprograming is a hallmark of cancer cells. However, the roles of pre‐existing differences in normal cells metabolism toward cancer risk is not known. In order to assess pre‐existing variations in normal cell metabolism, we have quantified the inter‐individual variation in oxidative metabolism of normal primary human mammary epithelial cells (HMECs). We then assessed their response to selected cytokines such as insulin growth factor 1 (IGF1) and tumor necrosis factor alpha (TNFα), which are associated with breast cancer risk. Specifically, we compared the oxidative metabolism of HMECs obtained from women with breast cancer and without cancer. Our data show considerable inter‐individual variation in respiratory activities of HMECs from different women. A bioenergetic parameter called pyruvate‐stimulated respiration (PySR) was identified as a key distinguishing feature of HMECs from women with breast cancer and without cancer. Samples showing PySR over 20% of basal respiration rate were considered PySR^+ve and the rest as PySR^?ve. By this criterion, HMECs from tumor‐affected breasts (AB) and non‐tumor affected breasts (NAB) of cancer patients were mostly PySR^?ve (88% and 89%, respectively), while HMECs from non‐cancer patients were mostly PySR^+ve (57%). This suggests that PySR^?ve/+ve phenotypes are individual‐specific and are not caused by field effects due to the presence of tumor. The effects of IGF1 and TNFα treatments on HMECs revealed that both suppressed respiration and extracellular acidification. In addition, IGF1 altered PySR^?ve/+ve phenotypes. These results reveal individual‐specific differences in pyruvate metabolism of normal breast epithelial cells and its association with breast cancer risk.

     

Ecological role of physical dormancy in seeds of Oxytropis racemosa in a semiarid sandland with unpredictable rainfall

Aims Seed dormancy and the soil seed bank are crucial to plant regeneration strategy, especially in semiarid ecosystems with unpredictable precipitation. The aim of this study was to investigate how seed dormancy is controlled by environmental factors and how it is correlated with the soil seed bank and regeneration of the perennial legume Oxytropis racemosa, a dominant perennial herb in Mu Us Sandland of semiarid China.Methods Germination and imbibition experiments on fresh intact and scarified seeds of O. racemosa were used to identify physical dormancy (PY) in seeds of this species. Soil seed bank dynamics, timing of seedling emergence and the fate of buried seeds in the natural habitat were investigated.Important findings PY was broken by mechanical scarification or wet heat/ice water cycles but not solely by dry heat or wet heat treatment. The soil seed bank exhibited seasonal changes in the number of seeds, which was highest in September and lowest in July. Seeds buried at different sand depths gradually lost dormancy; 20–42% of the seeds remained dormant after 20 months of burial. Dormancy break occurs gradually throughout the year. Our results indicate that O. racemosa exhibits hardcoatedness heterogeneity that spreads germination of a seed cohort between seasons and years in the semiarid environment, where the amount of precipitation during the growing season is highly variable.     

Mutations in a Novel CLN6-Encoded Transmembrane Protein Cause Variant Neuronal Ceroid Lipofuscinosis in Man and Mouse

The CLN6 gene that causes variant late-infantile neuronal ceroid lipofuscinosis (vLINCL), a recessively inherited neurodegenerative disease that features blindness, seizures, and cognitive decline, maps to 15q21-23. We have used multiallele markers spanning this approximately 4-Mb candidate interval to reveal a core haplotype, shared in Costa Rican families with vLINCL but not in a Venezuelan kindred, that highlighted a region likely to contain the CLN6 defect. Systematic comparison of genes from the minimal region uncovered a novel candidate, FLJ20561, that exhibited DNA sequence changes specific to the different disease chromosomes: a G-->T transversion in exon 3, introducing a stop codon on the Costa Rican haplotype, and a codon deletion in exon 5, eliminating a conserved tyrosine residue on the Venezuelan chromosome. Furthermore, sequencing of the murine homologue in the nclf mouse, which manifests recessive NCL-like disease, disclosed a third lesion-an extra base pair in exon 4, producing a frameshift truncation on the nclf chromosome. Thus, the novel approximately 36-kD CLN6-gene product augments an intriguing set of unrelated membrane-spanning proteins, whose deficiency causes NCL in mouse and man.     

Lateral clustering of platelet GP Ib-IX complexes leads to up-regulation of the adhesive function of integrin alpha IIbbeta 3.

Binding of von Willebrand factor (VWF) to GP Ib-IX mediates initial platelet adhesion and increases the subsequent adhesive function of alpha(IIb)beta(3). Because these responses are promoted most effectively by large VWF multimers, we hypothesized that receptor clustering modulates GP Ib-IX function. To test this, GP IX was fused at its cytoplasmic tail to tandem repeats of FKBP, and GP Ib-IX(FKBP)(2) and alpha(IIb)beta(3) were expressed in Chinese hamster ovary cells. Under flow conditions at wall shear rates of up to 2000 s(-1), GP Ib-IX(FKBP)(2) mediated cell tethering to immobilized VWF, just as in platelets. Conditional oligomerization of GP Ib-IX(FKBP)(2) by AP20187, a cell-permeable FKBP dimerizer, caused a decrease in cell translocation velocities on VWF (p < 0.001). Moreover, clustering of GP Ib-IX(FKBP)(2) by AP20187 led to an increase in alpha(IIb)beta(3) function, manifested under static conditions by increased cell adhesion to fibrinogen (p < 0.01) and under flow by increased stable cell adhesion to VWF (p < 0.04). Clustering of GP Ib-IX(FKBP)(2) also stimulated rapid tyrosine phosphorylation of ectopically expressed Syk, a putative downstream effector of GP Ib-IX in platelets. These studies establish that GP Ib-IX oligomerization, per se, affects the interaction of this receptor with VWF and its ability to influence the adhesive function of alpha(IIb)beta(3). By extrapolation, GP Ib-IX clustering in platelets may promote thrombus formation.     

Scent Marking in Voles: A Reassessment of Over Marking, Counter Marking, and Self-Advertisement

We conducted a series of experiments to discern among the counter-marking, over-marking, and self-advertisement hypotheses for secondary marking in male prairie voles, Microtus ochrogaster , and meadow voles, M. pennsylvanicus . Secondary scent marks (those placed in an area that has already been marked by a conspecific) were not significantly greater than initial marks placed on clean substrate (a substrate without any previous scent marks) for either species and thus did not support a counter-marking hypothesis. Similarly, overlapping of initial scent marks with secondary marks occurred less often than expected by chance and did not support an over-marking hypothesis. Secondary marks tended to avoid overlap with scent marks previously deposited by a potential competitor. Our results suggest that secondary scent marking functions to self-advertise by maximizing individual identity and avoiding masking or blending with previous donors. Future studies on secondary marking should be designed to quantify the observed and expected frequency and placement of original and secondary marks to discern among alternative hypotheses for the adaptive significance of secondary marking.     

The protein SET binds the neuronal Cdk5 activator p35nck5a and modulates Cdk5/p35nck5a activity.

The neuronal Cdk5 kinase is composed of the catalytic subunit Cdk5 and the activator protein p35(nck5a) or its isoform, p39(nck5ai). To identify novel p35(nck5a)- and p39(nck5ai)-binding proteins, fragments of p35(nck5a) and p39(nck5ai) were utilized in affinity isolation of binding proteins from rat brain homogenates, and the isolated proteins were identified using mass spectrometry. With this approach, the nuclear protein SET was shown to interact with the N-terminal regions of p35(nck5a) and p39(nck5ai). Our detailed characterization showed that the SET protein formed a complex with Cdk5/p35(nck5a) through its binding to p35(nck5a). The p35(nck5a)-interacting region was mapped to a predicted alpha-helix in SET. When cotransfected into COS-7 cells, SET and p35(nck5a) displayed overlapping intracellular distribution in the nucleus. The nuclear co-localization was corroborated by immunostaining data of endogenous SET and Cdk5/p35(nck5a) from cultured cortical neurons. Finally, we demonstrated that the activity of Cdk5/p35(nck5a), but not that of Cdk5/p25(nck5a), was enhanced upon binding to the SET protein. The tail region of SET, which is rich in acidic residues, is required for the stimulatory effect on Cdk5/p35(nck5a).