Effect of Ceramide Tail Length on the Structure of Model Stratum Corneum Lipid Bilayers

Lipid bilayers composed of non-hydroxy sphingosine ceramide (CER NS), cholesterol (CHOL), and free fatty acids (FFAs), which are components of the human skin barrier, are studied via molecular dynamics simulations. Since mixtures of these lipids exist in dense gel phases with little molecular mobility at physiological conditions, care must be taken to ensure that the simulations become decorrelated from the initial conditions. Thus, we propose and validate an equilibration protocol based on simulated tempering, in which the simulation takes a random walk through temperature space, allowing the system to break out of metastable configurations and hence become decorrelated from its initial configuration. After validating the equilibration protocol, which we refer to as random-walk molecular dynamics, the effects of the lipid composition and ceramide tail length on bilayer properties are studied. Systems containing pure CER NS, CER NS + CHOL, and CER NS + CHOL + FFA, with the CER NS fatty acid tail length varied within each CER NS-CHOL-FFA composition, are simulated. The bilayer thickness is found to depend on the structure of the center of the bilayer, which arises as a result of the tail-length asymmetry between the lipids studied. The hydrogen bonding between the lipid headgroups and with water is found to change with the overall lipid composition, but is mostly independent of the CER fatty acid tail length. Subtle differences in the lateral packing of the lipid tails are also found as a function of CER tail length. Overall, these results provide insight into the experimentally observed trend of altered barrier properties in skin systems where there are more CERs with shorter tails present.     

Young But Not Old Adult African Striped Mice Reduce Their Activity in the Dry Season When Food Availability is Low

An individual′s survival and fitness depend on its ability to effectively allocate its time between competing behaviors. Sex, social tactic, season and food availability are important factors influencing activity budgets. However, few field studies have tested their influences. The African striped mouse (Rhabdomys pumilio) lives in highly seasonal habitats in southern Africa, and individuals can adopt different social tactics. We investigated seasonal changes in activity budgets of different tactics and predicted that individuals will reduce their activity in the non‐breeding season to save energy when food availability is low and that young non‐breeding adults (‘philopatrics’) invest mainly in activities related to gaining body mass to increase survival probability. We predicted old adults (‘breeders’), which bred during the previous breeding season, to invest mainly in maintenance of their social status. We conducted 90 focal observations during the non‐breeding season and 73 during the breeding season. Activity budgets of striped mice were season and tactic specific, with philopatrics, but not breeders, reducing activity when food availability was low, possibly to decrease energy expenditure. Philopatrics of both sexes foraged and basked more in the breeding season than during the non‐breeding season. Male philopatrics gained body mass and female philopatrics maintained their body mass in both seasons. Sex‐specific differences occurred during the breeding season, when female breeders foraged more than male breeders, while male breeders chased other individuals more than female breeders. These findings indicate that individuals adopting different social tactics display distinct behaviors to fulfill tactic‐specific energetic needs .     

Novel Production Protocol for Small-scale Manufacture of Probiotic Fermented Foods

A novel dried bacterial consortium of Lactobacillus rhamnosus yoba 2012 and Streptococcus thermophilus C106 is cultured in 1 L of milk. This fresh starter can be used for the production of fermented milk and other fermented foods either at home or at small-scale in rural settings. For the fresh starter, 1 L of milk is pasteurized in a pan that fits into a larger pan containing water, placed on a source of heat. In this water bath, the milk is heated and incubated at 85 °C for 30 min. Thereafter, the milk is cooled down to 45 °C, transferred to a vacuum flask, inoculated with the dried bacteria and left for at least 16 hr between 30 °C and 45 °C. For the purpose of frequent home production, the fresh starter is frozen into ice cubes, which can be used for the production of small volumes of up to 2 L of fermented milk. For the purpose of small-scale production in resource-poor countries, pasteurization of up to 100 L of milk is conducted in milk cans that are placed in a large sauce pan filled with water and heated on a fire at 85 °C for 30 min, and subsequently cooled to 45 °C. Next, the 100 L batch is inoculated with the 1 L freshly prepared starter mentioned before. To assure an effective fermentation at a temperature between 30 and 45 °C, the milk can is covered with a blanket for 12 hr. For the production of non-dairy fermented foods, the fresh starter is left in a cheese cloth for 12 hr, and the drained-off whey can be subsequently used for the inoculation of a wide range of food raw materials, including vegetables and cereal-based foods.     

Enhancement by farnesol and farnesoic acid of juvenile-hormone biosynthesis in induced low-activity locust corpora allata

Exogenous farnesol or farnesoic acid (FA) stimulates juvenile hormone III (JH III) biosynthesis by isolated corpora allata from Locusta migratoria in a dose-dependent manner. Farnesol and FA also stimulate a dose-dependent accumulation of substantial amounts of methyl farnesoate (MF), identified by gas chromatography-mass spectroscopy (GCMS) analysis, in the corpora allata. Lower quantities of MF were found in the incubation medium. Corpora allata, denervated 2 days prior to assay, showed low spontaneous rates of JH biosynthesis which were stimulated by farnesol and FA. The dose-response curves for control and denervated corpora allata were similar. During oocyte maturation the rate of farnesol and FA stimulation of JH biosynthesis increased gradually. However, after transection of nervus corporis allati 1 (NCA-1), the rate of stimulated JH synthesis was maintained at preoperative levels. Although the spontaneous rate of JH biosynthesis decreased rapidly after NCA-1 transection, denervated glands could still be stimulated by farnesol or FA to produce large amounts of JH. These results suggest that the low spontaneous rate of JH biosynthesis in denervated corpora allata is not caused by inhibition of the final steps of JH biosynthesis.     

Attraction of the specialist parasitoid Cotesia rubecula to Arabidopsis thaliana infested by host or non-host herbivore species

In this study we investigated whether in a two‐choice set‐up the parasitoid Cotesia rubecula (Marshall) (Hymenoptera, Braconidae) distinguishes between volatiles emitted by Arabidopsis thaliana (L.) Heynh. (Brassicaceae) infested with its host, Pieris rapae (L.) (Lepidoptera: Pieridae) and Arabidopsis infested with non‐host herbivores. Four non‐host herbivore species were tested: the caterpillars Plutella xylostella (L.) (Lepidoptera: Plutellidae) and Spodoptera exigua (Hübner) (Lepidoptera: Noctuidae), both chewing insects, the spider mite Tetranychus urticae (Koch) (Acari: Tetranychidae), which punctures parenchymal cells, and the aphid Myzus persicae (Sulzer) (Hemiptera: Aphidoidea), which is a phloem‐feeder. Compared with undamaged plants, C. rubecula females were more attracted to Arabidopsis plants infested by P. rapae, P. xylostella, S. exigua, or T. urticae, but not to plants infested by M. persicae. The parasitoids preferred host‐infested plants to spider mite‐ or aphid‐infested plants, but not to plants infested with non‐host caterpillars (P. xylostella or S. exigua). The data show that when Arabidopsis plants are infested with a leaf tissue‐damaging herbivore they emit a volatile blend that attracts C. rubecula females and the wasps only discriminate between a host and non‐host herbivore when the type of damage is different (chewing vs. piercing). When Arabidopsis is infested with a herbivore that hardly damages leaf tissue, C. rubecula females are not attracted. These results may be explained by differences in the amount of damage and in the relative importance of different signal‐transduction pathways induced by different types of herbivores.     

Autoregulation of RCO by Low-Affinity Binding Modulates Cytokinin Action and Shapes Leaf Diversity

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Block of Nav1.8 by small molecules

Sodium channels are key proteins in regulating neuronal excitability and accumulating data suggest that specific subtypes of voltage-dependent sodium channels are important in signaling various types of pain. Consistent with this theme, Jarvis et al.(7) recently reported the identification of a subtype-selective Na(v)1.8 blocker that was active in several pre-clinical models of pain. During the course of these studies compounds were also identified that showed large differences in potency when tested on Na(v)1.8 channels from different species. This addendum illustrates one of these compounds along with the potency correlation between recombinant and native tetrodotoxin-resistant sodium channels for additional examples. These data show that significant differences can be observed for sodium channel blockers across species and highlight the importance of considering this possibility when searching for new compounds and research tools to probe sodium channel function.     

Online Peptide Fractionation Using a Multiphasic Microfluidic Liquid Chromatography Chip Improves Reproducibility and Detection Limits for Quantitation in Discovery and Targeted Proteomics

Comprehensive proteomic profiling of biological specimens usually requires multidimensional chromatographic peptide fractionation prior to mass spectrometry. However, this approach can suffer from poor reproducibility because of the lack of standardization and automation of the entire workflow, thus compromising performance of quantitative proteomic investigations. To address these variables we developed an online peptide fractionation system comprising a multiphasic liquid chromatography (LC) chip that integrates reversed phase and strong cation exchange chromatography upstream of the mass spectrometer (MS). We showed superiority of this system for standardizing discovery and targeted proteomic workflows using cancer cell lysates and nondepleted human plasma. Five-step multiphase chip LC MS/MS acquisition showed clear advantages over analyses of unfractionated samples by identifying more peptides, consuming less sample and often improving the lower limits of quantitation, all in highly reproducible, automated, online configuration. We further showed that multiphase chip LC fractionation provided a facile means to detect many N- and C-terminal peptides (including acetylated N terminus) that are challenging to identify in complex tryptic peptide matrices because of less favorable ionization characteristics. Given as much as 95% of peptides were detected in only a single salt fraction from cell lysates we exploited this high reproducibility and coupled it with multiple reaction monitoring on a high-resolution MS instrument (MRM-HR). This approach increased target analyte peak area and improved lower limits of quantitation without negatively influencing variance or bias. Further, we showed a strategy to use multiphase LC chip fractionation LC-MS/MS for ion library generation to integrate with SWATH^TM data-independent acquisition quantitative workflows. All MS data are available via ProteomeXchange with identifier PXD001464.Mass spectrometry based proteomic quantitation is an essential technique used for contemporary, integrative biological studies. Whether used in discovery experiments or for targeted biomarker applications, quantitative proteomic studies require high reproducibility at many levels. It requires reproducible run-to-run peptide detection, reproducible peptide quantitation, reproducible depth of proteome coverage, and ideally, a high degree of cross-laboratory analytical reproducibility. Mass spectrometry centered proteomics has evolved steadily over the past decade, now mature enough to derive extensive draft maps of the human proteome (1, 2). Nonetheless, a key requirement yet to be realized is to ensure that quantitative proteomics can be carried out in a timely manner while satisfying the aforementioned challenges associated with reproducibility. This is especially important for recent developments using data independent MS quantitation and multiple reaction monitoring on high-resolution MS (MRM-HR)¹ as they are both highly dependent on LC peptide retention time reproducibility and precursor detectability, while attempting to maximize proteome coverage (3). Strategies usually employed to increase the depth of proteome coverage utilize various sample fractionation methods including gel-based separation, affinity enrichment or depletion, protein or peptide chemical modification-based enrichment, and various peptide chromatography methods, particularly ion exchange chromatography (4–10). In comparison to an unfractionated “naive” sample, the trade-off in using these enrichments/fractionation approaches are higher risk of sample losses, introduction of undesired chemical modifications (e.g. oxidation, deamidation, N-terminal lactam formation), and the potential for result skewing and bias, as well as numerous time and human resources required to perform the sample preparation tasks. Online-coupled approaches aim to minimize those risks and address resource constraints. A widely practiced example of the benefits of online sample fractionation has been the decade long use of combining strong cation exchange chromatography (SCX) with C18 reversed-phase (RP) for peptide fractionation (known as MudPIT – multidimensional protein identification technology), where SCX and RP is performed under the same buffer conditions and the SCX elution performed with volatile organic cations compatible with reversed phase separation (11). This approach greatly increases analyte detection while avoiding sample handling losses. The MudPIT approach has been widely used for discovery proteomics (12–14), and we have previously shown that multiphasic separations also have utility for targeted proteomics when configured for selected reaction monitoring MS (SRM-MS). We showed substantial advantages of MudPIT-SRM-MS with reduced ion suppression, increased peak areas and lower limits of detection (LLOD) compared with conventional RP-SRM-MS (15).To improve the reproducibility of proteomic workflows, increase throughput and minimize sample loss, numerous microfluidic devices have been developed and integrated for proteomic applications (16, 17). These devices can broadly be classified into two groups: (1) microfluidic chips for peptide separation (18–25) and; (2) proteome reactors that combine enzymatic processing with peptide based fractionation (26–30). Because of the small dimension of these devices, they are readily able to integrate into nanoLC workflows. Various applications have been described including increasing proteome coverage (22, 27, 28) and targeting of phosphopeptides (24, 31, 32), glycopeptides and released glycans (29, 33, 34).In this work, we set out to take advantage of the benefits of multiphasic peptide separations and address the reproducibility needs required for high-throughput comparative proteomics using a variety of workflows. We integrated a multiphasic SCX and RP column in a “plug-and-play” microfluidic chip format for online fractionation, eliminating the need for users to make minimal dead volume connections between traps and columns. We show the flexibility of this format to provide robust peptide separation and reproducibility using conventional and topical mass spectrometry workflows. This was undertaken by coupling the multiphase liquid chromatography (LC) chip to a fast scanning Q-ToF mass spectrometer for data dependent MS/MS, data independent MS (SWATH) and for targeted proteomics using MRM-HR, showing clear advantages for repeatable analyses compared with conventional proteomic workflows.     

Heterologous expression of pentalenene synthase (PSS) from Streptomyces UC5319 in Xanthophyllomyces dendrorhous

For the first time, the pentalenene synthase (PSS) gene from Streptomyces UC5319 was expressed in Xanthophyllomyces dendrorhous, a native producer of astaxanthin. For the expression of the gene and the concurrent knock out of the native crtE or crtYB genes, two new vectors were engineered and used for the transformation of the wild-type strain of X. dendrorhous. The transformations resulted in white colonies, showing a complete shutdown of the carotenoid production. Furthermore, an additional vector was constructed for the insertion of the PSS gene in the rDNA of the yeast. All the mutant strains produce the sesquiterpene pentalenene and show no difference in growth when compared to the wild-type strain. In this report, we demonstrate that X. dendrorhous is a suitable host for the expression of heterologous terpene cyclases and for the production of foreign terpene compounds.