A protocol for culturing Drosophila melanogaster stage 9 egg chambers for live imaging

This protocol describes a method for the dissection of egg chambers from intact Drosophila females and culture conditions that permit live imaging of them, with a particular emphasis on stage 9. This stage of development is characterized by oocyte growth and patterning, outer follicle cell rearrangement and migration of border cells. Although in vitro culture of egg chambers of later developmental stages has long been possible, until recently stage 9 egg chambers could only be kept alive for short periods, did not develop normally, and border cell migration failed entirely. We have established culture conditions that support overall egg chamber development including border cell migration in vitro. This protocol makes possible direct observation of molecular and cellular dynamics in both wild-type and mutant egg chambers, and opens the door to testing of pharmacological inhibitors and the use of biosensors. The entire protocol takes approximately 24 h while the preparation of egg chambers for live imaging requires only 15-20 min.     

A three-stage discrete-time population model: continuous versus seasonal reproduction

We consider a three-stage discrete-time population model with density-dependent survivorship and time-dependent reproduction. We provide stability analysis for two types of birth mechanisms: continuous and seasonal. We show that when birth is continuous there exists a unique globally stable interior equilibrium provided that the inherent net reproductive number is greater than unity. If it is less than unity, then extinction is the population's fate. We then analyze the case when birth is a function of period two and show that the unique two-cycle is globally attracting when the inherent net reproductive number is greater than unity, while if it is less than unity the population goes to extinction. The two birth types are then compared. It is shown that for low birth rates the adult average number over a one-year period is always higher when reproduction is continuous. Numerical simulations suggest that this remains true for high birth rates. Thus periodic birth rates of period two are deleterious for the three-stage population model. This is different from the results obtained for a two-stage model discussed by Ackleh and Jang (J. Diff. Equ. Appl., 13, 261-274, 2007), where it was shown that for low birth rates seasonal breeding results in higher adult averages.     

Detection of proteins using a colorimetric bio-barcode assay

The colorimetric bio-barcode assay is a red-to-blue color change-based protein detection method with ultrahigh sensitivity. This assay is based on both the bio-barcode amplification method that allows for detecting miniscule amount of targets with attomolar sensitivity and gold nanoparticle-based colorimetric DNA detection method that allows for a simple and straightforward detection of biomolecules of interest (here we detect interleukin-2, an important biomarker (cytokine) for many immunodeficiency-related diseases and cancers). The protocol is composed of the following steps: (i) conjugation of target capture molecules and barcode DNA strands onto silica microparticles, (ii) target capture with probes, (iii) separation and release of barcode DNA strands from the separated probes, (iv) detection of released barcode DNA using DNA-modified gold nanoparticle probes and (v) red-to-blue color change analysis with a graphic software. Actual target detection and quantification steps with premade probes take approximately 3 h (whole protocol including probe preparations takes approximately 3 days).     

High frequency somatic embryogenesis and plant regeneration in root explant cultures of carnation

Root explants excised from carnation plants maintained in vitro formed off-white, friable calluses after three weeks of culture on Murashige and Skoog (MS) medium supplemented with 1 mg l⁻¹ thidiazuron (TDZ) and 1 mg l⁻¹ α-naphthalaneacetic acid (NAA). These calluses were subsequently transferred to MS basal medium where, after an additional four weeks of culture, approximately 50% of the calluses formed somatic embryos. However, calluses formed on root explants that had been cultured on MS medium supplemented with 2,4-dichlorophenoxyacetic acid did not produce somatic embryos upon transfer to MS basal medium. Somatic embryos developed into plantlets and subsequently were grown to maturity. These results indicate that root explants have a high competence for somatic embryogenesis in carnation. J. Seo and S.W. Kim contributed equally to this work.     

Discrimination of higher plant calluses based on embryogenic capacity and taxonomic classification by pyrolysis mass spectrometry

Pyrolysis mass spectrometry (PyMS) is a rapid, simple, high-resolution analytical method based on thermal degradation of complex material in a vacuum, and has been widely applied to the discrimination of closely related microbial strains. Minimally prepared samples of embryogenic and non-embryogenic calluses derived from various higher plants (sweet potato, morning glory, Korean ginseng, Siberian ginseng, and balloon flower) were subjected to PyMS for spectral fingerprinting. A dendrogram based on the unweighted pair group method, with arithmetic mean of pyrolysis mass spectra, divided the calluses into Siberian ginseng embryogenic callus and the others, which were subsequently divided into embryogenic and non-embryogenic callus groups, regardless of plant species from which the calluses were derived. In the non-embryogenic callus group, the dendrogram was in agreement with the known taxonomy of the plants. These results indicate that PyMS analysis could be applied for discriminating plant calluses based on embryogenic capacity and taxonomic classification.     

Membrane proteomic analysis of human mesenchymal stromal cells during adipogenesis

Mesenchymal stromal cells (MSCs) have proven useful for cell and immune therapy, but the molecular constituents responsible for their functionalities, in particular, those on the plasma membrane, remain largely unknown. Here we employed both gel and nongel based MS to analyze human MSCs' membrane proteome before and after adipogenesis. 2-DE of cells that were pretreated with membrane impermeable fluorescent dyes revealed that both the whole cell proteome and the cell surface subproteome were independent of donors. LC coupled with tandem MS analysis of the plasma membrane-containing fraction allowed us to identify 707 proteins, approximately half of which could be annotated as membrane-related proteins. Of particular interest was a subset of ectodomain-containing membrane-bound proteins that encompass most known surface markers for MSCs, but also contain a multitude of solute carriers and ATPases. Upon adipogenic differentiation, this proteomic profile was amended to include several proteins involved in lipid metabolism and trafficking, at the expense of, most noticeably, ectoenzymes. Our results here provide not only a basis for future studies of MSC-specific molecular mechanisms, but also a molecular inventory for the development of antibody-based cell isolation and identification procedures.     

Proteomic identification of macrophage migration-inhibitory factor upon exposure to TiO2 particles

Inhalation of particulate matter aggravates respiratory symptoms in patients with chronic airway diseases, but the mechanisms underlying this response remain poorly understood. We used a proteomics approach to examine this phenomenon. Treatment of epithelial cells with BSA-coated titanium dioxide (TiO(2)) particles altered 20 protein spots on the two-dimensional gel, and these were then analyzed by nano-LC-MS/MS. These proteins included defense-related, cell-activating, and cytoskeletal proteins implicated in the response to oxidative stress. The proteins were classified into four groups according to the time course of their expression patterns. For validation, RT-PCR was performed on extracts of in vitro TiO(2)-treated cells, and lung issues from TiO(2)-treated rats were analyzed by immunohistochemical staining and enzyme immunoassay. TiO(2) treatment was found to increase the amount of mRNA for macrophage migration-inhibitory factor (MIF). MIF was expressed primarily in epithelium and was elevated in lung tissues and bronchoalveolar lavage fluids of TiO(2)-treated rats as compared with sham-treated rats. Carbon black and diesel exhaust particles also induced expression of MIF protein in the epithelial cells.     

Relationships Between Catecholamine Levels and Stress or Intelligence

Catecholamines, including epinephrine (E), norepinephrine (NE), and dopamine (DA), are associated with the response to stressful conditions. However, the relationships of catecholamines with intelligence and their interactions with stress remain unclear. This study assessed stress, intelligence quotient (IQ), and catecholamine levels in 70 healthy subjects to elucidate associations between catecholamines and stress, and between catecholamines and IQ. Additionally, the associations of catecholamines with stress and IQ were analyzed according to hemispheric dominance using the Brain Preference Indicator (BPI). There were positive correlations between the NE/E ratio and the somatization of stress but negative correlations between the E/NE ratio and the somatization of stress among the total number of subjects. In the right-brain-dominant group, a high E/DA ratio was correlated with low levels of stress, somatization and depression, and high NE/E and DA/E ratios were associated with high levels of somatization. In the left-brain-dominant group, high E levels were correlated with low levels of depression. In the total subjects, there were positive correlations between the NE/E and DA/E ratios and the sum of the vocabulary, arithmetic, picture arrangement, and block design IQ subtests. Thus, these catecholamines were associated with stress and IQ, which suggests that the autonomic functional regulation of catecholamine levels in relation to stress may also affect cognitive functions related to intelligence in the brain. Furthermore, the relationships between catecholamines and stress or IQ differed depending on hemispheric dominance, which suggests that the present results could be used to inform the development of personalized therapies based on hemispheric asymmetry.

     

Caspase-cleaved TRAF1 negatively regulates the antiapoptotic signals of TRAF2 during TNF-induced cell death

Tumor necrosis factor (TNF) signaling leads to pleiotropic responses in a wide range of cell types, in part by activating antiapoptotic and proapoptotic pathways. Previous studies have suggested that TNF receptor-associated factor (TRAF) 2 can mediate crucial antiapoptotic signals during TNF stimulation. However, it is unclear how the antiapoptotic signals via TRAF2 in TNF-R1 signaling is regulated. Here we show that TRAF1 is cleaved by caspase-8 into two fragments during apoptosis induced by TNF. Overexpression of the C-terminal cleavage product, TRAF1-c, increased TNF-induced cell death of hybridoma T cells. Importantly, we demonstrate that the cleavage product of TRAF1 coimmunoprecipitates with TRAF2 that is released from the TNF-R1 complex in response to prolonged TNF treatment. These results indicate that caspase-dependent cleavage of TRAF1 generates TRAF1-c fragments that are able to bind TRAF2, and then sequester TRAF2 from the TNF-R1 complex, rendering cells, at least in part, sensitive to TNF.