Novel method for isolation of murine clara cell secretory protein-expressing cells with traces of stemness

Clara cells are non-ciliated, secretory bronchiolar epithelial cells that serve to detoxify harmful inhaled substances. Clara cells also function as stem/progenitor cells for repair in the bronchioles. Clara cell secretory protein (CCSP) is specifically expressed in pulmonary Clara cells and is widely used as a Clara cell marker. In addition CCSP promoter is commonly used to direct gene expression into the lung in transgenic models. The discovery of CCSP immunoreactivity in plasma membranes of airway lining cells prompted us to explore the possibility of enriching Clara cells by flow cytometry. We established a novel and simple method for the isolation of CCSP-expressing cell Clara cells using a combination of mechanical and enzymatic dissociation followed by flow cytometry sorting technology. We showed that ～25% of dissociated cells from whole lung expressed CCSP. In the resulting preparation, up to 98% of cells expressed CCSP. Notably, we found that several common stem cell markers including CD44, CD133, Sca-1 and Sox2 were expressed in CCSP(+) cells. Moreover, CCSP(+) cells were able to form spheroid colonies in vitro with 0.97‰ efficiency. Parallel studies in vivo confirmed that a small population of CCSP(-)expressing cells in mouse airways also demonstrates stem cell-like properties such as label retention and harboring rare bronchioalveolar stem cells (BASCs) in terminal bronchioles (TBs). We conclude that CCSP(+) cells exhibit a number of stem cell-like features including stem cell marker expression, bronchosphere colony formation and self-renewal ability. Clara cell isolation by flow cytometry sorting is a useful method for investigating the function of primary Clara cells in stem cell research and mouse models.     

Differences in Energy Expenditures and Growth Dilution Explain Higher PCB Concentrations in Male Summer Flounder

Comparison of polychlorinated biphenyl (PCB) concentrations between the sexes of mature fish may reveal important behavioral and physiological differences between the sexes. We determined whole-fish PCB concentrations in 23 female summer flounder Paralichthys dentatus and 27 male summer flounder from New Jersey coastal waters. To investigate the potential for differences in diet or habitat utilization between the sexes, carbon and nitrogen stable isotope ratios were also determined. In 5 of the 23 female summer flounder, PCB concentrations in the somatic tissue and ovaries were determined. In addition, we used bioenergetics modeling to assess the contribution of the growth dilution effect to the observed difference in PCB concentrations between the sexes. Whole-fish PCB concentrations for females and males averaged 87 and 124 ng/g, respectively; thus males were 43% higher in PCB concentration compared with females. Carbon and nitrogen stable isotope ratios did not significantly differ between the sexes, suggesting that diet composition and habitat utilization did not vary between the sexes. Based on PCB determinations in the somatic tissue and ovaries, we predicted that PCB concentration of females would increase by 0.6%, on average, immediately after spawning due to release of eggs. Thus, the change in PCB concentration due to release of eggs did not explain the higher PCB concentrations observed in males. Bioenergetics modeling results indicated that the growth dilution effect could account for males being 19% higher in PCB concentration compared with females. Thus, the bulk of the observed difference in PCB concentrations between the sexes was not explained by growth dilution. We concluded that a higher rate of energy expenditure in males, stemming from greater activity and a greater resting metabolic rate, was most likely the primary driver for the observed difference in PCB concentrations between the sexes.     

Frontiers in alley cropping: Transformative solutions for temperate agriculture

Annual row crops dominate agriculture around the world and have considerable negative environmental impacts, including significant greenhouse gas emissions. Transformative land‐use solutions are necessary to mitigate climate change and restore critical ecosystem services. Alley cropping (AC)—the integration of trees with crops—is an agroforestry practice that has been studied as a transformative, multifunctional land‐use solution. In the temperate zone, AC has strong potential for climate change mitigation through direct emissions reductions and increases in land‐use efficiency via overyielding compared to trees and crops grown separately. In addition, AC provides climate change adaptation potential and ecological benefits by buffering alley crops to weather extremes, diversifying income to hedge financial risk, increasing biodiversity, reducing soil erosion, and improving nutrient‐ and water‐use efficiency. The scope of temperate AC research and application has been largely limited to simple systems that combine one timber tree species with an annual grain. We propose two frontiers in temperate AC that expand this scope and could transform its climate‐related benefits: (i) diversification via woody polyculture and (ii) expanded use of tree crops for food and fodder. While AC is ready now for implementation on marginal lands, we discuss key considerations that could enhance the scalability of the two proposed frontiers and catalyze widespread adoption.     

Mitochondrial modulation of calcium signaling at the initiation of development

Fertilization triggers cytosolic Ca(2+) oscillations that activate mammalian eggs and initiate development. Extensive evidence demonstrates that Ca(2+) is released from endoplasmic reticulum stores; however, less is known about how the increased Ca(2+) is restored to its resting level, forming the Ca(2+) oscillations. We investigated whether mitochondria also play a role in activation-associated Ca(2+) signaling. Mitochondrial dysfunction induced by the mitochondrial uncoupler FCCP or antimycin A disrupted cytosolic Ca(2+) oscillations, resulting in sustained increase in cytosolic Ca(2+), followed by apoptotic cell death. This suggests that functional mitochondria may participate in sequestering the released Ca(2+), contributing to cytosolic Ca(2+) oscillations and preventing cell death. By centrifugation, mouse eggs were stratified and separated into fractions containing both endoplasmic reticulum and mitochondria and fractions containing endoplasmic reticulum with no mitochondria. The former showed Ca(2+) oscillations by activation, whereas the latter exhibited sustained elevation in cytosolic Ca(2+) but no Ca(2+) oscillations, suggesting that mitochondria take up released cytosolic Ca(2+). Further, using Rhod-2 for detection of mitochondrial Ca(2+), we found that mitochondria exhibited Ca(2+) oscillations, the frequency of which was not different from that of cytosolic Ca(2+) oscillations, indicating that mitochondria are involved in Ca(2+) signaling during egg activation. Therefore, we propose that mitochondria play a crucial role in Ca(2+) signaling that mediates egg activation and development, and apoptotic cell death.     

Effect of fatigue on hamstring coactivation during isokinetic knee extensions

We examined the effect of fatigue of the quadriceps muscles on coactivation of the hamstring muscles and determined if the response is different between two isokinetic speeds in ten males and ten females with no history of knee pathology. Electromyographic data were recorded from the vastus lateralis and biceps femoris muscles during 50 maximal knee extensions at isokinetic speeds of 1.75 rad · s⁻¹ (100° · s⁻¹) and 4.36 rad · s⁻¹ (250° · s⁻¹). A greater degree of coactivation was apparent at the higher speed, but the increase in coactivation of the hamstring muscles was similar at both speeds. The results revealed that: (1) coactivation is greater at a higher isokinetic speed, and (2) coactivation increases during fatigue, but the rate of increase is independent of contraction velocity. Accepted: 15 June 1998     

Epidermal growth factor: Characteristics of specific binding in membranes from liver,placenta, and other target tissues

Epidermal growth factor, a 6,400-dalton polypeptide from the mouse submaxillary gland, binds specifically to cells and membranes derived from a variety of human, rat, mouse, and bovine tissues. Liver, placenta, skin, cornea, and cultured chondrocytes, Hela cells, and Chang liver cells bind large amounts of epidermal growth factor, whereas fat cells, resting and lectin-stimulated human peripheral lymphocytes, mouse thymocytes, cultured rat hepatoma cells, and mammary cells from virgin and pregnant mice bind little or no epidermal growth factor. The binding site for epidermal growth factor is distinct from receptors for other anabolic peptides such as insulin, nerve growth factor, and growth hormone. The binding of epidermal growth factor is rapid and reversible. The rate constant of association is approximately 10⁶ mole^?1 sec^?1, the rate constant of dissociation is about 6 × 10^?4 sec^?1, and the apparent equilibrium dissociation constant is about 10^?9m. Trypsin at low concentrations (50–200 μg/ml) destroys the receptor site for epidermal growth factor. The binding of epidermal growth factor by membranes is not accompanied by appreciable degradation of the peptide present in the medium or of that bound to the membranes. Use can be made of the high affinity and specificity of membranes for epidermal growth factor to measure by a competitive binding assay as little as 200 pg of EGF per ml (3 × 10^?11m).     

Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin β-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6

There has been great progress in the development of technology for the conversion of lignocellulosic biomass to sugars and subsequent fermentation to fuels. However, plant lignin remains an untapped source of materials for production of fuels or high value chemicals. Biological cleavage of lignin has been well characterized in fungi, in which enzymes that create free radical intermediates are used to degrade this material. In contrast, a catabolic pathway for the stereospecific cleavage of β-aryl ether units that are found in lignin has been identified in Sphingobium sp. SYK-6 bacteria. β-Aryl ether units are typically abundant in lignin, corresponding to 50–70% of all of the intermonomer linkages. Consequently, a comprehensive understanding of enzymatic β-aryl ether (β-ether) cleavage is important for future efforts to biologically process lignin and its breakdown products. The crystal structures and biochemical characterization of the NAD-dependent dehydrogenases (LigD, LigO, and LigL) and the glutathione-dependent lyase LigG provide new insights into the early and late enzymes in the β-ether degradation pathway. We present detailed information on the cofactor and substrate binding sites and on the catalytic mechanisms of these enzymes, comparing them with other known members of their respective families. Information on the Lig enzymes provides new insight into their catalysis mechanisms and can inform future strategies for using aromatic oligomers derived from plant lignin as a source of valuable aromatic compounds for biofuels and other bioproducts.     

A novel approach for multi-domain and multi-gene family identification provides insights into evolutionary dynamics of disease resistance genes in core eudicot plants

Background

Recent advances in DNA sequencing techniques resulted in more than forty sequenced plant genomes representing a diverse set of taxa of agricultural, energy, medicinal and ecological importance. However, gene family curation is often only inferred from DNA sequence homology and lacks insights into evolutionary processes contributing to gene family dynamics. In a comparative genomics framework, we integrated multiple lines of evidence provided by gene synteny, sequence homology and protein-based Hidden Markov Modelling to extract homologous super-clusters composed of multi-domain resistance (R)-proteins of the NB-LRR type (for NUCLEOTIDE BINDING/LEUCINE-RICH REPEATS), that are involved in plant innate immunity.

Results

To assess the diversity of R-proteins within and between species, we screened twelve eudicot plant genomes including six major crops and found a total of 2,363 NB-LRR genes. Our curated R-proteins set shows a 50% average for tandem duplicates and a 22% fraction of gene copies retained from ancient polyploidy events (ohnologs). We provide evidence for strong positive selection and show significant differences in molecular evolution rates (Ka/Ks-ratio) among tandem- (mean = 1.59), ohnolog (mean = 1.36) and singleton (mean = 1.22) R-gene duplicates. To foster the process of gene-edited plant breeding, we report species-specific presence/absence of all 140 NB-LRR genes present in the model plant Arabidopsis and describe four distinct clusters of NB-LRR “gatekeeper” loci sharing syntenic orthologs across all analyzed genomes.

Conclusion

By curating a near-complete set of multi-domain R-protein clusters in an eudicot-wide scale, our analysis offers significant insight into evolutionary dynamics underlying diversification of the plant innate immune system. Furthermore, our methods provide a blueprint for future efforts to identify and more rapidly clone functional NB-LRR genes from any plant species.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-966) contains supplementary material, which is available to authorized users.     

Overexpression of IL-10 in C2D Macrophages Promotes a Macrophage Phenotypic Switch in Adipose Tissue Environments

Adipose tissue macrophages are a heterogeneous collection of classically activated (M1) and alternatively activated (M2) macrophages. Interleukin 10 (IL-10) is an anti-inflammatory cytokine, secreted by a variety of cell types including M2 macrophages. We generated a macrophage cell line stably overexpressing IL-10 (C2D-IL10) and analyzed the C2D-IL10 cells for several macrophage markers after exposure to adipocytes compared to C2D cells transfected with an empty vector (C2D-vector). C2D-IL10 macrophage cells expressed more CD206 when co-cultured with adipocytes than C2D-vector cells; while the co-cultured cell mixture also expressed higher levels of Il4, Il10, Il1β and Tnf. Since regular C2D cells traffic to adipose tissue after adoptive transfer, we explored the impact of constitutive IL-10 expression on C2D-IL10 macrophages in adipose tissue in vivo. Adipose tissue-isolated C2D-IL10 cells increased the percentage of CD206⁺, CD301⁺, CD11c⁻CD206⁺ (M2) and CD11c⁺CD206⁺ (M1b) on their cell surface, compared to isolated C2D-vector cells. These data suggest that the expression of IL-10 remains stable, alters the C2D-IL10 macrophage cell surface phenotype and may play a role in regulating macrophage interactions with the adipose tissue.