Yi-Bu Chen

GROWTH AND NITROGEN FIXATION OF THE DIAZOTROPHIC FILAMENTOUS NONHETEROCYSTOUS CYANOBACTERIUM TRICHODESMIUM SP. IMS 101 IN DEFINED MEDIA : EVIDENCE FOR A CIRCADIAN RHYTHM

Trichodesmium sp. IMS 101, originally isolated from coastal western Atlantic waters by Prufert‐Bebout and colleagues and maintained in seawater‐based media, was successfully cultivated in two artificial media. Its characteristics of growth, nitrogen fixation, and regulation of nitrogen fixation were compared to those of natural populations and Trichodesmium sp. NIBB 1067. Results indicate that the culture grown in artificial media had nitrogen fixation characteristics similar to those when the culture is grown in seawater‐based medium and to those of Trichodesmium sp. in the natural habitat. The study provides practical artificial media to facilitate the physiological studies of these important diazotrophic cyanobacteria, as well as the cultivation of other Trichodesmium species in future studies. Manipulations of the light/dark cycle were performed to determine whether or not the daily cycle of nitrogen fixation is a circadian rhythm. Cultures grown under continuous light maintained the cycle for up to 6 days. We demonstrated that the daily cycle of nitrogen fixation in Trichodesmium sp. IMS 101 was at least partially under the control of a circardian rhythm.

Extended carrier lifetimes and diffusion in hybrid perovskites revealed by Hall effect and photoconductivity measurements

Impressive performance of hybrid perovskite solar cells reported in recent years still awaits a comprehensive understanding of its microscopic origins. In this work, the intrinsic Hall mobility and photocarrier recombination coefficient are directly measured in these materials in steady-state transport studies. The results show that electron-hole recombination and carrier trapping rates in hybrid perovskites are very low. The bimolecular recombination coefficient (10−11 to 10−10 cm3 s−1) is found to be on par with that in the best direct-band inorganic semiconductors, even though the intrinsic Hall mobility in hybrid perovskites is considerably lower (up to 60 cm2 V−1 s−1). Measured here, steady-state carrier lifetimes (of up to 3 ms) and diffusion lengths (as long as 650 μm) are significantly longer than those in high-purity crystalline inorganic semiconductors. We suggest that these experimental findings are consistent with the polaronic nature of charge carriers, resulting from an interaction of charges with methylammonium dipoles.

Competitive balance of intrabulge BMP/Wnt signaling reveals a robust gene network ruling stem cell homeostasis and cyclic activation

Hair follicles facilitate the study of stem cell behavior because stem cells in progressive activation stages, ordered within the follicle architecture, are capable of cyclic regeneration. To study the gene network governing the homeostasis of hair bulge stem cells, we developed a Keratin 15-driven genetic model to directly perturb molecular signaling in the stem cells. We visualize the behavior of these modified stem cells, evaluating their hair-regenerating ability and profile their molecular expression. Bone morphogenetic protein (BMP)-inactivated stem cells exhibit molecular profiles resembling those of hair germs, yet still possess multipotentiality in vivo. These cells also exhibit up-regulation of Wnt7a, Wnt7b, and Wnt16 ligands and Frizzled (Fzd) 10 receptor. We demonstrate direct transcriptional modulation of the Wnt7a promoter. These results highlight a previously unknown intra-stem cell antagonistic competition, between BMP and Wnt signaling, to balance stem cell activity. Reduced BMP signaling and increased Wnt signaling tilts each stem cell toward a hair germ fate and, vice versa, based on a continuous scale dependent on the ratio of BMP/Wnt activity. This work reveals one more hierarchical layer regulating stem cell homeostasis beneath the stem cell–dermal papilla-based epithelial–mesenchymal interaction layer and the hair follicle–intradermal adipocyte-based tissue interaction layer. Although hierarchical layers are all based on BMP/Wnt signaling, the multilayered control ensures that all information is taken into consideration and allows hair stem cells to sum up the total activators/inhibitors involved in making the decision of activation.

Regulation of breast cancer metastasis by Runx2 and estrogen signaling: the role of SNAI2

IntroductionIn contrast to its role in breast cancer (BCa) initiation, estrogen signaling has a protective effect in later stages, where estrogen receptor (ER)α loss associates with aggressive metastatic disease. We asked whether the beneficial effect of estrogen signaling in late-stage BCa is attributable to the recently reported estrogen-mediated antagonism of the pro-metastatic transcription factor Runx2.MethodsMCF7/Rx2dox breast cancer cells were engineered with a lentivirus expressing Runx2 in response to doxycycline (dox). Cells treated with dox and/or estradiol (E2) were subjected to genome-wide expression profiling, RT-qPCR analysis of specific genes, and Matrigel™ invasion assays. Knockdown of genes of interest was performed using lentiviruses expressing appropriate shRNAs, either constitutively or in response to dox. Gene expression in BCa tumors was investigated using a cohort of 557 patients compiled from publicly available datasets. Association of gene expression with clinical metastasis was assessed by dichotomizing patients into those expressing genes of interest at either high or low levels, and comparing the respective Kaplan-Meier curves of metastasis-free survival.ResultsRunx2 induced epithelial-mesenchymal transition (EMT) evidenced by acquisition of a fibroblastic morphology, decreased expression of E-cadherin, increased expression of vimentin and invasiveness. Runx2 stimulated SNAI2 expression in a WNT- and transforming growth factor (TGF)β-dependent manner, and knockdown of SNAI2 abrogated the pro-metastatic activities of Runx2. E2 antagonized the pro-metastatic activities of Runx2, including SNAI2 upregulation. In primary BCa tumors, Runx2 activity, SNAI2 expression, and metastasis were positively correlated, and SNAI2 expression was negatively correlated with ERα. However, the negative correlation between SNAI2 and ERα in bone-seeking BCa cells was weaker than the respective negative correlation in tumors seeking lung. Furthermore, the absence of ERα in primary tumors was associated with lung- and brain- but not with bone metastasis, and tumor biopsies from bone metastatic sites displayed the unusual combination of high Runx2/SNAI2 and high ERα expression.ConclusionsE2 antagonizes Runx2-induced EMT and invasiveness of BCa cells, partly through attenuating expression of SNAI2, a Runx2 target required for mediating its pro-metastatic property. That ERα loss promotes non-osseous metastasis by unleashing Runx2/SNAI2 is supported by the negative correlation observed in corresponding tumors. Unknown mechanisms in bone-seeking BCa allow high Runx2/SNAI2 expression despite high ERα level

Hydrogen Sulfide Promotes Tet1- and Tet2-Mediated Foxp3 Demethylation to Drive Regulatory T Cell Differentiation and Maintain Immune Homeostasis

Regulatory T (Treg) cells are essential for maintenance of immune homeostasis. Here we found that hydrogen sulfide (H2S) was required for Foxp3(+) Treg cell differentiation and function and that H2S deficiency led to systemic autoimmune disease. H2S maintained expression of methylcytosine dioxygenases Tet1 and Tet2 by sulfhydrating nuclear transcription factor Y subunit beta (NFYB) to facilitate its binding to Tet1 and Tet2 promoters. Transforming growth factor-β (TGF-β)-activated Smad3 and interleukin-2 (IL-2)-activated Stat5 facilitated Tet1 and Tet2 binding to Foxp3. Tet1 and Tet2 catalyzed conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) in Foxp3 to establish a Treg-cell-specific hypomethylation pattern and stable Foxp3 expression. Consequently, Tet1 and Tet2 deletion led to Foxp3 hypermethylation, impaired Treg cell differentiation and function, and autoimmune disease. Thus, H2S promotes Tet1 and Tet2 expression, which are recruited to Foxp3 by TGF-β and IL-2 signaling to maintain Foxp3 demethylation and Treg-cell-associated immune homeostasis.

Identification of novel candidate genes involved in mineralization of dental enamel by genome-wide transcript profiling.

The gene repertoire regulating vertebrate biomineralization is poorly understood. Dental enamel, the most highly mineralized tissue in mammals, differs from other calcifying systems in that the formative cells (ameloblasts) lack remodeling activity and largely degrade and resorb the initial extracellular matrix. Enamel mineralization requires that ameloblasts undergo a profound functional switch from matrix‐secreting to maturational (calcium transport, protein resorption) roles as mineralization progresses. During the maturation stage, extracellular pH decreases markedly, placing high demands on ameloblasts to regulate acidic environments present around the growing hydroxyapatite crystals. To identify the genetic events driving enamel mineralization, we conducted genome‐wide transcript profiling of the developing enamel organ from rat incisors and highlight over 300 genes differentially expressed during maturation. Using multiple bioinformatics analyses, we identified groups of maturation‐associated genes whose functions are linked to key mineralization processes including pH regulation, calcium handling, and matrix turnover. Subsequent qPCR and Western blot analyses revealed that a number of solute carrier (SLC) gene family members were up‐regulated during maturation, including the novel protein Slc24a4 involved in calcium handling as well as other proteins of similar function (Stim1). By providing the first global overview of the cellular machinery required for enamel maturation, this study provide a strong foundation for improving basic understanding of biomineralization and its practical applications in healthcare. J. Cell. Physiol. 227: 2264–2275, 2012.

Plastid Regulation of Lhcb1 Transcription in the Chlorophyte Alga Dunaliella tertiolecta

We identify four novel DNA-binding complexes in the nuclear-encoded Lhcb1 promoter of the chlorophyte alga Dunaliella tertiolecta that are regulated by photosynthetic pathways in the plastid. The binding activities of three of the complexes were positively correlated with time-dependent changes in Lhcb1 transcript abundance, implicating their roles as transcriptional enhancers in a retrograde signal transduction pathway. Using a combination of inhibitors, uncouplers, and antimycin A, and by following the kinetic pattern of gene regulation, we infer two different sensors in the signal transduction pathway. On short time scales of 0.5 to about 4 h, the transthylakoid membrane potential appears to be a critical determinant of gene expression, whereas on time scales of 8 h or longer, the redox state of the plastoquinone pool becomes increasingly more important. The differentiation of these two types of signals was observed in parallel effects on gene transcription and on the patterns of DNA-binding activities in the Lhcb1 promoter. These signals appear to be transduced at the nuclear level via a coordinated ensemble of DNA-binding complexes located between −367 and −188 bp from the start codon of the gene. The regulation of these elements allows the cell to up- or down-regulate the expression on Lhcb1 in response to changes in irradiance.

Photoacclimation of Light Harvesting Systems in Eukaryotic Algae

Photoacclimation is a suite of phenotypically expressed, developmentally independent, reversible physiological feedback responses to short-term (minutes to days) variations in spectral irradiance. These responses are observed in all eukaryotic algal taxa and involve alterations in the optical absorption cross section, the effective absorption cross section, and the rate of electron transfer from water to a terminal acceptor (e.g., carbon dioxide or nitrate). In this chapter, we review the primary physical processes in aquatic ecosystems that provided selection pressure for photoacclimation responses. These processes include the passage of clouds across the sky, vertical mixing, and diel variability in incident solar irradiance. The physiological responses to variations in the spectral irradiance are transduced via the redox state of intersystem electron transport components, especially plastoquinone. In a ‘nested’ series, responses include state transitions, alterations in the xanthophylls, and net synthesis/degradation of light harvesting complexes. The three processes have different time constants and dynamic ranges, but all result in alterations of the effective absorption cross section of photochemistry, such that light absorption and electron transport are balanced. The balance between light absorption and electron transport optimizes (not maximizes) photosynthesis under a very wide range of light conditions found in natural aquatic ecosystems.

A stable cranial neural crest cell line from mouse.

Cranial neural crest cells give rise to ectomesenchymal derivatives such as cranial bones, cartilage, smooth muscle, dentin, as well as melanocytes, corneal endothelial cells, and neurons and glial cells of the peripheral nervous system. Previous studies have suggested that although multipotent stem-like cells may exist during the course of cranial neural crest development, they are transient, undergoing lineage restriction early in embryonic development. We have developed culture conditions that allow cranial neural crest cells to be grown as multipotent stem-like cells. With these methods, we obtained 2 independent cell lines, O9-1 and i10-1, which were derived from mass cultures of Wnt1-Cre; R26R-GFP-expressing cells. These cell lines can be propagated and passaged indefinitely, and can differentiate into osteoblasts, chondrocytes, smooth muscle cells, and glial cells. Whole-genome expression profiling of O9-1 cells revealed that this line stably expresses stem cell markers (CD44, Sca-1, and Bmi1) and neural crest markers (AP-2α, Twist1, Sox9, Myc, Ets1, Dlx1, Dlx2, Crabp1, Epha2, and Itgb1). O9-1 cells are capable of contributing to cranial mesenchymal (osteoblast and smooth muscle) neural crest fates when injected into E13.5 mouse cranial tissue explants and chicken embryos. These results suggest that O9-1 cells represent multipotent mesenchymal cranial neural crest cells. The O9-1 cell line should serve as a useful tool for investigating the molecular properties of differentiating cranial neural crest cells.

Regulation of nitrate reductase in Chlamydomonas reinhardtii by the redox state of the plastoquinone pool

In the chlorophyte alga Chlamydomonas reinhardtii, expression of the nuclear gene NIA1, encoding nitrate reductase, is regulated by light, but the signal transduction mechanism is poorly understood. Using inhibitors, mutants, and physiological manipulation, we searched for signals in the photosynthetic electron transport chain that potentially regulate NIA1 expression. In the NIA1 + wild-type clone CC-1692, nitrate reductase activity is strongly down-regulated when the reduction of plastoquinone is blocked by 3-(3′4′-dichlorophenyl)-1,1′-dimethyl urea (DCMU), but unaffected or stimulated when the oxidation of plastoquinol is inhibited by 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone (DBMIB). Simultaneously, although DBMIB reduced NIA1 expression by ∼30% over a 6-h period relative to the control, DCMU inhibited expression of the gene by over 80%. A cross between CC-1692 and a site-directed mutant, CC-3388 A251I, in which amino acid 251 in the PSII core protein, D1, was altered from alanine to isoleucine, thereby decreasing the binding affinity for QB, produced a cell with markedly reduced expression of NIA1. Our results indicate that expression of nitrate reductase is coupled to photosynthesis via a sensor related to the redox poise of the plastoquinone pool. When the pool is oxidized, carbon fixation is low and nitrate reductase is down-regulated; conversely, when the pool is reduced, carbon fixation is high and the gene and enzyme activity are up-regulated. These experimental observations suggest a model for the coupled light regulation of photosynthesis and nitrate assimilation.