The Light Responsive Transcriptome of the Zebrafish: Function and Regulation

Most organisms possess circadian clocks that are able to anticipate the day/night cycle and are reset or “entrained” by the ambient light. In the zebrafish, many organs and even cultured cell lines are directly light responsive, allowing for direct entrainment of the clock by light. Here, we have characterized light induced gene transcription in the zebrafish at several organizational levels. Larvae, heart organ cultures and cell cultures were exposed to 1- or 3-hour light pulses, and changes in gene expression were compared with controls kept in the dark. We identified 117 light regulated genes, with the majority being induced and some repressed by light. Cluster analysis groups the genes into five major classes that show regulation at all levels of organization or in different subset combinations. The regulated genes cover a variety of functions, and the analysis of gene ontology categories reveals an enrichment of genes involved in circadian rhythms, stress response and DNA repair, consistent with the exposure to visible wavelengths of light priming cells for UV-induced damage repair. Promoter analysis of the induced genes shows an enrichment of various short sequence motifs, including E- and D-box enhancers that have previously been implicated in light regulation of the zebrafish period2 gene. Heterologous reporter constructs with sequences matching these motifs reveal light regulation of D-box elements in both cells and larvae. Morpholino-mediated knock-down studies of two homologues of the D-box binding factor Tef indicate that these are differentially involved in the cell autonomous light induction in a gene-specific manner. These findings suggest that the mechanisms involved in period2 regulation might represent a more general pathway leading to light induced gene expression

The fallacy of placing confidence in confidence intervals

Interval estimates – estimates of parameters that include an allowance for sampling uncertainty – have long been touted as a key component of statistical analyses. There are several kinds of interval estimates, but the most popular are confidence intervals (CIs): intervals that contain the true parameter value in some known proportion of repeated samples, on average. The width of confidence intervals is thought to index the precision of an estimate; CIs are thought to be a guide to which parameter values are plausible or reasonable; and the confidence coefficient of the interval (e.g., 95 %) is thought to index the plausibility that the true parameter is included in the interval. We show in a number of examples that CIs do not necessarily have any of these properties, and can lead to unjustified or arbitrary inferences. For this reason, we caution against relying upon confidence interval theory to justify interval estimates, and suggest that other theories of interval estimation should be used instead

Fusion reaction 48Ca+249Bk leading to formation of the element Ts (Z=117)

The heaviest currently known nuclei, which have up to 118 protons, have been produced in 48Ca induced reactions with actinide targets. Among them, the element tennessine (Ts), which has 117 protons, has been synthesized by fusing 48Ca with the radioactive target 249Bk, which has a half-life of 327 d. The experiment was performed at the gas-filled recoil separator TASCA. Two long and two short α decay chains were observed. The long chains were attributed to the decay of 294Ts. The possible origin of the short-decay chains is discussed in comparison with the known experimental data. They are found to fit with the decay chain patterns attributed to 293Ts. The present experimental results confirm the previous findings at the Dubna Gas-Filled Recoil Separator on the decay chains originating from the nuclei assigned to Ts

Low-spin octahedral cobalt(II) complexes of CoN6 and CoN4P2 chromophores. Synthesis, spectroscopic characterisation and electron-transfer properties

The reaction of 2-(arylazo)pyridines (NC5H4)N=NC6H4R L-1-L-7 (R=H, o-Me/Cl, m-Me/Cl, p-Me/Cl) with cobalt(II) perchlorate hexahydrate in absolute ethanol under anaerobic conditions afforded low-spin [(CoL3)-L-II](2+) complexes, isolated as ClO4- salts. At room temperature the complexes are one-electron paramagnetic in nature, low-spin Co-II, t(2g)(6)e(g)(1), S=1/2 and behave as 1:2 electrolytes in acetonitrile solvent. In acetonitrile solvent they show a ligand-to-metal charge-transfer (LMCT) band near 400 nm, an intraligand transition near 300 nm and ligand-field d-d transitions in the range 860-600 nm. The complexes exhibit quasi-reversible Co-II-Co-III couples near 1 V and six sequential ligand reductions (N=N groups) in the range 0.2 to -1.8 V versus saturated calomel electrode (SCE). At room temperature in the solid state they exhibit isotropic EPR spectra but at 77 K, both in the polycrystalline state and in the dichloromethane solution, display rhombic spectra. Reaction of [(CoL3)-L-II](2+) with 2,2'-bipyridine (bpy) and 1,10-phenanthroline (phen) resulted in complete ligand-exchanged products with concomitant metal oxidation, low-spin [Co-III(bpy)(3)](3+) and low-spin [Co-III(phen)(3)](3+) respectively. The reaction of PPh3 with the [Ca-II(L-7)(3)](2+) [L-7=2-(p-chlorophenylazo)pyridine] yielded a partial ligand-exchanged product, low-spin [Co-II(L-7)(2)(PPh3)(2)](2+), isolated as its ClO4- salt. The complex is one-electron paramagnet and a 1 :2 electrolyte in acetonitrile solvent. It displays an LMCT band at 401 nm, an intraligand transition at 305 nm and four d-d transitions in the range 870-640 nm. It exhibits irreversible Co-II to Co-III oxidation at 1.33 V (E-pa) and four successive ligand reductions in the range -0.30 to -1.1 V versus SCE. At 77 K the complex displays an axial EPR spectrum

Ruthenium-, osmium- and cobalt-ion mediated selective activation of a C-Cl bond. Direct and spontaneous aromatic thiolation reaction via C-S bond cleavage

The reactions of KSC(S)OEt and NaSC(S)NEt2 with the complexes [RuL2Cl2] 1a, [OsL2Br2] 1b and [CoL3[ClO4](2).H2O 1c [L = 2-(o-chlorophenylazo)pyridine, 2-(o-ClC6H4N=N)C5H4N] in boiling dimethylformamide solvent resulted in [(RuL)-L-II'(2)] 3a, [(OsL)-L-II'(2)] 3b and [(CoL)-L-III'(2)][ClO4] 3c respectively [L' = 2-(o-SC6H4N=N)C5H4N]. In complexes 3 the o-carbon-chlorine bond of the pendant phenyl ring of the parent ligand L has been selectively and directly thiolated via carbon-sulfur bond cleavage of the dithiocarbonate and dithiocarbamate molecules, Two such newly formed tridentate thiolated ligands (L') are bound to the metal ions in a meridional fashion. The reactions are spontaneous in the case of dithiocarbonate as thiolating agent, but relatively slow and incomplete for dithiocarbamate. During the thiolation reaction the metal ion in the cobalt complex is oxidised from the starting Co-II in 1c to Co-III in the final product 3c. The reactions are highly sensitive to the nature of the solvent used, taking place only in those having high boiling points and polarities. The meridional configuration (cis-trans-cis with respect to sulfur, azo and pyridine nitrogens respectively) of 3 has been established by H-1 and C-13 NMR spectroscopy. The complexes exhibit two MLCT transitions in the visible region and intraligand (pi-pi*, n-pi*) transitions in the UV region. In acetonitrile solution they display reversible M-III-M-II reduction potentials at 0.43 V for Ru (3a), 0.36 V for Os (3b) and -0.14 V for Co (3c) versus the saturated calomel electrode

Impact of {Os(pap)(2)} in fine-tuning the binding modes and non-innocent potential of deprotonated 2,2 '-bipyridine-3,3 '-diol

The reaction of ctc-Os-II(pap)(2)Cl-2 (pap = 2-phenylazopyridine, ctc = cis-trans-cis with respect to chlorides and pyridine/azo nitrogens of pap, respectively) and ambidentate 2,2'-bipyridine-3,3'-diol (H2L) leads to the simultaneous formation of isomeric [Os-II(pap)(2)(HL-)](+) (2(+)/3(+)), seven-membered chelate containing Os-II(pap)(2)(L2-) (4) and diastereomeric [{Os-II(pap)(2)}(2)(mu-L2-)](2+) (5a(2+) (meso, Delta Lambda)/5b(2+) (rac, Delta Delta/Lambda Lambda)). The reaction of 2,2'-biphenol (H2L') and ctc-Os-II(pap)(2)Cl-2 yields Os-II(pap)(2)(L'(2-)) (6), an analogue of 4. The identities of the newly designed complexes have been established by different analytical, spectroscopic and X-ray diffraction techniques. H-1-NMR spectra of the complexes and single crystal X-ray structures of selective derivatives [2]ClO4, [3]ClO4, [5a](ClO4)(2), and 6 establish the retention of the tc-configuration of the precursor {Os(pap)(2)}. In isomeric 2(+) and 3(+), monodeprotonated HL- is linked to the {Os-II(pap)(2)} fragment through N, N and N, O- donors, resulting in nearly planar five- and six-membered chelates with O-H center dot center dot center dot O- and O-H center dot center dot center dot N hydrogen bonds at its back face, respectively. The O-, O- donating L'(2-) extends a severely twisted seven-membered chelate with the {Os(pap)(2)} unit in 6. The N, O-/O-, N donors of deprotonated L2- bridge the two {Os-II(pap)(2)} units in a symmetric fashion in 5a(2+), forming two moderately twisted six-membered chelates. Though the deprotonation of the O-H center dot center dot center dot N hydrogen bond in 2+ by another unit of {Os-II(pap)(2)} generates a diastereomeric mixture of 5a(2+) and 5b(2+), attempts to deprotonate the relatively stronger O-H center dot center dot center dot O- hydrogen bond in 2(+) have failed. The isomeric 2(+)/3(+), seven-membered chelate containing 4/6 and diastereomeric 5a(2+)/5b(2+) exhibit distinctive H-1-NMR and absorption spectra as well as electrochemical responses. The pap (N=N) based two successive reductions and the participation of HL-, L2-, L'(2-) in the oxidation processes of the respective complexes have been revealed using EPR and DFT calculated MOs and Mulliken spin density plots at the intermediate paramagnetic states

Metal ion-mediated selective activations of C-H and C-Cl bonds. Direct aromatic thiolation reactions via C-S bond cleavage of dithioacids

The reactions of potassium salt of dithiocarbonate, R'OCS2K, 4 (R' = Me, Et, Pr-n, Bu-n, Pr-i, Bu-i, -CH2Ph) with the low-spin ctc-Ru-II(L)(2)Cl-2 1, ctc-Os-II(L)(2)Br-2 2 and mer-[Co-II(L)(3)](ClO4)(2). H2O 3 [L = 2-(arylazo)pyridine, NC5H4-N=N-C6H4(R), R-H, o-Me/Cl, m-Me/Cl, p-Me/Cl; ctc: cis-trans-cis with respect to halides, pyridine and azo nitrogens respectively) in boiling dimethylformamide solvent resulted in low-spin diamagnetic Ru-II(L')(2), 5, Os-II(L')(2) 6 and [Co-III(L')(2)]ClO4 7 respectively (L' = o-S-C6H3(R)N=NC5H4N). In the complexes 5, 6 and 7 ortho carbon-hydrogen bond of the pendant phenyl ring of the ligands (L') has been selectively and directly thiolated via the carbon-sulphur bond cleavage of 4. The newly formed tridenate thiolated ligands (L') are bound to the me;al ion in a meridional fashion. In the case of cobalt complex (7), during the activation process the bivalent cobalt ion in the starting complex 3 has been oxidised to the trivalent Co-III state. The reactions are highly sensitive to the nature and the location of the substituents present in the active phenyl ring. The presence of electron donating Me group at the ortho and para positions of the pendant phenyl ring with respect to the activation points can only facilitate the thiolation process. The complexes (1c, 2c and 3c) having chloride group at the ortho position of the active phenyl ring underwent the thiolation reaction selectively via the carbon-chloride bond activation process. The rate of carbon-chloride activation process has been found to be much faster compared to the C-H bond activation. The reactions are sensitive to the nature of the solvent used, taking place only in those having high boiling and polar solvents. The rate of the reactions is also dependent on the nature of the R' group present in 4, following the order: Me similar to Et > Pr-n > Bu-n > Pr-i > Bu-i >> -CH2Ph. The molecular geometry of the complexes in solution has been established by H-1 and C-13 NMR spectroscopy. The thiolated complexes (5, 6, 7) exhibit metal to ligand charge-transfer transitions in the visible region and intraligand pi-pi* and n-pi* transitions in the UV region. In acetonitrile solution the complexes display reversible M(III)reversible arrow M-II reductions at 0.43 V for Ru (5a), 0.36 V for Os (6a) and -0.13 V for Co (7a) vs saturated calomel electrode (SCE)