Visual Annotation of Gene List with Functional Enrichment

The genes in NCBI databases are currently annotated with itemized text (Gene Reference Into Function, or GeneRIF). A previous work suggests that the visual presentation can be more effective when time and space are under heavy constraints. In this thesis we first report a novel annotation of the genome information using Web 2.0 technologies: GeneGIF (Gene Graphics Into Function). The users can quickly scan through important functions of each gene from a graph, and then go to detailed pages when they find interesting annotations. The modular implementation makes it easily pluggable into other widely used databases without reprogramming. Then we present another web based tool - ListGIF which derives over represented concepts for a list of genes from biomedical literature. ListGIF supports two literature resources: GeneRIF and Gene Ontology. Our strategy is based on the idea that the significance of a feature is associated with the number of literature co-occurrences among each gene's annotation in the list. To reduce the bias that unbalanced GeneRIF distribution among genes might bring to the result, we provide both gene level and GeneRIF level analysis. Result is also presented in a word-cloud like graph with traceability to original published evidence

Simultaneous determination of seven constituents in Si-Ni-San decoction and a compatibility comparison study using HPLC–UV

<div><p>A simple and accurate HPLC–UV method was developed for simultaneous determination of seven constituents in Si-Ni-San decoction. Separation was performed on a Hypersil C₁₈ column and detection was set with gradient wavelength at 240 nm (0–26 min) and 210 nm (26–30 min). The mobile phase consisted of 0.03% phosphoric acid in water (v/v), and acetonitrile was used with a flow rate of 1.0 ^− 1. This method provides good linearity (<i>r</i>>0.9992), precision (RSD < 1.9%), repeatability (RSD < 2.9%), stability (RSD < 2.9%) and recovery (97.6–102.0%), which has been successfully applied to quantitative determination of the seven constituents in Si-Ni-San decoction and different compatibility groups.</p></div

Rhodium(III)-Catalyzed Directed <i>ortho</i>-C–H Bond Functionalization of Aromatic Ketazines via C–S and C–C Coupling

Described herein is a convenient and efficient method for sulfuration and olefination of aromatic ketazines via rhodium-catalyzed oxidative C–H bond activation. A range of substituted substrates are supported, and a possible mechanism is proposed according to experimental results of kinetic isotopic effect, reversibility studies, and catalysis of rhodacycle intermediate <b>c1</b>

Supplemental Material - China’s Smoke-free Policies in Public Place and the Smoking Cessation Status of Smokers

Supplemental Material for China’s Smoke-free Policies in Public Place and the Smoking Cessation Status of Smokers by Jing Wen, Wenlu Shang, Yong Ding, Hui Qiao, and Jiangping Li in Tobacco Use Insights.</p

Electronic Structure Properties of Two-Dimensional π‑Conjugated Polymers

Two-dimensional (2D) π-conjugated microporous polymers recently attracted tremendous interest due to their unique structural and electronic properties compared with 1D polymers and also graphene. In this paper, we present a comprehensive electronic structure investigation of several representative 2D conjugated polymers by virtue of first-principles density functional theory (DFT) calculations. A comparison of how spatial distribution of frontier molecular orbitals and charge carriers evolves in 1D and 2D conjugated oligomers as a function of system size is given. We also report the relationships between HOMO–LUMO gaps/ionization potential (IP)/electron affinity (EA)/structural reorganization energy upon charge doping and the oligomer size. These findings are insightful for understanding the electronic structure difference between 1D and 2D π-conjugated polymers and informative for designing new functional materials

β-Catenin Is Critical for Cerebellar Foliation and Lamination

<div><p>The cerebellum has a conserved foliation pattern and a well-organized layered structure. The process of foliation and lamination begins around birth. β-catenin is a downstream molecule of Wnt signaling pathway, which plays a critical role in tissue organization. Lack of β-catenin at early embryonic stages leads to either prenatal or neonatal death, therefore it has been difficult to resolve its role in cerebellar foliation and lamination. Here we used <i>GFAP-Cre</i> to ablate <i>β-catenin</i> in neuronal cells of the cerebellum after embryonic day 12.5, and found an unexpected role of β-catenin in determination of the foliation pattern. In the mutant mice, the positions of fissure formation were changed, and the meninges were improperly incorporated into fissures. At later stages, some lobules were formed by Purkinje cells remaining in deep regions of the cerebellum and the laminar structure was dramatically altered. Our results suggest that β-catenin is critical for cerebellar foliation and lamination. We also found a non cell-autonomous role of β-catenin in some developmental properties of major cerebellar cell types during specific stages.</p></div

Proximate composition, amino acid and fatty acid composition of fish maws

<div><p>Fish maws are commonly recommended and consumed in Asia over many centuries because it is believed to have some traditional medical properties. This study highlights and provides new information on the proximate composition, amino acid and fatty acid composition of fish maws of <i>Cynoscion acoupa</i>, <i>Congresox talabonoides</i> and <i>Sciades proops</i>. The results indicated that fish maws were excellent protein sources and low in fat content. The proteins in fish maws were rich in functional amino acids (FAAs) and the ratio of FAAs and total amino acids in fish maws ranged from 0.68 to 0.69. Among species, croaker <i>C. acoup</i>a contained the most polyunsaturated fatty acids, arachidonic acid, docosahexaenoic acid and eicosapntemacnioc acid, showing the lowest value of index of atherogenicity and index of thrombogenicity, showing the highest value of hypocholesterolemic/hypercholesterolemic ratio, which is the most desirable.</p></div

<i>hGFAP-Cre</i> activity in the cerebellum.

<p>Sagittal sections were shown. (A) Xgal staining in an E12.5 <i>hGFAP-Cre, R26R</i> mouse, showing the absence of Cre activity in the cerebellum. (B) Xgal staining of an E13.5 <i>hGFAP-Cre, R26R, β-catenin^fl/fl</i> mouse. The rl (black arrowhead) showed Xgal labeling. (C) Xgal staining of an E14.5 <i>hGFAP-Cre, R26R, β-catenin^fl/wt</i> mouse. The rl and egl showed extensive Xgal labeling. Xgal labeling also appeared in the mhb, vz (black arrowhead) and the interior of cerebellum (white arrowhead). The inset is a lateral section from the same mouse, showing more staining in the vz region. There is no staining in the pm (white arrow). (D) Xgal staining of an E16.5 <i>hGFAP-Cre, R26R, β-catenin^fl/wt</i> mouse. The egl (arrow) and the interior of the cerebellum showed extensive Cre activity. (E) A P22 <i>hGFAP-Cre, R26R</i> mouse first stained with Xgal, and then stained with calbindin antibody using a fluorescent secondary antibody. Some cells were double-positive (arrows) and formed Xgal clusters. (F) Sections from E14.5, E17.5, and E18.5 <i>hGFAP-Cre, β-catenin^fl/fl</i> mice and control littermates stained with anti-β-catenin antibody. The level of β-catenin was normal in the E14.5 mutant mouse, but clearly decreased in the EGL of E17.5 or E18.5 mutant mice. The white dashed line in E17.5 sections indicates the inner border of the EGL. β-catenin was still expressed in the pm of mutant mice. Abbreviations: cp, choroid plexus; egl, external granule cell layer; mhb, mid-hindbrain boundary; pm, pia mater; rl, rhombic lip; vz, ventricular zone. Scale bar: 100 μm (A–E) and 50 μm (F).</p

Non cell-autonomous role of β-catenin in major cerebellar cell types.

<p>(A) Sections from P8 and P26 <i>L7-Cre, β-catenin^fl/wt</i> or <i>L7-Cre, β-catenin^fl/fl</i> cerebellum stained with anti-calbindin antibody and DAPI. Purkinje cells from the <i>L7-Cre, β-catenin^fl/fl</i> mouse had normal morphology and well-organized lamination, just like those from control cerebellum. (B) Wild-type C57/BL6 mice electroporated with pSuper vectors carrying either control siRNA or β-catenin siRNA at P4 and analyzed at P14. Most siRNA-transfected cells were able to migrate into the IGL. There was no significant difference between the two groups. (C) E13.5 <i>R26R, β-catenin^fl/wt</i> or <i>R26R, β-catenin^fl/fl</i> mice injected with AdCreM2. The mice were annalyzed at P16. Sections were first stained with Xgal and then with anti-NeuN antibody using the DAB method. Most of NeuN-positive cells were located in the IGL (arrows), indicating that Cre-expressing granule cells had migrated into the IGL. (D and E) <i>GFAP-CreER^T2, R26R, β-cat ^fl/fl</i> mice were induced twice between P0 and P3, and analyzed at P7 or P18, as indicated. Xgal staining showed extensive recombination in the BGL. The ml also had scattered Xgal+ cells, probably interneurons. The EGL had no Xgal+ cells. The insets are enlargements of the squares. (F and G) <i>GFAPCreER^T2, R26R, β-cat^fl/wt</i> mice or <i>GFAPCreER^T2, R26R, β-cat^fl/fl</i> mice were induced and analyzed on postnatal days as indicated, and immunostained with anti-GFAP (F) or anti-BLBP (G) antibody. In mutant cerebella, Bergmann glia also expressed BLBP and GFAP and extended fibers to the pial surface. Inset in G is the enlargement of the squared area showing glial cell bodies were seen in the BGL (arrows) and rarely seen in the ml. The slices in (E) and (G) were from the same mouse. Abbreviations: Bgl, Bergmann glia layer; egl, external granule cell layer; ml, molecular layer; pm, pia mater. Scale bars: 100 μm.</p

Developmental stage-dependent glial defects in the <i>hGFAP-Cre, β-catenin^fl/fl</i> mouse.

<p>(A) Sagittal sections immunolabeled with anti-BLBP antibody. At E14.5, radial glial fibers were attached to the pial surface in both control and mutant mice. The right panels were acquired under high power (60×). At E17.5, in the caudal part of the mutant cerebellum, the density of radial fibers decreased, and some BLBP-positive cell bodies appeared in the EGL (arrows). At E18.5, more ectopic glial cells were seen in the EGL (arrows). (B) Section of a P0 mutant cerebellum stained with anti-BLBP antibody and DAPI. Colocalization indicates they were indeed cell bodies (arrows). (C) Sections from P0 control and mutant mice stained with antibodies against BLBP and nestin. Many double-positive cells were found in the mutant EGL (arrows), with a polarized appearance. (D) Sections of P8 control or mutant cerebellum double-stained with anti-BLBP and anti-GFAP antibodies. In the control mouse, GFAP was expressed in the white matter glia (arrowhead in the upper panel), Bergmann glia (arrows in a) and glia in-between (short arrows in b). In the mutant mouse, GFAP was only expressed by white matter glia (arrowhead in the upper panel) and ectopic glia in the EGL (arrows in c), but not by glial cells in-between (short arrows in d). The lower panels are enlargements of the squares in the upper panels (a–d). Scale bars: 20 μm.</p