Molecular Cloning and Expression Analysis of a MADS-Box Gene (GbMADS2) from Ginkgo biloba

As a kind of transcription factors gene family, MADS-box genes play an important role in plant development processes. To find genes involved in the floral transition of Ginkgo biloba, a MADS-box gene, designated as GbMADS2, was cloned from G. biloba based on EST sequences by RT-PCR. Sequence analysis results showed that the cDNA sequence of GbMADS2 contained a 663 bp length ORF encoding 221 amino acids protein, which displayed typical structure of plant MADS-box protein including MADS, I, and K domains and C terminus. The sequence of GbMADS2 protein was highly homologous to those of MADS-box proteins from other plant species with the highest homologous to AGAMOUS (CyAG) from Cycas revoluta. The phylogenetic tree analysis revealed that GbMADS2 belonged to AGAMOUS clade genes. Real-time PCR analysis indicated that expression levels of GbMADS2 gene in female and male flower were significantly higher than those in root, stem, and leaves, and that GbMADS2 expression level increased along with time of flower development. The spatial and time-course expression profile of GbMADS2 implied that GbMADS2 might be involved in development of reproductive organs. The isolation and expression analysis of GbMADS2 provided basis for further studying the molecular mechanism of flower development in G. biloba

novoPathFinder: a webserver of designing novel-pathway with integrating GEM-model

To increase the number of value-added chemicals that can be produced by metabolic engineering and synthetic biology, constructing metabolic space with novel reactions/pathways is crucial. However, with the large number of reactions that existed in the metabolic space and complicated metabolisms within hosts, identifying novel pathways linking two molecules or heterologous pathways when engineering a host to produce a target molecule is an arduous task. Hence, we built a user-friendly web server, novoPathFinder, which has several features: (i) enumerate novel pathways between two specified molecules without considering hosts; (ii) construct heterologous pathways with known or putative reactions for producing target molecule within Escherichia coli or yeast without giving precursor; (iii) estimate novel pathways with considering several categories, including enzyme promiscuity, Synthetic Complex Score (SCScore) and LD50 of intermediates, overall stoichiometric conversions, pathway length, theoretical yields and thermodynamic feasibility. According to the results, novoPathFinder is more capable to recover experimentally validated pathways when comparing other rule-based web server tools. Besides, more efficient pathways with novel reactions could also be retrieved for further experimental exploration. novoPathFinder is available at http://design.rxnfinder.org/novopathfinder/

BGM-Net: Boundary-Guided Multiscale Network for Breast Lesion Segmentation in Ultrasound.

Automatic and accurate segmentation of breast lesion regions from ultrasonography is an essential step for ultrasound-guided diagnosis and treatment. However, developing a desirable segmentation method is very difficult due to strong imaging artifacts e.g., speckle noise, low contrast and intensity inhomogeneity, in breast ultrasound images. To solve this problem, this paper proposes a novel boundary-guided multiscale network (BGM-Net) to boost the performance of breast lesion segmentation from ultrasound images based on the feature pyramid network (FPN). First, we develop a boundary-guided feature enhancement (BGFE) module to enhance the feature map for each FPN layer by learning a boundary map of breast lesion regions. The BGFE module improves the boundary detection capability of the FPN framework so that weak boundaries in ambiguous regions can be correctly identified. Second, we design a multiscale scheme to leverage the information from different image scales in order to tackle ultrasound artifacts. Specifically, we downsample each testing image into a coarse counterpart, and both the testing image and its coarse counterpart are input into BGM-Net to predict a fine and a coarse segmentation maps, respectively. The segmentation result is then produced by fusing the fine and the coarse segmentation maps so that breast lesion regions are accurately segmented from ultrasound images and false detections are effectively removed attributing to boundary feature enhancement and multiscale image information. We validate the performance of the proposed approach on two challenging breast ultrasound datasets, and experimental results demonstrate that our approach outperforms state-of-the-art methods

Rare earth element transfer from soil to navel orange pulp (Citrus sinensis Osbeck cv. Newhall) and the effects on internal fruit quality.

The effects of soil rare earth element (REE) on navel orange quality and safety in rare earth ore areas have gained great attention. This study investigated the transfer characteristics of REE from soil to navel orange pulp (Citrus sinensis Osbeck cv. Newhall) and examined the effects of soil REE on internal fruit quality in Xinfeng County, Jiangxi province, China. Path analysis showed that soil REE, pH, cation exchange capacity (CEC), and Fe oxide (Feox) significantly affected pulp REE concentrations. A Freundlich-type prediction model for pulp REE was established: log[REEpulp] = -1.036 + 0.272 log[REEsoil] - 0.056 pH - 0.360 log[CEC] + 0.370 log[Feox] (n = 114, R2 = 0.60). From the prediction model, it was inferred that even when soil REE and Feox were as high as 1038 mg kg-1 and 96.4 g kg-1, respectively, and pH and CEC were as low as 3.75 and 5.08 cmol kg-1, respectively, pulp REE concentrations were much lower than the food limit standard. Additionally, soil REE levels were significantly correlated with selected fruit quality indicators, including titratable acidity (r = 0.52, P < 0.01), total soluble solids (r = 0.48, P < 0.01) and vitamin C (r = 0.56, P < 0.01). Generally, under routine methods of water and fertilization management, the cultivation of navel oranges in rare earth ore areas of south China with soil REE ranging from 38.6 to 546 mg kg-1 had improved in internal fruit quality

The path analysis diagram for the relationship between REE content in navel orange pulp and soil REE or soil properties.

<p>Single-headed arrows represent the direct effects (<i>P</i>_ij), and double-headed arrows indicate the coefficients of the correlations between soil REE and the soil properties (<i>r</i>_ij). Subscript designations for soil REE, the soil properties, and the REE content in the navel orange pulp are identified numerically as follows: (1) REE content in soil; (2) soil pH; (3) organic carbon (OC); (4) cation exchange capacity (CEC); (5) clay; (6) Fe oxide (Fe_ox); (7) REE content in the pulp.</p

The locations of the soil sampling sites in Xinfeng County.

<p>The locations of the soil sampling sites in Xinfeng County.</p

Descriptive statistics of measured soil properties in 114 navel orange orchards.

<p>Descriptive statistics of measured soil properties in 114 navel orange orchards.</p

Relationship between the measured log[REE_pulp] and the predicted log[REE_soil].

<p>Relationship between the measured log[REE_pulp] and the predicted log[REE_soil].</p

Stepwise multiple linear regression equations.

<p>Stepwise multiple linear regression equations.</p

Syntheses, Structures, Luminescence, and Magnetic Properties of a Series of Novel Coordination Polymers Constructed by Nanosized [Ln₈Fe₄] Rings

A total of five three-dimensional Ln-Fe coordination polymers (CPs) [(CH₃)₂NH]­[(CH₃)₂NH₂]­[Ln₂Fe­(SO₄)₄(L)]­·3H₂O (Ln = Eu, <b>1</b>; Dy, <b>2</b>; Gd, <b>3</b>; Sm, <b>4</b>; Er, <b>5</b>; H₂L = tartaric acid) have been successfully synthesized under solvothermal conditions and characterized by infrared spectroscopy, thermogravimetric analysis, elemental analyses, luminescence, and magnetic properties. Structural analysis indicates that the frameworks of <b>1</b>–<b>5</b> are constructed from novel [Ln₈Fe₄] rings. In the strcutures of <b>1</b>–<b>5</b>, Ln^III and Fe^III ions interconnect through O donors of sulfate anions to generate a one-dimensional chain, and the adjacent chains are joined together by ligand [L]^2– to form a two-dimensional zonary plane, which is further bridged by ligand [L]^2– to give a new topology and named as “<i><b>Xhd</b></i><b>1</b>”. Magnetic properties of <b>2</b> and <b>3</b> were investigated using variable temperature magnetic susceptibility, and weak ferromagnetic exchange between the Fe^III and Ln^III ions has been established for the Gd derivative. Meanwhile, we also studied luminescence spectra and luminescence lifetimes of <b>1</b> and <b>4</b> in the solid state at room temperature. The luminescence lifetime of <b>1</b> is 0.98 ms, which is significantly longer than the values in the reported Eu³⁺ coordination polymers