Genome-wide analysis of chromatin features identifies histone modification sensitive and insensitive yeast transcription factors.

We propose a method to predict yeast transcription factor targets by integrating histone modification profiles with transcription factor binding motif information. It shows improved predictive power compared to a binding motif-only method. We find that transcription factors cluster into histone-sensitive and -insensitive classes.

TIP: a probabilistic method for identifying transcription factor target genes from ChIP-seq binding profiles.

Motivation: ChIP-seq and ChIP-chip experiments have been widely used to identify transcription factor (TF) binding sites and target genes. Conventionally, a fairly 'simple' approach is employed for target gene identification e.g.

Design and synthesis of affinity ligands and relation of their structure with adsorption of proteins.

Affinity chromatography has played an increasingly important role both in the pharmaceutical industry and academic research. In the present study, we report our preliminary investigation on the relationship between the affinity ligand structure and its adsorption to multi-protein samples. The structure of the ligands, including the size of the ring (cyclic group) and the length of the chain (linear group), has a great impact on the adsorption of ligands to proteins.

[The expressions of alpha-enolase in the nasopharyngeal cancer tissue].

Objective: To study the meaning of expressions of ENO1 in the nasopharyngeal cancer tissue.

Method: By using SP immunohistochemical methods.

Result: The positive expressions for ENO1 were 60.

Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells.

Transcription factor (TF) binding and histone modification (HM) are important for the precise control of gene expression. Hence, we constructed statistical models to relate these to gene expression levels in mouse embryonic stem cells. While both TF binding and HMs are highly 'predictive' of gene expression levels (in a statistical, but perhaps not strictly mechanistic, sense), we find they show distinct differences in the spatial patterning of their predictive strength: TF binding achieved the highest predictive power in a small DNA region centered at the transcription start sites of genes, while the HMs exhibited high predictive powers across a wide region around genes.

[Design and application of inflatable pressure applicator on the treatment of femoral shaft fractures: case control study].

Objective: To compare the influence on the postoperative wound healing between inflatable pressure applicator and traditional pressure dressing.

Methods: From May 2009 to February 2010, 50 patients with closed femoral shaft fractures were randomly divided into group A and group B, with 25 patients in each group. There were 13 males and 12 females in group A, ranging in age from 38 to 60 years, with an average of (55.

Evaluation of organ-specific glucose metabolism by ¹⁸F-FDG in insulin receptor substrate-1 (IRS-1) knockout mice as a model of insulin resistance.

Objective: Insulin resistance (IR) is a physiological condition in which the body produces insulin but does not result in a sufficient biological effect. Insulin resistance is usually asymptomatic but is associated with health problems and is a factor in the metabolic syndrome. The aim of the present study is to clarify organ-specific insulin resistance in normal daily conditions using [(18)F]-2-fluoro-2-deoxy-D: -glucose ([(18)F]-FDG).

Hormonal regulation of galectin 3 in trophoblasts and its effects on endometrium.

Previous studies had shown important functions of galectin 3 (Gal-3) in endometrium during embryo implantation, in regulation of endometrial cell proliferation and adhesion by interacting with integrin β3. In this study, we investigated hormonal regulation of Gal-3 in trophoblasts and its extracellular effects on endometrium. We used BeWo and RL95-2 cells as a model of trophoblastic and endometrial epithelial cells, respectively, to create an in vivo model of embryo implantation.

Urchin-like Ni-P microstructures: facile synthesis, properties and application in the fast removal of heavy-metal ions.

Urchin-like Ni-P microstructures with room-temperature magnetism have been successfully synthesized via a simple water-DMF solvothermal route. The as-obtained product exhibits good capacity to rapidly remove heavy-metal ions such as Cd(2+) and Pb(2+) ions from water and can be easily recycled owing to their magnetism.

A cis-regulatory map of the Drosophila genome.

Systematic annotation of gene regulatory elements is a major challenge in genome science. Direct mapping of chromatin modification marks and transcriptional factor binding sites genome-wide has successfully identified specific subtypes of regulatory elements. In Drosophila several pioneering studies have provided genome-wide identification of Polycomb response elements, chromatin states, transcription factor binding sites, RNA polymerase II regulation and insulator elements; however, comprehensive annotation of the regulatory genome remains a significant challenge.

A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets.

We develop a statistical framework to study the relationship between chromatin features and gene expression. This can be used to predict gene expression of protein coding genes, as well as microRNAs. We demonstrate the prediction in a variety of contexts, focusing particularly on the modENCODE worm datasets.

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.

We systematically generated large-scale data sets to improve genome annotation for the nematode Caenorhabditis elegans, a key model organism. These data sets include transcriptome profiling across a developmental time course, genome-wide identification of transcription factor-binding sites, and maps of chromatin organization. From this, we created more complete and accurate gene models, including alternative splice forms and candidate noncoding RNAs.

Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data.

We present an integrative machine learning method, incRNA, for whole-genome identification of noncoding RNAs (ncRNAs). It combines a large amount of expression data, RNA secondary-structure stability, and evolutionary conservation at the protein and nucleic-acid level. Using the incRNA model and data from the modENCODE consortium, we are able to separate known C.

Phenazine-1-carboxylic acid derivatives: design, synthesis and biological evaluation against Rhizoctonia solani Kuhn.

Rhizoctonia solani Kuhn is the pathogen that causes sheath blight and results in significant yield reduction in rice and in nearly 50 other crops. In order to develop a new fungicide effective against this pathogen, a series of structurally diverse phenazine-1-carboxylic acid derivatives, 2a, 2b, 2c, 2d, 2e, 2f, 2g, 2h, 2i, 2j, and 2k, were designed, synthesized and evaluated for their antifungal activity. The two most active compounds 2i and 2j were selected as lead compounds for further antifungal research.

[Diagnosis and treatment of esthesioneuroblastoma in the nasal cavity and sinuses].

Objective: To discuss the clinical characteristics, diagnosis and treatment of esthesioneuroblastoma (ENB).

Methods: The clinical data of 7 patients with ENB were analyzed retrospectively, and the clinical characteristics, diagnosis, surgical approaches and prognosis of the disease were discussed.

Results: The 7 patients received surgical treatment combined with radiotherapy and chemotherapy.

Expression of SATB1 and heparanase in gastric cancer and its relationship to clinicopathologic features.

The purpose of this study was to investigate the expression of special AT-rich binding protein 1 (SATB1) and heparanase in human gastric cancer as well as its relationship to the clinicopathologic factors. Specimens from 102 patients who underwent radical gastrectomy between 2000 and 2002 were studied by immunohistochemistry for SATB1 and heparanase expression. SATB1 and heparanase were positively expressed in 48.

SATB1 is an independent prognostic marker for gastric cancer in a Chinese population.

Special AT-rich sequence binding protein 1 (SATB1), a new type of gene regulator, has been reported to express in various human cancers and may associate with the malignant potential. However, there are few data available on SATB1 expression and its relationship to tumor progression in gastric cancer. The current study was designed to examine the SATB1 expression in gastric cancer and to correlate it with clinical outcome.

Segmental duplications in the human genome reveal details of pseudogene formation.

Duplicated pseudogenes in the human genome are disabled copies of functioning parent genes. They result from block duplication events occurring throughout evolutionary history. Relatively recent duplications (with sequence similarity≥90% and length≥1 kb) are termed segmental duplications (SDs); here, we analyze the interrelationship of SDs and pseudogenes.

Network modeling identifies molecular functions targeted by miR-204 to suppress head and neck tumor metastasis.

Due to the large number of putative microRNA gene targets predicted by sequence-alignment databases and the relative low accuracy of such predictions which are conducted independently of biological context by design, systematic experimental identification and validation of every functional microRNA target is currently challenging. Consequently, biological studies have yet to identify, on a genome scale, key regulatory networks perturbed by altered microRNA functions in the context of cancer. In this report, we demonstrate for the first time how phenotypic knowledge of inheritable cancer traits and of risk factor loci can be utilized jointly with gene expression analysis to efficiently prioritize deregulated microRNAs for biological characterization.

The BH3-mimetic GX15-070 induces autophagy, potentiates the cytotoxicity of carboplatin and 5-fluorouracil in esophageal carcinoma cells.

Despite improvements in both surgical techniques and radio- and chemo-therapy regimens, the prognosis of esophageal cancer is poor. In pursuit of novel effective strategy, this study examined the effect of the BH3-mimetic GX15-070 on esophageal carcinoma cells. We discovered that GX15-070 inhibited the growth of esophageal cancer cells.

Yeast species associated with wine grapes in China.

Having more information on the yeast ecology of grapes is important for wine-makers to produce wine with high quality and typical attributes. China is a significant wine-consuming country and is becoming a serious wine-producer, but little has been reported about the yeast ecology of local ecosystems. This study provides the first step towards the exploitation of the yeast wealth in China's vine-growing regions.

[Repairing postoperative soft tissue defects of tibia and ankle open fractures with muscle flap pedicled with medial half of soleus].

Objective: To investigate the therapeutic effect of repairing postoperative soft tissue defects of tibia and ankle open fractures with muscle flap pedicled with medial half of soleus.

Methods: From February 1998 to January 2009, 15 male patients with postoperative soft tissue defects of internal fixation for tibia and ankle open fractures were treated. Their age was 18-54 years old (average 32 years old).

[Serum proteomics profiling for diagnosis of myasthenia gravis].

Objective: To identify the significant protein peaks and establish the diagnostic model of myasthenia gravis (MG) by serum proteomics profiling analysis.

Methods: The serum samples from 56 MG patients and 16 healthy controls were detected by the technology of surface-enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI-TOF MS). The differentially expressed protein peaks were identified to establish a MG diagnostic model.