Genome-Wide Mapping Targets of the Metazoan Chromatin Remodeling Factor NURF Reveals Nucleosome Remodeling at Enhancers, Core Promoters and Gene Insulators

NURF is a conserved higher eukaryotic ISWI-containing chromatin remodeling complex that catalyzes ATP-dependent nucleosome sliding. By sliding nucleosomes, NURF is able to alter chromatin dynamics to control transcription and genome organization. Previous biochemical and genetic analysis of the specificity-subunit of Drosophila NURF (Nurf301/Enhancer of Bithorax (E(bx)) has defined NURF as a critical regulator of homeotic, heat-shock and steroid-responsive gene transcription. It has been speculated that NURF controls pathway specific transcription by co-operating with sequence-specific transcription factors to remodel chromatin at dedicated enhancers. However, conclusive in vivo demonstration of this is lacking and precise regulatory elements targeted by NURF are poorly defined. To address this, we have generated a comprehensive map of in vivo NURF activity, using MNase-sequencing to determine at base pair resolution NURF target nucleosomes, and ChIP-sequencing to define sites of NURF recruitment. Our data show that, besides anticipated roles at enhancers, NURF interacts physically and functionally with the TRF2/DREF basal transcription factor to organize nucleosomes downstream of active promoters. Moreover, we detect NURF remodeling and recruitment at distal insulator sites, where NURF functionally interacts with and co-localizes with DREF and insulator proteins including CP190 to establish nucleosome-depleted domains. This insulator function of NURF is most apparent at subclasses of insulators that mark the boundaries of chromatin domains, where multiple insulator proteins co-associate. By visualizing the complete repertoire of in vivo NURF chromatin targets, our data provide new insights into how chromatin remodeling can control genome organization and regulatory interactions.

Determination of roxithromycin residues in the flounder muscle with electrospray liquid chromatography-mass spectrometry

A highly sensitive and specific method for the determination of roxithromycin in the flounder muscle by LC-MS was developed and validated. A dichloromethane extract of the sample was separated on C18 reversed-phase column with acetonitrile-50 mM ammonium acetate (80:20, v/v) as the mobile phase and analyzed by LC-MS via atmospheric pressure ionization/electrospray ionization interface. The limit of detection and limit of quantitation were 0.01 and 0.1 ng/g, respectively. Mean recoveries from spiked muscles were 81.1% (ranged from 71.0 to 90.3%) for roxithromycin. The method has been successfully applied to determine roxithromycin in the flounder muscle.

Exon junction complex proteins bind nascent transcripts independently of pre-mRNA splicing in Drosophila melanogaster

Although it is currently understood that the exon junction complex (EJC) is recruited on spliced mRNA by a specific interaction between its central protein, eIF4AIII, and splicing factor CWC22, we found that eIF4AIII and the other EJC core proteins Y14 and MAGO bind the nascent transcripts of not only intron-containing but also intronless genes on Drosophila polytene chromosomes. Additionally, Y14 ChIP-seq demonstrates that association with transcribed genes is also splicing-independent in Drosophila S2 cells. The association of the EJC proteins with nascent transcripts does not require CWC22 and that of Y14 and MAGO is independent of eIF4AIII. We also show that eIF4AIII associates with both polysomal and monosomal RNA in S2 cell extracts, whereas Y14 and MAGO fractionate separately. Cumulatively, our data indicate a global role of eIF4AIII in gene expression, which would be independent of Y14 and MAGO, splicing, and of the EJC, as currently understood.

Membrane type-1 matrix metalloproteinase is induced following cyclic compression of in vitro grown bovine chondrocytes

OBJECTIVE

To determine if membrane type-1 matrix metalloproteinase (MT1-MMP) will respond to cyclic compression of chondrocytes grown in vitro and the regulatory mechanisms underlying this response.

METHODS

Cyclic compression (30min, 1kPa, 1Hz) was applied to bovine chondrocytes (6-9-month-old animals) grown on top of a biodegradable substrate within 3 days of initiating culture. Luciferase assays using bovine articular chondrocytes were undertaken to demonstrate the mechanosensitivity of MT1-MMP. Semi-quantitative reverse-transcription polymerase chain reaction (RT-PCR) and western blot analysis were used to establish the time course of gene and protein upregulation in response to cyclic compression. The regulation of MT1-MMP was assessed by electrophoretic mobility shift assays, RT-PCR and western blot analysis. As well, an MT1-MMP decoy oligonucleotide and an extracellular signal-regulated kinase 1/2 (ERK1/2) pharmacological inhibitor were utilized to further characterize MT1-MMP regulation.

RESULTS

After cyclic compression, MT1-MMP showed a rapid and transient increase in gene expression. Elevated protein levels were detected within 2h of stimulation which returned to baseline by 6h. During cyclic compression, phosphorylation of the mitogen activated protein kinase ERK1/2 increased significantly. This was followed by increased gene and protein expression of the transcription factor; early growth factor-1 (Egr-1) and Egr-1 binding to the MT1-MMP promoter. Blocking Egr-1 DNA binding with a decoy MT1-MMP oligonucleotide, downregulated MT1-MMP gene expression. The ERK1/2 inhibitor U0126 also reduced Egr-1 DNA binding activity to MT1-MMP promoter sequences and subsequent transcription of MT1-MMP.

CONCLUSIONS

These data suggest that cyclic compression of chondrocytes in vitro upregulates MT1-MMP via ERK1/2 dependent activation of Egr-1 binding. Delineation of the regulatory pathways activated by mechanical stimulation will further our understating of the mechanisms influencing tissue remodeling.

Impact Analysis of Different CT Configurations of Carotid Artery Plaque Calcifications on Cerebrovascular Events

BACKGROUND AND PURPOSE

CT is considered the standard reference both for quantification and characterization of carotid artery calcifications. Our aim was to investigate the relationship among different types of calcium configurations detected with CT within the plaque with a novel classification and to investigate the prevalence of cerebrovascular events.

MATERIALS AND METHODS

Seven hundred ninety patients (men = 332; mean age, 69.7 [SD, 13] years; 508 symptomatic for cerebrovascular symptoms and 282 asymptomatic) who underwent computed tomography of the carotid arteries were retrospectively included in this institutional review board-approved study. The plaque was classified into 6 types according to the different types of calcium configurations as the following: type 1, complete absence of calcification within the plaque; type 2, intimal or superficial calcifications; type 3, deep or bulky calcifications; type 4, adventitial calcifications with internal soft plaque of <2 mm thickness; type 5, mixed patterns with intimal and bulky calcifications; and type 6, positive rim sign.

RESULTS

The highest prevalence of cerebrovascular events was observed for type 6, for which 89 of the 99 cases were symptomatic. Type 6 plaque had the highest degree of correlation with TIA, stroke, symptoms, and ipsilateral infarct for both sides with a higher prevalence in younger patients. The frequency of symptoms observed by configuration type significantly differed between right and left plaques, with symptoms observed more frequently in type 6 calcification on the right side (50/53; 94%) than on the left side (39/46; 85%, P < .001).

CONCLUSIONS

We propose a novel carotid artery plaque configuration classification that is associated with the prevalence of cerebrovascular events. If confirmed in longitudinal analysis, this classification could be used to stratify the risk of occurrence of ischemic events.

Temporal arteritis and fever: report of a case and a clinical reanalysis of 360 cases

The purposes of this article are to report a case with temporal arteritis (TA) and to summarize and reanalyze the cases of temporal arteritis associated with fever in published articles for understanding better the clinical features of TA. A case with biopsy-proven TA is reported. The publications with TA and fever were searched by using MEDLINE in English from 1966 to 1999. Three hundred sixty cases of temporal arteritis associated with fever were reanalyzed. The results showed that a case of biopsy-proven TA with typically clinical manifestation was initially misdiagnosed and that the reanalysis of 360 cases revealed that the common clinical findings at presentation were abnormal temporal arteries, headache, low fever, loss of weight, polymyalgia rheumatica, jaw claudication, vision disorder, arthralgis or myalyias, and ear pain and that the uncommon clinical findings at presentation were high fever, malaise, anorexia, breast pain, transient ischemic attack/stroke, cough, mental disorder, diarrhea, and uterine prolapse, etc. Laboratory findings were the range of erythrocyte sedimentation rate (ESR) 14 to 149 with a mean of 97.0 mm/hr, white blood cells being normal or increased in the range of 10.9 to 22.9 x 10(9)/L, hemoglobin level 7 to 16 g/dL, the platelets count increased to 785 x 10(9)/L, and microscopic hematuria. The diagnosis was made by a combination of clinical features, an increased ESR, a response to steroids, and, most specifically, temporal artery biopsy. The initial diagnosis was misdiagnosed in 38.2% of patients. In conclusion, the features of TA associated with fever have not been widely appreciated yet. TA is a common cause of fever of unknown origin (FUO) in the elderly. TA should be considered when patients complain of common and uncommon manifestations. An elevated ESR will aid in the diagnosis of TA, and temporal artery biopsy will provide certainty.

Angelica gigas NAKAI and Its Active Compound, Decursin, Inhibit Cellular Injury as an Antioxidant by the Regulation of AMP-Activated Protein Kinase and YAP Signaling

Natural products and medicinal herbs have been used to treat various human diseases by regulating cellular functions and metabolic pathways. Angelica gigas NAKAI (AG) helps regulate pathological processes in some medical fields, including gastroenterology, gynecology, and neuropsychiatry. Although some papers have reported its diverse indications, the effects of AG against arachidonic acid (AA)+ iron and carbon tetrachloride (CCl₄) have not been reported. In HepG2 cells, AA+ iron induced cellular apoptosis and mitochondrial damage, as assessed by mitochondrial membrane permeability (MMP) and the expression of apoptosis-related proteins. On the other hand, AG markedly inhibited these detrimental phenomena and reactive oxygen species (ROS) production induced by AA+ iron. AG activated the liver kinase B1 (LKB1)-dependent AMP-activated protein kinase (AMPK), which affected oxidative stress in the cells. Moreover, AG also regulated the expression of yes-associated protein (YAP) signaling as mediated by the AMPK pathways. In mice, an oral treatment of AG protected against liver toxicity induced by CCl₄, as indicated by the plasma and histochemical parameters. Among the compounds in AG, decursin had antioxidant activity and affected the AMPK pathway. In conclusion, AG has antioxidant effects in vivo and in vitro, indicating that natural products such as AG could be potential candidate for the nutraceuticals to treat various disorders by regulating mitochondrial dysfunction and cellular metabolic pathways.

Role of Drosophila EDEMs in the degradation of the alpha-1-antitrypsin Z variant

The synthesis of proteins in the endoplasmic reticulum (ER) that exceeds the protein folding capacity of this organelle is a frequent cause of cellular dysfunction and disease. An example of such a disease is alpha-1-antitrypsin (A1AT) deficiency, caused by destabilizing mutations in this glycoprotein. It is considered that the mutant proteins are recognized in the ER by lectins and are subsequently degraded through the proteasome, leading to a deficiency in this enzyme in the afflicted patients. We previously established a Drosophila model of this disease by overexpressing the null Hong Kong (NHK) allele of this gene and found that the Drosophila lectin, ER degradation-enhancing α-mannosidase-like protein 2 (EDEM2), can accelerate the degradation of A1AT when overexpressed. NHK is a rare allele, and in this study, we investigated in depth the mechanisms through which Drosophila EDEMs affect the degradation of the Z variant, which is the predominant disease allele. Specifically, we report that the Z allele does not activate ER stress signaling as prominently as the NHK allele, but similarly requires both Drosophila EDEM1 and EDEM2 for the degradation of the protein. We demonstrate that EDEMs are required for their ubiquitination, and without EDEMs, glycosylated A1AT mutants accumulate in cells. These results support the role of the EDEM-mediated ubiquitination of the alpha-1-antitrypsin Z (ATZ) allele, and establish a Drosophila model for the study of this protein and disease.

Evaluation of hybrid PET/CT gastrography in gastric cancer

AIM

With the recent advances in multidetector-row CT, a fusion of functional PET with three dimensional (3D) CT gastrography may provide enhanced diagnostic capability and help surgeons during preoperative planning. The diagnostic value of hybrid PET/CT gastrography was compared with that of conventional PET/CT alone in gastric cancer staging.

PATIENTS, METHODS

Patients with gastric cancer (n = 101) confirmed by endoscopic biopsy specimens underwent conventional PET/CT and regional PET with contrast enhanced CT, followed by gastrectomy with lymphadenectomy at our institution from November 2007 to November 2008. These images were fused into a hybrid PET/CT gastrography using the cardiac IQ fusion software. Conventional PET/CT and hybrid PET/CT gastrography were evaluated for staging of gastric cancer. After gastrectomy, these were compared with pathologic reports respectively.

RESULTS

Gastric cancer was diagnosed as 50 early gastric cancer (EGC) and 51 advanced gastric cancer (AGC) on pathologic examination. In EGC, hybrid PET/CT gastrography and PET/CT identified 36 (72%) and 7 (14%) tumours, respectively. Hybrid PET/CT gastrography correctly delineated the subtype of 25 EGC. In AGC, all 51 (100%) tumours were identified on the hybrid PET/CT gastrography compared to 39 (76.5%) tumours on PET/CT. Hybrid PET/CT gastrography correctly classified the morphology of 42 AGC using the Bormann classification. Additionally, depth of invasion was correctly presented in 38 of 51 AGC. Hybrid PET/CT gastrography for regional lymph node (LN) metastasis in the EGC and AGC showed the sensitivity of 75% and 83.9%, and specificity 90.5% and 55%, respectively.

CONCLUSION

Hybrid PET/CT gastrography is the more intuitive and comprehensive method for the preoperative evaluation of gastric cancer than conventional PET/CT.

Direct growth of horizontally aligned carbon nanotubes between electrodes and its application to field-effect transistors

This paper presents direct growth of horizontally-aligned carbon nanotubes (CNTs) between two predefined various inter-spacing up to tens of microns of electrodes (pads) and its use as CNT field-effect transistors (CNT-FETs). Using the conventional photolithography technique followed by thin film evaporation and lift off, the catalytic electrodes (pads) were prepared, consisting of Pt, Al and Fe triple layers on SiO2/Si substrate. The grown CNTs were horizontally-aligned across the catalytic electrodes on the modified gold image furnace hot stage (thermal CVD) at 800 degrees C by using an alcohol vapor as the carbon source. Scanning and transmission electron microcopies (SEM/TEM) were used to observe the structure, growth direction and density of CNTs, while Raman spectrum analysis was used to indicate the degree of amorphous impurity and diameter of CNTs. Both single- and multi-wall CNTs with diameters of 1.1-2.2 nm were obtained and the CNT density was controlled by thickness of Fe catalytic layer. Following horizontally-aligned growth of CNTs, the electrical properties of back-gate CNT-FETs were measured and showd p-type conduction behaviors of FET.

Numerical simulation and fabrication of silicon sheet via spin casting

A spin-casting process for fabricating polycrystalline silicon sheets for use as solar cell wafers is proposed, and the parameters that control the sheet thickness are investigated. A numerical study of the fluidity of molten silicon indicates that the formation of thin silicon sheets without a mold and via spin casting is feasible. The faster the rotation speed of graphite mold, the thinner the thickness of sheet. After the spread of the molten silicon to cover the graphite mold with rotation speed of above 500 rpm, the solidification has to start. Silicon sheets can be produced by using the centrifugal force under appropriate experimental conditions. The spin-cast sheet had a vertical columnar microstructure due to the normal heat extraction to the substrate, and the sheet lifetime varied from 0.1 microS to 0.3 microS measured by using the microwave photoconductance decay (MW-PCD) to confirm that the spin-cast silicon sheet is applicable to photovoltaics.

The ISWI chromatin remodelling factor NURF is not required for mitotic male X chromosome organisation

The nucleosome remodelling factor (NURF) is an ISWI-class ATP-dependent chromatin remodeling enzyme required both for gene expression and higher order chromatin organisation. NURF binds to histone modifications that decorate the Drosophila polytene male X chromosome and is required to maintain correct organisation of this chromosome. NURF mutants exhibit distorted and decondensed polytene male X chromosomes dependent on the presence of the male-specific lethal (MSL) complex. Here we tested whether mitotic chromosomes similarly require NURF to maintain correct morphology. Surprisingly, although the MSL complex remains associated with mitotic male X chromosomes, NURF is not required to maintain morphology. While the ISWI subunit of NURF is known to remain associated with mitotic chromosomes we show that the NURF specificity subunit Nurf301/BPTF dissociates from chromatin during both Drosophila and human mitosis, further illuminating that NURF is dispensable for mitotic chromosome organisation.

Development of a simple cell lysis method for recombinant DNA using bacteriophage lambda lysis genes

In this study, we describe the development of a simple and efficient method for cell lysis via the insertion of a bacteriophage lambda lysis gene cluster into the pET22b expression vector in the following order; the T7 promoter, a gene for a target protein intended for production, Sam7 and R. This insertion of R and Sam7 into pET22b exerted no detrimental effects on cellular growth or the production of a target protein. The induction of the T7 promoter did not in itself result in the autolysis of cells in culture but the harvested cells were readily broken by freezing and thawing. We compared the efficiency of the cell lysis technique by freezing and thawing to that observed with sonication, and determined that both methods completely disintegrated the cells and released proteins into the solution. With our modification of pET22b, the lysis of cells became quite simple, efficient, and reliable. This strategy may prove useful for a broad variety of applications, particularly in experiments requiring extensive cell breakage, including library screening and culture condition exploration, in addition to protein purification.

Study of the microstructures and lifetime of spin-cast silicon sheets for photovoltaics

Silicon sheets were fabricated by a new fabricating method, spin casting with various rotation speeds of the graphite mold. The microstructure of spin-cast silicon sheets were investigated using an electron probe microanalyzer (EPMA) and scanning electron microscope/electron backscatter diffraction/orientation image micrograph, and the lifetime of the sheets was mapped using microwave photoconductance decay. The silicon sheets were vertically aligned, with sizes ranging from tens of microns to one hundred microns. The as-grown lifetime was measured and found to range from 0.049 micros to 0.250 micros. The ASTM number was plotted against the lifetime using ASTM E112 to estimate the grain size. Approximately half of the grain boundaries seemed electrically inactive with meaning of no recombination center since the grains were growth directionally, especially in a longitudinal aligned. It was confirmed that the lifetime of spin-cast sheets makes them suitably applicable for photovoltaics compared to those produced by alternative ribbon-producing methods.

Numerical simulation of solid liquid interface behavior during continuous strip casting process

A new metal-strip-casting process called continuous strip-casting (CSC) has been developed for making thin metal strips. A numerical simulation model to help understand solid-liquid interface behavior during CSC has been developed and used to identify the solidification morphologies of the strips and to determine the optimum processing conditions. In this study, we used a modified level contour reconstruction method (LCRM) and the sharp interface method to modify interface tracking, and performed a simulation analysis of the CSC process. The effects of process parameters such as heat-transfer coefficient and extrusion velocity on the behavior of the solid-liquid interface were estimated and used to improve the apparatus. A Sn (Tin) plate of dimensions 200 x 50 x 1 mm3 was successfully produced by CSC for a heat-transfer coefficient of 104 W/m2 K and an extrusion velocity of 0.2 m/s.

Formation of silicon sheet on a rotating substrate

A spin casting process to fabricate polycrystalline silicon sheets for use as solar cell wafers is presented and the parameters that control the sheet thickness are investigated. The computational model for the spin casting is proposed in order to understand the melt flow and solidification behaviors in the mold. The effect of the rotating speed of the mold and substrate morphology on the silicon sheets is studied via computer simulations, and the simulation results are compared with the experimental results. The numerical study of the fluidity and solidification behavior of the silicon predicted that the formation of rectangular sheets via spin casting is feasible, and the subsequent experiment confirmed this prediction. Using a square mold, rectangular silicon sheets can be produced under appropriate experimental conditions. Microstructural analyses verified the presence of long columnar structures on the sheets.

Identifying Herbal Candidates and Active Ingredients Against Postmenopausal Osteoporosis Using Biased Random Walk on a Multiscale Network

Postmenopausal osteoporosis is a major global health concern, particularly affecting aging women, and necessitates innovative treatment options. Herbal medicine, with its multi-compound, multi-target characteristics, offers a promising approach for complex diseases. In this study, we applied multiscale network and random walk-based analyses to identify candidate herbs and their active ingredients for postmenopausal osteoporosis, focusing on their underlying mechanisms. A dataset of medicinal herbs, their active ingredients, and protein targets was compiled, and diffusion profiles were calculated to assess the propagation effects. Through correlation analysis, we prioritized herbs based on their relevance to osteoporosis, identifying the top candidates like Benincasae Semen, Glehniae Radix, Corydalis Tuber, and Houttuyniae Herba. Gene Set Enrichment Analysis (GSEA) revealed that the 49 core protein targets of these herbs were significantly associated with pathways related to inflammation, osteoclast differentiation, and estrogen metabolism. Notably, compounds such as falcarindiol from Glehniae Radix and tetrahydrocoptisine from Corydalis Tuber-previously unstudied for osteoporosis-were predicted to interact with inflammation-related proteins, including IL6, IL1B, and TNF, affecting key biological processes like apoptosis and cell proliferation. This study advances the understanding of herbal therapies for osteoporosis and offers a framework for discovering novel therapeutic agents.