PubMed Assistant: a biologist-friendly interface for enhanced PubMed search

MEDLINE is one of the most important bibliographical information sources for biologists and medical workers. Its PubMed interface supports Boolean queries, which are potentially expressive and exact. However, PubMed is also designed to support simplicity of use at the expense of query expressiveness and exactness. Many PubMed users have never tried explicit Boolean queries. We developed a Java program, PubMed Assistant, to make literature access easier in several ways. PubMed Assistant provides an interface that efficiently displays information about the citations and includes useful functions such as keyword highlighting, export to citation managers, clickable links to Google Scholar and others that are lacking in PubMed.     

Comparative studies of intracellular Ca2+ in strongly and weakly metastatic rat prostate cancer cell lines

The metastatic ability of prostate cancer cells involves differential expression of ionic mechanisms. In the present study, using electrophysiological recordings and intracellular Ca2+ measurements, we investigated Ca2+ related signalling in two rat prostate cancer (MAT-LyLu and AT-2) cell lines of markedly different metastatic potential. Whole-cell voltage clamp experiments indicated the absence of an inward current carried through voltage-dependent Ca2+ channels in either cell line. A Ca2+-dependent component was also absent in the voltage-activated outward K+ currents. Indo-1 microfluorimetry confirmed these results and also revealed marked differences in the resting level of intracellular Ca2+ and the ability of the two cell lines to regulate intracellular Ca2+. The weakly metastatic AT-2 cells displayed a significantly higher resting intracellular Ca2+ than the related but strongly metastatic MAT-LyLu cell line. Increasing extracellular K+ decreased intracellular Ca2+ in the AT-2 but had no effect on intracellular Ca2+ levels in the MAT-LyLu cells. Furthermore, increasing extracellular Ca2+ increased intracellular Ca2+ in AT-2 but, again, had no effect on MAT-LyLu cells. These results suggested the presence of a tonic, voltage-independent Ca2+ permeation mechanism operating specifically in the AT-2 cells. The influx of Ca2+ into the AT-2 cells was suppressed by both CdCl2 (100-300 microM) and SKF-96365 (10-30 microM). It is concluded that the strongly metastatic MAT-LyLu cell line lacks a voltage-independent basal Ca2+ influx mechanism that is present in the weakly metastatic AT-2 cells.     

A novel thermoacidophilic endoglucanase, Ba-EGA, from a new cellulose-degrading bacterium, Bacillus sp.AC-1

A newly discovered bacterium, strain AC1, containing cellulase was isolated from the gastric juice of the mollusca, Ampullaria crosseans. Analysis of the 16S rDNA sequence and carbon sources revealed that the bacterium belonged to the genus Bacillus. A novel endoglucanase (Ba-EGA) was purified from culture supernatants of the bacterium growing in CMC-Na (low viscosity) induction medium. The cellulase was purified about 150-fold by ammonium sulfate fractionation, ion exchange, hydrophobic, and gel filtration chromatography, with a specific activity of 35.0 IU/mg. The molecular mass of the enzyme was 67 kDa. N-terminal amino acid sequencing revealed a sequence of SDYNYVEVLQKSILF, which had high homology with endoglucanases from the Bacillus and Clostridium species. The maximal activity of the enzyme with the substrate of CM-cellulose is at pH 4.5–6.5 and 70°C, respectively. The studies on pH and temperature stability showed that the Ba-EGA is stable enough between pH 7.5 and 10.5 at 30°C for 2 h, and more than 80% of the activity still remains when incubation was prolonged to 1 h at 50°C. The activity of the enzyme was significantly inhibited by Fe²⁺, Cu²⁺ (5.0 mM of each), and sodium dodecyl sulfate (SDS) (0.5%) and obviously activated by Tween 20 and Triton X-100 (0.25% each). Binding studies revealed that the Ba-EGA had cellulose-binding domain.     

Differential regulation of proteasome activity in the nucleus and the synaptic terminals

Proteasome is a multi-subunit proteolytic complex that degrades proteins covalently linked to multiple molecules of ubiquitin. Earlier studies showed a role for the ubiquitin-proteasome pathway in several models of long-term memory and other forms of synaptic plasticity. In Aplysia, the ubiquitin-proteasome pathway has been shown to contribute to the induction of long-term facilitation. In other model systems, ubiquitin-proteasome-mediated proteolysis has also been shown to play a role in synapse development. Previous studies of synaptic plasticity focused on changes in components or the substrates of the ubiquitin-proteasome pathway in whole neurons. Modification of specific synapses would require precise spatial and temporal regulation of the components of the ubiquitin-proteasome pathway within the subcellular compartments of neurons during learning. As a first step towards testing the idea of local regulation of the ubiquitin-proteasome pathway in neurons, we investigated proteasome activity in nuclear and synaptosomal fractions. Here we show that proteasome activity in the synaptic terminals is higher compared to the activity in the nucleus in the Aplysia nervous system as well as in the mouse brain. Furthermore, the proteasome activity in the two neuronal compartments is differentially modulated by protein kinases. Differential regulation of proteasome activity in neuronal compartments such as the synaptic terminals is likely to be a key mechanism underlying synapse-specific plasticity.     

Nox2 and Rac1 regulate H2O2-dependent recruitment of TRAF6 to endosomal interleukin-1 receptor complexes

Reactive oxygen species (ROS) generated by NADPH oxidases (Nox) have been implicated in the regulation of signal transduction. However, the cellular mechanisms that link Nox activation with plasma membrane receptor signaling remain poorly defined. We have found that Nox2-derived ROS influence the formation of an active interleukin-1 (IL-1) receptor complex in the endosomal compartment by directing the H2O2-dependent binding of TRAF6 to the IL-1R1/MyD88 complex. Clearance of both superoxide and H2O2 from within the endosomal compartment significantly abrogated IL-1beta-dependent IKK and NF-kappaB activation. MyD88-dependent endocytosis of IL-1R1 following IL-1beta binding was required for the redox-dependent formation of an active endosomal receptor complex competent for IKK and NF-kappaB activation. Small interfering RNAs to either MyD88 or Rac1 inhibited IL-1beta induction of endosomal superoxide and NF-kappaB activation. However, MyD88 and Rac1 appear to be recruited independently to IL-1R1 following ligand stimulation. In this context, MyD88 binding was required for inducing endocytosis of IL-1R1 following ligand binding, while Rac1 facilitated the recruitment of Nox2 into the endosomal compartment and subsequent redox-dependent recruitment of TRAF6 to the MyD88/IL-1R1 complex. The identification of Nox-active endosomes helps explain how subcellular compartmentalization of redox signals can be used to direct receptor activation from the plasma membrane.     

Respiratory pattern of captive Yangtze finless porpoises (Neophocaena phocaenoides asiaeorientalis)

Cetacean respiration usually happen in bouts. The most widely applied quantitative method used to analyze the structure of these bouts is the log_e-survivorship analysis, based on the assumption that the respiratory intervals are distributed as negative exponentials. However, for the data collected from three captive Yangtze finless porpoises (Neophocaena phocaenoides asiaeorientalis), we failed to obtain a convergent result with the application of log_e-survivorship analysis. However, the two-Gaussian model, which was recently proposed to analyze the feeding behavior of cows, was successfully fitted to the data. According to the fitting results, the overall respiratory pattern of the captive Yangtze finless porpoises can be described as a dive with a mean duration of around 30–40 s, followed by two or three ventilations with a mean interval of approximately 9 s. The average intra-bout intervals during both active and inactive periods are constant at 7.7–9.9 s for all individuals. However, when shifting from active to inactive states, the adult male and female decrease their mean numbers of respirations per bout and average length of inter-bout respiratory intervals, while the estimates of both parameters increase for the juvenile female. It was pointed out that the two-Gaussian model might be more adequate for cetacean respiratory-bout structure analyses than the log_e-survivorship technique.     

Expression of Discoidin Domain Receptor 2 (DDR2) Extracellular Domain in Pichia Pastoris and Functional Analysis in Synovial Fibroblasts and NIT3T3 Cells

Discoidin domain receptor 2 (DDR2) is a kind of protein tyrosine kinases associated with cell proliferation and tumor metastasis, and collagen, identified as a ligand for DDR2, up-regulates matrix metallloproteinase 1 (MMP-1) and MMP-2 expression in cellular matrix. To investigate the roles of DDR2 in destruction of cartilage in rheumatoid arthritis (RA) and tumor metastasis, we tried to express extracellular domain of DDR2 fused with a His tag to increase protein solubility and facilitate purification (without signal peptide and transmembrane domain, designated DR) in Pichia pastoris, purify the expressed protein, and characterize its function, for purpose of future application as a specific DDR2 antagonist. Two clones of relative high expression of His-DR were obtained, After purification by a Ni-NTA (nitric-tri-acetic acid) chromatographic column, soluble fused His-DR over 90% purity were obtained. Competitive binding inhibition assay demonstrated that expressed His-DR could block the binding of DDR2 and natural DDR2 receptors on NIT3T3 and synovial cell surfaces. Results of RT-PCR, Western blotting, and gelatinase zymography showed that His-DR was capable of inhibiting MMP-1 and MMP-2 secretion from NIT3T3 cells and RA synoviocytes stimulated by collagen II. For MMP-1, the inhibitory effect was displayed at the levels of mRNA and protein, whereas for MMP-2 it was demonstrated at the level of protein physiological activity. All these findings suggested that the fused expressed His-DR inhibited the activity of natural DDR2, and relevant MMP-1 and MMP-2 expression in synoviocytes and NIH3T3 cells provoked by collagen II. Wei Zhang and Tianbing Ding equally contributed to this work.     

Expression and distribution of trihydrophobin 1 in postnatal developing mouse testis

The human trihydrophobin 1 (TH1) is a highly conserved and widely expressed protein. It is clear that TH1 serves as a new specific negative regulator of A-Raf kinase. In this study, we found that TH1 associated with A-Raf in mouse testis by using coimmunoprecipitation analysis. Then we characterized the gene expression of TH1 in mouse testis and analyzed the changes of TH1 protein during postnatal development. The protein expression of TH1 in mouse testis was further analyzed by immunohistochemistry staining. Strong signals were detected in the seminiferous tubules and the distribution patterns varied with the different ages of postnatal mouse testis. TH1 was distributed in spermatocytes and Sertoli cells at 2 weeks postnatal, and was abundant in spermatogonia at 8 weeks postnatal. Leydig cells were positive to TH1 throughout testicular development. A high expression of TH1 in both Leydig cells and mouse Leydig tumor cells (mLTC-1cells) was found to be concentrated in the cytoplasm. The colocalization of TH1 and A-Raf in mLTC-1 cells or in adult testis was also observable.