SjTPdb: integrated transcriptome and proteome database and analysis platform for Schistosoma japonicum

<p>Abstract</p> <p>Background</p> <p><it>Schistosoma japonicum </it>is one of the three major blood fluke species, the etiological agents of schistosomiasis which remains a serious public health problem with an estimated 200 million people infected in 76 countries. In recent years, enormous amounts of both transcriptomic and proteomic data of schistosomes have become available, providing information on gene expression profiles for developmental stages and tissues of <it>S. japonicum</it>. Here, we establish a public searchable database, termed SjTPdb, with integrated transcriptomic and proteomic data of <it>S. japonicum</it>, to enable more efficient access and utility of these data and to facilitate the study of schistosome biology, physiology and evolution.</p> <p>Description</p> <p>All the available ESTs, EST clusters, and the proteomic dataset of <it>S. japonicum </it>are deposited in SjTPdb. The core of the database is the 8,420 <it>S. japonicum </it>proteins translated from the EST clusters, which are well annotated for sequence similarity, structural features, functional ontology, genomic variations and expression patterns across developmental stages and tissues including the tegument and eggshell of this flatworm. The data can be queried by simple text search, BLAST search, search based on developmental stage of the life cycle, and an integrated search for more specific information. A PHP-based web interface allows users to browse and query SjTPdb, and moreover to switch to external databases by the following embedded links.</p> <p>Conclusion</p> <p>SjTPdb is the first schistosome database with detailed annotations for schistosome proteins. It is also the first integrated database of both transcriptome and proteome of <it>S. japonicum</it>, providing a comprehensive data resource and research platform to facilitate functional genomics of schistosome. SjTPdb is available from URL: <url>http://function.chgc.sh.cn/sj-proteome/index.htm</url>.</p

Colorectal cancer screening with fecal occult blood test: A 22-year cohort study.

The aim of the present study was to investigate the efficacy of colorectal cancer (CRC) screening with a three-tier fecal occult blood test (FOBT) in the Chinese population. The study was performed between 1987 and 2008 at the Beijing Military General Hospital, in a cohort of army service males and females aged &gt;50 years. Between 1987 and 2005, a three-tier screening program, comprising guaiac-based FOBTs (gFOBTs), followed by immunochemical FOBTs for positive guaiac test samples and then colonoscopy for positive immunochemical test subjects, was performed annually. The cohort was followed up until 2008. The cohort included 5,104 subjects, of which, 3,863 subjects participated in screening (screening group) and 1,241 did not (non-screening group). The two groups did not differ in age, gender or other major risk factors for colon cancer. Overall, 36 CRCs occurred in the screening group and 21 in the non-screening group. Compared with the non-screening group, the relative risk for the incidence and mortality of CRC was 0.51 [95% confidence interval (CI), 0.30-0.87] and 0.36 (95% CI, 0.18-0.71), respectively, in the screening group. The general sensitivity of this three-tier FOBT was 80.6% (95% CI, 65.3-91.1). Thus, annual screening using the three-tier FOBT program may reduce the CRC incidence and mortality rate

Demonstration of chronometric leveling using transportable optical clocks beyond laser coherence limit

Optical clock network requires the establishment of optical frequency transmission link between multiple optical clocks, utilizing narrow linewidth lasers. Despite achieving link noise levels of 10${^{-20}}$, the final accuracy is limited by the phase noise of the clock laser. Correlation spectroscopy is developed to transmit frequency information between two optical clocks directly, enabling optical clock comparison beyond the phase noise limit of clock lasers, and significantly enhancing the measurement accuracy or shorten the measurement time. In this letter, two compact transportable ${^{40}}$Ca${^+}$ clocks are employed to accomplish the correlation spectroscopy comparison, demonstrating an 10 cm level measurement accuracy of chronometric leveling using a mediocre clock laser with linewidth of 200 Hz. The relative frequency instability reaches $6.0\times10{^{-15}}/\sqrt{\tau/s}$, which is about 20 times better than the result with Rabi spectroscopy using the same clock laser. This research greatly reduces the harsh requirements on the performance of the clock laser, so that an ordinary stable-laser can also be employed in the construction of optical clock network, which is essential for the field applications, especially for the chronometric leveling

The α1‐adrenergic receptor is involved in hepcidin upregulation induced by adrenaline and norepinephrine via the STAT3 pathway

Elevated body iron stores are associated with hypertension progression, while hypertension is associated with elevated plasma catecholamine levels in patients. However, there is a gap in our understanding of the connection between catecholamines and iron regulation. Hepcidin is a key iron‐regulatory hormone, which maintains body iron balance. In the present study, we investigated the effects of adrenaline (AD) and norepinephrine (NE) on hepatic hepcidin regulation. Mice were treated with AD, NE, phenylephrine (PE, α1‐adrenergic receptor agonist), prazosin (PZ, α1‐adrenergic receptor antagonist), and/or propranolol (Pro, β‐adrenergic receptor antagonist). The levels of hepcidin, as well as signal transducer and activator of transcription 3 (STAT3), ferroportin 1 (FPN1), and ferritin‐light (Ft‐L) protein in the liver or spleen, were assessed. Six hours after AD, NE, or PE treatment, hepatic hepcidin mRNA levels increased. Pretreatment with PZ, but not Pro, abolished the effects of AD or NE on STAT3 phosphorylation and hepatic hepcidin expression. When mice were treated with AD or NE continuously for 7 days, an increase in hepatic hepcidin mRNA levels and serum hepcidin concentration was also observed. Meanwhile, the expected downstream effects of elevated hepcidin, namely decreased FPN1 expression and increased Ft‐L protein and non‐heme iron concentrations in the spleen, were observed after the continuous AD or NE treatments. Taken together, we found that AD or NE increase hepatic hepcidin expression via the α1‐adrenergic receptor and STAT3 pathways in mice. The elevated hepatic hepcidin decreased FPN1 levels in the spleen, likely causing the increased iron accumulation in the spleen

Regression of Gastric Cancer by Systemic Injection of RNA Nanoparticles Carrying Both Ligand and siRNA

Gastric cancer is the second leading cause of cancer-related death worldwide. RNA nanotechnology has recently emerged as an important field due to recent finding of its high thermodynamic stability, favorable and distinctive in vivo attributes. Here we reported the use of the thermostable three-way junction (3WJ) of bacteriophage phi29 motor pRNA to escort folic acid, a fluorescent image marker and BRCAA1 siRNA for targeting, imaging, delivery, gene silencing and regression of gastric cancer in animal models. In vitro assay revealed that the RNA nanoparticles specifically bind to gastric cancer cells, and knock-down the BRCAA1 gene. Apoptosis of gastric cancer cells was observed. Animal trials confirmed that these RNA nanoparticles could be used to image gastric cancer in vivo, while showing little accumulation in crucial organs and tissues. The volume of gastric tumors noticeably decreased during the course of treatment. No damage to important organs by RNA nanoparticles was detectible. All the results indicated that this novel RNA nanotechnology can overcome conventional cancer therapeutic limitations and opens new opportunities for specific delivery of therapeutics to stomach cancer without damaging normal cells and tissues, reduce the toxicity and side effect, improve the therapeutic effect, and exhibit great potential in clinical tumor therapy

The pyruvate decarboxylase activity of IpdC is a limitation for isobutanol production by Klebsiella pneumoniae

BACKGROUND: Klebsiella pneumoniae contains an endogenous isobutanol synthesis pathway. The ipdC gene annotated as an indole-3-pyruvate decarboxylase (Kp-IpdC), was identified to catalyze the formation of isobutyraldehyde from 2-ketoisovalerate. RESULTS: Compared with 2-ketoisovalerate decarboxylase from Lactococcus lactis (KivD), a decarboxylase commonly used in artificial isobutanol synthesis pathways, Kp-IpdC has an 2.8-fold lower Km for 2-ketoisovalerate, leading to higher isobutanol production without induction. However, expression of ipdC by IPTG induction resulted in a low isobutanol titer. In vitro enzymatic reactions showed that Kp-IpdC exhibits promiscuous pyruvate decarboxylase activity, which adversely consume the available pyruvate precursor for isobutanol synthesis. To address this, we have engineered Kp-IpdC to reduce pyruvate decarboxylase activity. From computational modeling, we identified 10 amino acid residues surrounding the active site for mutagenesis. Ten designs consisting of eight single-point mutants and two double-point mutants were selected for exploration. Mutants L546W and T290L that showed only 5.1% and 22.1% of catalytic efficiency on pyruvate compared to Kp-IpdC, were then expressed in K. pneumoniae for in vivo testing. Isobutanol production by K. pneumoniae T290L was 25% higher than that of the control strain, and a final titer of 5.5 g/L isobutanol was obtained with a substrate conversion ratio of 0.16 mol/mol glucose. CONCLUSIONS: This research provides a new way to improve the efficiency of the biological route of isobutanol production

The LAMOST Survey of Background Quasars in the Vicinity of the Andromeda and Triangulum Galaxies -- II. Results from the Commissioning Observations and the Pilot Surveys

We present new quasars discovered in the vicinity of the Andromeda and Triangulum galaxies with the LAMOST during the 2010 and 2011 observational seasons. Quasar candidates are selected based on the available SDSS, KPNO 4 m telescope, XSTPS optical, and WISE near infrared photometric data. We present 509 new quasars discovered in a stripe of ~135 sq. deg from M31 to M33 along the Giant Stellar Stream in the 2011 pilot survey datasets, and also 17 new quasars discovered in an area of ~100 sq. deg that covers the central region and the southeastern halo of M31 in the 2010 commissioning datasets. These 526 new quasars have i magnitudes ranging from 15.5 to 20.0, redshifts from 0.1 to 3.2. They represent a significant increase of the number of identified quasars in the vicinity of M31 and M33. There are now 26, 62 and 139 known quasars in this region of the sky with i magnitudes brighter than 17.0, 17.5 and 18.0 respectively, of which 5, 20 and 75 are newly-discovered. These bright quasars provide an invaluable collection with which to probe the kinematics and chemistry of the ISM/IGM in the Local Group of galaxies. A total of 93 quasars are now known with locations within 2.5 deg of M31, of which 73 are newly discovered. Tens of quasars are now known to be located behind the Giant Stellar Stream, and hundreds behind the extended halo and its associated substructures of M31. The much enlarged sample of known quasars in the vicinity of M31 and M33 can potentially be utilized to construct a perfect astrometric reference frame to measure the minute PMs of M31 and M33, along with the PMs of substructures associated with the Local Group of galaxies. Those PMs are some of the most fundamental properties of the Local Group.Comment: 26 pages, 6 figures, AJ accepte