A comprehensive assessment of N-terminal signal peptides prediction methods

Background: Amino-terminal signal peptides (SPs) are short regions that guide the targeting of secretory proteins to the correct subcellular compartments in the cell. They are cleaved off upon the passenger protein reaching its destination. The explosive growth in sequencing technologies has led to the deposition of vast numbers of protein sequences necessitating rapid functional annotation techniques, with subcellular localization being a key feature. Of the myriad software prediction tools developed to automate the task of assigning the SP cleavage site of these new sequences, we review here, the performance and reliability of commonly used SP prediction tools. Results: The available signal peptide data has been manually curated and organized into three datasets representing eukaryotes, Gram-positive and Gram-negative bacteria. These datasets are used to evaluate thirteen prediction tools that are publicly available. SignalP (both the HMM and ANN versions) maintains consistency and achieves the best overall accuracy in all three benchmarking experiments, ranging from 0.872 to 0.914 although other prediction tools are narrowing the performance gap. Conclusion: The majority of the tools evaluated in this study encounter no difficulty in discriminating between secretory and non-secretory proteins. The challenge clearly remains with pinpointing the correct SP cleavage site. The composite scoring schemes employed by SignalP may help to explain its accuracy. Prediction task is divided into a number of separate steps, thus allowing each score to tackle a particular aspect of the prediction.12 page(s

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Correlation between lumbar lordosis and the treatment of chronic low back pain with pulsed radiofrequency applied to the L2 dorsal root ganglion

Background: Percutaneous pulsed radiofrequency (PRF) applied to the L2 dorsal root ganglion (DRG) is an alternative procedure for treating patients with chronic discogenic pain. It is assumed that afferent nerve fibers innervating the degenerated disc and facet joint might travel in the same pathway and finally enter into the L2 DRG. Blocking the L2 DRG with PRF might alleviate discogenic pain and facet joint pain concurrently. Purpose: The purpose of this study was to investigate the correlation between different types of lumbar lordosis (LL) and the treatment of chronic low back pain with PRF applied to the L2 DRG. Materials and Methods: Between 2008 and 2013, 84 patients (29 men and 55 women) were enrolled. Their mean age was 56.03 ± 9.04 years. All patients suffered from low back pain for more than 6 months that worsened on prolonged sitting or standing and did not improve with at least 3 months of conservative treatment. LL was classified into four types based on Roussouly's classification. The L2 DRG was blocked with 2-Hz PRF waves lasting for 120 s at 45 V with the temperature of the electrode tip not above 42°C. The functional outcomes were assessed pre- and post-operatively using a visual analog scale (VAS) and the Oswestry Disability Index (ODI). Results: Twenty-four patients were Type 1 LL, 26 were Type 2 LL, 21 were Type 3 LL, and 13 were Type 4 LL. The mean age of patients with each type of LL was type 1 (56.63 ± 12.09 years), Type 2 (55.39 ± 11.05 years), Type 3 (55.86 ± 11.40 years), and Type 4 (56.54 ± 12.73 years). There were similar improvements in the VAS and ODI scores for all LL types. Two patients experienced cerebrospinal fluid leakage when the needle was moved toward the L2 DRG, but neither patient experienced a neurological deficit. Conclusion: PRF applied to the L2 DRG is an alternative procedure for treating patients with chronic low back pain, regardless of which type of LL the patients have. Chronic low back pain, including discogenic pain and facet joint pain, may be treated by PRF applied to the L2 DRG

Effects of Taraxacum mongolicum on in vitro response of milk somatic cells stimulated by lipopolysaccharide and subclinical mastitis in dairy cows in vivo

The anti-inflammatory effects of Taraxacum mongolicum (TM) were investigated in Holstein-Friesian dairy cows, in vitro and in vivo. In vitro, isolated milk somatic cells were pretreated with various concentrations (31 to 500, μg/ml) of TM extract (TME) and subsequently incubated with lipopolysaccharide (LPS, 1 μg/ml). The results show that TME treatment had no effect on cell viability; however, it significantly suppressed LPS-induced expression of nitric oxide (NO), interleukin(IL)-8, IL-1β, and tumor necrosis factor (TNF)-α in milk somatic cells, in a dose-dependent manner. In vivo, 14 lactating Holstein-Friesian cows, with subclinical mastitis, were randomly assigned to two groups and fed a diet with (treatment group, n=7, 150 g TM powder per head per day) or without (control group, n=7) TM supplementation for 14 days. Cows fed with TM powder had a significantly (P<0.05) reduced somatic cell count, total bacteria count and IL-8 in milk compared to the control group. In conclusion, the anti-inflammatory effects of TM were associated with down-regulation of NO and pro-inflammatory cytokines. Addition of TM as a dietary supplement might minimize the impact of subclinical bovine mastitis.Keywords: Cytokine, mastitis, somatic cell count, Taraxacum mongolicum, traditional Chinese medicineAfrican Journal of Biotechnology Vol. 12(10), pp. 1155-116

Ginger and Zingerone Ameliorate Lipopolysaccharide-Induced Acute Systemic Inflammation in Mice, Assessed by Nuclear Factor-κB Bioluminescent Imaging

Ginger is a commonly used spice in cooking. In this study, we comprehensively evaluated the anti-inflammatory activities of ginger and its component zingerone in lipopolysaccharide (LPS)-induced acute systemic inflammation in mice via nuclear factor-κB (NF-κB) bioluminescent imaging. Ginger and zingerone significantly suppressed LPS-induced NF-κB activities in cells in a dose-dependent manner, and the maximal inhibition (84.5% ± 3.5% and 96.2% ± 0.6%) was observed at 100 μg/mL ginger and zingerone, respectively. Moreover, dietary ginger and zingerone significantly reduced LPS-induced proinflammatory cytokine production in sera by 62.9% ± 18.2% and 81.3% ± 6.2%, respectively, and NF-κB bioluminescent signals in whole body by 26.9% ± 14.3% and 38.5% ± 6.2%, respectively. In addition, ginger and zingerone suppressed LPS-induced NF-κB-driven luminescent intensities in most organs, and the maximal inhibition by ginger and zingerone was observed in small intestine. Immunohistochemical staining further showed that ginger and zingerone decreased interleukin-1β (IL-1β)-, CD11b-, and p65-positive areas in jejunum. In conclusion, our findings suggested that ginger and zingerone were likely to be broad-spectrum anti-inflammatory agents in most organs that suppressed the activation of NF-κB, the production of IL-1β, and the infiltration of inflammatory cells in mice