DBMLoc: a Database of proteins with multiple subcellular localizations

<p>Abstract</p> <p>Background</p> <p>Subcellular localization information is one of the key features to protein function research. Locating to a specific subcellular compartment is essential for a protein to function efficiently. Proteins which have multiple localizations will provide more clues. This kind of proteins may take a high proportion, even more than 35%.</p> <p>Description</p> <p>We have developed a database of proteins with multiple subcellular localizations, designated DBMLoc. The initial release contains 10470 multiple subcellular localization-annotated entries. Annotations are collected from primary protein databases, specific subcellular localization databases and literature texts. All the protein entries are cross-referenced to GO annotations and SwissProt. Protein-protein interactions are also annotated. They are classified into 12 large subcellular localization categories based on GO hierarchical architecture and original annotations. Download, search and sequence BLAST tools are also available on the website.</p> <p>Conclusion</p> <p>DBMLoc is a protein database which collects proteins with more than one subcellular localization annotation. It is freely accessed at <url>http://www.bioinfo.tsinghua.edu.cn/DBMLoc/index.htm</url>.</p

Sensitive and easily recyclable plasmonic SERS substrate based on Ag nanowires in mesoporous silica

Raman spectra were obtained by a Renishaw inVia with a laser of 532 nm and 0.5% strength, samples were arranged on the silica plate. X-ray diffraction (XRD) patterns of the samples were recorded on a Rigaku D/MAX- 2550 diffractometer using Cu Kα radiation of wavelength 1.5406 Å, typically run at a voltage of 40 kV and current of 100 mA. UV-visible absorbance spectra were achieved for the dry pressed disk samples using a Scan UV-Vis spectrophotometer (Varian, Cary 500) equipped with an integrating sphere assembly, using BaSO4 as a reflectance sample. Transmission electron microscopy (TEM) images were collected on a JEOL JEM 2010F, electron microscope operated at an acceleration voltage of 200 kV. By utilizing the Barrett−Joyner−Halenda (BJH) model, the pore volumes and pore size distributions were got from the adsorption branches of isotherms

Probing hidden Mott gap and incommensurate charge modulation on the polar surfaces of PdCrO2_2

Here we report a combined study of low-temperature scanning tunneling microscopy (STM) and dynamical mean-field theory (DMFT) on PdCrO$_2$, a delafossite metal with an antiferromagnetic order below ~37.5 K. First, on the CrO$_2$-terminated polar surface we detect a gap-like feature both below and above the N\'eel temperature. The DMFT calculations indicate that this gap is opened due to the strong correlations of Cr-3d electrons, suggesting the hidden Mott nature of the gap. Then, we observe two kinds of Pd-terminated polar surfaces. One is a well-ordered Pd surface with the Fermi-surface-nesting-induced incommensurate charge modulation, while the other one is a reconstructed Pd surface with the individual nano-scale non-periodic domain structures. On the well-ordered Pd surface, the interference between the incommensurate charge modulation and the atomic lattice forms the periodic moir\'e pattern. Our results provide important microscopic information for fully understanding the correlated electronic properties of this class of materials.Comment: 11 pages, 4 figure

Optimization and scale-up of cell culture and purification processes for production of an adenovirus-vectored tuberculosis vaccine candidate

Tuberculosis (TB) is the second leading cause of death by infectious disease worldwide. The only available TB vaccine is the Bacille Calmette-Guerin (BCG). However, parenterally administered Mycobacterium bovis BCG vaccine confers only limited immune protection from pulmonary tuberculosis in humans. There is a need for developing effective boosting vaccination strategies. AdAg85A, an adenoviral vector expressing the mycobacterial protein Ag85A, is a new tuberculosis vaccine candidate, and has shown promising results in pre-clinical studies and phase I trial. This adenovirus vectored vaccine is produced using HEK 293 cell culture. Here we report on the optimization of cell culture conditions, scale-up of production and purification of the AdAg85A at different scales. Four commercial serum-free media were evaluated under various conditions for supporting the growth of HEK293 cell and production of AdAg85A. A culturing strategy was employed to take advantages of two culture media with respective strengths in supporting the cell growth and virus production, which enabled to maintain virus productivity at higher cell densities and resulted in more than two folds of increases in culture titer. The production of AdAg85A was successfully scaled up and validated at 60L bioreactor under the optimal conditions. The AdAg85A generated from the 3L and 60L bioreactor runs was purified through several purification steps. More than 98% of total cellular proteins was removed, over 60% of viral particles was recovered after the purification process, and purity of AdAg85A was similar to that of the ATCC VR-1516 Ad5 standard. Vaccination of mice with the purified AdAg85A demonstrated a very good level of Ag85A-specific antibody responses. The optimized production and purification conditions were transferred to a GMP facility for manufacturing of AdAg85A for generation of clinical grade material to support clinical trials

Construction of an efficient Claviceps paspali cell factory for lysergic acid production

Lysergic acid (LA) is the key precursor of ergot alkaloids, and its derivatives have been used extensively for the treatment of neurological disorders. However, the poor fermentation efficiency limited its industrial application. At the same time, the hardship of genetic manipulation has hindered the metabolic engineering of Claviceps strains to improve the LA titer further. In this study, an efficient genetic manipulation system based on the protoplast-mediated transformation was established in the industrial strain Claviceps paspali. On this basis, the gene lpsB located in the ergot alkaloids biosynthetic gene cluster was deleted to construct the LA-producing cell factory. Plackett-Burman and Box-Behnken designs were used in shaking flasks, achieving an optimal fermentation medium composition. The final titer of LA and iso-lysergic acid (ILA) reached 3.7 g·L−1, which was 4.6 times higher than that in the initial medium. Our work provides an efficient strategy for the biosynthesis of LA and ILA and lays the groundwork for its industrial production

Wearable rehabilitation wristband for distal radius fractures

BackgroundDistal radius fractures are a common type of fracture. For patients treated with closed reduction with splinting, a period of rehabilitation is still required after the removal of the splint. However, there is a general lack of attention and low compliance to rehabilitation training during this period, so it is necessary to build a rehabilitation training monitoring system to improve the efficiency of patients’ rehabilitation.MethodsA wearable rehabilitation training wristband was proposed, which could be used in the patient’s daily rehabilitation training scenario and could recognize four common wrist rehabilitation actions in real-time by using three thin film pressure sensors to detect the pressure change curve at three points on the wrist. An algorithmic framework for classifying rehabilitation training actions was proposed. In our framework, an action pre-detection strategy was designed to exclude false detections caused by switching initial gestures during rehabilitation training and wait for the arrival of the complete signal. To classify the action signals into four categories, firstly an autoencoder was used to downscale the original signal. Six SVMs were then used for evaluation and voting, and the final action with the highest number of votes would be used as the prediction result.ResultsExperimental results showed that the proposed algorithmic framework achieved an average recognition accuracy of 89.62%, an average recognition recall of 88.93%, and an f1 score of 89.27% on the four rehabilitation training actions.ConclusionThe developed device has the advantages of being small size and easy to wear, which can quickly and accurately identify and classify four common rehabilitation training actions. It can easily be combined with peripheral devices and technologies (e.g., cell phones, computers, Internet) to build different rehabilitation training scenarios, making it worthwhile to use and promote in clinical settings

Periodic Mechanical Stress Stimulates Cav-1-Dependent IGF-1R Mitogenic Signals in Rat Chondrocytes Through ERK1/2

Background/Aims: The biological effects of periodic mechanical stress on the mitogenesis of chondrocytes have been studied extensively over the past few years. However, the mechanisms underlying the ability of chondrocytes to sense and respond to mechanical stimuli remain to be determined. In the current study, we analyzed the mechanisms by which periodic mechanical stress is translated into biochemical signals and verified the key role of non-integrin mechanosensors including Caveolin-1 (Cav-1), and insulin-like growth factor-1 receptor (IGF-1R) in chondrocyte proliferation. Methods: Two steps were undertaken in the experiment. In the first step, the cells were maintained under static conditions or periodic mechanical stress for 0 h and 1 h prior to Western blot analysis. In the second step, the cells were pretreated with short hairpin RNA (shRNA) targeted to Cav-1 or IGF-1R or control scrambled shRNA. Moreover, they were pretreated with their selective inhibitors methyl β-cyclodextrin (MCD) or Linsitinib (OSI-906). They were maintained under static conditions or periodic mechanical stress for 1 h prior to Western blot analysis, and for 3 days, 8 h per day, prior to direct cell counting and CCK-8 assay, respectively. Results: Periodic mechanical stress significantly induced sustained phosphorylation of Cav-1 at Tyr14 and IGF-1R at Tyr1135/1136. Proliferation was inhibited by pretreatment with Cav-1 inhibitor MCD and by shRNA targeted to Cav-1 in chondrocytes in response to periodic mechanical stress. Meantime, MCD and shRNA targeted to Cav-1 also attenuated IGF-1R, and extracellular signal-regulated kinase (ERK)1/2 activation. In addition, inhibiting IGF-1R activity by Linsitinib and shRNA targeted to IGF-1R abrogated chondrocyte proliferation and phosphorylation level of ERK1/2 subjected to periodic mechanical stress, while the phosphorylation site of Cav-1 was not affected. Conclusion: These findings collectively suggested that periodic mechanical stress promoted chondrocyte proliferation through Cav-1-IGF-1R-ERK1/2

Periodic Mechanical Stress Stimulates GIT1-Dependent Mitogenic Signals in Rat Chondrocytes Through ERK1/2 Activity

Background/Aims: The mitogenic effects of periodic mechanical stress on chondrocytes have been studied extensively, but the mechanisms whereby chondrocytes sense and respond to mechanical stimuli remain to be determined. We explored the question and verified the key role of G protein coupled receptor kinase interacting protein 1 (GIT1) signaling in periodic mechanical stress-induced chondrocyte proliferation. Methods: Two steps were undertaken in the experiment. In the first step, the cells were maintained under non-pressure conditions or periodic mechanical stress for 1 h prior to Western blot analysis. In the second step, the cells were pretreated with short hairpin RNA (shRNA) targeted to GIT1 or Src or control scrambled shRNA, or transfected with GIT1 wild-type or GIT1 mutant Y321F, or focal adhesion kinase (FAK) wild-type or FAK mutants Y397F or Y576F/Y577, respectively. Moreover, the cells were pretreated with blocking antibody against integrin β1 or PP2. Then the cells were maintained under non-pressure conditions or periodic mechanical stress for 1 h prior to Western blot analysis, and for 3 days, 8 h per day, prior to direct cell counting and CCK-8 assay, respectively. Results: Periodic mechanical stress significantly induced sustained phosphorylation of GIT1 at Tyr321. Reduction of GIT1 with shRNA targeted to GIT1 and GIT1 mutant Y321F inhibited periodic mechanical stress-promoted chondrocyte proliferation, accompanied by attenuated extracellular signal-regulated kinase (ERK)1/2 and FAK phosphorylation at Tyr576/577. However, activation of Src and FAK-Tyr397 was not prevented upon GIT1 suppression. Furthermore, pretreatment with blocking antibody against integrin β1, Src-selective inhibitor, PP2, and shRNA targeted to Src blocked GIT1 activation under periodic mechanical stress. In addition, GIT1 phosphorylation at Tyr321 was not reduced upon pretreatment with FAK mutants Y397F or Y576F/Y577 under conditions of periodic mechanical stress. Conclusion: These findings collectively suggested that periodic mechanical stress promoted chondrocyte proliferation through at least two separate pathways, integrin β1-Src-GIT1-FAK(Tyr576/577)-ERK1/2, and the other parallel GIT1-independent integrin β1-FAK(Tyr397)-ERK1/2

Entropy regulation in LaNbO4-based fergusonite to implement high-temperature phase transition and promising dielectric properties

High-entropy effect is a novel design strategy to optimize properties and explore novel materials. In this work, (La1/5Nd1/5Sm1/5Ho1/5Y1/5)NbO4 (5RNO) high-entropy microwave dielectric ceramics were successfully prepared in the sintering temperature (S.T.) range of 1210–1290 ℃ via a solid-phase reaction route, and medium-entropy (La1/3Nd1/3Sm1/3)NbO4 and (La1/4Nd1/4Sm1/4Ho1/4)NbO4 (3RNO and 4RNO) ceramics were compared. The effects of the entropy (S) on crystal structure, phase transition, and dielectric performance were evaluated. The entropy increase yields a significant increase in a phase transition temperature (from monoclinic fergusonite to tetragonal scheelite structure). Optimal microwave dielectric properties were achieved in the high-entropy ceramics (5RNO) at the sintering temperature of 1270 ℃ for 4 h with a relative density of 98.2% and microwave dielectric properties of dielectric permittirity (εr) = 19.48, quality factor (Q×f) = 47,770 GHz, and resonant frequency temperature coefficient (τf) = –13.50 ppm/℃. This work opens an avenue for the exploration of novel microwave dielectric material and property optimization via entropy engineering