Molecular docking and molecular simulation studies for N-degron selectivity of chloroplastic ClpS from Chlamydomonas reinhardtii.

Regarding the importance of N-degron pathway in protein degradation network, the adaptor protein ClpS recognizes the substrates bearing classical N-degrons, and delivers them to caseinolytic protease complex ClpAP for degradation. Interestingly, the majority of N-degrons located near the N-terminus of protein substrate are belonged to the hydrophobic type amino acids. Chloroplast, an important organelle for plant photosynthesis, contain a diversified Clp degradation system. Despite several studies have confirmed that chloroplastic ClpS is able to interact with classical N-degrons derived from prokaryotes, whereas, the molecular mechanism underlying how the chloroplastic ClpS protein could recognize the substrate tagged by N-degrons is still unclear until now. Chlamydomonas reinhardtii is a kind of unicellular model organism for photosynthesis researches, which possesses a large cup-shaped chloroplast, and the corresponding genome data indicates that it owns bacterial homologous adaptor protein, named CrClpS1. However, the relevant biochemical knowledges, and protein structure researches for CrClpS1 adaptor aren't reported up to date. The molecular interactions between CrClpS1 and possible N-degrons are undefined as well. Here, we build a reliable homology model of CrClpS1 and find a hydrophobic pocket for N-degron binding. We combine molecular docking, molecular dynamic simulations, and MM/PBSA, MM/GBSA binding free energy estimations to elucidate the molecular properties of CrClpS1-N-degron interactions. Besides, we investigate the conformational changes for CrClpS1-apo in water-solvent environment and analyze its possible biological significances through a long time molecular dynamic simulation. Specifically, the adaptor CrClpS1 displays the stronger interactions with Phe, Trp, Tyr, His and Ile with respect to other amino acids. Using the residue decomposition analysis, the interactions between CrClpS1 and N-degrons are heavily depended on several conservative residues, which are located around the hydrophobic pocket, implying that chloroplast isolated from Chlamydomonas reinhadtii adopts a relatively conservative N-degron recognition mode. Besides, the opening-closure of hydrophobic pocket of CrClpS1 might be beneficial for the N-degron selectivity.

Angioplasty for Supra-Aortic Arterial Lesions from Takayasu Arteritis: Efficacy of Cutting Balloon Angioplasty Versus Conventional Balloon Angioplasty.

BACKGROUND: This retrospective study aimed to evaluate the safety and efficacy of cutting balloon angioplasty and conventional balloon angioplasty in supra-aortic arterial lesions caused by Takayasu arteritis. METHODS: A total of 46 patients with supra-aortic arterial lesions between January 2011 and December 2018 were included. Cutting balloon angioplasty was applied for 17 patients with 24 supra-aortic arterial lesions (group A), while 29 patients with 36 supra-aortic arterial lesions received conventional balloon angioplasty (group B). The preoperative clinical manifestation, operation result, and postoperative outcomes were recorded and compared in the 2 groups. RESULTS: Dizziness, visual disturbance, and unequal/absent pulses were the most common manifestations. The technical success of revascularization was 93.5% (43/46) in patients and 93.3% (56/60) in lesions. The stent implantation rate in group A was significantly lower than that in group B (4.2% vs. 50% in lesions, P < 0.05). Restenosis was the most common complication in both groups. Although the early (≤30 days) and late (>30 days) complications in group A were less than those in group B, there was no significant difference between the 2 groups (P > 0.05). Moreover, the primary-assisted patency of cutting balloon angioplasty and conventional balloon angioplasty at 1, 2, and 5 years were 66.7%, 62.5%, and 62.5% and 61.1%, 58.2%, and 49.8%, there was no significant difference between the 2 groups (P > 0.05), respectively. CONCLUSIONS: Compared with conventional balloon angioplasty, cutting balloon angioplasty could be considered a safe and effective alternative for supra-aortic arterial lesions caused by Takayasu arteritis, demonstrating better patency and clinical benefit.

Improved Mechanical and Corrosion Properties of Powder Metallurgy Austenitic, Ferritic, and Martensitic Stainless Steels by Liquid Phase Sintering.

Powder metallurgy (PM) has been widely used to produce various steels in industry, mainly due to its capabilities for manufacturing nearly net-shaped products and mass production. To improve the performances of PM stainless steels, the roles of 0.6 wt% B additive in the microstructures, mechanical properties, and corrosion resistances of PM 304L austenitic, 410L ferritic, and 410 martensitic stainless steels were investigated. The results showed that adding 0.6 wt% B significantly improved the sintered densities of the three kinds of stainless steels due to the liquid phase sintering (LPS) phenomenon. The borides in 304L + 0.6B, 410L + 0.6B, and 410 + 0.6B were rich in B and Cr atoms but deficient in Fe, Ni, or C atoms, as analyzed by electron probe micro-analysis. Furthermore, the B additive contributed to the improved apparent hardness and corrosion resistance of PM stainless steels. In the 410L stainless steel, the 0.6 wt% B addition increased the corrosion voltage from -0.43 VSCE to -0.24 VSCE and reduced the corrosion current density from 2.27 × 10-6 A/cm2 to 1.93 × 10-7 A/cm2. The effects of several factors, namely: porosity; the generation of boride; the matrix/boride interfacial areas; Cr depletion; and the microstructure on the corrosion performances are discussed. The findings clearly indicate that porosity plays a predominant role in the corrosion resistances of PM austenitic, ferritic, and martensitic stainless steels.

Cereal Endosperms: Development and Storage Product Accumulation.

The persistent triploid endosperms of cereal crops are the most important source of human food and animal feed. The development of cereal endosperms progresses through coenocytic nuclear division, cellularization, aleurone and starchy endosperm differentiation, and storage product accumulation. In the past few decades, the cell biological processes involved in endosperm formation in most cereals have been described. Molecular genetic studies performed in recent years led to the identification of the genes underlying endosperm differentiation, regulatory network governing storage product accumulation, and epigenetic mechanism underlying imprinted gene expression. In this article, we outline recent progress in this area and propose hypothetical models to illustrate machineries that control aleurone and starchy endosperm differentiation, sugar loading, and storage product accumulations. A future challenge in this area is to decipher the molecular mechanisms underlying coenocytic nuclear division, endosperm cellularization, and programmed cell death.

The Microstructure of Fe-Based Laminated Metal Composite Produced by Powder Metallurgy.

Powder metallurgy (PM) is a versatile process to manufacture nearly net-shaped metallic materials in industry. In this study, the PM process was used to fabricate two Fe-based laminated metal composites (LMCs), Fe-4Ni-3Cr-0.5Mo-0.5C/Fe and 410/304L. The results showed that after sintering, the LMCs were free of interfacial cracks and distortion, indicating that the PM process is a feasible means for producing these LMCs. In the Fe-4Ni-3Cr-0.5Mo-0.5C/Fe LMC, the diffusion of C resulted in the generation of a continuous pearlite layer between the Fe-4Ni-3Cr-0.5Mo-0.5C and Fe layers and a ferrite/pearlite mixture in the Fe layer. In the 410/304L LMC, the difference in the chemical potentials of C between the 304L and 410 layers led to the uphill diffusion of C from the 410 layer to the 304L layer. A continuous ferrite layer was thus formed near the interface of the 410 layer. Furthermore, a martensite layer of about 50 µm thickness was generated at the interface due to the high Cr and Ni content.

Wear Behavior of a Heat-Treatable Al-3.5Cu-1.5Mg-1Si Alloy Manufactured by Selective Laser Melting.

In this study, the wear behavior of a heat-treatable Al-7Si-0.5Mg-0.5Cu alloy fabricated by selective laser melting was investigated systematically. Compared with the commercial homogenized AA2024 alloy, the fine secondary phase of the SLM Al-Cu-Mg-Si alloy leads to a low specific wear rate (1.8 ± 0.11 × 10-4 mm3(Nm)-1) and a low average coefficient of friction (0.40 ± 0.01). After the T6 heat treatment, the SLM Al-Cu-Mg-Si alloy exhibits a lower specific wear rate (1.48 ± 0.02 × 10-4 mm3(Nm)-1), but a similar average coefficient of friction (0.34 ± 0.01) as the heat-treated AA2024 alloy. Altogether, the SLM Al-3.5Cu-1.5Mg-1Si alloy is suitable for the achievement of not only superior mechanical performance, but also improved tribological properties.

RADICLELESS 1 (RL1)-mediated nad4 intron 1 splicing is crucial for embryo and endosperm development in rice (Oryza sativa L.).

Pentatricopeptide repeat (PPR) proteins are one of the largest protein families in land plants. PPR proteins exhibit sequence-specific RNA-binding activity and are implicated in plant growth and development related processes. In this study, we report that the radicleless 1 (rl1) mutant in rice (Oryza sativa L.) exhibited defective radicle emergence in embryos and compromised grain filling in endosperms. Gene cloning and confirmation via genetic complementation analyses showed that RL1 encodes a P-type PPR protein, which is localized to mitochondria. The RL1 protein was specifically involved in the splicing of intron 1 of the mitochondrial nad4 transcript, which encodes a subunit of the mitochondrial NADH dehydrogenase complex. Consistent with this observation, the rl1 mutant exhibited altered mitochondrial morphology and lower ATP accumulation compared with the wild type. Thus, our findings suggest that RL1-mediated nad4 splicing is crucial for embryo and endosperm development in rice.

Local and Global Feature Learning for Blind Quality Evaluation of Screen Content and Natural Scene Images.

The blind quality evaluation of screen content images (SCIs) and natural scene images (NSIs) has become an important, yet very challenging issue. In this paper, we present an effective blind quality evaluation technique for SCIs and NSIs based on a dictionary of learned local and global quality features. First, a local dictionary is constructed using local normalized image patches and conventional -means clustering. With this local dictionary, the learned local quality features can be obtained using a locality-constrained linear coding with max pooling. To extract the learned global quality features, the histogram representations of binary patterns are concatenated to form a global dictionary. The collaborative representation algorithm is used to efficiently code the learned global quality features of the distorted images using this dictionary. Finally, kernel-based support vector regression is used to integrate these features into an overall quality score. Extensive experiments involving the proposed evaluation technique demonstrate that in comparison with most relevant metrics, the proposed blind metric yields significantly higher consistency in line with subjective fidelity ratings.

Performance of laser inter-satellite links with dynamic beam waist adjustment.

In this paper, we propose the idea of dynamic beam waist adjustment for laser inter-satellite communications, and study the performance of this dynamic-beam scheme. The beam waist adjustment is based on continuous detection of the instantaneous pointing error angle, which is performed at the transmitter side. Using a square to approximate the circular detector region, we obtain a closed-form expression for calculating the proportion of power that can be collected by the receiver aperture, and derive a simple algebraic solution for the optimum dynamic beam waist. Due to its simple form, the dynamic beam waist value can be computed in real time at the transmitter, and therefore, the adjustment is practically implementable. It is shown that the performance of laser inter-satellite links with dynamic beam waist is better than that with fixed beam waist.

Simulating binocular vision for no-reference 3D visual quality measurement.

Perceptual quality measurement of three-dimensional (3D) visual signals has become a fundamental challenge in 3D imaging fields. This paper proposes a novel no-reference (NR) 3D visual quality measurement (VQM) metric that uses simulations of the primary visual cortex (V1) of binocular vision. As the major technical contribution of this study, perceptual properties of simple and complex cells are considered for NR 3D-VQM. More specifically, the metric simulates the receptive fields of simple cells (one class of V1 neurons) using Gaussian derivative functions, and the receptive fields of complex cells (the other class of V1 neurons) using disparity energy responses and binocular rivalry responses. Subsequently, various quality-aware features are extracted from the primary visual cortex; these will change in the presence of distortions. Finally, those features are mapped to the subjective quality score of the distorted 3D visual signal by using support vector regression (SVR). Experiments on two publicly available 3D databases confirm the effectiveness of our proposed metric, compared to the relevant full-reference (FR) and NR metrics.

Effect of shikonin on multidrug resistance in HepG2: The role of SIRT1.

CONTEXT: Overexpression of SIRT1 is considered to enhance the resistance of HepG2 cells to irradiation. Shikonin, a naturally occurring naphthoquinone compound, displays anticancer effects and circumvents cancer drug resistance. OBJECTIVES: This study investigated the MDR reversal effect of shikonin induced by the overexpression of SIRT1. MATERIALS AND METHODS: The overexpression of SIRT1 in HepG2 cells was established by lentivirus infection. Five days after transduction, real-time quantitative polymerase chain reaction and western blotting were used to detect the expression of SIRT1 and MDR1/P-gp. Drug resistance was also evaluated by flow cytometry after rhodamine-123 staining. On day 5, the multidrug resistance cells were treated by shikonin (10(-7), 10(-6), and 10(-5) µmol/L) one time. The cell viability was detected by the MTT assay, and apoptosis was evaluated by Hoechst 33342 staining and caspase-3 activity 24 h after shikonin treatment. RESULTS: Overexpression of SIRT1 decreased rhodamine-123 staining and successfully produced the R-HepG2 cell line. Compared with HepG2, the expression of MDR1/P-gp mRNA (3.45 ± 0.35) and protein (1.40 ± 0.05) were both upregulated in R-HepG2. Shikonin inhibited cell viability (from 93.9 ± 2.1 to 66.7 ± 1.5%), induced apoptosis of R-HepG2 (apoptotic ratio from 3.5 ± 0.8 to 47.5 ± 2.7%, caspase-3 activity from 103.5 ± 1.9 to 329.2 ± 14.9%, respectively), downregulated the mRNA and protein expression of SIRT1 and MDR1/P-gp, and decreased rhodamin 123 efflux. DISCUSSION AND CONCLUSION: In the present study, we demonstrated that shikonin is able to overcome drug resistance in hepatocellular carcinoma cells, and the mechanism is related to the SIRT1-MDR1/P-gp signaling pathway.

Histone deacetylase inhibitor, 2-propylpentanoic acid, increases the chemosensitivity and radiosensitivity of human glioma cell lines in vitro.

BACKGROUND: Treatment for malignant glioma generally consists of cytoreductive surgery followed by radiotherapy and chemotherapy. In this study, we intended to investigate the effects of 2-propylpentanoic acid (VPA), a histone deacetylase inhibitor, on chemosensitivity and radiosensitivity in human glioma cell lines. METHODS: Human glioma cell lines, T98-G, and SF295, were treated with temozolomide (TMZ) or irradiation (IR), with or without VPA (1.0 mmol/L). Then, cytotoxicity and clonogenic survival assay was performed. Cell cycle stage, apoptosis, and autophagy were also detected using flow cytometry and dansyl monocadaverin (MDC) incorporation assay. One-way analysis of variance (ANOVA) and t-test were used to analyze the differences among variant groups. RESULTS: Mild cytotoxicity of VPA was revealed in both cell lines, T98-G and SF295, with the 50% inhibiting concentration (IC50) value of (3.85 ± 0.58) mmol/L and (2.15 ± 0.38) mmol/L, respectively; while the IC50 value of TMZ was (0.20 ± 0.09) mmol/L for T98-G and (0.08 ± 0.02) mmol/L for SF295. Moreover, if combined with VPA (1.0 mmol/L) for 96 hours, the sensitivity of glioma cells to TMZ was significant increased (P < 0.05). The surviving fractions at 2 Gy (SF2) of T98-G and SF295 cells exposed to IR alone were 0.52 and 0.58. However, when VPA was combined with IR, the SF2 of T98-G and SF295 dropped to 0.39 (P = 0.047) and 0.49 (P = 0.049), respectively. Treatment with VPA plus TMZ or IR also resulted in a significant decrease in the proportion of cells in the G2 phase and increased apoptotic rates as well as autophagy in T98-G and SF295 cell lines (P < 0.01). CONCLUSION: VPA may enhance the activities of TMZ and IR on glioma cells possibly through cell cycle block and promote autophagy, and thus could be a potential sensitizer of glioma treatment.

Clinical features and outcomes of head and neck castleman disease.

PURPOSE: To increase the understanding of head and neck Castleman disease (CD) and to improve its diagnosis and management. PATIENTS AND METHODS: A retrospective study was performed on the medical records of 14 patients with cervical CD treated at the Sun Yat-sen University Cancer Center from January 2000 through December 2009. The predictor variables were age, gender, site, size, and treatment modality. The outcome variables were survival time and recurrence. RESULTS: Neck level II (9/14) was the most common site for CD. On computed tomogram, all 14 cases appeared as nodular and cylindrical-shaped lesions growing along the neck. Computed tomogram showed a uniform density and clear margins of the lesions. Thirteen cases with hyaline-vascular type CD showed significant enhancement on enhancing computed tomographic scans. One case with plasma-cell type CD accompanied by Hodgkin lymphoma showed mild heterogeneous enhancement and a strong vascular shadow inside the lesion. Thirteen patients with unicentric CD underwent regional resection. Follow-up time ranged from 14 to 132 months, during which none of the patients relapsed. CONCLUSIONS: The results of this study suggest that head and neck CD has a low incidence and that the most common site is unilateral level II. Regional resection was the first choice for the treatment of unicentric CD. Overall, chemotherapy was associated with a poor prognosis in patients with multicentric CD. Future studies will focus on the early diagnosis and treatment of multicentric CD. Long-term follow-up is also necessary.

Inflammatory myofibroblastic tumor of the head and neck.

Inflammatory myofibroblastic tumor (IMT) is a rare benign neoplasm. The aim of this study was to enhance the understanding of head and neck IMT and to improve its diagnosis and management. Clinical features and related treatment of 10 IMT cases were retrospectively analyzed and the literature was reviewed. Tumor sites identified included four in the maxillary space, two in the buccal space, two in the parotid gland, one in the post aurem, and one in the neck. Nine of ten patients received local resection, and one of ten patients received a total maxillectomy. One patient had a local recurrence and died, while the other nine patients had no distant metastases and survived. A computed tomography (CT) exam performed on nine of the ten patients showed that six of these nine cases were heterogeneous in density, while the other three cases were homogeneous. Four cases showed marked heterogeneous enhancement, two cases showed mild heterogeneous enhancement, and three cases showed moderate homogeneous enhancement on contrast-enhanced CT images. The incidence of IMT in the head and neck is low, and local resection is currently the best treatment. A prolonged postoperative follow-up period is necessary for patients with IMT.

COX-2 Gene increases tongue cancer cell proliferation and invasion through VEGF-C pathway.

COX-2 induces the proliferation and invasion of oral squamous cell carcinoma. In the present study, the role of the COX-2 gene in the tongue cancer cell proliferation and invasion was investigated. A short hairpin RNA (shRNA)method was used to knock down COX-2 gene expression and investigate the relationship between COX-2 and VEGF-C, and the role of the COX-2 gene for proliferation and invasion was also investigated in the tongue cancer cell Tca8113. COX-2 gene overexpressed in tongue cancer cell line. Suppressing the expression of COX-2 by shRNA could decrease cell proliferation comparing with control shRNA. Nevertheless, depressing COX-2 gene expression by shRNA reduced VEGF-C expression on both mRNA and protein levels. VEGF-C gene expression could be regulated by COX-2 gene. Our results suggested that COX-2 played essential roles in the proliferation and metastasis of tongue cancer, and COX-2 could serve as a potential chemotherapy target for tongue cancer.

[Impacts on nutrient export by landscape heterogeneity based on sub-watershed].

Landscape features of a watershed are important factors affecting non-point source (NPS) pollution. Sub-watershed bounds were delineated and landscape heterogeneity was analyzed based on GIS and RS in Xitiaoxi watershed which located the upper reach of Taihu Lake area. Nutrient export intensity of sub-watersheds was estimated by revised export coefficient model. Then the relationships between nutrient export and main landscape types, as well as Shannon diversity index (SHDI) in sub-watershed units were analyzed. Results show, TN and TP export intensity have obvious spatial difference, which changed from 3.01 kg/(hm2 x a) to 15.44 kg/(hm2 x a) and 0.049 kg/(hm2 x a) to 0.355 kg/(hm2 x a) respectively. The dominated landscape types including cultivated land and forest land quantitatively related with nutrient export intensity. TN and TP export intensity will decrease 0.203 1 kg/(hm2 x a) and 0.0152 kg/(hm2 x a) respectively with 10% increased of forest area, and will increase 0.5726 kg/(hm2 x a) and 0.0273 kg/(hm2 x a) with 10% increased of cultivated land area. The relationship between nutrient export intensity and SHDI exhibited second-degree polynomial, export intensity increased by SHDI increasing and to maximum when SHDI equals 1.5, then decreased with SHDI increasing. This research results will provide an important reference value for NPS management.

Effects of the biological clock gene Bmal1 on tumour growth and anti-cancer drug activity.

The Bmal1 gene plays a key role in controlling circadian rhythms. To better understand how the Bmal1 gene affects tumour growth and the response to anti-cancer drugs, we examined the effect of knockdown of Bmal1 by RNAi both in vitro and in vivo. Down-regulation of Bmal1 gene expression accelerated cell proliferation in vitro and promoted tumour growth in mice. Suppressing Bmal1 expression in murine colon cancer cells (C26) and fibroblast cells (L929) decreased apoptosis induced by Etoposid, reduced the distribution of cells in the G2/M phases treated by Docetaxel and decreased DNA damage induced by Cisplatin. Loss of Bmal1 reduced the expression of per1, per2, per3, wee1 and p53. The expression of p21 and c-myc was also altered in certain cell lines. However, Bmal1 deficiency increased the protein levels of cdc2, cyclin B1, cyclin D1 and cyclin E. Wee1 and cyclin A expression was minimally altered. Thus, the circadian clock gene Bmal1 plays a role in regulating tumour cell apoptosis, cell-cycle progression and DNA damage response and in homoeostasis regulation. Down-regulation of Bmal1 accelerates the development of tumours and may influence the response to anti-cancer drugs.

Two-dimensional difference fluorescence gel electrophoresis to verify the scale-up of a non-affinity-based downstream process for isolation of a therapeutic recombinant antibody.

For therapeutic antibody production Protein A chromatography is often replaced by non-affinity-based purification sequences, which are considered as more economical. 2-D DIGE was applied for evaluation of scale-up of non-affinity based process of a humanized monoclonal antibody, anti-Rh(D) IgG(1), in comparison with other conventional analytical methods, like SDS-PAGE, Western blot, or SEC. Due to a high sensitivity of this technique (125 pg protein/spot) and high dynamic range of five orders of magnitude, low molecular weight impurities were detected in purified samples. Cation exchange chromatography was efficient capture step for IgG(1) purification in laboratory and pilot scale. The differences between samples after first purification step in laboratory and pilot scale were compensated with second purification step where almost the same protein pattern was observed. 2-D DIGE is a helpful tool for monitoring of purification effects and for scale-up verification of downstream processes.

Replacers of barcodes for small application areas by using grating dots to diffractively form bright points.

Although barcodes can be used to manage data conveniently, they cannot be applied to small areas. Therefore, pointcodes are used to overcome the issue in this article. A pointcode uses a pointcode pattern to encode data and uses a pointcode image to decode data. A pointcode pattern is composed of many grating dots with different specified grating pitches and grating orientations. Moreover, there are two grating-dot sizes generated. When a laser beam illuminates a pointcode pattern with correct illuminating conditions, a pointcode image corresponding to the hidden data is diffractively reconstructed. A pointcode image is composed of many bright points with different positions. There are two possible bright-point sizes generated. A bright point or two bright points at specified positions are used to denote a number. Small pointcode patterns are enough to diffractively form pointcode images.