Using cellular automata images and pseudo amino acid composition to predict protein subcellular location

The avalanche of newly found protein sequences in the post-genomic era has motivated and challenged us to develop an automated method that can rapidly and accurately predict the localization of an uncharacterized protein in cells because the knowledge thus obtained can greatly speed up the process in finding its biological functions. However, it is very difficult to establish such a desired predictor by acquiring the key statistical information buried in a pile of extremely complicated and highly variable sequences. In this paper, based on the concept of the pseudo amino acid composition (Chou, K. C. PROTEINS: Structure, Function, and Genetics, 2001, 43: 246–255), the approach of cellular automata image is introduced to cope with this problem. Many important features, which are originally hidden in the long amino acid sequences, can be clearly displayed through their cellular automata images. One of the remarkable merits by doing so is that many image recognition tools can be straightforwardly applied to the target aimed here. High success rates were observed through the self-consistency, jackknife, and independent dataset tests, respectively.

Using complexity measure factor to predict protein subcellular location

Recent advances in large-scale genome sequencing have led to the rapid accumulation of amino acid sequences of proteins whose functions are unknown. Because the functions of these proteins are closely correlated with their subcellular localizations, it is vitally important to develop an automated method as a high-throughput tool to timely identify their subcellular location. Based on the concept of the pseudo amino acid composition by which a considerable amount of sequence-order effects can be incorporated into a set of discrete numbers (Chou, K. C., Proteins: Structure, Function, and Genetics, 2001, 43: 246-255), the complexity measure approach is introduced. The advantage by incorporating the complexity measure factor as one of the pseudo amino acid components for a protein is that it can more effectively reflect its overall sequence-order feature than the conventional correlation factors. With such a formulation frame to represent the samples of protein sequences, the covariant-discriminant predictor (Chou, K. C. and Elrod, D. W., Protein Engineering, 1999, 12: 107-118) was adopted to conduct prediction. High success rates were obtained by both the jackknife cross-validation test and independent dataset test, suggesting that introduction of the concept of the complexity measure into prediction of protein subcellular location is quite promising, and might also hold a great potential as a useful vehicle for the other areas of molecular biology.

Using pseudo amino acid composition to predict protein subcellular location: Approached with Lyapunov index, Bessel function, and Chebyshev filter

With the avalanche of new protein sequences we are facing in the post-genomic era, it is vitally important to develop an automated method for fast and accurately determining the subcellular location of uncharacterized proteins. In this article, based on the concept of pseudo amino acid composition (Chou, K.C. Proteins: Structure, Function, and Genetics, 2001, 43: 246-255), three pseudo amino acid components are introduced via Lyapunov index, Bessel function, Chebyshev filter that can be more efficiently used to deal with the chaos and complexity in protein sequences, leading to a higher success rate in predicting protein subcellular location.

Damage-tolerant nanotwinned metals with nanovoids under radiation environments

Material performance in extreme radiation environments is central to the design of future nuclear reactors. Radiation induces significant damage in the form of dislocation loops and voids in irradiated materials, and continuous radiation often leads to void growth and subsequent void swelling in metals with low stacking fault energy. Here we show that by using in situ heavy ion irradiation in a transmission electron microscope, pre-introduced nanovoids in nanotwinned Cu efficiently absorb radiation-induced defects accompanied by gradual elimination of nanovoids, enhancing radiation tolerance of Cu. In situ studies and atomistic simulations reveal that such remarkable self-healing capability stems from high density of coherent and incoherent twin boundaries that rapidly capture and transport point defects and dislocation loops to nanovoids, which act as storage bins for interstitial loops. This study describes a counterintuitive yet significant concept: deliberate introduction of nanovoids in conjunction with nanotwins enables unprecedented damage tolerance in metallic materials.

Using cellular automata to generate image representation for biological sequences

A novel approach to visualize biological sequences is developed based on cellular automata (Wolfram, S. Nature 1984, 311, 419-424), a set of discrete dynamical systems in which space and time are discrete. By transforming the symbolic sequence codes into the digital codes, and using some optimal space-time evolvement rules of cellular automata, a biological sequence can be represented by a unique image, the so-called cellular automata image. Many important features, which are originally hidden in a long and complicated biological sequence, can be clearly revealed thru its cellular automata image. With biological sequences entering into databanks rapidly increasing in the post-genomic era, it is anticipated that the cellular automata image will become a very useful vehicle for investigation into their key features, identification of their function, as well as revelation of their "fingerprint". It is anticipated that by using the concept of the pseudo amino acid composition (Chou, K.C. Proteins: Structure, Function, and Genetics, 2001, 43, 246-255), the cellular automata image approach can also be used to improve the quality of predicting protein attributes, such as structural class and subcellular location.

Ferulic acid induces heme oxygenase-1 via activation of ERK and Nrf2

This study investigated the effect of ferulic acid (FA) on the up-regulation of heme oxygenase-1 (HO-1) in lymphocytes and the molecular mechanisms involved. Lymphocytes were treated with FA (0.001-0.1 μM) for certain times. Cell viability, the activity and level of expression of HO-1, and signal pathways were analyzed. FA significantly upregulated HO-1 expression both at the level of mRNA and protein in lymphocytes. Moreover, FA induced NF-E2-related factor (Nrf2) nuclear translocation and transcriptional activity, which is upstream of FA induced HO-1 expression. In addition, lymphocytes treated with FA exhibited activation of extracellular regulated kinase (ERK) and treatments with U0126 (an ERK kinase inhibitor) attenuated the FA induced activation of Nrf2, resulting in a decrease in HO-1 expression. Zinc protoporphyrin (ZnPP, a HO-1 inhibitor) markedly suppressed cytoprotection from radiation-induced cell damage by FA. Results suggested that the ERK signaling pathway controlled the anti-oxidation of FA by regulating the expression of the antioxidant enzyme HO-1.

Characterizing the boundary lateral to the shear direction of deformation twins in magnesium

The three-dimensional nature of twins, especially the atomic structures and motion mechanisms of the boundary lateral to the shear direction of the twin, has never been characterized at the atomic level, because such boundary is, in principle, crystallographically unobservable. We thus refer to it here as the dark side of the twin. Here, using high-resolution transmission electron microscopy and atomistic simulations, we characterize the dark side of deformation twins in magnesium. It is found that the dark side is serrated and comprised of coherent twin boundaries and semi-coherent twist prismatic–prismatic boundaries that control twin growth. The conclusions of this work apply to the same twin mode in other hexagonal close-packed materials, and the conceptual ideas discussed here should hold for all twin modes in crystalline materials.

Twin propagation involves three-dimensional normal, forward and lateral motion of twin interfaces with respect to the twinning shear direction. Here, the authors combine electron microscopy and atomistic simulations to study the until now unknown lateral structure of tensile deformation twins in magnesium.

In vivo targeted delivery of CD40 shRNA to mouse intestinal dendritic cells by oral administration of recombinant Sacchromyces cerevisiae

Short hairpin RNA (shRNA)-mediated gene regulation is a commonly used technique for gene manipulation. An efficient and safe delivery system is indispensable when shRNA is delivered into living organisms for gene therapy. Previous studies have proved that DNA and protein can be delivered into dendritic cells (DCs) by non-pathogenic Saccharomyces cerevisiae without being degraded. CD40 is closely related to apoptosis of tumor cells and some immune mechanisms. In this study, we demonstrated that recombinant yeast S. cerevisiae efficiently delivered the shRNA of immune-associated gene (CD40) into mouse intestinal DCs via oral administration. Western blot analysis of isolated intestinal DCs indicated that the inhibition of CD40 gene expression reached up to 56-91%. The secretion of cytokines such as interleukin-2 (IL-2), IL-6, IL-10, IL-12, tumor necrosis factor-α and interferon-γ in intestinal DCs had varying degrees of changes. In conclusion, we found that orally administered recombinant yeast can be used as an efficient shRNA delivery system for intestinal DC-specific gene silencing and immunomodulation in vivo.

Prevalence and cardiovascular risk factors of asymptomatic intracranial arterial stenosis: the Kongcun Town Study in Shandong, China

BACKGROUND AND PURPOSE

This study was to investigate the prevalence and cardiovascular risk factors (CRFs) of asymptomatic intracranial atherosclerotic stenosis (aICAS) amongst middle-aged and older adults living in rural communities in China.

METHODS

This population-based study included 2019 subjects (aged ≥40 years, 52.3% women) who were free of stroke and living in rural communities in China. From October 2017 to May 2018, data on demographics, CRFs and health conditions were collected through face-to-face interviews, physical examination and laboratory tests. Asymptomatic ICAS was detected through a two-phase procedure: a screening phase with transcranial Doppler ultrasound, followed by a diagnostic phase with magnetic resonance angiography examination. Multivariable logistic regression models were used to analyse CRFs associated with aICAS.

RESULTS

Of the 2019 participants, aICAS was detected in 153 persons. The overall prevalence of aICAS was 7.6%, and the prevalence of moderate-to-severe aICAS was 5.0%. The multi-adjusted odds ratio (95% confidence interval) of aICAS associated with CRFs was 2.40 (1.56-3.69) for hypertension, 1.91 (1.32-2.76) for high hypersensitive C-reactive protein, 1.68 (1.14-2.49) for diabetes and 1.61 (1.08-2.41) for overweight or obesity. When these four CRFs were aggregated, compared with participants without any of these factors, the multi-adjusted odds ratios (95% confidence interval) of aICAS for persons concurrently having one, two and three or more of these factors were 1.14 (0.52-2.48), 2.91 (1.42-5.99) and 5.51 (2.64-11.50), respectively (P for linear trend <0.001).

CONCLUSIONS

Asymptomatic ICAS is common amongst rural-dwelling middle-aged and older Chinese people. Hypertension, diabetes, overweight or obesity and high hypersensitive C-reactive protein, especially when coexisting, are strongly associated with aICAS.

A proposed computer diagnostic system for malignant melanoma (CDSMM)

This paper describes a computer diagnostic system for malignant melanoma. The diagnostic system is a rule base system based on image analyses and works under the PC windows environment. It consists of seven modules: I/O module, Patient/Clinic database, image processing module, classification module, rule base module and system control module. In the system, the image analyses are automatically carried out, and database management is efficient and fast. Both final clinic results and immediate results from various modules such as measured features, feature pictures and history records of the disease lesion can be presented on screen or printed out from each corresponding module or from the I/O module. The system can also work as a doctor's office-based tool to aid dermatologists with details not perceivable by the human eye. Since the system operates on a general purpose PC, it can be made portable if the I/O module is disconnected.

A triple-classification radiomics model for the differentiation of pleomorphic adenoma, Warthin tumour, and malignant salivary gland tumours on the basis of diffusion-weighted imaging

AIM

To develop and validate a triple-classification radiomics model for the preoperative differentiation of pleomorphic adenoma (PA), Warthin tumour (WT), and malignant salivary gland tumour (MSGT) based on diffusion-weighted imaging (DWI).

MATERIALS AND METHODS

Data from 217 patients with histopathologically confirmed salivary gland tumours (100 PAs, 68 WTs, and 49 MSGTs) from January 2015 to March 2019 were analysed retrospectively and divided into a training set (n=173), and a validation set (n=44). A total of 396 radiomic features were extracted from the DWI of all patients. Analysis of variance (ANOVA) and least absolute shrinkage and selection operator (LASSO) regression were used to select radiomic features, which were then constructed using three classification models, namely, logistic regression method (LR), support vector machine (SVM), and K-nearest neighbor (KNN). The diagnostic performance of the radiomics model was quantified by the receiver operating characteristic (ROC) curve and area under the ROC curve (AUC) of the training and validation data sets.

RESULTS

The 20 most valuable features were investigated based on the LASSO regression. LR and SVM methods exhibited better diagnostic ability than KNN for multiclass classification. LR and SVM had the best performance and yielded the AUC values of 0.857 and 0.824, respectively, in the training data set and the AUC values of 0.932 and 0.912, respectively, in the validation data set of MSGT diagnosis.

CONCLUSION

DWI-based triple-classification radiomics model has predictive value in distinguishing PA, WT, and MSGT, which can be used for preoperative auxiliary diagnosis in clinical practice.

Single crystalline nanostructures of topological crystalline insulator SnTe with distinct facets and morphologies

Topological crystalline insulators (TCIs) are a new class of topological materials that possess unique metallic surface states protected by crystalline mirror symmetry. Their topological surface properties are expected to strongly depend on the surface orientation. By combining density functional theory (DFT) calculations and synthesis experiments, we demonstrate the controlled growth of single crystalline nanostructures of the prototypical TCI SnTe with distinct facets and morphologies. Our calculations suggest that the excess energy of the {111} surfaces can be either higher or lower than that of the {100} surfaces, depending on the stoichiometry, while the {110} is always higher than the {100}. In our synthesis experiment, we qualitatively controlled the stoichiometry by tailoring the growth temperature and obtained two types of single crystalline nanowires: smooth nanowires dominated by {100} facets at high temperatures and zigzag nanowires composed of both {100} and {111} surfaces at low temperatures. Notably, there is no {110} facet in our nanostructures, strongly supporting the DFT calculations. Our device fabrication and electrical characterizations suggest that both types of nanowires are suitable for transport studies of topological surface states.

Association of Toll like receptor 9 expression with lymph node metastasis in human breast cancer

The toll like receptor 9(TLR9) has been suggested to play an important role in the invasion and metastasis of cancer cells in vitro. However, the expression of TLR9 in human cancer specimens has never been characterized. In this study, we investigated the expression of TLR9 in breast cancer specimens and determined the association between its expression and the clinicopathological features observed. We found that TLR9 expression was significantly higher in patients with breast cancers displaying large tumor size (P = 0.040), lymph node metastasis (P < 0.001) or advanced pathological stage (P = 0.006). TLR9 expression was also increased in ER negative breast cancer specimens (P = 0.043). Logistic regression analysis revealed that pathological stage (P = 0.007) and TRL9 (P = 0.001) expression were independent factors that influenced axillary lymph node metastasis of breast cancer. Patients with positive TLR9 expression had a higher progress free survival compared with the TLR9-negative cohort (P = 0.037). Therefore we concluded that Lymph node metastasis more likely occur in breast cancer patients with a positive TLR9 status and its expression might serve as an indicator of poor prognosis in patients with breast cancer.

Layer-by-Layer Assembly of Lipid Nanobubbles on Microneedles for Ultrasound-Assisted Transdermal Drug Delivery

Microneedles as a typical device for transdermal drug delivery provide an alternative route for drug administration with minimal digestion by organs and better patient compliance. However, diffusion of passively released drug molecules within the skin tissue mainly depends on the interstitial fluid, which may be affected by different physiological conditions of individuals. Herein, we propose a nanobubble-modified microneedle patch for ultrasound-assisted drug delivery, which provides additional driving force for penetration and diffusion of the drug molecules. Layer-by-layer self-assembled drug-containing nanobubbles on the surfaces of microneedles trigger active drug release upon application of ultrasound. The concomitant microstreaming caused by cavitation effects facilitates the penetration and diffusion of drug molecules in the gelatin gel model and the ex vivo porcine skin model. The proposed drug delivery strategy holds great promise for rapid transdermal drug delivery with enhanced penetration and diffusion of the released drugs.

Ectopic thymic carcinoma of the parotid gland

Ectopic thymic carcinoma (ETC) of the parotid gland is a rare entity. This report describes the case of a 52-year-old man with a painless mass in the right parotid gland. Magnetic resonance imaging (MRI) showed a biphasic mass consisting of a central segment and a peripheral segment. The patient underwent a superficial parotidectomy, and point-to-point correspondence sampling for analysis based on MRI findings was performed. The pathological finding was ETC, and there was an excellent association between MRI characteristics and histopathological findings. Subsequently, the patient underwent postoperative radiation therapy. At the 9-month follow-up, he had recovered well without facial paralysis, and there was no evidence of recurrence or metastasis. This report describes the clinical, radiological, and pathological features of the ETC.

High-Cholesterol Diet Disrupts the Levels of Hormones Derived from Anterior Pituitary Basophilic Cells

Emerging evidence shows that elevated cholesterol levels are detrimental to health. However, it is unclear whether there is an association between cholesterol and the pituitary. We investigated the effects of a high-cholesterol diet on pituitary hormones using in vivo animal studies and an epidemiological study. In the animal experiments, rats were fed a high-cholesterol or control diet for 28 weeks. In rats fed the high-cholesterol diet, serum levels of thyroid-stimulating hormone (TSH; also known as thyrotrophin), luteinising hormone (LH) and follicle-stimulating hormone (FSH) produced by the basophilic cells of the anterior pituitary were elevated in a time-dependent manner. Among these hormones, TSH was the first to undergo a significant change, whereas adrenocorticotrophic hormone (ACTH), another hormone produced by basophilic cells, was not changed significantly. As the duration of cholesterol feeding increased, cholesterol deposition increased gradually in the pituitary. Histologically, basophilic cells, and especially thyrotrophs and gonadotrophs, showed an obvious increase in cell area, as well as a potential increase in their proportion of total pituitary cells. Expression of the β-subunit of TSH, FSH and LH, which controls hormone specificity and activity, exhibited a corresponding increase. In the epidemiological study, we found a similar elevation of serum TSH, LH and FSH and a decrease in ACTH in patients with hypercholesterolaemia. Significant positive correlations existed between serum total cholesterol and TSH, FSH or LH, even after adjusting for confounding factors. Taken together, the results of the present study suggest that the high-cholesterol diet affected the levels of hormones derived from anterior pituitary basophilic cells. This phenomenon might contribute to the pituitary functional disturbances described in hypercholesterolaemia.

Ncor1 Deficiency Promotes Osteoclastogenesis and Exacerbates Periodontitis

Nuclear receptor corepressor 1 (Ncor1) has been reported to regulate different transcription factors in different biological processes, including metabolism, inflammation, and circadian rhythms. However, the role of Ncor1 in periodontitis has not been elucidated. The aims of the present study were to investigate the role of Ncor1 in experimental periodontitis and to explore the underlying mechanisms through an experimental periodontitis model in myeloid cell-specific Ncor1-deficient mice. Myeloid cell-specific Ncor1 knockout (MNKO) mice were generated, and experimental periodontitis induced by ligation using 5-0 silk sutures was established. Ncor1 flox/flox mice were used as littermate controls (LC). Histological staining and micro-computed tomography scanning were used to evaluate osteoclastogenesis and alveolar bone resorption. Flow cytometry was conducted to observe the effect of Ncor1 on myeloid cells. RNA sequencing was used to explore the differentially targeted genes in osteoclastogenesis in the absence of Ncor1. Coimmunoprecipitation (Co-IP), chromatin immunoprecipitation (ChIP) experiments, and dual luciferase assays were performed to explore the relationship between NCoR1 and the targeted gene. Alveolar bone resorption in the MNKO mice was significantly greater than that in the LC mice after periodontitis induction and osteoclastogenesis in vitro. The percentage of CD11b+ cells, particularly CD11b+ Ly6G+ neutrophils, was substantially higher in gingival tissues in the MNKO mice than in the LC mice. Results of RNA sequencing demonstrated that CCAAT enhancer binding protein α (Cebpα) was one of the most differentially expressed genes between the MNKO and LC groups. Mechanistically, Co-IP assays, ChIP experiments, and dual luciferase assays revealed that NCOR1 interacted with peroxisome proliferator-activated receptor gamma (PPARγ) and cooperated with HDAC3 to control the transcription of Cebpα. In conclusion, Ncor1 deficiency promoted osteoclast and neutrophil formation in mice with experimental periodontitis. It regulated the transcription of Cebpα via PPARγ to promote osteoclast differentiation.

A nanoparticle-containing polycaprolactone implant for combating post-resection breast cancer recurrence

The recurrence and metastasis of tumor after surgery is the main cause of death for patients with breast cancer. Systemic chemotherapy suffered from low delivery efficiency to tumors and the side effects of chemo drugs. Localized chemotherapy using drug-containing implants is an alternative, while the reconstruction of breast tissue is generally considered after chemotherapy, resulting in a second surgery for patients. Here, we describe a strategy using implantable drug-containing polymeric scaffolds to deliver chemo drugs directly to the post-resection site, and simultaneously provide mechanical support and regenerative niche for breast tissue reconstruction. When doxorubicin was loaded in mesoporous silica nanoparticles and subsequently incorporated into polycaprolactone scaffolds (DMSN@PCL), a 9-week sustained drug release was achieved post implantation in mice. The local recurrence of residual tumor after surgery was significantly inhibited within 4 weeks in a post-surgical mouse model bearing xenograft MDA-MB-231 tumor. DMSN@PCL scaffolds exhibited good biocompatibility in mice during the treatment. We believe our strategy holds great promise as an adjuvant localized chemotherapy in clinics for combating post-resection breast cancer recurrence.

An observational analysis of insulinoma from a single institution

BACKGROUND

Insulinoma is the commonest functioning pancreatic neuroendocrine tumor causing hyperinsulinemic hypoglycemia.

AIM

This study is aimed to evaluate the clinical features, preoperative laboratory and imaging diagnosis and pathologic findings of insulinoma.

METHODS

Data of the patients from 2001 to 2016 diagnosed as insulinoma in Tongji Hospital, China were retrospectively extracted and analyzed.

RESULTS

A total of 40 patients were diagnosed as insulinoma with a male/female ratio of 0.68:1. The median onset age was 46.5 years. Nearly all the included patients presented neurological symptoms and 60% presented autonomic symptoms. More than 95% of the patients met the functional European Neuroendocrine Tumor Society criteria including glucose, insulin and C-peptide levels. The preoperative detection rates of ultrasonography, enhanced computed tomography, magnetic resonance imaging, and endoscopic ultrasonography were 60.50%, 84.95%, 80% and 83.3% respectively. The joint imaging examinations can markedly increase the detection rate. The mean tumor size was 1.89 ± 0.72 cm. Ki-67 index by histopathological diagnosis were all less than 20%. The positive rates of insulin, synaptophysin and chromogranin A were close to 100%.

CONCLUSION

Laboratory tests of glucose, insulin and C-peptide are reliable for preoperative diagnosis. Combination of the imaging examinations can improve the diagnosis.

Live-cell and super-resolution imaging reveal that the distribution of wall-associated protein A is correlated with the cell chain integrity of Streptococcus mutans

Streptococcus mutans is a primary pathogen responsible for dental caries. It has an outstanding ability to form biofilm, which is vital for virulence. Previous studies have shown that knockout of Wall-associated protein A (WapA) affects cell chain and biofilm formation of S. mutans. As a surface protein, the distribution of WapA remains unknown, but it is important to understand the mechanism underlying the function of WapA. This study applied the fluorescence protein mCherry as a reporter gene to characterize the dynamic distribution of WapA in S. mutans via time-lapse and super-resolution fluorescence imaging. The results revealed interesting subcellular distribution patterns of WapA in single, dividing and long chains of S. mutans cells. It appears at the middle of the cell and moves to the poles as the cell grows and divides. In a cell chain, after each round of cell division, such dynamic relocation results in WapA distribution at the previous cell division sites, resulting in a pattern where WapA is located at the boundary of two adjacent cell pairs. This WapA distribution pattern corresponds to the breaking segmentation of wapA deletion cell chains. The dynamic relocation of WapA through the cell cycle increases our understanding of the mechanism of WapA in maintaining cell chain integrity and biofilm formation.