User guides for biologists to learn computational methods

Journal of Microbiology - System-wide studies of a given molecular type are referred to as “omics.” These include genomics, proteomics, and metabolomics, among others. Recent...     

Platelet‐rich plasma inhibits osteoblast apoptosis and actin cytoskeleton disruption induced by gingipains through upregulating integrin β1

The aim of this study was to explore the effects of platelet‐rich plasma on gingipain‐caused changes in cell morphology and apoptosis of osteoblasts. Mouse osteoblasts MC3T3‐E1 cells were treated with gingipain extracts from Porphyromonas gingivalis in the presence or absence of platelet‐rich plasma. Apoptosis was detected with terminal deoxynucleotidyl transferase‐mediated dUTP nick‐end labeling staining. F‐actin was determined by phalloidin‐fluorescent staining and observed under confocal microscopy. Western blot analysis was used to detect integrin β1, F‐actin, and G‐actin protein expressions. A knocking down approach was used to determine the role of integrin β1. The platelet‐rich plasma protected osteoblasts from gingipain‐induced apoptosis in a dose‐dependent manner, accompanied by upregulation of integrin β1. Platelet‐rich plasma reversed the loss of F‐actin integrity and decrease of F‐actin/G‐actin ratio in osteoblasts in the presence of gingipains. By contrast, the effects of platelet‐rich plasma were abrogated by knockdown of integrin β1. The platelet‐rich plasma failed to reduce cell apoptosis and reorganize the cytoskeleton after knockdown of integrin β1. In conclusion, platelet‐rich plasma inhibits gingipain‐induced osteoblast apoptosis and actin cytoskeleton disruption by upregulating integrin β1 expression.     

Astragaloside IV alleviates atherosclerosis through targeting circ_0000231/miR-135a-5p/CLIC4 axis in AS cell model in vitro

Molecular and Cellular Biochemistry - Non-coding RNAs (ncRNAs) have shown to act as crucial mediators in atherosclerosis (AS) development. The purpose of our study was to explore the role of...     

Platycodin D Inhibits β-Amyloid-Induced Inflammation and Oxidative Stress in BV-2 Cells Via Suppressing TLR4/NF-κB Signaling Pathway and Activating Nrf2/HO-1 Signaling Pathway

Neurochemical Research - Alzheimer’s disease (AD) is a common neurodegenerative disease associated with deposition of β-amyloid peptide (Aβ). Platycodin D (PLD), a...     

Suppression of DRR1 results in the accumulation of insoluble ubiquitinated proteins,which impairs drought stress tolerance

Drought stress has detrimental effects on plants. Although the abscisic acid (ABA)‐mediated drought response is well established, defensive mechanisms to cope with dehydration‐induced proteotoxicity have been rarely studied. DRR1 was identified as an Arabidopsis drought‐induced gene encoding an ER‐localized RING‐type E3 Ub ligase. Suppression of DRR1 markedly reduced tolerance to drought and proteotoxic stress without altering ABA‐mediated germination and stomatal movement. Proteotoxicity‐ and dehydration‐induced insoluble ubiquitinated protein accumulation was more obvious in DRR1 loss‐of‐function plants than in wild‐type plants. These results suggest that DRR1 is involved in an ABA‐independent drought stress response possibly through the mitigation of dehydration‐induced proteotoxic stress.     

Evaluation of the efficacy and safety of hydroxychloroquine in comparison with chloroquine in moderate and severe patients with COVID-19

Science China Life Sciences -     

ARL4C might serve as a prognostic factor and a novel therapeutic target for gastric cancer: bioinformatics analyses and biological experiments

The ADP-ribosylation factor-like proteins (ARLs) have been proved to regulate the malignant phenotypes of several cancers. However, the exact role of ARLs in gastric cancer (GC) remains elusive. In this study, we systematically investigate the expression status, interactive relations, potential pathways, genetic variations and clinical values of ARLs in GC. We find that ARLs are significantly dysregulated in GC and involved in various cancer-related pathways. Subsequently, machine learning models identify ARL4C as one of the two most significant clinical indicators among ARLs for GC. Furthermore, ARL4C silencing remarkably inhibits the growth and metastasis of GC cells both in vitro and in vivo. Moreover, enrichment analysis indicates that ARL4C is highly correlated with TGF-β1 signalling. Correspondingly, TGF-β1 treatment dramatically increases ARL4C expression and ARL4C knockdown inhibits the phosphorylation level of Smads, downstream factors of TGF-β1. Meanwhile, the coexpression of ARL4C and TGF-β1 worsens the prognosis of GC patients. Our work comprehensively demonstrates the crucial role of ARLs in the carcinogenesis of GC and the specific mechanisms underlying the GC-promoting effects of TGF-β1. More importantly, we uncover the great promise of ARL4C-targeted therapy in improving the efficacy of TGF-β1 inhibitors for GC patients.     

Characteristics of Refractive-Index Sensor in Graphene-Modified Long-Range Surface Exciton-Polaritons

The organic non-crystalline medium of 5,6-dichloro-2-[[5,6-dichloro-1-ethyl-3-(4-sulfobutyl)-benzimidazol-2-ylidene]-propenyl]-1-ethyl-3-(4-sulfobutyl)-benzimidazolium hydroxide (TDBC) is emerging as possible alternative plasmonic material for noble metal in visible region. In this paper, a novel long-range surface exciton-polariton (LRSEP) sensor based on TDBC film covered with graphene is reported. To enhance the imaging sensitivity, the thickness of TDBC film and the number of graphene layers are optimized. The result shows that the optimized imaging sensitivity is enhanced to 3243 RIU⁻¹ when n_s = 1.34. Compared with the traditional noble metal film-based sensor, the proposed LRSEP sensor demonstrates that the imaging sensitivity has been greatly improved. This is the first study of the TDBC film-based LRSEP sensor, which we hope to support the potential development of chemical sensing and bio-sensing.

     

ROI-Based Compression Strategy of 3D MRI Brain Datasets for Wireless Communications

ObjectivesBecause of the large amount of medical imaging data, the transmission process becomes complicated in telemedicine applications. Thus, in order to adapt the data bit streams to the constraints related to the limitation of the bandwidths a reduction of the size of the data by compression of the images is essential. Despite the improvements in the field of compression, the transmission itself can also introduce errors. For this reason, it is important to develop an adequate strategy which will help reduce this volume of data without having to introduce some distortion and resist the errors introduced by the channel noise during transmission. Thus, in this paper, we propose a ROI-based coding strategy and unequal bit stream protection to meet this dual constraint.Material and methodsThe proposed ROI-based compression strategy with unequal bit stream protection is composed of three parts: the first one allows the extraction of the ROI region, the second one consists of a ROI-based coding and the third one allows an unequal protection of the ROI bit stream.First, the Regions Of Interest (ROI) are extracted by hierarchical segmentation of these regions according to a segmentation method based on the technique of Marker-based-watershed combined with the technique of active contours by level set. The resulting regions are selectively encoded by a 3D coder based on a shape adaptive discrete wavelet transform 3D-BISK, where the compression ratio of each region depends on its relevance in diagnosis. These obtained regions of interest are protected with an error-correcting code of Reed-Solomon type with a code rate that varies according to the relevance of the region by an unequal protection strategy (UEP).ResultsThe performance of the proposed compression scheme is evaluated in several ways. First, tests are performed to study the impact of errors on the different bit streams. In the first place, these tests are carried out in order to study the effect of the variation of the compression rates on the different bit streams. Secondly, different Reed Solomon error-correcting codes of different code rates are tested at different compression rates on a BSC channel. Finally, the performances of this coding strategy are compared with those of SPIHT 3D in the case of transmission on a BSC channel.ConclusionThe obtained results show that the proposed method is quite efficient in transmission time reduction. Therefore, our proposed scheme will reduce the volume of data without having to introduce some distortion and resist the errors introduced by the channel noise in the case of telemedicine.