Vol.45, No.6, 2021-Table of Contents

On the Cover


Gene signatures associated with clinical traits identified by Weighted gene coexpression network analysis (WGCNA) guide the recent development of biomarkers for the diagnosis and function mechanism exploration of cancers. A 9-gene signature related to both stemness index (mRNAsi) and prognosis of hepatocellular carcinoma (HCC) is identified, which may control the metastasis and drug resistance in HCC.
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  • A novel nine gene signature integrates stemness characteristics associated with prognosis in hepatocellular carcinoma
  • Abstract Cancer stem cells (CSCs) are heterogeneous with self-renewal and differentiation ability. The mRNA expression-based stemness index (mRNAsi) described the similarity between tumor cells and CSCs, which is positively associated with the poor prognosis of cancer patients. However, the key prognostic genes related to mRNAsi in hepatocellular carcinoma (HCC) remains unclear. A 9-gene signature related to mRNAsi and HCC prognosis including PSMG3, SNRPD1, DTYMK, PIGU, NME1, TXNL4A, IPO4, PES1, and REXO4 was obtained. High expression of this signature indicates poor prognosis of HCC. PIGU was an independent prognostic factor of HCC, which was significantly associated with progression of HCC. Among them,… More
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  • Real-Time analysis of exosome secretion of single cells with single molecule imaging
  • Abstract The exosome-mediated response can promote or restrain the diseases by regulating the intracellular pathways, making the exosome become an effective marker for diagnosis and therapeutic control at the single-cell level. However, real-time analysis is hard to be achieved with traditional approaches because the exosomes usually need to be enriched by ultracentrifugation for a measurable signal-to-noise ratio. Recently developed label-free single-molecule imaging approaches may become an real-time quantitative tool for the analysis of single exosomes and related secretion behaviors of single living cells owing to their extreme sensitivity. More
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  • Implications of enolase in the RANKL-mediated osteoclast activity following spinal cord injury
  • Abstract Spinal Cord Injury (SCI) is a debilitating condition characterized by damage to the spinal cord, resulting in loss of function, mobility, and sensation. Although increasingly prevalent in the US, no FDA-approved therapy exists due to the unfortunate complexity of the condition, and the difficulties of SCI may be furthered by the development of SCI-related complications, such as osteoporosis. SCI demonstrates two crucial stages for consideration: the primary stage and the secondary stage. While the primary stage is suggested to be immediate and irreversible, the secondary stage is proposed as a promising window of opportunity for therapeutic intervention. Enolase, a metabolic… More
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  • Proteogenomics for pediatric brain cancer
  • Abstract Pediatric central nervous system tumors are the most common tumors in children, it constitute 15%–20% of all malignancies in children and are the leading cause of cancer related deaths in children. Proteogenomics is an emerging field of biological research that utilizes a combination of proteomics, genomics, and transcriptomics to aid in the discovery and identification of biomarkers for diagnosis and therapeutic purposes. Integrative proteogenomics analysis of pediatric tumors identified underlying biological processes and potential treatments as well as the functional effects of somatic mutations and copy number variation driving tumorigenesis. More
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  • Delineating the role of phytocompounds against anti-bacterial drug resistance–An update
  • Abstract Antibacterial resistance developed by bacteria due to the unlimited use of antibiotics has posed a challenge for human civilization. This kind of problem is not limited to India only, but it is a global concern. Nowadays, many treatments and medicines for bacterial diseases have been developed. However, they possess some drawbacks. Therefore, the alternative medicine has been used to target the drug resistant mechanisms and such medicines have less side effects which is becoming necessary. Natural products have traditionally or historically been of importance for the development of antibacterial agents and are also known to overcome bacterial drug resistance by… More
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  • Nanoscale interactions between the nicotinic acetylcholine receptor and cholesterol
  • Abstract Cholesterol is a major lipid in biological membranes. It not only plays a structural role but also modulates a wide range of functional properties of neurotransmitter and hormone receptors and ion channels. The membraneembedded segments of the paradigm neurotransmitter receptor for acetylcholine (nAChR) contain linear sequences of amino acids with the capacity to recognize cholesterol. These cholesterol consensus domains have been designated as “CARC” and its mirror sequence “CRAC”. CARC preferentially occurs in the exoplasmic-facing membrane leaflet, and CRAC, in the cytoplasmic-facing hemilayer. Both motifs are highly conserved among ion-channel and neurotransmitter receptor proteins in vertebrate nervous systems, where they… More
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  • Role of GM3 ganglioside in the pathology of some progressive human diseases and prognostic importance of serum anti-GM3 antibodies
  • Abstract Glycosphingolipids (gangliosides) have been characterized as important biological molecules with a key role as regulators in many physiological processes on cellular, tissue, organ, and organism levels. The deviations in their normal amounts, production, and metabolism are very often related to the development of many multi-factor socially important diseases. GM3 ganglioside, as a small molecule, plays important roles in the cascade regulatory pathways in the pathology of many disorders like neurodegenerative diseases, autoimmune diseases, inflammation, diabetes, malignant transformation, and others. Ganglioside GM3 and its derivatives are membrane-bound glycosphingolipids composed of an oligosaccharide head structure containing one sialic acid residue. These molecules… More
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  • Viral integration detection strategies and a technical update on Virus-Clip
  • Abstract Oncovirus infection is crucial in human malignancies. Certain oncoviruses can lead to structural variations in the human genome known as viral genomic integration, which can contribute to tumorigenesis. Existing viral integration detection tools differ in their underlying algorithms pinpointing different aspects or features of viral integration phenomenon. We discuss about major procedures in performing viral integration detection. More importantly, we provide a technical update on Virus-Clip to facilitate its usage on the latest human genome builds (hg19 and hg38) and the adoption of multi-thread mode for faster initial read alignment. By comparing the execution of Virus-Clip using single-thread and multi-thread… More
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  • Targeted editing of intronic-splicing silencer enhancement of SMN2 Exon 7 inclusion by CRISPR/Case 9
  • Abstract Spinal muscular atrophy (SMA) is an autosomal recessive hereditary neuromuscular disease. Exon 7 and 8 of survival of motor neuron 1 (SMN1) gene or only exon 7 homology deletion leads to the failure to produce a full-length SMN gene. The copy number of SMN2 gene with high homology of SMN1 affects the degree of disease and was the target gene for targeting therapy, in which splicing silencer in intron 7 was the key to suppress the inclusion of exon 7. In this study, we projected to use CRISPR/Case 9 for the targeted editing of intronic-splicing silencer (ISS) sequence to promote… More
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  • The signaling pathway in modulating bone metabolism after dental implant in diabetes
  • Abstract Diabetes Mellitus is a systematic disease with complications in multi-organs, including decreased implant osseointegration and a high failure rate of dental transplants. Accumulating evidence indicates that the signaling pathway directly impacts the process of bone metabolism and inflammatory response implicated with dental implants in diabetic patients. This review summarizes the recent advance in signaling pathways regulate osseointegration and inflammatory response in dental transplantation, aiming to identify the potential therapeutic target to reduce the dental transplant failure in diabetes patients, with emphasis on the surface characteristics of the implant, inflammatory signaling, AMPK, PPARγ, WNT, ROS, and adiponectin signaling. More
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  • High level of circPTN promotes proliferation and stemness in gastric cancer
  • Abstract Increasing evidence proves that circular RNAs (circRNAs) play an important role in regulating the biological behaviors of tumors. The central purpose of this research was to investigate the functions of circRNA in gastric cancer. The utilization of real-time PCR was to test circPTN expression in gastric cancer cells. Cell counting colony formation assays, CCK-8 assay, and EdU assay were used to investigate proliferation. Transwell assay was applied to investigate migration. We discovered that circPTN was highly expressed in gastric cancer cells. Low expression of circPTN inhibits gastric cancer cell proliferation and migration. Elevated expression of circPTN promotes gastric cancer cell… More
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  • Immune prognostic implications of PSMD14 and its associated genes signatures in hepatocellular carcinoma
  • Abstract PSMD14 played a vital role in initiation and progression of hepatocellular carcinoma (HCC). However, PSMD14 and its-related genes for the immune prognostic implications of HCC patients have rarely been analyzed. Messenger RNA expression profiles and clinicopathological data were downloaded from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) database-Liver Hepatocellular Carcinoma (LIHC). Additionally, we used multi-dimensional bioinformatics analysis to construct and validate a PSMD14-based immune prognostic signature (including RBM45, PSMD1, OLA1, CCT6A, LCAT and IVD) for HCC prognosis prediction. Patients in the high-risk group shown significantly poorer survival than patients in the low-risk group. Calibration curves confirmed… More
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  • Basal cell carcinoma stem cells exhibit osteogenic and chondrogenic differentiation potential
  • Abstract Specific cell subpopulations identified as cancer stem cells (CSCs) can be found in basal cell carcinoma (BCC). Generally, CSCs have a marked trans-differentiation potential that could potentially be used in differentiation therapies. However, there are no studies regarding BCC CSCs multipotency. The aim of the study was to analyze the characteristic of CSCs of BCC with emphasis on their differentiation potential upon specific induction. Specific staining and cell morphology were used for differentiation confirmation, along with the expression analysis of osteogenic (ALP, BSP, Runx2, OCN, BMP2), chondrogenic (COL1 and COL2A1), adipogenic (PPAR-γ) and neurogenic (Nestin and MAP2) markers. BCC CSCs… More
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  • Astragaloside IV improves melanocyte differentiation from mouse bone marrow mesenchymal stem cells
  • Abstract Vitiligo results in an autoimmune disorder destructing skin pigment cells, melanocytes (Mcs). This study aimed to investigate whether Astragaloside IV (AIV) could efficiently induce differentiation of bone marrow mesenchymal stem cells (BMMSCs) into Mcs. BMMSCs were induced and differentiated into Mcs with 0.1, 0.2, and 0.4 mg/L AIV during 150-day. Morphologic changes of differentiated cells were observed. Levels of some melanocytic specific genes (TRP-1, TRP-2, MART-1, Mitf) were measured with quantitative polymerase chain reaction (qPCR) at 90, 120, and 150 days of induction. After 90-day induction, the differentiated cells with 0.4 mg/L AIV demonstrated the typical morphology of Mcs, positive… More
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  • Repurposing of FDA-Approved drugs to predict new inhibitors against key regulatory genes in Mycobacterium tuberculosis
  • Abstract

    Tuberculosis (TB) disease has become one of the major public health concerns globally, especially in developing countries. Numerous research studies have already been carried out for TB, but we are still struggling for a complete and quick cure for it. The progress of Mycobacterium tuberculosis (MTB) strains resistant to existing drugs makes its cure and control very complicated. Therefore, it is the need of the hour to search for newer and effective drugs that can inhibit an increasing number of putative drug targets. We applied the drug repurposing concept to identify promising FDA-approved drugs against five key-regulatory genes (FurB, IdeR,… More

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  • Propofol inhibits cells migration and invasion via HOTAIR/miR-93/HIF-1α-mediated lactate secretion in colon cancer
  • Abstract Propofol, a common intravenous anesthetic used in clinical, has been shown to regulate cells proliferation, inflammation, angiogenesis and metastasis as well as exerting anti-cancer effect in several different types of cancer. However, the functions and mechanisms of propofol in lactate secretion and invasion of cancer cells remain unknown. The primary aim of this study was to investigate the role of propofol in cells migration and invasion of colon cancer (CRC). Scratches assay, Transwell assay were used to detect colon cells migration and invasion. Real-time Quantitative Polymerase Chain Reaction (RT-qPCR), Western blotting were utilized to detect the expression of related molecules.… More
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  • Identification of potential inhibitors for Sterol C-24 reductase of Leishmania donovani through virtual screening of natural compounds
  • Abstract Leishmaniasis is a vector-borne parasitic neglected tropical disease caused by a group of about 30 different species of the genus Leishmania. It is transmitted by the bite of female phlebotomies sand fly. Three main clinical manifestations of leishmaniasis include cutaneous, visceral, and mucocutaneous leishmaniasis. Visceral leishmaniasis (VL) caused by Leishmania donovani, is an infection of reticuloendothelial system and fatal if untreated. Cholesterol, a sterol that is prominent in the mammalian cell membranes whereas stigmasterol and ergosterol are more prevalent in plants, yeast, and protozoa, respectively. Ergosterols which is absent in human being, is an important constituent of parasite membrane. Sterol… More
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  • RNA-sequencing indicates high hemocyanin expression as a key strategy for cold adaptation in the Antarctic amphipod Eusirus cf. giganteus clade g3
  • Abstract We here report the de novo transcriptome assembly and functional annotation of Eusirus cf. giganteus clade g3, providing the first database of expressed sequences from this giant Antarctic amphipod. RNA-sequencing, carried out on the whole body of a single juvenile individual likely undergoing molting, revealed the dominant expression of hemocyanins. The mRNAs encoding these oxygen-binding proteins cumulatively accounted for about 40% of the total transcriptional effort, highlighting the key biological importance of high hemocyanin production in this Antarctic amphipod species. We speculate that this observation may mirror a strategy previously described in Antarctic cephalopods, which compensates for the decreased ability… More
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  • Oxidative stress indicators in human and bottlenose dolphin leukocytes in response to a pro-inflammatory challenge
  • Abstract Marine mammals undergo cycles of tissue ischemia and reperfusion during the dive response. Reperfusion injury can result in oxidative tissue damage and the activation of a pro-inflammatory immune response. The risk of oxidative damage is reduced by antioxidants. Our hypothesis is that the reported higher antioxidant defenses within marine mammal tissues provide additional protection in situations that produce oxidative stress, like inflammation, in comparison to terrestrial mammal tissues. Leukocytes were isolated from the whole blood of Pacific bottlenose dolphins (Tursiops truncatus gilli) and humans (Homo sapiens) and were exposed to lipopolysaccharides (LPS, 10 µg/mL) in vitro to simulate a pro-inflammatory… More
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  • Application of ferrous sulfate alleviates negative impact of cadmium in rice (Oryza sativa L.)
  • Abstract Soil contamination with toxic heavy metals [such as cadmium (Cd)] is becoming a serious global problem due to rapid development of social economy. Iron (Fe), being an important element, has been found effective in enhancing plant tolerance against biotic and abiotic stresses. The present study investigated the extent to which different levels of Ferrous sulphate (FeSO4) modulated the Cd tolerance of rice (Oryza sativa L.), when maintained in artificially Cd spiked regimes. A pot experiment was conducted under controlled conditions for 146 days, by using natural soil, mixed with different levels of CdCl2 [0 (no Cd), 0.5 and 1 mg/kg]… More
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  • Biosynthesis of raw starch degrading β-cyclodextrin glycosyltransferase by immobilized cells of Bacillus licheniformis using potato wastewater
  • Abstract The study was sought to enhance the synthesis of thermal stable β-cyclodextrin glycosyltransferase (β-CGTase) using potato wastewater as a low-cost medium and assess the degree to which it is efficient for industrial production of β-cyclodextrin (β-CD) from raw potato starch. Thermophilic bacteria producing β-CGTase was isolated from Saudi Arabia and the promising strain was identified as Bacillus licheniformis using phylogenetic analysis of the 16S rRNA gene. Alginate-encapsulated cultures exhibited twice-fold of β-CGTase production more than free cells. Scanning electron microscopy (SEM) of polymeric capsules indicated the potential for a longer shelf-life, which promotes the restoration of activity in bacterial cells… More
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  • Identification of PtGai (a DELLA protein) in trifoliate orange and expression patterns in response to drought stress
  • Abstract Gibberellins (GAs) are an important hormone in regulating plant growth and development, and DELLA protein is an essential negative regulator of GA signal transduction. The aim of the study was to clone a GA-inhibiting protein DELLA from trifoliate orange (Poncirus trifoliata L. Raf.) and to analyze the bioinformations and expression patterns of the protein gene in tissues and in response to drought stress. A DELLA protein was isolated from trifoliate orange and named as PtGai (Genebank number: MZ170959). The PtGai protein had 1731 bp open reading frames, along with 576 amino acid codes, and also grouped with sweet orange (XM_006430552.4).… More
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  • Complete genome sequence of two strawberry vein banding virus isolates from China
  • Abstract It was rarely reported about strawberry vein banding virus (SVBV) genome sequence in China and most countries worldwide. In this work, we determined the complete genome sequences of two SVBV isolates in China, designated SVBV-AH and SVBV-BJ, that were obtained from naturally infected strawberry samples from Anhui province and Beijing city of China, respectively. The complete genomes of SVBV-AH and SVBV-BJ were 7,862 nucleotides (nts) and 7,863 nts long, respectively, and both constituted with seven genes typical of the caulimoviruses. Alignment of complete nucleotide sequences showed that SVBV-AH and SVBV-BJ shared a significant nucleotide sequence identity of 97.7% of each… More
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