Showing papers in "Journal of Biosciences in 2021"

SARS-CoV-2 genomics: An Indian perspective on sequencing viral variants

Abstract: Since its emergence as a pneumonia-like outbreak in the Chinese city of Wuhan in late 2019, the novel coronavirus disease COVID-19 has spread widely to become a global pandemic. The first case of COVID-19 in India was reported on 30 January 2020 and since then it has affected more than ten million people and resulted in around 150,000 deaths in the country. Over time, the viral genome has accumulated mutations as it passes through its human hosts, a common evolutionary mechanism found in all microorganisms. This has implications for disease surveillance and management, vaccines and therapeutics, and the emergence of reinfections. Sequencing the viral genome can help monitor these changes and provides an extraordinary opportunity to understand the genetic epidemiology and evolution of the virus as well as tracking its spread in a population. Here we review the past year in the context of the phylogenetic analysis of variants isolated over the course of the pandemic in India and highlight the importance of continued sequencing-based surveillance in the country.

Advances in Bone tissue engineering: A fundamental review.

Abstract: Bone is a dynamic tissue that can always rebuild itself by modeling and remodeling to maintain functionality. This tissue is responsible for several vital functions in the body, such as providing structural support for soft tissues and the body, being the central region of hematopoiesis in human adults, and contributing to mineral homeostasis. Besides, it has an innate ability of auto-regeneration when damaged. All of these processes involve several molecular cues related to biochemical and mechanical stimulus. However, when the lesion is complicated or too big, it is necessary to intervene surgically, which may not effectively solve the problem. Bone tissue engineering seeks to provide resources to resolve these clinical issues and has been advancing in recent years, presenting promising devices for bone tissue repair. The understanding of some important biofactors and bone stem-cells influence might be crucial for an effective regenerative medicine, since bone is one of the most transplanted tissues. So, the purpose of this article is to provide an overview of the bone tissue, including the role of stem cells and some of the bioactive molecules associated with these processes. Finally, we will suggest future directions for bone tissue engineering area that might be helpful in order to produce biomimetic bone substitutes that become a real alternative to translational medicine.

Polymyxins, the last-resort antibiotics: Mode of action, resistance emergence, and potential solutions.

Abstract: Infections caused by multi-drug resistant (MDR) bacterial pathogens are a leading cause of mortality and morbidity across the world. Indiscriminate use of broad-spectrum antibiotics has seriously affected this situation. With the diminishing discovery of novel antibiotics, new treatment methods are urgently required to combat MDR pathogens. Polymyxins, the cationic lipopeptide antibiotics, discovered more than half a century ago, are considered to be the last-line of antibiotics available at the moment. This antibiotic shows a great bactericidal effect against Gram-negative bacteria. Polymyxins primarily target the bacterial membrane and disrupt them, causing lethality. Because of their membrane interacting mode of action, polymyxins cause nephrotoxicity and neurotoxicity in humans, limiting their usability. However, recent modifications in their chemical structure have been able to reduce the toxic effects. The development of better dosing regimens has also helped in getting better clinical outcomes in the infections caused by MDR pathogens. Since the mid-1990s the use of polymyxins has increased manifold in clinical settings, resulting in the emergence of polymyxin-resistant strains. The risk posed by the polymyxin-resistant nosocomial pathogens such as the Enterobacteriaceae group, Pseudomonas aeruginosa, and Acinetobacter baumannii, etc. is very serious considering these pathogens are resistant to almost all available antibacterial drugs. In this review article, the mode of action of the polymyxins and the genetic regulatory mechanism responsible for the emergence of resistance are discussed. Specifically, this review aims to update our current understanding in the field and suggest possible solutions that can be pursued for future antibiotic development. As polymyxins primarily target the bacterial membranes, resistance to polymyxins arises primarily by the modification of the lipopolysaccharides (LPS) in the outer membrane (OM). The LPS modification pathways are largely regulated by the bacterial two-component signal transduction (TCS) systems. Therefore, targeting or modulating the TCS signalling mechanisms can be pursued as an alternative to treat the infections caused by polymyxin-resistant MDR pathogens. In this review article, this aspect is also highlighted.

Epigenetic variation in animal populations: Sources, extent, phenotypic implications, and ecological and evolutionary relevance

Abstract: Laboratory experiments and fieldwork with asexually reproducing invertebrates and vertebrates clearly revealed that animal populations can produce substantial phenotypic variation despite genetic identity. This epigenetically caused phenotypic variation comes from two different sources, namely directional environmental induction and bed-hedging developmental stochasticity. Both occur together and are mediated by molecular epigenetic mechanisms like DNA methylation, histone modifications and microRNAs. These epigenetic mechanisms are also involved in insect polyphenism, phenotypic changes in early domestication, and gene expression change and chromatin rearrangement during speciation. Epigenetic variation is particularly important for asexual populations helping them to stay in the game of life when the environmental conditions change. However, it is also relevant for sexually reproducing populations, as shown for genetically impoverished invasive groups, cave animals and sessile taxa that cannot evade unfavourable environmental conditions. Experiments revealed that epigenetic marks can be transgenerationally inherited and persist for several generations. First evidence suggests that inherited epimutations with phenotypic effects may end-up in phenotype-fixing genetic mutations by accelerated mutation of methylated nucleotides. Refined concepts, suitable animal models, fast and affordable new omics techniques that require only small tissue samples, and appropriate data interpretation tools are now available enabling future investigations in ecological and evolutionary epigenetics with high accuracy.

Pattern of genomic variation in SARS-CoV-2 (COVID-19) suggests restricted nonrandom changes: Analysis using Shewhart control charts

Abstract: SARS-CoV-2 is a member of the Coronavirus family which recently originated from the Wuhan province of China and spread very rapidly through the world infecting more than 4 million people. In the past, other Coronaviruses have also been found to cause human infection, but not as widespread as COVID-19. Since Coronavirus sequences constantly change due to mutation and recombination, it is important to understand the pattern of changes and likely path the virus can take in the future. In this study, we have used the Shewhart control chart to identify and analyze hypervariable (hotspots) and hypovariable (coldspots) regions of the virus. Our analysis shows that SARS-CoV-2 has changed in a few regions of the genome. Analysis of SARS-CoV-1 and MERS sequences suggests that over time, mutations start accumulating in different regions and most likely SARS-CoV-2 may also follow a similar path. The results suggest a possible emergence of modified viruses over some time.

Protein expression and secretion by filamentous fungi

Abstract: In the search for optimal platforms for protein expression and secretion, filamentous fungi in principle provide some of the best microbial cell factories. They are inherently endowed with the ability to secrete proteins. Fungi belonging to Aspergillus and Trichoderma species are well-studied for industrial production of proteins and enzymes. Our understanding of these organisms at the level of transcription, translation, post-translational processing and the secretory pathways has improved significantly in recent years. Despite this, the ability of these fungal secretion platforms has not yet been able to match their intrinsic secretion capacity to produce foreign proteins. Details of the molecular mechanisms of the secretory pathways in filamentous fungi are emerging. This knowledge can be gainfully employed to enhance protein production in filamentous fungi, particularly in the secretion of heterologous proteins of value.

Nutraceutical and therapeutic potential of Phycocyanobilin for treating Alzheimer's disease.

Abstract: Alzheimer's disease (AD) is a devastating neurodegenerative condition provoking the loss of cognitive and memory performances. Despite huge efforts to develop effective AD therapies, there is still no cure for this neurological condition. Here, we review the main biological properties of Phycocyanobilin (PCB), accounting for its potential uses against AD. PCB, given individually or released in vivo from C-Phycocyanin (C-PC), acts as a bioactive-molecule-mediating antioxidant, is anti-inflammatory and has immunomodulatory activities. PCB/C-PC are able to scavenge reactive oxygen and nitrogen species, to counteract lipid peroxidation and to inhibit enzymes such as NADPH oxidase and COX-2. In animal models of multiple sclerosis and ischemic stroke, these compounds induce remyelination as demonstrated by electron microscopy and the expression of genes such as Mal up-regulation of and Lingo-1 down-regulation. These treatments also reduce pro-inflammatory cytokines levels and induce immune suppressive genes. PCB/C-PC protects isolated rat brain mitochondria and inactivate microglia, astrocytes and neuronal apoptosis mediators. Such processes are all involved in the pathogenic cascade of AD, and thus PCB may effectively mitigate the injury in this condition. Furthermore, PCB can be administered safely by oral or parenteral routes and therefore, could be commercially offered as a nutraceutical supplement or as a pharmaceutical drug.

Conjugation of imipenem to silver nanoparticles for enhancement of its antibacterial activity against multi-drugresistant isolates of Pseudomonas aeruginosa .

Abstract: Due to the broad-spectrum of antibiotic resistance, herein we investigated the possibility of using imipenem-conjugated silver nanoparticles (IMP-AgNPs) against multidrug-resistant isolates of Pseudomonas aeruginosa. For this purpose, 200 clinical isolates were tested against different antibiotics to determine the antimicrobial susceptibility. To identify blaVIM and blaIMP resistance genes, PCR was used. The synthesized AgNPs and conjugants were characterized using UV-vis spectroscopy, XRD, SEM, TEM, DLS, and FTIR. The stability, drug release kinetics, cytotoxicity, hemolytic and apoptotic effects of NPs were also investigated. MIC of the imipenem, AgNPs, and conjugants were evaluated versus P. aeruginosa isolates. Finally, the effects of the IMP-AgNPs to heal burn wounds in rats was evaluated. According to the results, about 68% of isolates showed resistance to imipenem (MIC ≥ 64 μg/ml to ≥ 512 μg/ml). Analytical results verified the synthesis of AgNPs and IMP-AgNPs. A Dose-dependent decrease happened in terms of the MIC values of IMP-AgNPs were also affected by the existence of resistant genes. Low cytotoxic was observed regarding AgNPs which lead to apoptosis. The histopathological results showed a considerable epithelization in treated groups with IMP-AgNPs. Accordingly, IMP-AgNPs can be considered as a powerful antibacterial agent to treat the infections caused by multidrug-resistant P. aeruginosa.

Circ_0002711 knockdown suppresses cell growth and aerobic glycolysis by modulating miR-1244/ROCK1 axis in ovarian cancer.

Abstract: It has been well investigated that circular RNAs (circRNAs) play important roles in various cancers. The function of circ_0002711 and its underlying mechanisms in ovarian cancer (OC) remain unknown. qRT-PCR and western blot were performed to detect the expressions of circ_0002711, microRNA-1244 (miR-1244), and Rho kinase 1 (ROCK1) in OC tissues and cells. MTT assay and colony formation assay were employed to evaluate cell proliferation. Detection of lactate production, glucose uptake, and ATP level and oxygen consumption were used to determine Warburg effect. Western blot was used to examine glycolysis or proliferationrelated genes. Dual-luciferase reporter assay and RIP pull down assay were used to address the relationship among circ_0002711, miR-1244, and ROCK1. In vivo tumor growth was evaluated in nude mice. Circ_0002711 was upregulated in OC tissues and cell lines. Circ_0002711 downregulation inhibited cell viability, colony formation ability and aerobic glycolysis. Circ_0002711 contained binding sites with miR1244. Moreover, loss of miR-1244 undermined circ_0002711 downregulation-mediated function. ROCK1 contained binding sites with miR-1244. MiR-1244 upregulation suppressed cell proliferation and aerobic glycolysis, which was rescued by enhanced expression of ROCK1. Circ_0002711 knockdown hampered ROCK1 expression by upregulating miR-1244 expression. Finally, decreased expression of circ_0002711 inhibited tumor growth in vivo. Circ_0002711/miR-1244/ROCK1 axis regulated Warburg effect and tumor growth in vivo.

Why are some coronavirus variants more infectious

Abstract: Since the start of the pandemic, SARS-CoV-2 has infected almost 200 million human hosts and is set to encounter and gain entry in many more in the coming months. As the coronavirus flourish, the evolutionary pressure selects those variants that can complete the infection cycle faster and reproduce in large numbers compared to others. This increase in infectivity and transmissibility coupled with the immune response from high viral load may cause moderate to severe disease. Whether this leads to enhanced virulence in the prevalent Alpha and Delta variants is still not clear. This review describes the different types of SARS-CoV-2 variants that are now prevalent, their emergence, the mutations responsible for their growth advantages, and how they affect vaccine efficacy and increase chances of reinfection. Finally, we have also summarized the efforts made to recognize and predict the mutations, which can cause immune escape and track their emergence through impactful genomic surveillance.

Research advances and prospects of legume lectins

Abstract: Lectins are widely distributed proteins having ability of binding selectively and reversibly with carbohydrates moieties and glycoconjugates. Although lectins have been reported from different biological sources, the legume lectins are the best-characterized family of plant lectins. Legume lectins are a large family of homologous proteins with considerable similarity in amino acid sequence and their tertiary structures. Despite having strong sequence conservation, these lectins show remarkable variability in carbohydrate specificity and quaternary structures. The ability of legume lectins in recognizing glycans and glycoconjugates on cells and other intracellular structures make them a valuable research tool in glycomic research. Due to variability in binding with glycans, glycoconjugates and multiple biological functions, legume lectins are the subject of intense research for their diverse application in different fields such as glycobiology, biomedical research and crop improvement. The present review specially focuses on structural and functional characteristics of legume lectins along with their potential areas of application.

CircRNA expression profiling and bioinformatics analysis indicate the potential biological role and clinical significance of circRNA in influenza A virus-induced lung injury.

Abstract: Circular RNA (circRNA) plays an important role in the regulation of multiple biological processes. However, circRNA profiling and the potential biological role of circRNA in influenza A virus (IAV)-induced lung injury have not been investigated. In the present study, circRNA expression profiles in lung tissues from mice with and without IAV-induced lung injury were analyzed using high-throughput sequencing, and differentially expressed circRNAs were verified by quantitative PCR. The gene homology of candidate circRNAs was investigated and the expression of plasma circRNAs from patients with IAV-induced acute respiratory distress syndrome (ARDS) was detected. The target microRNAs (miRNAs) of circRNAs were predicted. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed. In total, 781 circRNAs were differentially expressed between ARDS mice and control (467 were up-regulated and 314 were down-regulated). Moreover, the candidate circRNAs (Slco3a1, Nfatc2, Wdr33, and Dmd) expression showed the same trend with the sequencing results. The isoforms of circRNA Slco3a1 and Wdr33 were highly conserved between humans and mice. Plasma circRNA Slco3a1 and Wdr33 presented differential expression in patients with IAV-induced ARDS compared to control. The circRNAmiRNA interaction network and GO and KEGG analyses indicated the potential biological role of circRNAs in the development of IAV-induced lung injury. Taken together, a large number of differentially expressed circRNAs were identified in our study. CircRNA Slco3a1 and Wdr33 had significantly different expression in specimens from mice and humans, and showed a potential biological role in IAV-induced lung injury by bioinformatics analysis.

New insights into the activation of Radiation Desiccation Response regulon in Deinococcus radiodurans

Abstract: The highly radiation-resistant bacterium Deinococcus radiodurans responds to gamma radiation or desiccation through the coordinated expression of genes belonging to Radiation and Desiccation Resistance/Response (RDR) regulon. RDR regulon is operated through cis-acting sequence RDRM (Radiation Desiccation Response Motif), trans-acting repressor DdrO and protease IrrE (also called PprI). The present study evaluated whether RDR regulon controls the response of D. radiodurans to various other DNA damaging stressors, to which it is resistant, such as UV rays, mitomycin C (MMC), methyl methanesulfonate (MMS), ethidium bromide (EtBr), etc. Activation of 3 RDR regulon genes (ddrB, gyrB and DR1143) was studied by tagging their promoter sequences with a highly sensitive GFP reporter. Here we demonstrated that all the DNA damaging stressors elicited activation of RDR regulon of D. radiodurans in a dose-dependent and RDRM-/IrrE-dependent manner. However, ROS-mediated indirect effects [induced by hydrogen peroxide (H2O2), methyl viologen (MV), heavy metal/metalloid (zinc or tellurite), etc.] did not activate RDR regulon. We also showed that level of activation was inversely proportional to cellular abundance of repressor DdrO. Our data strongly suggests that direct DNA damage activates RDR regulon in D. radiodurans.

LncRNA-SNHG16 promotes proliferation and migration of acute myeloid leukemia cells via PTEN/PI3K/AKT axis through suppressing CELF2 protein

Abstract: The silence of lncRNA small nucleolar RNA host gene 16 (SNHG16) suppressed acute lymphoblastic leukemia (ALL) cell proliferation and migration, whereas its role in acute myeloid leukemia (AML) still lacks clarity. This study showed that SNHG16 was upregulated in AML patients and cells. And SNHG16 overexpression remarkably enhanced the proliferation and migration capacities of HL60 and AML-193 cells, while SNHG16 knockdown acted the opposite way. Subsequently, we revealed that SNHG16 directly bound to CELF2 (CUGBP Elav-like family member 2) protein, and caused CELF2 mRNA unstably and proteins reducing. CELF2 was decreased both in AML patients and cells. CELF2 overexpression or interference weakened the effect of overexpressing or silencing SNHG16 on proliferation and migration. Moreover, the transfection of pcDNA-CELF2 elevated PTEN (phosphatase and tensin homolog) activity and hindered the phosphoinositide 3-kinase (PI3K)/AKT signaling. And SNHG16 reduced PTEN activity and promoted the PI3K/AKT pathway activation by restraining CELF2. Furthermore, GDC-0941 (a specific inhibitor of the PI3K/AKT pathway) impeded the effect of SNHG16 increase, and bpV(pic) (a specific PTEN inhibitor) declined the effect of SNHG16 decrease on cell proliferation and migration. Taken together, the present study indicated that SNHG16 promoted proliferation and migration of AML cells via PTEN/PI3K/AKT axis through suppressing CELF2 protein.

Relationship between polyamines conjugated to mitochondrion membrane and mitochondrion conformation from developing wheat embryos under drought stress

Abstract: The mitochondrion conformation and the contents of conjugated polyamines were investigated using the embryos of developing wheat (Triticum aestivum L.) grains of two cultivars differing in drought tolerance as experiment materials. After drought stress treatment for 7 days, the relative water content of embryo and relative increase rate of embryo dry weight of the drought-sensitive Yangmai No. 9 cv. decreased more significantly than those of the drought-tolerant Yumai No. 18 cv. Furthermore, the changes in mitochondrion conformation of Yangmai No. 9 were more marked. Meanwhile, the increases of the contents of conjugated non-covalently spermidine (CNC-Spd) and conjugated covalently putrescine (CC-Put) of Yumai No. 18 were more obvious than those of Yangmai No. 9. Treatment with exogenous Spd not only alleviated the injury of drought stress to Yangmai No. 9, but also enhanced the increase of CNC-Spd content and inhibited the change in the mitochondrion conformation of this cultivar. The treatments of Yumai No. 18 with two inhibitors, methylglyoxyl-bis (guanylhydrazone) and phenanthrolin, significantly inhibited the drought stress-induced increases of CNC-Spd and CC-Put contents of the cultivar, respectively. Meanwhile, the treatments with the two inhibitors aggravated the injury of drought stress to Yumai No. 18 and enhanced the change in the mitochondrion conformation of this cultivar. These results mentioned above suggested that the CNC-Spd and CC-Put in embryo mitochondrion membrane isolated from developing grains could enhance the wheat tolerance to drought stress by maintaining the mitochondrion conformation.

Exosomal circRNA HIPK3 knockdown inhibited cell proliferation and metastasis in prostate cancer by regulating miR-212/BMI-1 pathway

Abstract: Prostate cancer (PCa) is the second frequent malignancy among men in the world. Exosomal circular RNAs (circRNAs) have been reported to function in PCa progression. The current study aimed to investigate the role of exosomal circRNA homeodomain-interacting protein kinase 3 (circHIPK3) in PCa development. Exosomes were extracted from serum and cells utilizing commercial kit, and identified by transmission electron microscopy (TEM), Western blot assay and nanoparticle tracking analyzer. Relative expression of circHIPK3, microRNA (miR)-212 and B-cell specific MMLV insertion site-1 (BMI-1) was examined by quantitative realtime PCR or Western blot assay. Receiver Operating Characteristic (ROC) analysis was conducted to assess the diagnostic potential of exosomal miR-212. Cell viability, and metastasis including migration and invasion, were detected by Methyl thiazolyl tetrazolium (MTT) assay and Transwell assay, respectively. Cell apoptosis was monitored using flow cytometry. The interaction between miR-212 and circHIPK3 or BMI-1 was validated by dual-luciferase reporter assay. Xenograft tumor assay was employed to explore the role of exosomal circHIPK3 in vivo. Exosomal circHIPK3 was increased in serum of PCa patients, and could discriminate PCa patients from normal volunteers. Depletion of exosomal circHIPK3 or overexpression of exosomal miR-212 reduced viability, migration and invasion, but promoted cell apoptosis in PCa cells, which was attenuated by miR-212 inhibition or BMI-1, respectively. MiR-212 targeted BMI-1, and downregulated BMI-1 expression. Exosomal circHIPK3 knockdown also suppressed tumor growth in vivo. Exosomal circHIPK3 knockdown inhibited PCa progression by regulating miR-212/BMI-1 axis, at least in part, offering a new insight into the molecular mechanism of PCa.

Chloroplast genome analysis of Angiosperms and phylogenetic relationships among Lamiaceae members with particular reference to teak (Tectona grandis L.f).

Abstract: Availability of comprehensive phylogenetic tree for flowering plants which includes many of the economically important crops and trees is one of the essential requirements of plant biologists for diverse applications. It is the first study on the use of chloroplast genome of 3265 Angiosperm taxa to identify evolutionary relationships among the plant species. Sixty genes from chloroplast genome was concatenated and utilized to generate the phylogenetic tree. Overall the phylogeny was in correspondence with Angiosperm Phylogeny Group (APG) IV classification with very few taxa occupying incongruous position either due to ambiguous taxonomy or incorrect identification. Simple sequence repeats (SSRs) were identified from almost all the taxa indicating the possibility of their use in various genetic analyses. Large proportion (95.6%) of A/T mononucleotide was recorded while the di, tri, tetra, penta and hexanucleotide amounted to less than 5%. Ambiguity of the taxonomic status of Tectona grandis L.f was assessed by comparing the chloroplast genome with closely related Lamiaceae members through nucleotide diversity and contraction/expansion of inverted repeat regions. Although the gene content was highly conserved, structural changes in the genome was evident. Phylogenetic analysis suggested that Tectona could qualify for a subfamily Tectonoideae. Nucleotide diversity in intergenic and genic sequences revealed prominent hyper-variable regions such as, rps16-trnQ, atpH-atpI, psc4-psbJ, ndhF, rpl32 and ycf1 which have high potential in DNA barcoding applications.

COVID-19 and central nervous system interplay: A big picture beyond clinical manifestation

Abstract: The coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV2) has been declared a pandemic. Global research updates confirm that the infected patients manifest a range of clinical symptoms and sometimes remain entirely asymptomatic, posing a greater threat to the people coming in contact. Despite several case reports coming up every day, our knowledge about the neurotropic mechanism of the SARS-CoV-2, immunological responses, and the mode of disease progression and mechanism of crosstalk between the central nervous system (CNS), heart, lungs, and other major organs is not complete. Report of anosmia, ataxia, dysgeusia, and altered psychological status of the infected COVID-19 patients offers some clue to the possible route of viral entry and multiplication. In this review, we have critically assessed the involvement of CNS dysregulation in COVID-19 patients. The probable mechanism of immunological responses, the impairment of the coagulation pathway, the onset of cytokine storm, its interplay with the HPA axis, and hypoxia are discussed in detail here. Based on the latest research findings and some case reports of hospitalized COVID-19 patients, it is evident that the CNS involvement in disease progression is alarming. Accurate and timely detection of viral load in CNS is necessary to allow prompt and effective treatment modalities.

Circ-HIPK3 regulates YAP1 expression by sponging miR-381-3p to promote oral squamous cell carcinoma development

Abstract: Circular RNAs (circRNAs) have been reported to play important roles in human cancers. Circular RNA homeodomain interacting protein kinase 3 (Circ-HIPK3) was investigated to be involved in tumorigenesis. However, the functions of circ-HIPK3 in oral squamous cell carcinoma (OSCC) remain vague. The expression of circ-HIPK3, microRNA (miR)-381-3p and Yes-associated protein1 (YAP1) was detected by qRT-PCR or western blot. Cell proliferation, apoptosis, invasion and migration were measured by MTT assay, flow cytometry, or transwell assay. The dual-luciferase reporter assay was employed to test the target correlations miR-381-3p and circ-HIPK3 or YAP1. Murine xenograft model was established to conduct in vivo assay. CircHIPK3 was elevated in OSCC tissues and cell lines, and decrease of circ-HIPK3 suppressed OSCC cell proliferation, invasion, migration and induced apoptosis in vitro as well as inhibited tumor growth in vivo. Rescue assay indicated circ-HIPK3 silence mediated OSCC progression inhibition by sponging miR-381-3p, which was a target of circ-HIPK3. Furthermore, miR-381-3p directly interacted with YAP1 and miR-381-3p inhibition could attenuate YAP1 deletion-induced suppression on cell malignant biological behavior in OSCC. Meanwhile, co-expression analysis showed circ-HIPK3 could regulate YAP1 expression by competing for miR-381-3p. Circ-HIPK3 contributed to OSCC growth and development through regulating YAP1 expression by sponging miR-381-3p, indicating a promising therapeutic strategy for OSCC.

MALAT1 knockdown protects from bronchial/tracheal smooth muscle cell injury via regulation of microRNA-133a/ryanodine receptor 2 axis

Abstract: Asthma has significant impacts on living quality particularly in children. Long noncoding RNA (lncRNA) MALAT1 plays a crucial role in neonatal respiratory diseases. Meanwhile, MALAT1 knockdown could induce viability and attenuate apoptosis of airway-related cells. However, the role of MALAT1 in neonatal asthma, asthma-related cell, and its possible mechanism is unclear. This study aims to investigate MALAT1 level in asthma and to identify the effects of MALAT1 on bronchial/tracheal smooth muscle cells (B/TSMCs). Newborn asthma modeling rat was constructed by introducing ovalbumin (OVA). MALAT1 levels in tissues or B/TSMCs were determined by RT-qPCR. Exogenous changes of MALAT1, RyR2 or miR-133a in B/TSMCs were fulfilled by cell transfection; cell apoptosis was measured by using Cell Death Detection ELISA kit and Hochest33342; IL-6, TNF-α and IL-1β level was detected by using corresponding ELISA kit; ryanodine receptor 2 (RyR2) mRNA and miR-133a level was determined by RT-qPCR; cleaved caspase-3 (c-caspase-3) and RyR2 expression was detected by Western blot; luciferase reporter assay was performed to confirm the target regulation of miR-133a on RyR2. We found that MALAT1 was significantly upregulated in tracheal tissues of newborn asthma modeling rats. In MALAT1-silenced or -overexpressed B/TSMCs, we found a synchronous change of cell apoptosis, inflammatory factor secretion (IL-6, TNF-α, and IL-1β) or RyR2 level, but a reverse change of miR-133a level with MALAT1. Besides, MALAT1 induced B/TSMCs apoptosis and inflammation increase could be partially reversed when RyR2 was silenced or when miR-133a was overexpressed. The luciferase reporter assay confirmed that RyR2 is a direct target gene of miR-133a in B/TSMCs. Finally, we conclude that MALAT1 knockdown could protect from B/TSMCs injury via regulating miR-133a/RyR2 axis.

Integration of advanced technologies for plant variety and cultivar identification.

Abstract: Identification of plant variety and cultivar is pivotal in the agricultural sector due to the abundance of plant varieties and cultivars developed in many crop species. However, plant variety and cultivar identification via basic morphological features is problematic and challenging when differentiating closely related species not only due to their limited differences but also due to technical limitations of the process being time-consuming, labour-intensive and costly, and statistically imprecise information being available due to phenotypic plasticity. Therefore, it is imperative to have rapid and highly efficient techniques to mitigate these limitations. This review provides an overview and summarization of the development and application of molecular markers such as Random Amplified Polymorphic DNA (RAPD), Restriction Fragment Length Polymorphism (RFLP), Simple Sequence Repeats (SSR), Inter-simple sequence repeats (ISSR), Amplified Fragment Length Polymorphism (AFLP), Single nucleotide polymorphism (SNP) and DNA barcoding, High-resolution melting (HRM) and biosensor technology as potential tools in the identification of plant variety and cultivar.

Rapid diagnosis of Leishmania infection with a portable loopmediated isothermal amplification device

Abstract: L. donovani is an intracellular protozoan parasite, that causes visceral leishmaniasis (VL), and consequently, post-kala azar dermal leishmaniasis (PKDL). Diagnosis and treatment of leishmaniasis is crucial for decreasing its transmission. Various diagnostic techniques like microscopy, enzyme-linked immunosorbent assays (ELISA) and PCR-based methods are used to detect leishmaniasis infection. More recently, loop-mediated isothermal amplification (LAMP) assay has emerged as an ideal diagnostic measure for leishmaniasis, primarily due to its accuracy, speed and simplicity. However, point-of-care diagnosis is still not been tested with the LAMP assay. We have developed a portable LAMP device for the monitoring of Leishmania infection. The LAMP assay performed using our device can detect and amplify as little as 100 femtograms of L. donovani DNA. In a preliminary study, we have shown that the device can also amplify L. donovani DNA present in VL and PKDL patient samples with high sensitivity (100%), specificity (98%) and accuracy (99%), and can be used both for diagnostic and prognostic analysis. To our knowledge, this is the first report to describe the development and application of a portable LAMP device which has the potential to evolve as a point-of-care diagnostic and prognostic tool for Leishmania infections in future.

Metastable biomolecular condensates of interferon-inducible antiviral Mx-family GTPases: A paradigm shift in the last three years

Abstract: Membraneless organelles (MLOs) in the cytoplasm and nucleus in the form of phase-separated biomolecular condensates are increasingly viewed as critical in regulating diverse cellular functions. We summarize a paradigm shift over the last 3 years in the field of interferon (IFN)-inducible antiviral Mx-family GTPases. Expression of the ‘myxovirus resistance proteins’ MxA in human cells and its ortholog Mx1 in murine cells is increased 50- to 100-fold by Type I (IFN-α and -β) and III IFNs (IFN-λ). Human MxA forms cytoplasmic structures, while murine Mx1 forms nuclear bodies. Since 2002, it has been widely thought that human (Hu) MxA is associated with the membraneous smooth endoplasmic reticulum (ER). In a paradigm shift, our recent data showed that HuMxA formed membraneless phase-separated biomolecular condensates in the cytoplasm. Some of the HuMxA condensates adhered to intermediate filaments generating a reticular pattern. Murine (Mu) Mx1, which was predominantly nuclear, was also confirmed to be in phase-separated nuclear biomolecular condensates. A subset of Huh7 cells showed association of GFP-MuMx1 with intermediate filaments in the cytoplasm. While cells with cytoplasmic GFP-HuMxA condensates and cytoplasmic GFP-MuMx1 filaments showed an antiviral phenotype towards vesicular stomatitis virus (VSV), those with only nuclear GFP-MuMx1 bodies did not. The new data bring forward the paradigm that both human MxA and murine Mx1 give rise to phase-separated biomolecular condensates, albeit in different subcellular compartments, and that differences in the subcellular localization of condensates of different Mx proteins determines the spectrum of their antiviral activity.

MiR-296-3p inhibits cell proliferation by the SOX4-Wnt/β-catenin pathway in triple-negative breast cancer

Abstract: MicroRNAs (miRNAs) have been demonstrated to play critical roles in the tumorigenesis of triple-negative breast cancer (TNBC). In this work, we addressed the sepecific role of miR-296-3p in TNBC. The levels of miR-296-3p and SOX4 were determined using RT-qPCR. The function of miR-296-3p overexpression on TNBC cell proliferation, migration, invasion, cancer stem cell (CSC)-like proterties, and Wnt pathway activation was investigated by MTT, EdU, wound healing, Transwell, sphere formation assays and western blot. Mechanistic investigations, including luciferase reporter, RNA pull-down, and RIP assays, were conducted to explore the regulatory mechanisms of miR-296-3p. We found that miR-296-3p was downregulated in TNBC tissues and cells. Overexpression of miR-296-3p suppressed TNBC cell proliferation, migration, invasion, and CSC-like proterties. Furthermore, miR-296-3p could bind to SOX4 and negatively modulate SOX4 expression. In addition, miR-296-3p was verified to inhibit Wnt/β-catenin pathway by downregulating SOX4. Moreover, overexpression of SOX4 or activation of Wnt pathway rescued the miR-296-3p upregulation-mediated suppressive effect on cellular processes in TNBC. In conclusion, miR‑296‑3p inhibits Wnt/β-catenin pathway by targeting SOX4 and exerts anti-tumor effects in TNBC.

Knockdown of circ_0008344 contributes to radiosensitization in glioma via miR-433-3p/RNF2 axis.

Abstract: Numerous studies have identified that circular RNAs (circRNAs) functioned as important regulators in tumor initiation, carcinogenesis, drug or radiation resistance. This study aims to reveal the function of circ_0008344 on radiosensitivity in glioma. The quantitative real-time polymerase chain reaction (qRT-PCR) was implemented for detecting the circ_0008344 and microRNA-433-3p (miR-433-3p) levels. Cell survival intensity and apoptosis were analyzed through colony formation assay and flow cytometry respectively. The protein levels were examined via Western blot. Dual-luciferase reporter assay was exploited for the analysis of target combination. Xenograft models were established in mice for circ_0008344 research in vivo. Our data showed that circ_0008344 level was signally increased in radioresistant glioma tissues and its down-regulation facilitated the susceptibility of glioma cells to radiation. Additionally, we found that circ_0008344 could interact with miR-433-3p and regulated radiosensitivity of glioma cells via sponging miR-433-3p. Ring finger protein 2 (RNF2) was proved to be a target of miR-433-3p and it was regulated by circ_0008344/miR-433-3p axis. The promotion of circ_0008344 knockdown on radiosensitivity was counteracted by RNF2 overexpression in glioma cells. Further experiment in vivo indicated that circ_0008344 down-regulation inhibited glioma growth and acted on miR-433-3p/RNF2 axis to enhance the radiosensitivity in glioma. These evidences manifested that knockdown of circ_0008344 exerted the radiosensitivity-promoting effect on glioma via the miR-433-3p-mediated RNF2 down-regulation, identifying circ_0008344 as a novel diagnostic biomarker of radioresistance and therapeutic target in glioma radiotherapy.

Metabolite profiling of violet, white and pink flowers revealing flavonoids composition patterns in Rhododendron pulchrum Sweet.

Abstract: Flower color is the major characteristics and critical breeding program for most Rhododendron species. However, little is known about their coloration mechanism and color inheritance. In this study, petal pigment constituents of three Rhododendron pulchrum Sweet cultivars with different colors were clarified based on LCESI- MS/MS method. Using a broad-targeted metabolomic approach, a total of 149 flavonoids and their glycosylated or methylated derivatives were identified, including 18 anthocyanins (Pg, Cy, Dp, Pn, Pt, and Mv) and 32 flavonols (mainly kaempferol 3-O-glycosides and quercetin 3-O-glycosides). Moreover, anthocyanins were mainly represented by anthocyanidin-3-O-glycosides (glucoside, rutinoside, galactoside, and di-glycosides). Flavone and C-glycosylated flavone were major second metabolites responsible for the difference among three different R. pulchrum cultivars. The accumulation of total flavonoids displayed a clear phenotypic variation: cultivars 'zihe' and 'fenhe' were clustered together, while 'baihe' was clustered alone in the HCA analysis. The composition and content of anthocyanins were more complex in colored flowers ('zehe' and 'fenhe') than in white flower ('baihe'). This study further enhanced our understanding on the flavonoids profile of flower coloration and will provide biochemical basis for further genetic breeding in Rhododendron species.

Connecting primitive phase separation to biotechnology, synthetic biology, and engineering

Abstract: One aspect of the study of the origins of life focuses on how primitive chemistries assembled into the first cells on Earth and how these primitive cells evolved into modern cells. Membraneless droplets generated from liquid-liquid phase separation (LLPS) are one potential primitive cell-like compartment; current research in origins of life includes study of the structure, function, and evolution of such systems. However, the goal of primitive LLPS research is not simply curiosity or striving to understand one of life’s biggest unanswered questions, but also the possibility to discover functions or structures useful for application in the modern day. Many applicational fields, including biotechnology, synthetic biology, and engineering, utilize similar phase-separated structures to accomplish specific functions afforded by LLPS. Here, we briefly review LLPS applied to primitive compartment research and then present some examples of LLPS applied to biomolecule purification, drug delivery, artificial cell construction, waste and pollution management, and flavor encapsulation. Due to a significant focus on similar functions and structures, there appears to be much for origins of life researchers to learn from those working on LLPS in applicational fields, and vice versa, and we hope that such researchers can start meaningful cross-disciplinary collaborations in the future.

Dietary conjugated linoleic acid and medium-chain triglycerides for obesity management

Abstract: Obesity is considered a serious global health issue. Patients have been predisposed to comorbidities such as dyslipidemia, cardiovascular diseases, diabetes, cancers, and osteoarthritis. Certain fats in the diet have been linked with an increase in obesity, such as saturated and trans-fats. Meanwhile, some dietary fats such as conjugated linoleic acids (CLAs) and medium-chain triglycerides (MCTs) could potentially reduce energy intake. Various mechanisms for reducing weight by CLAs and MCTs, such as increased lipolysis, improved intestinal microbiota, up-regulating peroxisome proliferator-activated receptors (PPARs), increased the expression of uncoupling protein of respiratory chain-1 (UCP-1), and affected satiety hormones are included. These bioactive compounds, CLAs and MCTs, should be used in moderate concentrations to prevent harmful effects such as insulin resistance for CLAs and hypercholesterolemia for MCTs. However, several studies have proposed CLAs or MCTs as adjuvants to the protocol used to minimize bodyweight. Our objective is to summarize the different causes of obesity and to discuss the effects of CLAs or MCTs on body weight and fat deposition in obese animals or humans.

Prenatal stress effects on offspring brain and behavior: Mediators, alterations and dysregulated epigenetic mechanisms.

Abstract: Prenatal environment significantly influences mammalian fetal development and adverse in utero conditions have life-long consequences for the offspring health. Research has revealed that a wide variety of prenatal stress factors lead to increased risk of vulnerability to neuropsychiatric disorders in the individuals. Multiple mediators are involved in stress transfer from mother to the developing fetus, with stress hormone cortisol being a chief player. Further, the developmental programming effects of prenatal stress have been observed in the form of alterations in the offspring brain at different levels. This review covers stress transfer mediators such as cortisol, serotonin, maternal cytokines, reactive oxygen species (ROS) and the maternal microbiota, and their role in fetal programming. Prenatal stress leads to alterations in the offspring brain at multiple levels, from molecular and cellular to structural. These alterations eventually result in lasting phenotypic alterations such as in the offspring behavior and cognition. Different brain alterations induced by prenatal stress such as in neural pruning processes, neural circuit formation, brain structural connectivity and epigenetic systems regulating neural gene expression are under focus in the second part of the review. The latter constitutes a key molecular mechanism involved in prenatal stress effects and has been discussed in more detail.

Central nervous system as a target of novel coronavirus infections: Potential routes of entry and pathogenic mechanisms

Abstract: Since the COVID-19 pandemic started in December 2019, there have been several reports of patients succumbing to neurological complications. Early reports were suggestive of a possibility, while by early 2020 it was clearly evident that although SARS-CoV-2 primarily attacks the respiratory system, the brain is one of the most affected organs post-recovery. Although it may be premature to comment on the long-term effects of COVID-19 in brain, some reliable predictions can be made based on the data currently available. Further, exploring the CNS connections of SARS-CoV-2 is of keen interest for neuroscience researchers. As soon as the virus enters the nasal region, it is exposed to the olfactory nervous system which is interlinked with the visual system, and hence we explore the mechanism of entry of this virus into CNS, including brain, olfactory and retinal nervous systems. In this review, we have thoroughly reviewed reports about both SARS-CoV-1 and SARS-CoV-2 with respect to their ability to breach the blood-brain and blood-retinal barriers. We have compiled different neurological conditions resulting from COVID-19 and looked into viral infections related to COVID-19 to understand how the virus may gain control of the olfactory and visual systems. Once the dust settles on the pandemic, it would be interesting to explore the extent of viral infection in the CNS. The longterm effects of this virus in the CNS are not yet known, and several scientific research papers evolving in this field will throw light on the same.