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Physiological response and transcriptome changes were observed to investigate the effects on the growth, metabolism and genetic changes of

Global climate change is heavily affected by an increase in CO2. As one of several efforts to cope with this, research on poplar, a representative, fast growing, and model organism in plants, is actively underway. The effects of elevated atmospheric CO2 on the metabolism, growth, and transcriptome of poplar were investigated to predict productivity in an environment where CO2 concentrations are increasing. Poplar trees were grown at ambient (400 ppm) or elevated CO2 concentrations (1.4× ambient, 560 ppm, and 1.8× ambient, 720 ppm) for 16 weeks in open-top chambers (OTCs). We analyzed the differences in the transcriptomes of Populusalba × Populus glandulosa clone “Clivus” and Populus euramericana clone “I-476” using high-throughput sequencing techniques and elucidated the functions of the differentially expressed genes (DEGs) using various functional annotation methods. About 272,355 contigs and 207,063 unigenes were obtained from transcriptome assembly with the Trinity assembly package. Common DEGs were identified which were consistently regulated in both the elevated CO2 concentrations. In Clivus 29, common DEGs were found, and most of these correspond to cell wall proteins, especially hydroxyproline-rich glycoproteins (HRGP), or related to fatty acid metabolism. Concomitantly, in I-476, 25 were identified, and they were related to heat shock protein (HSP) chaperone family, photosynthesis, nitrogen metabolism, and carbon metabolism. In addition, carbohydrate contents, including starch and total soluble sugar, were significantly increased in response to elevated CO2. These data should be useful for future gene discovery, molecular studies, and tree improvement strategies for the upcoming increased-CO2 environments.

Antimicrobial peptides (AMPs) are the frontline innate defense system evolutionarily preserved in insects to combat invading pathogens. These AMPs could serve as an alternative to classical antibiotics to overcome the burden of treating multidrug resistant bacteria. Psacotheasin, a knottin type AMP was isolated from Psacothea hilaris and shown to exhibit antimicrobial activity, especially against fungi through apoptosis mediated cell death. In this study, we aimed to identify novel probable AMPs from Psacothea hilaris, the yellow spotted longicorn beetle. The beetle was immunized with the two bacterial strains (E. coli and S. aureus), and the yeast strain C. albicans. After immunization, total RNA was isolated and sequenced in Illumina platform. Then, beetle transcriptome was de novo assembled and searched for putative AMPs with the known physiochemical features of the AMPs. A selection of AMP candidates were synthesized and tested for antimicrobial activity. Four peptides showed stronger activity against E. coli than the control AMP, melittin while one peptide showed similar activity against S. aureus. Moreover, four peptides and two peptides showed antifungal activity stronger than and similar to melittin, respectively. Collectively one peptide showed both antibacterial and antifungal activity superior to melittin, thus, it provides a potent antimicrobial peptide. All the peptides showed no hemolysis in all the tested concentrations. These results suggest that in silico mining of insects&rsquo, transcriptome could be a promising tool to obtain and optimize novel AMPs for human needs.

The isomers of citral (cis-citral and trans-citral) were isolated from the Cymbopogon citratus (DC.) Stapf oil demonstrates many therapeutic properties including anticancer properties. However, the effects of citral on suppressing human prostate cancer and its underlying molecular mechanism have yet to be elucidated. The citral was isolated from lemongrass oil using various spectroscopic analyses, such as electron ionized mass spectrometry (EI-MS) and nuclear magnetic resonance (NMR) spectroscopy respectively. We carried out 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay to evaluate the cell viability of citral in prostate cancer cells (PC-3 and PC3M). Furthermore, to confirm that PC3 undergoes apoptosis by inhibiting lipogenesis, we used several detection methods including flow cytometry, DNA fragmentation, Hoechst staining, PI staining, oil staining, qPCR, and Western blotting. Citral impaired the clonogenic property of the cancer cells and altered the morphology of cancer cells. Molecular interaction studies and the PASS biological program predicted that citral isomers tend to interact with proteins involved in lipogenesis and the apoptosis pathway. Furthermore, citral suppressed lipogenesis of prostate cancer cells through the activation of AMPK phosphorylation and downregulation of fatty acid synthase (FASN), acetyl coA carboxylase (ACC), 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGR), and sterol regulatory element-binding protein (SREBP1) and apoptosis of PC3 cells by upregulating BAX and downregulating Bcl-2 expression. In addition, in silico studies such as ADMET predicted that citral can be used as a safe potent drug for the treatment of prostate cancer. Our results indicate that citral may serve as a potential candidate against human prostate cancer and warrants in vivo studies.

Background Coumarin plays a vital role in drug discovery process due to its diverse biologically active components. Recently, coumarin derivatives are paying attention to treat various diseases including cancer. The effect of coumarin derivatives on gastric cancer is not well established although gastric cancer being the fourth leading cancer. Therefore, we attempt to study the effect of styrene substituted biscoumarin (SSBC) to induce apoptosis and inhibit cancer proliferation using in silico and in vitro approaches. Methods We performed 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay to identify the anti-proliferative activity of SSBC in stomach cancer cell lines (AGS) and toxicity of the compared was also assessed using lung normal cell lines (L-132 and MRC-5). A docking study was carried out between anti-apoptotic protein (BCL2) and SSBC compound. Furthermore, we analyzed the drug likeliness by screening pharmacological properties (ADME) and biological activity of SSBC by performing spectrum prediction analysis (PASS). The apoptotic effect of SSBC in AGS cell lines were detected using flow cytometry (FACS), Hoechst staining and DAPI/PI staining. Later, the regulation of apoptotic pathway by SSBC was also confirmed by qRT-PCR and western blotting analysis. Results The inhibition concentration (IC50) of SSBC was assayed against AGS and lung normal cell lines (L-132 and MRC-5). The IC50 value of SSBC toward AGS, L -132 and MRC-5 was 4.56, 268 and 285 μg/ml, respectively. In silico analysis predicted SSBC could bind to the active site of BH3 domain of anti-apoptotic protein and thus resulted in apoptotic mediated cell death. ADME prediction of SSBC exhibit strong binding capacity of 99.08% and showed absorption rate about 95.57% in the intestine. In addition, biological activity of SSBC was also predicted using PASS program and we found SSBC exhibit high activity for various cancer related protein expression including apoptosis pathway proteins such as caspase 3 stimulant, apoptosis agonist. Furthermore, apoptosis of AGS was also assessed using Hoechst staining, DAPI/PI analysis, flow-cytometric analysis, qRT-PCR and western blot analysis. Conclusion Our study denotes that SSBC could be very effective against AGS by inducing apoptosis through intrinsic pathway and recommended for in vivo and human trials.

Fleshy fruits are the most demanded fruits because of their organoleptic qualities and nutritional values. The genus Prunus is a rich source of diversified stone/drupe fruits such as almonds, apricots, plums, sweet cherries, peaches, and nectarines. The fruit-ripening process in Prunus involves coordinated biochemical and physiological changes resulting in changes in fruit texture, aroma gain, color change in the pericarp, sugar/organic acid balance, fruit growth, and weight gain. There are different varieties of peaches with unique palatable qualities and gaining knowledge in the genetics behind these quality traits helps in seedling selection for breeding programs. In addition, peaches have shorter post-harvest life due to excessive softening, resulting in fruit quality reduction and market loss. Many studies have been executed to understand the softening process at the molecular level to find the genetic basis. To summarize, this review focused on the molecular aspects of peach fruit quality attributes and their related genetics to understand the underlying mechanisms.

Classical antibiotics are the foremost treatment strategy against microbial infections. Overuse of this has led to the evolution of antimicrobial resistance. Antimicrobial peptides (AMPs) are natural defense elements present across many species including humans, insects, bacteria, and plants. Insect AMPs are our area of interest, because of their stronger abilities in host defense. We have deciphered AMPs from an endangered species Parnassius bremeri, commonly known as the red spotted apollo butterfly. It belongs to the second largest insect order Lepidoptera, comprised of butterflies and moths, and lives in the high altitudes of Russia, China, and Korea. We aimed at identifying the AMPs from the larvae stages. The rationale of choosing this stage is that the P. bremeri larvae development occurs at extremely low temperature conditions, which might serve as external stimuli for AMP production. RNA was isolated from larvae (L1 to L5) instar stages and subjected to next generation sequencing. The transcriptomes obtained were curated in in-silico pipelines. The peptides obtained were screened for requisite AMP physicochemical properties and in vitro antimicrobial activity. With the sequential screening and validation, we obtained fifteen candidate AMPs. One peptide TPS–032 showed promising antimicrobial activity against Porphyromonas gingivalis, a primary causative organism of periodontitis.

Background Phyllanthus emblica L. (Indian gooseberry) is widely used in the Ayurveda for thousands of years to treat health complications including disorders of the immune system, diabetes, and obesity. Purpose For the first time, our study aims to demonstrate the molecular mechanisms of the fruit extract of Phyllanthus emblica (PEFE) involved in the promotion of fat cell apoptosis and alleviation of adipogenesis. Methods The active constituents from PEFE were identified using high performance liquid chromatography-mass spectrometry (HPLC-MS). We carried out the 3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyl tetrazolium bromide (MTT) assay to evaluate the cytotoxic effects of PEFE using 3T3-L1 pre-adipocytes. The colonogenic assay was carried out to determine the inhibitory effect of 3T3-L1 adipocytes after PEFE treatment. In addition, inhibition of pancreatic lipase activity was performed and the lipolytic activity of PEFE and digallic acid was compared with the well-known standard drug orlistat. Besides, the molecular interaction and ligand optimization between digallic and adipogenesis/apoptosis markers were also carried out. Furthermore, to confirm fat cell apoptosis we have used several detection methods that includes Hoechst staining, PI staining, Oil staining and qPCR respectively. Results Digallic acid was identified as a major component in the PEFE. The IC50 values of digallic acid and PEFE were found to be 3.82 µg/ml and 21.85 µg/ml respectively. PEFE and digallic acid showed significant anti-lipolytic activity compared to the standard drug orlistat. In the mature adipocytes, PEFE significantly decreased triglyceride accumulation by downregulating adiponectin, PPARγ, cEBPα, and FABP4 respectively. We further analyzed the expression of apoptosis related genes upon PEFE treatment. Apoptotic process initiated through upregulation of BAX and downregulation of BCL2 resulting in an increased caspase-3 activity. In addition, we have also confirmed the apoptosis and DNA fragmentation in 3T3-L1 cells using Hoechst, PI and TUNEL assays. Conclusion PEFE negatively regulates adipogenesis by initiating fat cell apoptosis and therefore it can be considered as a potential herbal medicinal product for treating obesity.

The isomers of citral (cis-citral and trans-citral) were isolated from the Cymbopogon citratus (DC.) Stapf oil demonstrates many therapeutic properties including anticancer properties. However, the effects of citral on suppressing human prostate cancer and its underlying molecular mechanism have yet to be elucidated. The citral was isolated from lemongrass oil using various spectroscopic analyses, such as electron ionized mass spectrometry (EI-MS) and nuclear magnetic resonance (NMR) spectroscopy respectively. We carried out 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay to evaluate the cell viability of citral in prostate cancer cells (PC-3 and PC3M). Furthermore, to confirm that PC3 undergoes apoptosis by inhibiting lipogenesis, we used several detection methods including flow cytometry, DNA fragmentation, Hoechst staining, PI staining, oil staining, qPCR, and Western blotting. Citral impaired the clonogenic property of the cancer cells and altered the morphology of cancer cells. Molecular interaction studies and the PASS biological program predicted that citral isomers tend to interact with proteins involved in lipogenesis and the apoptosis pathway. Furthermore, citral suppressed lipogenesis of prostate cancer cells through the activation of AMPK phosphorylation and downregulation of fatty acid synthase (FASN), acetyl coA carboxylase (ACC), 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGR), and sterol regulatory element-binding protein (SREBP1) and apoptosis of PC3 cells by upregulating BAX and downregulating Bcl-2 expression. In addition, in silico studies such as ADMET predicted that citral can be used as a safe potent drug for the treatment of prostate cancer. Our results indicate that citral may serve as a potential candidate against human prostate cancer and warrants in vivo studies.

An insect’s innate immune system is the front line of defense against many invading microorganisms. One of the important components of this defense system is antimicrobial peptides (AMPs). Papiliocin is a well-studied antimicrobial peptide (AMP) isolated from the swallowtail butterfly, Papilio xuthus, and it was previously reported to be effective against Gram-positive bacteria, Gram-negative bacteria, and fungi, particularly in drug resistant Gram-negative bacteria. Hence, we aimed to identify novel AMPs from Papilio xuthus using its transcriptome. We immunized the swallowtail butterfly with Escherichia coli, Staphylococcus aureus, Candida albicans, and the total RNA was isolated. De novo transcriptome assembly and functional annotations were conducted, and AMPs were predicted using an in-silico pipeline. The obtained 344,804,442 raw reads were then pre-processed to retrieve 312,509,806 (90.6%) total clean reads. A total of 38,272 unigenes were assembled with the average length of 1010 bp. Differential gene expression analysis identified 584 and 1409 upregulated and downregulated genes, respectively. The physicochemical, aggregation, and allergen propensity were used as filtration criteria. A total of 248 peptides were predicted using our in-house pipeline and the known AMPs were removed, resulting in 193 novel peptides. Finally, seven peptides were tested in vitro and three peptides (Px 5, 6, and 7) showed stronger antimicrobial activity against Gram-negative bacteria and yeast. All the tested peptides were non-allergens. The identified novel AMPs may serve as potential candidates for future antimicrobial studies.

The purpose of this study was to evaluate the anticancer efficacy of interferon β in combination with low dose of cisplatin on human cervical cancer progression, as well as its principal action mechanism. The combination treatment synergistically potentiated the effect of interferon β on cell growth inhibition and DNA damage on HeLa cells by repressing NF-κB/p-Akt signaling. Synergistic targeting of these pathways has a therapeutic potential. Further, the combination treatment ameliorated the expression of pro-apoptotic Bax, and decreased the expression of anti-apoptotic protein Bcl-2. Additionally, the expression of active PARP was significantly increased and MMP-9 level was decreased in combination group as compared to the expression seen for the treatment with interferon β or cisplatin alone. Results demonstrate that the synergistic inhibitory effects of interferon β and low dose of cisplatin on human cervical cancer cells and also suggest that the inhibition of NF-κB/p-Akt signaling pathway plays a critical role in the anticancer effects of combination treatment along with the induction of PARP. Therefore, the combination of interferon β and cisplatin may be a useful treatment for human cervical cancer, with a greater effectiveness than other treatments.

Context: Alzheimer’s disease (AD) is the most common form of dementia affecting the aged population and neuroinflammation is one of the most observed AD pathologies. NF-κB is the central regulator of inflammation and inhibitor κB kinase (IKK) is the converging point in NF-κB activation. Celastrol is a natural triterpene used as a treatment for inflammatory conditions. Objective: This study determines the neuroprotective and inhibitory effect of celastrol on amyloid beta1-42 (Aβ1-42) induced cytotoxicity and IKKβ activity, respectively. Materials and methods: Retinoic acid differentiated IMR-32 cells were treated with celastrol (1 μM) before treatment with Aβ1-42 (IC30 10 μM) for 24 h. The cytotoxicity and IKK phosphorylation were measured by MTT and western blotting analysis, respectively. We screened 36 celastrol analogues for the IKKβ inhibition by molecular docking and evaluated their drug like properties to delineate the neuroprotective effects. Results: Celastrol (1 μM) inhibited Aβ1-42 (10 μM) induced IκBα phosphorylation and protected IMR-32 cells from cell death. Celastrol and 25 analogues showed strong binding affinity with IKKβ as evidenced by strong hydrogen-bonding interactions with critical active site residues. All the 25 analogues displayed strong anti-inflammatory properties but only 11 analogues showed drug-likeness. Collectively, molecule 15 has highest binding affinity, CNS activity and more drug likeness than parent compound celastrol. Discussion and conclusion: The decreased expression of pIκBα in celastrol pretreated cells affirms the functional representation of inhibited IKKβ activity in these cells. The neuroprotective potentials of celastrol and its analogues may be related to IKK inhibition.

Powdery mildew is one of the most common fungal diseases in the world. This disease frequently affects melon (Cucumis melo L.) and other Cucurbitaceous family crops in both open field and greenhouse cultivation. One of the goals of genomics is to identify the polymorphic loci responsible for variation in phenotypic traits. In this study, powdery mildew disease assessment scores were calculated for four melon accessions, ‘SCNU1154’, ‘Edisto47’, ‘MR-1’, and ‘PMR5’. To investigate the genetic variation of these accessions, whole genome re-sequencing using the Illumina HiSeq 2000 platform was performed. A total of 754,759,704 quality-filtered reads were generated, with an average of 82.64% coverage relative to the reference genome. Comparisons of the sequences for the melon accessions revealed around 7.4 million single nucleotide polymorphisms (SNPs), 1.9 million InDels, and 182,398 putative structural variations (SVs). Functional enrichment analysis of detected variations classified them into biological process, cellular component and molecular function categories. Further, a disease-associated QTL map was constructed for 390 SNPs and 45 InDels identified as related to defense-response genes. Among them 112 SNPs and 12 InDels were observed in powdery mildew responsive chromosomes. Accordingly, this whole genome re-sequencing study identified SNPs and InDels associated with defense genes that will serve as candidate polymorphisms in the search for sources of resistance against powdery mildew disease and could accelerate marker-assisted breeding in melon.