Distinct evolution of toll-like receptor signaling pathway genes in cetaceans Abstract Background The relatively rapid spread and diversity of marine pathogens posed an initial and ongoing challenge for cetaceans (whales, dolphins, and porpoises), descendants of terrestrial mammals that transitioned from land to sea approximately 56 million years ago. Toll-like receptors (TLRs) play important roles in regulating immunity against pathogen infections by detecting specific molecular patterns and activating a wide range of downstream signaling pathways. The ever-increasing catalogue of mammalian genomes offers unprecedented opportunities to reveal genetic changes associated with evolutionary and ecological processes. Objective This study aimed to explore the molecular evolution of TLR signaling pathway genes in cetaceans. Methods Genes involved in the TLR signaling pathway were retrieved by BLAST searches using human coding sequences as queries. We tested each gene for positive selection along the cetacean branches using PAML and Hyphy. Physicochemical property changes of amino acids at all positively selected residues were assessed by TreeSAAP and visualized with WebLogo. Bovine and dolphin TLR4 was assessed using human embryonic kidney cell line HEK293, which lacks TLR4 and its co-receptor MD-2. Results We demonstrate that eight TLR signaling pathway genes are under positive selection in cetaceans. These include key genes in the response to Gram-negative bacteria: TLR4, CD14, and LY96 (MD-2). Moreover, 41 out of 65 positively selected sites were inferred to harbor substitution that dramatically changes the physicochemical properties of amino acids, with most of them situated in or adjacent to functional regions. We also found strong evidence that positive selection occurred in the lineage of the Yangtze finless porpoise, likely reflecting relatively recent adaptions to a freshwater milieu. Species-specific differences in TLR4 response were observed between cetacean and terrestrial species. Cetacean TLR4 was significantly less responsive to lipopolysaccharides from a terrestrial E. coli strain, possibly a reflection of the arms race of host–pathogen co-evolution faced by cetaceans in an aquatic environment. Conclusion This study provides further impetus for studies on the evolution and function of the cetacean immune system.

A thiosemicarbazone derivative induces triple negative breast cancer cell apoptosis: possible role of miRNA-125a-5p and miRNA-181a-5p Abstract Background Breast cancer, the most commonly diagnosed malignancy in women, accounts for the highest cancer-related deaths worldwide. Triple negative breast cancer (TNBC), lacking the expression of estrogen, progesterone and HER2 receptors, has an aggressive clinical phenotype and is susceptible to chemotherapy but not to hormonal or targeted immunotherapy. In an attempt to identify potent and selective anti-TNBC agents, a set of thiosemicarbazone derivatives were screened for their cytotoxic activity against MDA-MB 231 breast cancer cell line. Methods MTT assay was used to examine cell viability. P53 phosphorylation status, poly (ADP-ribose) polymerase (PARP) cleavage as well as Bcl2 and Bax protein levels were assessed by Western blot. Quantitative Real Time-PCR was carried out to characterize miRNAs expression levels. Results Combining Cisplatin + thiosemicarbazone compound 4 showed potent anti-TNBC potential. Cisplatin + compound 4 significantly enhanced p53 phosphorylation, induced Bax amount, reduced Bcl2 protein levels, enhanced PARP cleavage and modulated miRNAs expression profile in TNBCs, with a particular overexpression of miR-125a-5p and miR-181a-5p. Intriguingly, miR-125a-5p and miR-181a-5p could significantly downregulate BCL2 expression by binding to their target sites in the 3′UTR. Conclusions Collectively, our results demonstrate an anti-TNBC activity of Cisplatin + thiosemicarbazone compound 4 combination mediated via induction of apoptosis.

Transcriptome analysis to characterize the genes related to gonad growth and fatty acid metabolism in the sea urchin Strongylocentrotus intermedius Abstract Background Sea urchin gonads of both sexes, commonly termed “roe”, are highly valued seafood delicacies, and Strongylocentrotus intermedius is considered one of the tastiest sea urchins. In order to produce high-quality gonads for consumption and clarify the mechanism of gonad growth and development of the sea urchin, more genetic information, especially at the transcriptome level, is needed. Objective A more thorough understanding of sea urchin gonad growth and development in both sexes could enable regulation of these processes at several stages with the aim of suppressing gametogenesis in order to produce high-quality gonads for consumption. Methods The adult sea urchins S. intermedius were cultured for 3 months, and were sampled for the gonadal transcriptome analysis which has been performed on the RNAs of three male and female adults of S. intermedius in each gonad development stage. Results Illumina sequencing raw sequence data was deposited in the NCBI Sequence Read Archive (SRA) database (PRJNA532998). It generated 560,196,356 raw reads and 548,956,944 clean reads were acquired, which were assembled into 107,850 transcripts with 44,124 genes. Comparative analysis showed the differentially expressed genes (DEGs) from 114 to 2566. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were used to determine the functional significance of these DEGs. We have selected 9 genes related to growth and 12 genes related to fatty acid biosynthesis and metabolism in sea urchin gonads. Conclusion These data for sea urchins were intended to provide markers for gonad growth and development that can be accumulated for use in aquaculture applications.

Study on the differential gene expression of elm leaves fed on by Tetraneura akinire Sasaki Abstract Background To study the essential molecular mechanism of gall formation is very important. Objective To investigate the differential gene expression in leaves fed on by Tetraneura akinire Sasaki and to provide a basis for the better understanding of the essential molecular mechanism of gall formation. Methods The infected leaves of the elm were divided into three periods: initial formation period (T2), growth and differentiation period (T3), and cracking period (T4). The untouched leaves were used as the control (T1). RNA-Seq was performed, and the high-quality sequences were mapped to the reference genome and the elm gene database to obtain the gene expression profiles. The expression level of each gene was calculated by the RPKM method. A combination of FDR ≤ 0.01 and the absolute value of |log2 ratio (T/CK)| ≥ 2 was used as the threshold to determine the significance of gene expression. Finally, GO and pathway enrichment analyses were used to identify the significantly enriched functional classification and metabolic pathways in DEGs. Results The results revealed that approximately 244 mRNAs were detected between T1 and T2, including 192 up-regulated and 52 down-regulated mRNAs; approximately 175 mRNAs were detected between T1 and T3, including 145 up-regulated and 30 down-regulated mRNAs; and approximately 372 mRNAs were detected between T1 and T4, including 360 up-regulated and 12 down-regulated mRNAs. Approximately 34 differentially expressed genes were identified by Venn analysis. Comparing the three infection periods to the control, there were 28 up-regulated and six down-regulated mRNAs. Additionally, 562 genes were used for cluster analysis, which revealed that the gene expression in T2 and T3 changed greatly. Genes related to cell proliferation and respiration, such as microtubulin and 6-phosphoric acid fructose kinase were mainly up-regulated during the T2 period. Genes encoding lipoxygenase, glutathione-S-transferase, superoxide dismutase and protease inhibitor were up-regulated during T2 and T3. Genes encoding lignocellulose synthase were up-regulated during T4, which suggests the reinforcement of the cell wall to improve the resistance to the damage of the Tetraneura akinire Sasaki. Conclusions The results showed that the feeding of Tetraneura akinire Sasaki caused the differential expression of elm genes and influenced cellular energy metabolism. These changes in physiological response and gene expression of the elm compose the physiological and molecular basis of the gall formation and may improve the resistance of elm to Tetraneura akinire Sasaki.

A core set of microsatellite loci for yellow-throated marten, Martes flavigula : a case of inferences of family relationships Abstract Background Microsatellite markers are an ideal molecular marker for population genetic studies such as population structure, pedigree, and kinship. The yellow-throated marten (Martes flavigula) is widely distributed in coniferous and deciduous forests of eastern Asia and plays the role of an indicator and umbrella species in South Korea, given the absence of top predators such as tiger and leopard. Objective The aim of our study was to establish a core set of microsatellite markers that could be used for a population genetics study on M. flavigula. Methods We characterized 21 di-motif microsatellites for M. flavigula by Illumina next-generation sequencing. We evaluated them for a population genetics study against five established criteria together with 33 previously developed microsatellites. We calculated relatedness values between individual yellow-throated martens in two groups that were suspected to be siblings using the selected core set of markers to confirm applicability. Results Twenty-three loci were determined as the core set of microsatellite markers. The probability of identity P(ID) and probability of identity between siblings P(ID)sib of the core set was estimated as 2−15 and 2.2−7, respectively. Relatedness values between individuals in the two groups of M. flavigula revealed that one of the pairs was sisters, confirming that the core set can be applied to kinship studies. Conclusion The developed microsatellite core set in this study is expected to contribute to studies on molecular ecology and population structure of M. flavigula.

Comparative transcript profiling and cytological observation of the newly bred recessive genic male sterility non-heading Chinese cabbage ( Brassica rapa ssp. chinensis) line WS24-3A Abstract Background WS24-3A is a newly bred non-heading Chinese cabbage genic male-sterile line, in which sterility is controlled by a recessive gene, designated as Bra2ms. WS24-3A has been used for hybrid breeding. Objective To reveal the underlying molecular mechanisms responsible for the sterility of WS24-3A. Methods Cytological observation of the process of sterile/fertile anther development was performed to determine the tissue and stage in which sterility occurs. Phenotyping and transcriptomic analyses were performed to identify differentially expressed genes (DEGs) between sterile and fertile flower buds at different stages. Results Cytological analysis revealed no tetrads at stage 7 or at later stages of anther development, and the degradation of callose was delayed. Abnormal meiocytes were surrounded by sustaining callose that degenerated gradually in WS24-3A. Comparative transcript profiling identified 3282 DEGs during three anther developmental stages, namely, pre-meiotic anther, meiotic anther, and anthers with single-celled pollen stage. The difference in DEG percentage between up-regulated and down-regulated at meiotic anther stage was obviously larger than at the other two stages; further, most DEGs are important for male meiosis, callose synthesis and dissolution, and tapetum development. Ten DEGs were found to be involved in anther and pollen development, which were analyzed by quantitative PCR. Conclusion Bra2ms affected gene expression in meiocytes and associated with callose synthesis, degradation and tapetum development. Our results provide clues to elucidate the molecular mechanism of genic male sterility in non-heading Chinese cabbage.

A transcriptome analysis uncovers Panax notoginseng resistance to Fusarium solani induced by methyl jasmonate Abstract Background Panax notoginseng is a famous Chinese herbal medicine, but the root rot disease mainly caused by Fusarium solani severely reduces the yield and quality of its medicinal materials. Objective The defense priming in P. notoginseng through exogenous application of signaling molecule will supply theoretical support for the exogenous regulation of disease resistance in P. notoginseng. Methods In this study, the exogenous application of methyl jasmonate (MeJA) increased P. notoginseng’s resistance to F. solani. Furthermore, the P. notoginseng transcriptome during F. solani infection was investigated through next-generation sequencing to uncover the resistance mechanism of P. notogingseng induced by MeJA. Results The de novo assembly of transcriptome sequences produced 80,551 unigenes, and 36,771 of these unigenes were annotated by at least one database. A differentially expressed gene analysis revealed that a large number of genes related to terpenoid backbone biosynthesis, phenylalanine metabolism, and plant–pathogen interactions were predominantly up-regulated by MeJA. Moreover, jasmonic acid (JA) biosynthesis-related genes and the JA signaling pathway genes, such as linoleate 13S-lipoxygenase, allene oxide cyclase, allene oxide synthase, TIFY, defensin, and pathogenesis-related proteins, showed increased transcriptional levels after inoculation with F. solani. Notably, according to the gene expression analysis, JA and ethylene signaling pathways may act synergistically to positively regulate the defense responses of P. notoginseng to F. solani. Conclusion JA signaling appears to play a vital role in P. notoginseng responses to F. solani infection, which will be helpful in improving the disease resistance of P. notoginseng cultivars as well as in developing an environmentally friendly biological control method for root rot disease.

Up-regulation of miR-27 extenuates lipopolysaccharide-induced injury in H9c2 cells via modulating ICAM1 expression Abstract Background MiR-27 has been found to present an overt myocardial expression during cardiogenesis. However, whether miR-27 involves in myocarditis development and the possible molecular mechanism remain unknown. The purpose of this study was to investigate the biological characteristic of miR-27 in LPS-damaged H9c2 cells. Methods H9c2 cells were treated with lipopolysaccharide (LPS, 10 µg/ml) for 12 h to form cell injury. MiR-27 mimic and inhibitor were used to up-regulate or down-regulate miR-27 expression. MTT assay and flow cytometry analysis were conducted to test cell viability and apoptosis. The relative RNA expression level of miR-27 and intercellular adhesion molecule 1 (ICAM1) was determined by qRT-PCR. Luciferase reporter gene assay was utilized to confirm the interaction between miR-27 and ICAM1. Western blot was used to determine the protein expression levels. Results We observed that LPS treatment significantly decreased the level of miR-27 in H9c2 cells. Moreover, LPS exposure suppressed cell viability, promoted cell apoptosis and increased the relative expression of p-NF-κB p65/NF-κB p65 and p-IκBα/IκBα. Up-regulation of miR-27 increased cell proliferation and reduced cell apoptosis, while down-regulation of miR-27 suppressed cell growth and promoted cell apoptosis. ICAM1 was predicted and verified as a target of miR-27, and the expression of ICAM1 is negatively regulated by miR-27. The relative expression of p-NF-κB p65/NF-κB p65 and p-IκBα/IκBα was dramatically decreased by miR-27 mimic and increased by miR-27 inhibitor. Conclusion Our study illustrated that up-regulation of miR-27 exhibits a protective effect on LPS-damaged H9c2 cells, which may be achieved by regulating ICAM1 and NF-κB signaling.

Integrated analysis of quantitative proteome and transcriptional profiles reveals abnormal gene expression and signal pathway in bladder cancer Abstract Background Bladder cancer (BCa) is a tumor associated with high morbidity and mortality and its incidence is increasing worldwide. However, the pathogenesis of bladder cancer is not well understood. Objective To further illustrate the molecular mechanisms involved in the pathogenesis of BCa and identify potential therapeutic targets, we combined the transcriptomic analysis with RNA sequencing and tandem mass tags (TMT)-based proteomic methods to quantitatively screen the differentially expressed genes and proteins between bladder cancer tissues (BC) and adjacent normal tissues (AN). Results Transcriptome and proteome studies indicated 7094 differentially expressed genes (DEGs) and 596 differentially expressed proteins (DEPs) between BC and AN, respectively. GO enrichment analyses revealed that cell adhesion, calcium ion transport, and regulation of ATPase activity were highly enriched in BCa. Moreover, several key signaling pathway were identified as of relevance to BCa, in particular the ECM-receptor interaction, cell adhesion molecules (CAMs), and PPAR signaling pathway. Interestingly, 367 genes were shared by DEGs and DEPs, and a significant positive correlation between mRNA and translation profiles was found. Conclusion In summary, this joint analysis of transcript and protein profiles provides a comprehensive reference map of gene activity regarding the disease status of BCa.

Analysis of differential gene expression in cold-tolerant vs. cold-sensitive varieties of snap bean ( Phaseolus vulgaris L.) in response to low temperature stress Abstract Background Snap bean, Phaseolus vulgaris L., as a warm-season vegetable, low temperature stress seriously affect the yield and quality. At present, little is known about the genes and molecular regulation mechanism in cold response in snap bean exposed to low temperature. Objectives Our objectives were to identify the low temperature response genes in snap bean and to examine differences in the gene response between cold-tolerant and cold-sensitive genotypes. Methods We used two highly inbred snap bean lines in this study, the cold-tolerant line ‘120’, and the cold-sensitive line ‘093’. The plants were grown to the three leaf and one heart stage and exposed to 4 °C low temperature. We used RNA sequencing (RNA-seq) to analyze the differences of gene expression. Results 988 and 874 cold-responsive genes were identified in ‘T120 vs CK120’ and ‘T093 vs CK093’ (‘T’ stands for low temperature treatment, and ‘CK’ stands for control at room temperature), respectively. Of these, 555 and 442 genes were unique to cold-stressed lines ‘120’ and ‘093’, respectively compared to the control. Our analysis of these differentially expressed genes indicates that Ca2+, ROS, and hormones act as signaling molecules that play important roles in low temperature response in P. vulgaris. Altering the expression of genes in these signaling pathways activates expression of downstream response genes which can interact with other signaling regulatory networks. This may maintained the balance of ROS and hormones, making line ‘120’ more cold-tolerant than line ‘093’. Conclusion Our results provide a preliminarily understanding of the molecular basis of low temperature response in snap bean, and also establish a foundation for the future genetic improvement of cold sensitivity in snap bean by incorporating genes for cold tolerance.