Identification and characterisation of tobacco microRNA transcriptome using high-throughput sequencing

MicroRNAs (miRNAs) are post-transcriptional regulators that are involved in numerous biological processes in plants. In this study, we investigate miRNAs in Honghua Dajinyuan, an agronomically important species of tobacco in China. Here, we report a comprehensive analysis of miRNA expression profiles in the leaf, stem and root using a high-throughput sequencing approach. A total of 165 miRNAs, representing 55 conserved families, and 50 novel miRNAs, representing 19 families, were identified in three libraries. In addition, 12 miRNAs were randomly selected from a differentially expressed conserved miRNA family in three libraries with expression alterations and subjected to qRT-PCR validation. Of these, the expression level of nta-miR167d is highly enriched in the leaf tissue. In addition, the expression level of nta-miR319a is prominently enriched in the stem, while nta-miR160c is highly enriched in the root. Moreover, the target prediction showed that most of the targets coded for transcription factors that are involved in cellular and metabolic processes. GO analysis showed that most of the targets were involved in organelle function, served binding functions, and take part in cellular and metabolic processes. This study helps shed new light on understanding the role of miRNAs in different parts of the tobacco plant and adds a significant number of novel miRNAs to the tobacco miRNA transcriptome.

Correction: a tale of two recent spills-comparison of 2014 Galveston Bay and 2010 Deepwater Horizon Oil Spill Residues

[This corrects the article DOI: 10.1371/journal.pone.0118098.].

Long-term monitoring data to describe the fate of polycyclic aromatic hydrocarbons in Deepwater Horizon oil submerged off Alabama's beaches

The 2010 Deepwater Horizon (DWH) catastrophe had considerable impact on the ∼ 50 km long sandy beach system located along the Alabama shoreline. We present a four-year dataset to characterize the temporal evolution of various polycyclic aromatic hydrocarbons (PAHs) and their alkylated homologs trapped in the residual oil buried along the shoreline. Field samples analyzed include the first arrival oil collected from Perdido Bay, Alabama in June 2010, and multiple oil spill samples collected until August 2014. Our field data show that, as of August 2014, DWH oil is still trapped along Alabama's beaches as submerged oil, predominately in the form of surface residual oil balls (SRBs). Chemical characterization data show that various PAHs present in the spilled oil (MC252 crude) weathered by about 45% to 100% when the oil was floating over the open ocean system in the Gulf of Mexico. Light PAHs, such as naphthalenes, were fully depleted, whereas heavy PAHs, such as chrysenes, were only partially depleted by about 45%. However, the rate of PAH weathering appears to have decreased significantly once the oil was buried within the partially-closed SRB environment. Concentration levels of several heavy PAHs have almost remained constant over the past 4 years. Our data also show that evaporation was most likely the primary weathering mechanism for PAH removal when the oil was floating over the ocean, although photo-degradation and other physico-chemical processes could have contributed to some additional weathering. Chemical data presented in this study indicate that submerged oil containing various heavy PAHs (for example, parent and alkylated chrysenes) is likely to remain in the beach system for several years. It is also likely that the organisms living in these beach environments would have an increased risk of exposure to heavy PAHs trapped in the non-recoverable form of buried DWH oil spill residues.

A tale of two recent spills--comparison of 2014 Galveston Bay and 2010 Deepwater Horizon oil spill residues

Managing oil spill residues washing onto sandy beaches is a common worldwide environmental problem. In this study, we have analyzed the first-arrival oil spill residues collected from two Gulf of Mexico (GOM) beach systems following two recent oil spills: the 2014 Galveston Bay (GB) oil spill, and the 2010 Deepwater Horizon (DWH) oil spill. This is the first study to provide field observations and chemical characterization data for the 2014 GB oil spill. Here we compare the physical and chemical characteristics of GB oil spill samples with DWH oil spill samples and present their similarities and differences. Our field observations indicate that both oil spills had similar shoreline deposition patterns; however, their physical and chemical characteristics differed considerably. We highlight these differences, discuss their implications, and interpret GB data in light of lessons learned from previously published DWH oil spill studies. These analyses are further used to assess the long-term fate of GB oil spill residues and their potential environmental impacts.

Fate of Deepwater Horizon oil in Alabama's beach system: understanding physical evolution processes based on observational data

The impact of MC252 oil on northern Gulf of Mexico (GOM) beaches from the 2010 Deepwater Horizon (DWH) catastrophe was extensive along Alabama's beaches. While considerable amount of cleanup has occurred along these beaches, as of August 2014, DWH oil spill residues continue to be found as surface residual balls (SRBs), and also occasionally as submerged oil mats (SOMs). Four years of field observations informing the fate and transport of DWH SRBs in Alabama's beach system are presented here, along with a conceptual framework for describing their physical evolution processes. The observation data show that SRBs containing MC252 residues currently remain in Alabama's beach system, although their relationship to SOMs is not fully known. Based on our field observations we conclude that small DWH SRBs are likely to persist for several years along the Alabama shoreline.

Investigation of methanogenic community structures in rural biogas digesters from different climatic regions in Yunnan, southwest China

Understanding of the microbial community structures of the biogas digesters in different climatic regions can help improve the methane production in the fermentation process. The methanogenic archaeal diversity in four rural biogas digesters (BNA, JSA, LJA, and XGA) was investigated by a culture-independent rRNA approach in different climatic regions in Yunnan. Community structure composed of 711 clones in the all libraries. A total of 33 operational taxonomic units (OTUs) were detected, and major groups of methanogens were the orders Methanosarcinales and Methanomicrobiales. 63.2 % of all archaeal OTUs belong to the order Methanosarcinales which mostly contain acetotrophic methanogens. Methanomicrobiales (19.5 % in all OTUs) were detected in considerable number. Additionally, there were minor rates of uncultured archaea. The principal component analysis indicated that the genus Methanosaeta was mainly affected by the fermentation temperatures.

Immune Function Alterations during 12 Weeks of Abstinence in Heroin Users

The intent of the study was to evaluate immune system changes during 12 weeks of abstinence in heroin users. We recruited men (N = 65) aged 18-45 years and collected demographic and heroin use pattern data. Serum blood levels of total interleukin 2 (IL-2), interferon γ (IFN-γ), immunoglobulin (Ig) A, IgG, and IgM were assessed at five time points. The IL-2 level was increased on day 84 as compared to that in healthy controls. The IFN-γ level was higher in heroin users than in healthy controls between days 0 and 28, and was decreased on day 84. IgG and IgM levels in heroin users were higher than those in healthy controls in our 12-week study, and were in positive correlation with the way of using the drug, duration of heroin dependence, and daily heroin intake. Our data revealed that the immune system was not restored during the 12 weeks of heroin withdrawal.

Bone marrow mesenchymal stromal cells to treat tissue damage in allogeneic stem cell transplant recipients: correlation of biological markers with clinical responses

Bone marrow mesenchymal stromal cells (BMSCs) have been used to treat acute graft-versus-host disease (GVHD) and other complications following allogeneic hematopoietic stem cell transplantation (SCT). We conducted a phase I trial using third party, early passage BMSCs for patients with steroid-refractory GVHD, tissue injury, or marrow failure following SCT to investigate safety and efficacy. To identify mechanisms of BMSC immunomodulation and tissue repair, patients were serially monitored for plasma GVHD biomarkers, cytokines, and lymphocyte phenotype. Ten subjects were infused a fixed dose of 2 × 10(6) BMSCs/kg intravenously weekly for three doses. There was no treatment-related toxicity (primary endpoint). Eight subjects were evaluable for response at 4 weeks after the last infusion. Five of the seven patients with steroid-refractory acute GVHD achieved a complete response, two of two patients with tissue injury (pneumomediastinum/pneumothorax) achieved resolution but there was no response in two subjects with delayed marrow failure. Rapid reductions in inflammatory cytokines were observed. Clinical responses correlated with a fall in biomarkers (Reg 3α, CK18, and Elafin) relevant for the site of GVHD or tissue injury. The GVHD complete responders survived significantly longer and had higher baseline absolute lymphocyte and central memory CD4 and CD8 counts. Cytokine changes also segregated with survival. These results confirm that BMSCs are associated with rapid clinical and biomarker responses in GVHD and tissue injury. However, BMSCs were ineffective in patients with prolonged GVHD with lower lymphocyte counts, which suggest that effective GVHD control by BMSCs requires a relatively intact immune system.

Identification of a novel cytochrome P450 gene, CYP321E1 from the diamondback moth, Plutella xylostella (L.) and RNA interference to evaluate its role in chlorantraniliprole resistance

Insect cytochrome P450 monooxygenases (P450s) play an important role in catalysis of many reactions leading to insecticides resistance. Our previous studies on transcriptome analysis of chlorantraniliprole-resistant development in the diamondback moth, Plutella xylostella revealed that up-regulation of cytochrome P450s are one of the main factors leading to the development of chlorantraniliprole resistance. Here, we report for the first time a novel cytochrome P450 gene CYP321E1, which belongs to the cytochrome P450 gene family CYP321. Real-time quantitative PCR (RT-qPCR) analyses indicated that CYP321E1 was expressed at all developmental stages of P. xylostella but was highest in the fourth-instar larvae; furthermore, the relatively high expression was observed in the midgut of the fourth-instar larvae, followed by fat bodies and epidermis. The expression of CYP321E1 in P. xylostella was differentially affected by three representative insecticides, including alphamethrin, abamectin and chlorantraniliprole. Among them, the exposure to chlorantraniliprole resulted in the largest transcript level of this cytochrome P450 gene. The findings suggested potential involvement of CYP321E1 in chlorantraniliprole resistance of P. xylostella. To assess the functional link of CYP321E1 to chlorantraniliprole resistance, RNA interference (RNAi)-mediated gene silencing by double stranded RNA (dsRNA) injecting was used. Results revealed that injection delivery of dsRNA can greatly reduce gene expression after 24 h. As a consequence of RNAi, a significant increment in mortality of larvae injected CYP321E1 dsRNA was observed after 24 h of exposure to chlorantraniliprole. These results strongly support our notion that this novel cytochrome P450 gene plays an important role in chlorantraniliprole detoxification in the diamondback moth and is partly responsible for its resistance.

Abstract 1730: A study on EGFR gene amplification and protein expression in Chinese esophagus cancer patients and antitumor effect of an EGFR inhibitor in patient-derived esophagus cancer models

Esophagus cancer is the fifth most common malignancy and the fourth leading cause of cancer mortality in China. According to Chinese cancer registry annual report in 2012, esophagus cancer accounts for nearly 1 in 10 of all cancer deaths. Despite the fact that much progress has been made in diagnosis and systemic chemotherapy regimens, the overall prognosis of esophagus cancer is disappointing. The 5-year survival rate, all stages included, is around 15∼25%. There remains a significant unmet medical need for esophagus cancer treatment.

EGFR expression was reported in 30∼90% esophagus cancers and overexpression of EGFR was found to be associated with poorer survival. Unlike colon cancer, K-ras mutation was less frequently found in esophagus cancer (5∼10%), suggesting EGFR pathway blockade might bring therapeutic benefit to those patients with EGFR activation or overexpression. In this study, as of November 2013, 35 surgical esophagus tumor samples were collected from a local hospital in Shanghai. 31 of the 35 samples were identified as squamous cell carcinoma. EGFR gene amplification, protein expression and K-ras mutation were studied. In addition, 9 patient derived esophagus cancer xenograft models (PDX) were developed and anti-tumor effect of a novel and highly potent EGFR inhibitor was evaluated in 6 PDX models.

Positive EGFR protein expression was found in 66% (23/35) of esophageal cancer samples. EGFR gene amplifications were observed in 9% patients (3/35). In 9 established PDX models, 7 of them showed EGFR expression and 2 with EGFR gene amplification. No K-ras mutation was observed in the 9 models. A novel and highly potent EGFR inhibitor (EGFRi), developed by Hutchison and currently being evaluated in phase I clinical trials in China, demonstrated potent anti-tumor activity in several PDX models with tumor growth inhibition in a range of 70% to >100%. One PDX model with EGFR gene amplification and overexpression exhibited the highest sensitivity to EGFRi with remarkable tumor regression. EGFR signaling transduction was evaluated and the EGFRi inhibited phosphorylation of EGFR and downstream signaling molecules AKT and ERK.

In conclusion, EGFR expression and/or gene amplification was frequently found in Chinese esophagus cancer. EGFR inhibition resulted in potent anti-tumor effect in multiple patient derived esophagus cancer models carrying EGFR amplifications or high expression, suggesting the potential benefit that anti-EGFR agents might bring to esophagus cancer patients with abnormal EGFR activation.

Citation Format: Yongxin Ren, Jianming Zheng, Linfang Wang, Wei Zhang, Fang Yin, Jinghong Zhou, Xuelei Ge, Shiming Fan, Renxiang Tang, Junen Sun, Weiguo Qing, Weiguo Su. A study on EGFR gene amplification and protein expression in Chinese esophagus cancer patients and antitumor effect of an EGFR inhibitor in patient-derived esophagus cancer models. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1730. doi:10.1158/1538-7445.AM2014-1730

Timing and intensity of exposure to interferon-γ critically determines the function of monocyte-derived dendritic cells

A growing body of evidence suggests that inflammatory cytokines have a dualistic role in immunity. In this study, we sought to determine the direct effects of interferon-γ (IFN-γ) on the differentiation and maturation of human peripheral blood monocyte-derived dendritic cells (moDC). Here, we report that following differentiation of monocytes into moDC with granulocyte-macrophage colony-stimulating factor and interleukin-4, IFN-γ induces moDC maturation and up-regulates the co-stimulatory markers CD80/CD86/CD95 and MHC Class I, enabling moDC to effectively generate antigen-specific CD4(+) and CD8(+) T-cell responses for multiple viral and tumour antigens. Early exposure of monocytes to high concentrations of IFN-γ during differentiation promotes the formation of macrophages. However, under low concentrations of IFN-γ, monocytes continue to differentiate into dendritic cells possessing a unique gene-expression profile, resulting in impairments in subsequent maturation by IFN-γ or lipopolysaccharide and an inability to generate effective antigen-specific CD4(+) and CD8(+) T-cell responses. These findings demonstrate that IFN-γ imparts differential programmes on moDC that shape the antigen-specific T-cell responses they induce. Timing and intensity of exposure to IFN-γ can therefore determine the functional capacity of moDC.

Interaction of diet and the masou salmon Δ5-desaturase transgene on Δ6-desaturase and stearoyl-CoA desaturase gene expression and N-3 fatty acid level in common carp (Cyprinus carpio)

The masou salmon Δ5-desaturase-like gene (D5D) driven by the common carp β-actin promoter was transferred into common carp (Cyprinus carpio) that were fed two diets. For P1 transgenic fish fed a commercial diet, Δ6-desaturase-like gene (D6D) and stearoyl-CoA desaturase (SCD) mRNA levels in muscle were up-regulated (P < 0.05) 12.7- and 17.9-fold, respectively, and the D6D mRNA level in the gonad of transgenic fish was up-regulated 6.9-fold (P < 0.05) compared to that of non-transgenic fish. In contrast, D6D and SCD mRNA levels in transgenic fish were dramatically down-regulated (P < 0.05), 50.2- and 16.7-fold in brain, and 5.4- and 2.4-fold in liver, respectively, in comparison with those of non-transgenic fish. When fed a specially formulated diet, D6D and SCD mRNA levels in muscle of transgenic fish were up-regulated (P < 0.05) 41.5- and 8.9-fold, respectively, and in liver 6.0- and 3.3-fold, respectively, compared to those of non-transgenic fish. In contrast, D6D and SCD mRNA levels in the gonad of transgenic fish were down-regulated (P < 0.05) 5.5- and 12.4-fold, respectively, and D6D and SCD mRNA levels in the brain were down-regulated 14.9- and 1.4-fold (P < 0.05), respectively, compared to those of non-transgenic fish. The transgenic common carp fed the commercial diet had 1.07-fold EPA, 1.12-fold DPA, 1.07-fold DHA, and 1.07-fold higher observed total omega-3 fatty acid levels than non-transgenic common carp. Although these differences were not statistically different (P > 0.05), there were significantly (P < 0.10) higher omega-3 fatty acid levels when considering the differences for all of the individual omega-3 fatty acids. The genotype × diet interactions observed indicated that the potential of desaturase transgenesis cannot be realized without using a well-designed diet with the needed amount of substrates.

Review: Chinese herbs as alternatives to antibiotics in feed for swine and poultry production: Potential and challenges in application

Gong, J., Yin, F., Hou, Y. and Yin, Y. 2014. Chinese herbs as alternatives to antibiotics in feed for swine and poultry production: Potential and challenges in application. Can. J. Anim. Sci. 94: 223–241. Traditional Chinese medicine (TCM) has a long history of clinical practice, and its own theoretical framework focused on functions at the whole-body level. However, due to cultural differences, TCM has not been fully recognized in Western countries. With the recent development of the theory of whole-body systems biology and “-omics”, there is a new opportunity to study TCM and to close the gap between TCM and Western medicine, because of the similarity in the theoretical foundations between TCM and whole-body systems biology. The uniqueness of TCM theory and practice is the approach to maintain and restore the body balance as a whole with no or little unfavourable side effects. Recent studies have also shown that Chinese herbs used as feed additives can modulate nutritional metabolism, immune responses, and intestinal health of food-producing animals, demonstrating good potential as substitutes for dietary antibiotics. Nonetheless, some issues need to be addressed before Chinese herbs can reach their full application. This article has critically reviewed recent progresses in scientific research of Chinese herbs as feed additives and their potential to replace dietary antibiotics. Possible challenges in future application for swine and poultry production are also discussed.