Hedgehog pathway negatively regulated depleted uranium-induced nephrotoxicity.

Depleted uranium (DU) retains the radiological toxicities, which accumulates preferentially in the kidneys. Hedgehog (Hh) pathway plays a critical role in tissue injury. However, the role of Hh in DU-induced nephrotoxicity was still unclear. This study was carried out to investigate the effect of Gli2, which was an important transcription effector of Hh signaling, on DU induced nephrotoxicity. To clarify it, CK19 positive tubular epithelial cells specific Gli2 conditional knockout (KO) mice model was exposed to DU, and then histopathological damage and Hh signaling pathway activation was analyzed. Moreover, HEK-293 T cells were exposed to DU with Gant61 or Gli2 overexpression, and cytotoxicity of DU as analyzed. Results showed that DU caused nephrotoxicity accompanied by activation of Hh signaling pathway. Meanwhile, genetic KO of Gli2 reduced DU-induced nephrotoxicity by normalizing biochemical indicators and reducing Hh pathway activation. Pharmacologic inhibition of Gli1/2 by Gant61 reduced DU induced cytotoxicity by inhibiting apoptosis, ROS formation and Hh pathway activation. However, overexpression of Gli2 aggravated DU-induced cytotoxicity by increasing the levels of apoptosis and ROS formation. Taken together, these results revealed that Hh signaling negatively regulated DU-inducted nephrotoxicity, and that inhibition of Gli2 might serve as a promising nephroprotective target for DU-induced kidney injury.

Extracellular RNA profiles in non-small cell lung cancer plasma.

Background: Non-small cell lung cancer (NSCLC) has a high mortality rate and poor prognosis. The early detection of high-risk patients is essential to improve patient prognosis. Thus, the identification of a non-invasive, non-radiative, convenient, and fast diagnostic approach should be a top priority in NSCLC research. Circulating extracellular RNAs (exRNAs) in the plasma are potential biomarkers for NSCLC. Methods: We used RNA-sequencing (RNA-seq) technology to explore the NSCLC-related RNAs, especially the circular RNAs (circRNAs). The circRNA-targeted micro RNAs (miRNAs) were predicted using 3 circRNA databases [i.e., the Cancer-Specific CircRNA Database (CSCD), circBank, and Circular RNA Interactome]. The circRNA-miRNA-messenger RNA (mRNA) network was constructed using Cytoscape V3.8.0 (Cytoscape Consortium, San Diego, CA, USA). The expression levels of some differentially expressed genes were validated by a quantitative real-time polymerase chain reaction (qRT-PCR) analysis. Results: The results showed that the RNA biotypes of the mitochondrial ribosomal RNAs (mt-rRNAs) and mitochondrial transfer RNAs (mt-tRNAs) were upregulated in the NSCLC plasma. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) terms of the differentially expressed transcripts of NSCLC included oxidative phosphorylation, proton transmembrane transport, and the response to oxidative stress. Additionally, the qRT-PCR validation indicated that hsa_circ_0000722 had significantly higher expression in the NSCLC plasma than the control plasma, but hsa_circ_0006156 did not differ between the NSCLC plasma and the control plasma. The expression levels of miR-324-5p and miR-326 were higher in the NSCLC plasma than the control plasma. Conclusions: In this study, an exRNA-sequencing strategy was used to identify the expression of NSCLC-specific transcription factors in clinical plasma samples, and hsa_circ_0000722 and hsa-miR-324-5p were identified as potential biomarkers in NSCLC.

Single-cell multi-omics sequencing and its application in tumor heterogeneity.

In recent years, the emergence and development of single-cell sequencing technologies have provided unprecedented opportunities to analyze deoxyribonucleic acid, ribonucleic acid and proteins at single-cell resolution. The advancements and reduced costs of high-throughput technologies allow for parallel sequencing of multiple molecular layers from a single cell, providing a comprehensive insight into the biological state and behavioral mechanisms of cells through the integration of genomics, transcriptomics, epigenomics and proteomics information. Researchers are actively working to further improve the cost-effectiveness, stability and high-throughput capabilities of single-cell multi-omics sequencing technologies and exploring their potential in precision medicine through clinical diagnostics. This review aims to survey the cutting-edge advancements in single-cell multi-omics sequencing, summarizing the representative technologies and their applications in profiling complex diseases, with a particular focus on tumors.

N-acetyl-L-cysteine attenuated the toxicity of ZIF-8 on EA.hy926 endothelial cells by wnt/ß-catenin pathway.

As kinds of porous crystalline compounds, zeolitic imidazolate frameworks (ZIFs) have been developed quickly and attracted considerable attention for use in nano drug delivery systems, which raised concerns about cardiovascular disorders. At the present, the cytotoxic mechanism of ZIFs in cardiovascular disorders was still unclear. Our experiment explored the toxicity of ZIF-8, a typical kind of ZIFs, on human EA.hy926 vascular endothelial cells. The cell viability, ROS formation, apoptosis level, inflammatory response level, wound healing ability and atherosclerosis-related indicators of EA.hy926 endothelial cells were analyzed after ZIF-8 treatment. Meanwhile, we evaluated the ability of antioxidant N-Acetyl-L-cysteine (NAC) to attenuate the toxicity of ZIF-8 on EA.hy926 endothelial cells. As results, NAC attenuated ROS formation, cell apoptosis, LDH formation and endothelial dysfunction caused by ZIF-8. As the Wnt/ß-catenin pathway was involved in endothelial cell dysfunction, we also studied the expression level of ß-catenin and LEF1 in ZIF-8 and/or NAC treated EA.hy926 cells. As expected, ZIF-8 increased the protein expressions of ß-catenin and LEF1in the IC50 group, which was significantly inhibited by co-treatment with NAC. Taken together, this study could help improve our understanding about the mechanism of ZIF-8-induced endothelial cells injury and NAC had therapeutic potential in preventing ZIF-8-associated endothelial dysfunction by wnt/ß-catenin pathway.

Analysis approaches for the identification and prediction of N6-methyladenosine sites.

The global dynamics in a variety of biological processes can be revealed by mapping transcriptional m6A sites, in particular full-transcriptome m6A. And individual m6A sites have contributed to biological function, which can be evaluated by stoichiometric information obtained from the single nucleotide resolution. Currently, the identification of m6A sites is mainly carried out by experiment and prediction methods, based on high-throughput sequencing and machine learning model respectively. This review summarizes the recent topics and progress made in bioinformatics methods of deciphering the m6A methylation, including the experimental detection of m6A methylation sites, techniques of data analysis, the way of predicting m6A methylation sites, m6A methylation databases, and detection of m6A modification in circRNA. At the end, the essay makes a brief discussion for the development perspective in this area.

Tumor-derived exosomal HOTAIRM1 regulates SPON2 in CAFs to promote progression of lung adenocarcinoma.

OBJECTIVE: SPON2 is one of the extracellular matrix proteins, which is closely related to the progression of a variety of tumors including non-small cell lung cancer (NSCLC), but its upstream regulation mechanism remains unclear. Our research aims to find the specific regulatory pathway of SPON2 by exploring the potential crosstalk between tumor cells and cancer-associated fibroblasts (CAFs) in tumor microenvironment (TME) of NSCLC. METHODS: We analyzed T1 lung adenocarcinoma samples from TCGA and screened extracellular matrix proteins that indicate poor prognosis. Expression level of SPON2 was verified by qPCR in clinical samples. The exosomes of NSCLC cell supernatant were extracted and identified by nanoparticle tracking analysis (NTA) and transmission electron microscope, western blots. The exosomes and CAFs were co-cultured, and cell migration and Matrigel invasion assay were used to evaluate the effect of CAFs on the migration and invasion of NSCLC cells. The interaction between LncRNA and miRNA was verified by Targetscan prediction, luciferase reporter assay, and RNA binding protein immunoprecipitation (RIP). RESULTS: We found that the expression of SPON2 was up-regulated in clinical T1a stage NSCLC patients. The expression of lnc HOTAIRM1 (HOTAIRM1) in exosomes secreted by NSCLC tissues increased. After exosomal HOTAIRM1 entered CAFs, HOTAIRM1 can adsorb miR-328-5p to up-regulate the expression of SPON2 in CAFs. Up-regulation of SPON2 in CAFs could promote the migration and invasion of NSCLC cells. CONCLUSION: Tumor-derived exosomal HOTAIRM1 can transfer into CAFs and competitively adsorb miR-328-5p, and regulate the SPON2 expression of CAFs cells, ultimately promote the progression of NSCLC. The discovery of this regulatory pathway can provide a new potential therapeutic target for the diagnosis and treatment of NSCLC.

Identification of the Phosphorus-Solubilizing Bacteria Strain JP233 and Its Effects on Soil Phosphorus Leaching Loss and Crop Growth.

Phosphorus (P) is one of the most limiting nutrients in global agricultural ecosystems, and phosphorus-solubilizing bacteria (PSB) can convert insoluble P into soluble P, thereby improving the absorption and use of soil P by plants. Increasing leaching loss of soil P due to PSB that could lead to water eutrophication is a major concern, although no direct experimental evidence is available to evaluate these effects. In this study, a highly efficient PSB strain, Pseudomonas sp. JP233, was isolated from soil and its P-solubilizing agent was identified by metabolomics and HPLC analyses. The effects of JP233 on P contents in soil leachates were also analyzed by microcosm leaching experiments in the absence and presence of maize. JP233 could solubilize insoluble P into soluble forms, and the molybdate reactive phosphorus (MRP) content reached 258.07 mg/L in NBRIP medium containing 5 g/L Ca3(PO4)2 within 48 h. Metabolomics analysis demonstrated that the organic acid involved in JP233 P solubilization was primarily 2-keto gluconic acid (2KGA). Further, HPLC analysis revealed that 2KGA contents rapidly accumulated to 19.33 mg/mL within 48 h. Microcosm leaching experiments showed that MRP and total phosphorus (TP) contents in soil leaching solutions were not significantly higher after JP233 inoculation. However, inoculation with JP233 into maize plant soils significantly decreased MRP and TP contents in the soil leaching solutions on days 14 (P < 0.01), 21 (P < 0.01), and 28 (P < 0.05). Inoculation with strain JP233 also significantly increased the biomass of maize aerial components and that of whole plants (P < 0.05). Thus, strain JP233 exhibited a significant plant-growth-promoting effect on maize development. In conclusion, the application of PSB into soils does not significantly increase P leachate loss. Rather, the application of PSB can help reduce P leachate loss, while significantly promoting plant absorption and use of soil P.

Five new species of Trichoderma from moist soils in China.

Trichoderma isolates were collected from moist soils near a water source in different areas of China. ITS sequences were submitted to MIST (Multiloci Identification System for Trichoderma) and meets the Trichoderma [ITS76] standard. Combined analyses of phylogenetic analyses of both phylograms (tef1-α and rpb2) and morphological characteristics, revealed five new species of Trichoderma, namely Trichodermahailarense, T.macrofasciculatum, T.nordicum, T.shangrilaense and T.vadicola. Phylogenetic analyses showed T.macrofasciculatum and T.shangrilaense belong to the Polysporum clade, T.hailarense, while T.nordicum and T.vadicola belong to the Viride clade. Each new taxon formed a distinct clade in phylogenetic analysis and have unique sequences of tef1-α and rpb2 that meet the Trichoderma new species standard. The conidiation of T.macrofasciculatum typically appeared in white pustules in concentric rings on PDA or MEA and its conidia had one or few distinctly verrucose. Conidiophores of T.shangrilaense are short and rarely branched, phialides usually curved and irregularly disposed. The aerial mycelium of T.hailarense and T.vadicola formed strands to floccose mat, conidiation tardy and scattered in tufts, conidiophores repeatedly rebranching in dendriform structure. The phialides of T.nordicum lageniform are curved on PDA and its conidia are globose to obovoidal and large.

Nigirpexin E, a new azaphilone derivative with anti-tobacco mosaic virus activity from soil-derived fungus Trichoderma afroharzianum LTR-2.

A new compound classified as one new azaphilone derivative, nigirpexin E (1), was obtained from the soil-derived fungus Trichoderma afroharzianum LTR-2, together with seven known compounds (2-8). The structures of 1-8 were determined by their HRESIMS, optical rotation, and NMR spectroscopic data. The absolute configuration of nigirpexin E (1) was determined on the basis of comparisons of experimental and theoretically calculated ECD spectra. Compound 3 was firstly isolated from Trichoderma. Bioactivities of the isolated compounds were assayed their anti-tobacco mosaic virus (anti-TMV) activities. The results showed that compound 1 exhibited significant inactivation effect against TMV with an inhibition rate of 67.25% (0.5 mg ml-1), which was higher than that of positive control ribavirin (56.74%). This is the first report of the anti-TMV activity of azaphilone derivatives.

Tumor-associated macrophages secret exosomal miR-155 and miR-196a-5p to promote metastasis of non-small-cell lung cancer.

BACKGROUND: Understanding the molecular basis underlying metastasis of non-small cell lung cancer (NSCLC) may provide a new therapeutic modality for the treatment of NSCLC. However, the mechanisms by which tumor-associated macrophages (TAMs) affect NSCLC metastasis remain undefined. In this study, we aimed to discover a novel regulatory pathway involved in NSCLC metastasis. METHODS: Cell Counting Kit-8 (CCK-8), Transwell, western blot assays were used to assess cell viability, migration, invasion and epithelial-mesenchymal transition (EMT). Exosomes from macrophages medium were characterized, and in vitro cell coculture was further conducted to investigate M2 derived exosomes mediated crosstalk between TAMs and tumor cells. Besides, miRNA microarray was used to analyze miRNA expression profiles of M0 and M2 derived exosomes. Luciferase reporter assay was used to verify the potential binding between miRNA and mRNA. Moreover, 6-week-old male BALB/c nude mice were performed to establish transplantation tumor model using tail vein injection. Hematoxylin & eosin staining was used to detect the metastasis of tumor tissues. RESULTS: We found that M2 TAMs were the main TAMs in metastatic tissues of NSCLC patients and exosomes derived from M2 TAMs were able to promote cell viability, cell migration, cell invasion and EMT in NSCLC. We demonstrated that miR-155 and miR-196a-5p were abundant in M2 TAMs and exosomes secreted by M2 TAMs. Functional experiments demonstrated that the deletion of miR-155 and miR-196a-5p in M2 TAMs significantly prevented NSCLC metastasis in vitro and in vivo. To clarify the mechanism governing miR-155 and miR-196a-5p from M2 TAMs, we carried out bioinformatics analysis to predict potential target genes. Mechanistically, miR-155 and miR-196a-5p directly bound to the 3'-UTR of Ras association domain family member 4 (RASSF4), and negatively regulating RASSF4 expression. At last, rescue assays demonstrated that miR-155 and miR-196a-5p exerted its performance by RASSF4. CONCLUSIONS: Overall, we revealed a new regulatory pathway that was M2 TAMs secreted exosomal miR-155 and miR-196a-5p to promote NSCLC metastasis. This dynamic and reciprocal cross-talk between NSCLC and macrophages innovatively provided a potential opportunity for diagnosis and treatment of NSCLC.

First Report of Phytopythium helicoides Causing Stalk Rot on Corn in China.

Corn (Zea mays L.) is one of the most important grain crops in the world, especially in China. Besides, corn stalks are often used in production of bio-fuels (Xue et al., 2017). Recently, the production and quality of corn have been severely influenced by corn stalk rot in China caused by Fusarium spp. (Yu et al., 2017). At the end of June of 2019, a field survey of corn was carried out in Tai'an City, western Shandong Province, China. During the survey, the average day time temperature ranged between 22-28°C with intermittent rainfall, the relative humidity was 50-70%. In this survey, the symptomatic corn plants showed signs of necrosis and rotting on stalks and root collars. Five fields were surveyed and symptomatic corn plants were observed in three fields. The incidence rate of disease was about 5%, and the disease was more of a problem in low-lying areas. A total of twenty-eight symptomatic corn plants (7-12 per field), hybrid Denghai-618, at the 3-4 leaf stage were collected and tested for the presence of pathogens. The diseased tissues were excised, surface-sterilized with 75% ethanol for 30 seconds, rinsed for 3 to 5 times with sterile distilled water, and plated on potato dextrose agar (PDA). All plates were incubated at 28°C for 48 hours, emerging colonies were sub-cultured onto PDA plates. Forty-two isolates were obtained, and twenty-seven isolates were identified as Fusarium spp. The remaining fifteen isolates had similar morphology, with colonies that were white and cottony in texture after incubation at 28°C for three days on PDA. The suitable temperature range for growth of hyphae was between 15°C to 40°C, and sporangia were ellipsoidal, papillate, and 23 - 34×21 - 31 µm in diameter. Oogonia (smooth, 22 - 30 µm in diameter) were present in the cultures after 28 days at 28°C. The isolates were identified using both morphological characteristics and DNA sequencing. Identity of the oomycete was confirmed using the BLAST algorithm available through the GenBank with the DNA sequences of rDNA internal transcribed spacer region (ITS), cytochrome c oxidase Ⅰ (coxⅠ) gene and cytochrome c oxidase Ⅱ (coxⅡ) gene, which were amplified using the primers ITS1/ITS4 (White et al. 1990), FM35/FM59 and FM66/FM58 (Martin 2000), respectively. The fifteen isolates selected for sequence analysis had identical gene sequences, and hence, only sequences for isolate RMSD1 were submitted to GenBank (ITS - MW440691, coxI - MW450815 and cox II - MW450816). The ITS, coxI and coxII sequences of the isolate RMSD1 showed 97% identity (751/774 bp), 99% identity (1087/1098 bp) and 99% identity (548/554 bp) with Phytopythium helicoides Accession nos: HQ643382, FR774199, and AB108014, respectively. The pathogenicity of RMSD1 was tested on the corn hybrid Denghai-618. Three-leaf-stage corn plants (N = 15) were inoculated with mycelial agar disks (3 to 4 mm in diameter) colonized with RMSD1 placed on their root-collars. Sterile PDA disks (3 to 4 mm in diameter) served as the negative control (N = 9). Inoculated plants were placed in the growth chamber at 28°C, 60% relative humidity, 16 h / 8 h light regime cycle. Ten days post-inoculation, the inoculated plants showed necrosis, with symptoms of stem rot similar to those observed in the field. The inoculation experiments were repeated twice with the same results, fulfilling Koch's postulates. The root-collars and stems of negative control remained asymptomatic, and P. helicoides was not isolated. Previously, P. helicoides has been reported as a pathogen of strawberry (Zhan et al. 2020) and kiwi fruits (Wang et al. 2015) from China, but not from corn. To our knowledge, it is the first report of P. helicoides causing corn stalk rot in China. In the future, P. helicoides can be considered as a potential candidate causing stem and collar-rot of corn in China, but not the only one. There are other microbes that can produce similar symptoms on corn, and control methods for pathogenic oomycetes differ from those for fungi.

Denoising Autoencoder, A Deep Learning Algorithm, Aids the Identification of A Novel Molecular Signature of Lung Adenocarcinoma.

Precise biomarker development is a key step in disease management. However, most of the published biomarkers were derived from a relatively small number of samples with supervised approaches. Recent advances in unsupervised machine learning promise to leverage very large datasets for making better predictions of disease biomarkers. Denoising autoencoder (DA) is one of the unsupervised deep learning algorithms, which is a stochastic version of autoencoder techniques. The principle of DA is to force the hidden layer of autoencoder to capture more robust features by reconstructing a clean input from a corrupted one. Here, a DA model was applied to analyze integrated transcriptomic data from 13 published lung cancer studies, which consisted of 1916 human lung tissue samples. Using DA, we discovered a molecular signature composed of multiple genes for lung adenocarcinoma (ADC). In independent validation cohorts, the proposed molecular signature is proved to be an effective classifier for lung cancer histological subtypes. Also, this signature successfully predicts clinical outcome in lung ADC, which is independent of traditional prognostic factors. More importantly, this signature exhibits a superior prognostic power compared with the other published prognostic genes. Our study suggests that unsupervised learning is helpful for biomarker development in the era of precision medicine.

MiR-486-5p Serves as a Good Biomarker in Nonsmall Cell Lung Cancer and Suppresses Cell Growth With the Involvement of a Target PIK3R1.

MicroRNAs are a class of noncoding RNAs that can be involved in the regulation of gene expression in cancers, including lung cancer. Our previous research has shown that miR-486-5p is one of the most downregulated microRNAs in tissue and serum samples of lung cancer as a good diagnostic biomarker. The objective of this study is to investigate the roles of miR-486-5p in the progression of lung cancer. In this study, miR-486-5p was further validated to be significantly downregulated in additional nonsmall cell lung cancer (NSCLC) tissue, serum, and cell samples by quantitative reverse transcription-polymerase chain reaction (RT-PCR), and the expression level of miR-486-5p was significantly associated with clinical phenotype of NSCLC. The PIK3R1 gene was confirmed to be a direct target of miR-486-5p by dual-luciferase reporter assay, and the expression level of miR-486-5p was inversely correlated with that of PIK3R1 in tumor tissues (r = -0.774, p < 0.01). Overexpressed miR-486-5p effectively inhibited cell proliferation and invasion and successfully induced apoptosis in vitro. PIK3R1 was involved in the suppression of miR-486-5p on cell growth. It can be concluded that miR-486-5p may act as a tumor suppressor contributing to the progression of NSCLC, and miR-486-5p would be a diagnostic and prognostic biomarker and a potential therapeutic target for lung cancer.

A Pathway-Based Strategy to Identify Biomarkers for Lung Cancer Diagnosis and Prognosis.

Current research has identified several potential biomarkers for lung cancer diagnosis or prognosis. However, most of these biomarkers are derived from a relatively small number of samples using algorithms at the gene level. Hence, gene expression signatures discovered in these studies have little overlaps. In this study, we proposed a new strategy to identify biomarkers from multiple datasets at the pathway level. We integrated the genome-wide expression data of lung cancer tissues from 13 published studies and applied our strategy to identify lung cancer diagnostic and prognostic biomarkers. We identified a 32-gene signature that differentiates lung adenocarcinomas from other lung cancer subtypes. We also discovered a 43-gene signature that can predict the outcome of human lung cancers. We tested their performance in several independent cohorts, which confirmed their robust prognostic and diagnostic power. Furthermore, we showed that the proposed gene expression signatures were independent of several traditional clinical indicators in lung cancer management. Our results suggest that the pathway-based strategy is useful to identify transcriptomic biomarkers from large-scale gene expression datasets that were collected from multiple sources.

Rat BodyMap transcriptomes reveal unique circular RNA features across tissue types and developmental stages.

Circular RNAs (circRNAs) are a novel class of regulatory RNAs. Here, we present a comprehensive investigation of circRNA expression profiles across 11 tissues and four developmental stages in rats, along with cross-species analyses in humans and mice. Although the expression of circRNAs is positively correlated with that of cognate mRNAs, highly expressed genes tend to splice a larger fraction of circular transcripts. Moreover, circRNAs exhibit higher tissue specificity than cognate mRNAs. Intriguingly, while we observed a monotonic increase of circRNA abundance with age in the rat brain, we further discovered a dynamic, age-dependent pattern of circRNA expression in the testes that is characterized by a dramatic increase with advancing stages of sexual maturity and a decrease with aging. The age-sensitive testicular circRNAs are highly associated with spermatogenesis, independent of cognate mRNA expression. The tissue/age implications of circRNAs suggest that they present unique physiological functions rather than simply occurring as occasional by-products of gene transcription.

Potential Diagnostic Power of Blood Circular RNA Expression in Active Pulmonary Tuberculosis.

BACKGROUND: Circular RNAs (circRNAs) are a class of novel RNAs with important biological functions, and aberrant expression of circRNAs has been implicated in human diseases. However, the feasibility of using blood circRNAs as disease biomarkers is largely unknown. METHODS: We explored the potential of using human peripheral blood mononuclear cell (PBMC) circRNAs as marker molecules to diagnose active pulmonary tuberculosis (TB). FINDINGS: First, we demonstrated that circRNAs are widely expressed in human PBMCs and that many are abundant enough to be detected. Second, we found that the magnitude of PBMC circRNAs in TB patients was higher than that in the paired healthy controls. Compared with host linear transcripts, the circRNAs within several pathways are disproportionately upregulated in active TB patients, including "Cytokine-cytokine receptor interaction", "Chemokine signaling pathway", "Neurotrophin signaling pathway", and "Bacterial invasion of epithelial cells". Based on the differentially expressed circRNAs within these pathways, we developed a PBMC circRNA-based molecular signature differentiating active TB patients from healthy controls. We validated the classification power of the PBMC circRNA signature in an independent cohort with the area under the receiver operating characteristic curve (AUC) at 0.946. INTERPRETATION: Our results suggest that PBMC circRNAs are potentially reliable marker molecules in TB diagnosis.

Metatranscriptomics analysis of cyanobacterial aggregates during cyanobacterial bloom period in Lake Taihu, China.

Molecular mechanism of interaction between the bloom-forming cyanobacterial species and attached microbios within cyanobacterial aggregates has not been elucidated yet and understanding of which would help to unravel the cyanobacteria bloom-forming mechanism. In this study, we profiled the metabolically active community by high-throughput metatranscriptome sequencing from cyanobacterial aggregates during cyanobacterial bloom period in Lake Taihu, China. A total of 308 million sequences were obtained using the HiSeq 2500 sequencing platform, which provided a great sequence coverage to carry out the in-depth taxonomic classification, functional classification, and metabolic pathway analysis of the cyanobacterial aggregates. The results show that bacteria dominated in cyanobacterial aggregates, accounting for more than 96.66% of total sequences. Microcystis was the most abundant genus, accounted for 26.80% of total assigned sequences at the genus level in cyanobacterial aggregates community; however, Proteobacteria (46.20%) was found to be as the most abundant active bacterial populations at the phylum level. More importantly, nitrogen, phosphonate, and phosphinate metabolism which associated with eutrophication were found in this study. Especially, the enzymes and organisms relating to denitrification and anammox of nitrogen metabolism, which reduced nitrogen concentration by reducing nitrate to nitrogen to inhibit the eutrophication, were first discovered in Lake Taihu during cyanobacterial bloom period. The present study provides a snapshot of metatranscriptome for cyanobacterial aggregates in Lake Taihu and demonstrates that cyanobacterial aggregates could play a key role in the nitrogen cycle in eutrophic water.

Personalized Peptide Arrays for Detection of HLA Alloantibodies in Organ Transplantation.

In organ transplantation, the function and longevity of the graft critically rely on the success of controlling immunological rejection reactivity against human leukocyte antigens (HLA). Histocompatibility guidelines are based on laboratory tests of anti-HLA immunity, which presents either as pre-existing or de novo generated HLA antibodies that constitute a major transplantation barrier. Current tests are built on a single-antigen beads (SAB) platform using a fixed set of ~100 preselected recombinant HLA antigens to probe transplant sera. However, in humans there exist a far greater variety of HLA types, with no two individuals other than identical twins who can share the same combination of HLA sequences. While advanced technologies for HLA typing and direct sequencing can precisely capture any mismatches in DNA sequence between a donor's and recipient's HLA, the SAB assay, due to its limited variety in sequence representation, is unable to precisely detect alloantibodies specifically against the donor HLA mismatches. We sought to develop a complementary method using a different technology to detect and characterize anti-donor HLA antibodies on a personalized basis. The screening tool is a custom peptide array of donor HLA-derived sequences for probing post-transplant sera of the organ recipient to assess the risk for antibody-mediated rejection. On a single array for one donor-recipient pair, up to 600 unique peptides are made based on the donor's HLA protein sequences, each peptide carrying at least one mismatched residue in a 15-amino acid sequence. In our pilot experiments to compare antigen patterns for pre- and post-transplant sera on these arrays, we were able to detect anti-HLA signals with the resolution that also allowed us to pinpoint the immune epitopes involved. These personalized antigen arrays allow high-resolution detection of donor-specific HLA epitopes in organ transplantation.

Selection of reliable reference genes for gene expression studies in Botrytis cinerea.

Botrytis cinerea is an important plant pathogen causing grey mold disease in a wide range of plant species. The aim of this study was to identify reliable reference genes that can be used for the analysis of relative gene expression in B. cinerea with quantitative real-time reverse transcription PCR (qRT-PCR). Six commonly used housekeeping genes including actin (ACT), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), ubiquitin (UBQ), ubiquitin-conjugating enzyme (UCE), α-tubulin (α-TUB) and ß-tubulin (ß-TUB) were selected to test their expression stabilities in B. cinerea treated with different concentration of oxalic acid (1, 5 and 10mM) and confronted with antagonistic Trichoderma afroharzianum. Four in silico algorithms (geNorm, BestKeeper, NormFinder and Comparative ΔCt) were applied to evaluate the expression stabilities of these genes, and the UBQ gene was identified as the most stably expressed. It was used to normalize the expression levels of three genes related to oxalic acid production (NADPH, VEL1 and OAH) when B. cinerea was challenged by T. afroharzianum. The results of this study are useful for gene expression analysis in B. cinerea.