Comparative Genomics and Functional Studies of Putative m6A Methyltransferase (METTL) Genes in Cotton.

N6-methyladenosine (m6A) RNA modification plays important regulatory roles in plant development and adapting to the environment, which requires methyltransferases to achieve the methylation process. However, there has been no research regarding m6A RNA methyltransferases in cotton. Here, a systematic analysis of the m6A methyltransferase (METTL) gene family was performed on twelve cotton species, resulting in six METTLs identified in five allotetraploid cottons, respectively, and three to four METTLs in the seven diploid species. Phylogenetic analysis of protein-coding sequences revealed that METTL genes from cottons, Arabidopsis thaliana, and Homo sapiens could be classified into three clades (METTL3, METTL14, and METTL-like clades). Cis-element analysis predicated the possible functions of METTL genes in G. hirsutum. RNA-seq data revealed that GhMETTL14 (GH_A07G0817/GH_D07G0819) and GhMETTL3 (GH_A12G2586/GH_D12G2605) had high expressions in root, stem, leaf, torus, petal, stamen, pistil, and calycle tissues. GhMETTL14 also had the highest expression in 20 and 25 dpa fiber cells, implying a potential role at the cell wall thickening stage. Suppressing GhMETTL3 and GhMETTL14 by VIGS caused growth arrest and even death in G. hirsutum, along with decreased m6A abundance from the leaf tissues of VIGS plants. Overexpression of GhMETTL3 and GhMETTL14 produced distinct differentially expressed genes (DEGs) in A. thaliana, indicating their possible divergent functions after gene duplication. Overall, GhMETTLs play indispensable but divergent roles during the growth of cotton plants, which provides the basis for the systematic investigation of m6A in subsequent studies to improve the agronomic traits in cotton.

Characterization of cotton ARF factors and the role of GhARF2b in fiber development.

BACKGROUND: Cotton fiber is a model system for studying plant cell development. At present, the functions of many transcription factors in cotton fiber development have been elucidated, however, the roles of auxin response factor (ARF) genes in cotton fiber development need be further explored. RESULTS: Here, we identify auxin response factor (ARF) genes in three cotton species: the tetraploid upland cotton G. hirsutum, which has 73 ARF genes, and its putative extent parental diploids G. arboreum and G. raimondii, which have 36 and 35 ARFs, respectively. Ka and Ks analyses revealed that in G. hirsutum ARF genes have undergone asymmetric evolution in the two subgenomes. The cotton ARFs can be classified into four phylogenetic clades and are actively expressed in young tissues. We demonstrate that GhARF2b, a homolog of the Arabidopsis AtARF2, was preferentially expressed in developing ovules and fibers. Overexpression of GhARF2b by a fiber specific promoter inhibited fiber cell elongation but promoted initiation and, conversely, its downregulation by RNAi resulted in fewer but longer fiber. We show that GhARF2b directly interacts with GhHOX3 and represses the transcriptional activity of GhHOX3 on target genes. CONCLUSION: Our results uncover an important role of the ARF factor in modulating cotton fiber development at the early stage.

Genome-wide characterization of the GRF family and their roles in response to salt stress in Gossypium.

BACKGROUND: Cotton (Gossypium spp.) is the most important world-wide fiber crop but salt stress limits cotton production in coastal and other areas. Growth regulation factors (GRFs) play regulatory roles in response to salt stress, but their roles have not been studied in cotton under salt stress. RESULTS: We identified 19 GRF genes in G. raimondii, 18 in G. arboreum, 34 in G. hirsutum and 45 in G. barbadense, respectively. These GRF genes were phylogenetically analyzed leading to the recognition of seven GRF clades. GRF genes from diploid cottons (G. raimondii and G. arboreum) were largely retained in allopolyploid cotton, with subsequent gene expansion in G. barbadense relative to G. hirsutum. Most G. hirsutum GRF (GhGRF) genes are preferentially expressed in young and growing tissues. To explore their possible role in salt stress, we used qRT-PCR to study expression responses to NaCl treatment, showing that five GhGRF genes were down-regulated in leaves. RNA-seq experiments showed that seven GhGRF genes exhibited decreased expression in leaves under NaCl treatment, three of which (GhGRF3, GhGRF4, and GhGRF16) were identified by both RNA-seq and qRT-PCR. We also identified six and three GRF genes that exhibit decreased expression under salt stress in G. arboreum and G. barbadense, respectively. Consistent with its lack of leaf withering or yellowing under the salt treatment conditions, G. arboreum had better salt tolerance than G. hirsutum and G. barbadense. Our results suggest that GRF genes are involved in salt stress responses in Gossypium. CONCLUSION: In summary, we identified candidate GRF genes that were involved in salt stress responses in cotton.

Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton.

Allotetraploid cotton is an economically important natural-fiber-producing crop worldwide. After polyploidization, Gossypium hirsutum L. evolved to produce a higher fiber yield and to better survive harsh environments than Gossypium barbadense, which produces superior-quality fibers. The global genetic and molecular bases for these interspecies divergences were unknown. Here we report high-quality de novo-assembled genomes for these two cultivated allotetraploid species with pronounced improvement in repetitive-DNA-enriched centromeric regions. Whole-genome comparative analyses revealed that species-specific alterations in gene expression, structural variations and expanded gene families were responsible for speciation and the evolutionary history of these species. These findings help to elucidate the evolution of cotton genomes and their domestication history. The information generated not only should enable breeders to improve fiber quality and resilience to ever-changing environmental conditions but also can be translated to other crops for better understanding of their domestication history and use in improvement.

microRNA-340 influences cell proliferation, apoptosis and invasion by targeting NF-κB1 in gastric cancer.

Gastric cancer is a serious threat to human health, and its pathogenesis may be regulated by a variety of mRNAs. Abnormal expression of microRNA-340 has been frequently reported in many malignant neoplasms, while the molecular mechanism of miR-340 has not been explored in gastric cancer. In this study, the mRNA level of miR-340 was determined by real-time PCR in GC cell lines. The miR-340 mimic was transiently transfected into GC cells by using Lipofectamine™ 2000 reagent. The BrdU-ELISA results showed that introduction of miR-340 inhibited cell proliferation. It was demonstrated that miR-340 mimic arrested cell cycle progression and promoted apoptosis of MKN-45 and BGC-823 cells. In addition, the overexpression of miR-340 could inhibit invasion and EMT of MKN-45 and BGC-823 cells. The expression of NF-κB1 was evidently reduced by up-regulation of miR-340. Luciferase reporter assay further confirmed that miR-340 could directly target the 3'UTR of NF-κB1. Moreover, overexpression of NF-κB1 transfected with miR-340 mimic partially reversed the inhibitory of miR-340 mimic in MKN-45 and BGC-823 cells. In conclusion, miR-340 induced cell apoptosis and inhibited invasion by down-regulation of NF-κB1, which might be a potential target in treatment and prevention of gastric cancer.

Role of LncRNA RP11-513G11.1 in chemoresistance and prognosis evaluation in patients with small cell lung cancer / 中国肿瘤生物治疗杂志

@#Objective: To investigate the role of LncRNA RP11-513G11.1 in the chemoresistance and evaluation of prognosis in small cell lung cancer (SCLC). Methods: From June 2012 to June 2017，98 cases of SCLC tissue, 30 cases of paracancerous tissue and 30 cases of normal lung tissue were performed by surgery, puncture biopsy or bronchoscopic biopsy from the Affiliated Hospital of Southwest Medical University. QRT-PCR was used to detect the expression of LncRNA RP11-513G11.1 in SCLC tissue, paracancerous tissue, normal lung tissue and SCLC sensitive cell strain H69, drug resistance cell strain H69AR.All patients received EP regimen (etoposide+cisplatin). According to their chemosensitivity, they were divided into chemosensitivity group and drug resistance group. The expression of LncRNA RP11-513G11.1 in two groups was detected. The relationship between RP11-513G11.1 expression and prognosis, survival time and risk factors of OS in patients were analyzed. Results: The expression of LncRNA RP11-513G11.1 in H69AR chemoresistant cells (13.790±2.830) was significantly higher than that in H69AR chemosensitive cells (1.080±0.090) (P<0.01),the expression level of LncRNA RP11-513G11.1 in SCLC tissues (8.558±1.130) was significantly higher than that in adjacent tissues (1.188±0.090) and normal lung tissues (1.636±0.150) (all P<0.01), the expression of RP11-513G11.1 in chemoresistant patients was significantly higher than that in chemosensitive patients (4.974±0.313) (P<0.01). The expression of RP11-513G11.1 was not related to gender and age, but was related to disease stage, lymph node metastasis, distant metastasis and chemotherapy resistance in SCLC patients (all P<0.05); High expression RP11-513G11.1 patients was shorter PFS [(12.59 ±2.08) months] and OS [(24.98 ±1.56) months] than those with low expression [(25.47±1.23) months] and [(39.03±2.67) months] (P<0.01). Univariate and multivariate analysis showed that RP11513G11.1 expression, disease stage and distant metastasis were independent prognostic risk factors for SCLC patients (all P<0.05). Conclusion: LncRNARP11-513G11.1 may be a potential biomarker of chemosensitivity and prognosis in SCLC patients.

99Tc-MDP-induced human osteoblast proliferation, differentiation and expression of osteoprotegerin.

The aim of the present study was to examine the influence of technetium methylenediphosphonate (99Tc-MDP) on the proliferation and differentiation of human osteoblasts. Human iliac cancellous bone was isolated and cultured with either 99Tc­MDP, ß fibroblast growth factor (as a positive control) or medium only (as a negative control). Proliferation was assessed by direct cell counting, CCK­8 assay and bromodeoxyuridine staining. The cell cycle and rate of apoptosis was assessed by propidium iodide staining and flow cytometry. Alkaline phosphatase (ALP) activity was assessed by the p­nitrophenyl phosphate method and mineralized nodules were stained with Alizarin Red. Expression of osteocalcin (OCN) and bone morphogenetic protein­2 (BMP­2) was assessed by reverse transcription­quantitative polymerase chain reaction (RT­qPCR), and expression levels of osteoprotegerin (OPG) and receptor activator of NF­κB ligand (RANKL) were assessed by RT­qPCR and ELISA. Isolated human osteoblasts stained positively for ALP and developed mineralized nodules. Treatment with 10­5­10­10 M 99Tc­MDP enhanced proliferation and 48 h incubation with 10­8 M 99Tc­MDP increased the proportion of cells in S­phase, decreased the proportion in G0/G1 phase, and increased the cell proliferation index. The rate of apoptosis also increased, but the increase was not significant. Cells incubated with 10­6­10­9 M 99Tc­MDP for 3­9 days exhibited increased ALP activity and mineralized nodule development. 10­8 M 99Tc­MDP increased BMP­2 and OPG expression levels and OPG secretion, but OCN mRNA expression levels and RANKL secretion were not significantly altered at 72 h. 99Tc­MDP treatment induced osteoblast proliferation and differentiation without affecting apoptosis. These findings provide proof of concept for the future use of 99Tc­MDP in the treatment of bone­destructive diseases.

Gossypium barbadense genome sequence provides insight into the evolution of extra-long staple fiber and specialized metabolites.

Of the two cultivated species of allopolyploid cotton, Gossypium barbadense produces extra-long fibers for the production of superior textiles. We sequenced its genome (AD)2 and performed a comparative analysis. We identified three bursts of retrotransposons from 20 million years ago (Mya) and a genome-wide uneven pseudogenization peak at 11-20 Mya, which likely contributed to genomic divergences. Among the 2,483 genes preferentially expressed in fiber, a cell elongation regulator, PRE1, is strikingly At biased and fiber specific, echoing the A-genome origin of spinnable fiber. The expansion of the PRE members implies a genetic factor that underlies fiber elongation. Mature cotton fiber consists of nearly pure cellulose. G. barbadense and G. hirsutum contain 29 and 30 cellulose synthase (CesA) genes, respectively; whereas most of these genes (>25) are expressed in fiber, genes for secondary cell wall biosynthesis exhibited a delayed and higher degree of up-regulation in G. barbadense compared with G. hirsutum, conferring an extended elongation stage and highly active secondary wall deposition during extra-long fiber development. The rapid diversification of sesquiterpene synthase genes in the gossypol pathway exemplifies the chemical diversity of lineage-specific secondary metabolites. The G. barbadense genome advances our understanding of allopolyploidy, which will help improve cotton fiber quality.

The deficiency of Gαq leads to enhanced T-cell survival.

We have previously reported that Gαq, the α subunit of the Gq protein, had important roles in dendritic cell migration, B-cell survival and autoimmunity. In this study, we showed that the deficiency of Gαq led to enhanced T-cell survival. Cultured Gnaq(-/-) T cells exhibited survival advantages both in medium alone and in the presence of anti-CD3 stimulation. Gnaq(-/-) T cells still exhibited a survival advantage when they were cultured in the presence of interleukin (IL)-2 or IL-7. Gnaq(-/-) T cells were more resistant to activation-induced cell death (AICD) in vitro. The survival advantage of Gnaq(-/-) T cells was further confirmed by transferring T cells into syngeneic hosts in vivo. Gαq deficiency might promote T-cell survival by upregulated Bcl-xL expression and downregulated Fas and FasL expressions. Furthermore, upon T-cell receptor (TCR) ligation, Akt activity was increased in Gnaq(-/-) T cells in comparison with wild-type (WT) T cells. The survival advantage of Gnaq(-/-) T cells was significantly attenuated after adding Akt inhibitor. Taken together, our data demonstrated a negative role of Gαq in regulating T-cell survival.

High throughput screening (HTS) in identification new ligands and drugable targets of G protein-coupled receptors (GPCRs).

G protein-coupled receptors (GPCRs) which constitute one of the largest and most versatile families of cell surface receptors are involved in a wide spectrum of physiological functions, such as, neuronal transmission, chemotaxis, pacemaker activity and embryonic development. Therefore, in the past a few years GPCR families have become very important targets in pharmaceutical design. However, according to the human genome project, there are approximately 1000 genes encoding GPCRs, only about 200 of GPCRs have known ligands and functions. Searching for ligands of the unknown GPCRs and better modulators of known GPCRs are currently attracting lots of interest. High throughput screening (HTS), which is commonly defined as an automatic process of testing potential drug candidates efficiently, is widely used in drug discovery. In this review, the use of high throughput screening (HTS) in studying GPCRs and the choice of screening technology in different G-protein signaling pathways were summarized.

Textiles wastewater treatment using anoxic filter bed and biological wriggle bed-ozone biological aerated filter.

In this study, the performance of the anoxic filter bed and biological wriggle bed-ozone biological aerated filter (AFB-BWB-O(3)-BAF) process treating real textile dyeing wastewater was investigated. After more than 2 month process operation, the average effluent COD concentration of the AFB, BWB, O(3)-BAF were 704.8 mg/L, 294.6 mg/L and 128.8 mg/L, with HRT being 8.1-7.7h, 9.2h and 5.45 h, respectively. Results showed that the effluent COD concentration of the AFB decreased with new carriers added and the average removal COD efficiency was 20.2%. During operation conditions, HRT of the BWB and O(3)-BAF was increased, resulting in a decrease in the effluent COD concentration. However, on increasing the HRT, the COD reduction capability expressed by the unit carrier COD removal loading of the BWB reactor increased, while that of the O(3)-BAF reactor decreased. This study is a beneficial attempt to utilize the AFB-BWB-O(3)-BAF combine process for textile wastewater treatment.

A novel anti-tissue factor monoclonal antibody with anticoagulant potency derived from synthesized multiple antigenic peptide through blocking FX combination with TF.

Tissue factor (TF) has been implicated in the pathogenesis of various thrombotic disorders. Monoclonal antibodies (mAb) that specifically target TF may have potential as antithrombotic therapy. We designed a unique TF peptide (TFP) that was specific for the binding site to factor X (FX). This peptide was used to develop TF mAb that block the coagulation cascade by interfering with the combination of FX with the TF/FVIIa complex. Chemically synthesized TFP coupled to polylysine matrix was used as multiple antigenic peptide (TF-MAP) and this was used to immunize Balb/c mice for the preparation of hybridomas. One hybridoma cell line released an antibody, named TF4A12, which had high anticoagulant potency (by dilute prothrombin time assay). Western blotting showed that TF4A12 could bind TF-MAP and the soluble TF extracellular domain (sTF(1-219)). Results of FX activation assay and amidolytic activity assay showed that the anticoagulant ability of TF4A12 is due to blocking FX, but not FVII, binding to TF. Our study identified an efficient method of developing TF mAb that could block the coagulation cascade.

Design of a novel plasminogen activator based on the structure of hirudin.

Using a phage library, seven peptide sequences with high affinity to human microplasminogen were obtained. Caseinolytic assay indicated that only the synthesized peptide P07 had slight fibrinolytic activity. To enhance its plasminogen activation ability, peptide P07 was fused into loop 32-35 of hirudin. In vitro assay demonstrated that this hirudin-like fusion protein can activate human plasminogen and retain the function of thrombin inhibition. Fusing the sequence ''SPDASRL'' into hirudin generated a plasminogen activation activity 100 times higher than peptide P07 in chromogenic and radial caseinolytic assay. This significant functional improvement might originate from a more specific active structure due to the hirudin scaffold.

Molecular design and characterization of recombinant long half-life mutants of human tissue factor pathway inhibitor.

Tissue factor pathway inhibitor (TFPI) is a physiological inhibitor of extrinsic pathway of coagulation and has biological functions of anticoagulation and anti-inflammation. Although TFPI has been proved to be a good therapeutic agent of sepsis, inflammatory shock, and DIC, the clinical application and therapeutic effects of TFPI are impeded because of its short half-life in vivo. In order to prolong the half-life of TFPI, homology modeling and molecule docking were performed on a computer workstation principally in protein structural biology and binding characteristics between TFPI and its receptor LRP (low-density lipoprotein receptor related protein). Two recombinant long half-life human TFPI mutants coined TFPI-Mut1 and TFPI-Mut4 were designed and expressed in E.coli. In comparison with the wild-type TFPI, TFPI-Mut1 and TFPI-Mut4 presented a few of changes in spatial configuration and a decrease in relative Gibbs free energy of docking complex by 17.3% and 21.5%, respectively, as indicated by a computer simulation. After refolding and purification, anticoagulant activities, anti-TF/FVIIa and anti-FXa activities of the mutants were found to be the same as those of wide-type TFPI. The pharmacokinetics research indicated that alpha phase half-life (t1/2 alpha) of TFPI-Mut1 and TFPI-Mut4 were prolonged 1.33-fold and 1.96-fold respectively, beta phase half-life (t1/2 beta) of TFPI-Mut1 and TFPI-Mut4 were prolonged 1.62-fold and 4.22-fold respectively. These results suggested that TFPI-Mut1 and TFPI-Mut4 maintained the bioactivities of wild-type TFPI, prolonged half-life in vivo simultaneously and were expected for better clinical value and therapeutic effect.

Construction and characterization of novel staphylokinase variants with antiplatelet aggregation activity and reduced immunogenecity.

To develop target thrombolytic agents with fibrinolytic activity, antiplatelet aggregation activity and reduced immunogenicity, two staphylokinase variants containing Arg-Gly-Asp (RGD) motif were constructed. Gene expression was induced in E. coli JF1125 and the variants, designated DGR and RL1, were purified with gel filtration and ion-exchange chromatography and the purity was over 95%. The fibrinolytic activity and kinetic constants of the two variants were comparable to those of recombinant wild-type staphylokinase. Both the variants can inhibit the platelet aggregation at a final concentration of 2 microM. The titers of antibodies against variants were much lower than those against recombinant staphylokinase in guinea pigs, which indicated that the immunogenicity of the variants was greatly reduced. These results confirm that it is possible to design and produce a bifunctional protein that possesses fibrinolytic and antiplatelet aggregation activities.

[The binding sites of estrogen receptor for miyabenol C and kobophenol A].

To examine the binding sites of miyabenol C (Miy C) and kobophenol A ( Kob A) with estrogen receptor (ER), computer modeling was applied to determine 3D structure of Miy C and Kob A. Molecular docking of the components to ER was carried out to find the binding sites between them. PCR mutagenesis was used to change the structure of ER cDNA. After the mutated sites were confirmed by DNA sequencing, report gene assay was used to study the effects of Miy C and Kob A on the trans-activating ability of ER. Results indicated that the effect of Miy C on the trans-activating ability of mutant 1 of ER [M1ER (ER M(517)AG(521)D)] was decreased, and Kob A had no stimulating effects on the trans-activating ability of M1ER. Miy C and Kob A had no stimulating effects on the trans-activating ability of mutant 2 of ER [M2ER (ER E(353)GR(394)G)]. Therefore, the ER sites for Miy C and Kob A may be located at Glu(353), Arg(394), Met(517) and Gly(521).