Genome-wide analyses of direct target genes of an ERF11 transcription factor involved in plant defense against bacterial pathogens.

Ethylene responsive factor ERF11 containing the ERF-associated amphiphilic repression (EAR) motif enhances plant resistance to bacterial pathogens. However, the underlying molecular mechanisms regulated by transcription factor ERF11 are poorly understood, in tobacco or other model plants. Here, we revealed the genome-wide binding landscape of BrERF11b in Nicotiana benthamian by conducting chromatin immunoprecipitation experiments followed by high-throughput sequencing (ChIP-seq) and bioinformatic analyses. Our results also revealed a GCCbox-like consensus BrERF11b-binding DNA motif: VCGCCGCC. By further integrative analysis of ChIP-seq and RNA-seq data, and the confirmation of electrophoretic mobility shift assay (EMSA), we screened three direct target genes NbNIMIN2, NbTAF15b and NbERF4. These results suggest that ERF11 may be involved in NPR1-mediated systemic acquired resistance (SAR), nucleotide-binding leucine-rich repeat immune receptors (NLR) -mediated autoimmunity, and H2O2 generation, by direct transcriptional repression of NIM1-INTERACTING2 (NIMIN2), and transcriptional activation of TATA-binding protein-associated factor 15b (TAF15b) and ERF4. Our findings provide insightful information and valuable gene resource in unraveling the regulatory networks of plant defense responses to bacterial pathogens.

Using exosomal miRNAs extracted from porcine follicular fluid to investigate their role in oocyte development.

BACKGROUND: Follicular development is crucial to normal oocyte maturation, with follicular size closely related to oocyte maturation. To better understand the molecular mechanisms behind porcine oocyte maturation, we obtained exosomal miRNA from porcine follicular fluid (PFF). These miRNA samples were then sequenced and analyzed regarding their different follicular sizes, as described in the methods section. RESULTS: First, these results showed that this process successfully isolated PFF exosomes. Nearly all valid reads from the PFF exosomal sequencing data were successfully mapped to the porcine genome database. Second, we used hierarchical clustering methods to determine that significantly expressed miRNAs were clustered into A, B, C, and D groups in our heatmap according to different follicle sizes. These results allowed for the targeting of potential mRNAs genes related to porcine oocyte development. Third, we chose ten, significantly expressed miRNAs and predicted their target genes for further GO analysis. These results showed that the expression levels of neurotransmitter secretion genes were greatly changed, as were many target genes involved in the regulation of FSH secretion. Notably, these are genes that are very closely related to oocyte maturation in growing follicles. We then used pathway analysis for these targeted genes based on the originally selected ten miRNAs. Results indicated that the pathways were mainly related to the biosynthesis of TGF-beta and its signaling pathway, which are very closely related to reproductive system functions. CONCLUSIONS: Finally, these exosomal miRNAs obtained from PFF may provide a valuable addition to our understanding of the mechanism of porcine oocyte maturation. It is also likely that these exosomal miRNAs could function as molecular biomarkers to choose high-quality oocytes and allow for in vitro porcine embryo production.

First polar body morphology affects potential development of porcine parthenogenetic embryo in vitro.

Previous studies have reported that the first polar body (PB1) morphology reflects embryo development competence, but the effects of PB1 on porcine embryo development remain unknown. This study aims to determine whether the ability of porcine embryo development is related to oocytes' PB1 in vitro. The distribution of type II cortical granules (CGs) of porcine matured oocytes in grade B PB1 is significantly greater compared with those in grades A and C PB1 (71.43% versus 52.46% and 50%; P 0.05). The acetylation level of porcine embryos in the group with grade B PB1 is significantly greater compared with those in the other groups (P < 0.05), and is almost 2.5 times higher than that in grade A. Therefore, porcine oocytes with PB1 in grade B are more competitive in cytoplasmic maturation and further embryo development in vitro.

Molecular characterization and expression patterns of MTP genes under heavy metal stress in mustard (Brassica juncea L.).

Members of the Metal Tolerance Protein (MTP) family are critical in mediating the transport and tolerance of divalent metal cations. Despite their significance, the understanding of MTP genes in mustard (Brassica juncea) remains limited, especially regarding their response to heavy metal (HM) stress. In our study, we identified MTP gene sets in Brassica rapa (17 genes), Brassica nigra (18 genes), and B. juncea (33 genes) using the HMMER (Cation_efflux; PF01545) and BLAST analysis. For the 33 BjMTPs, a comprehensive bioinformatics analysis covering the physicochemical properties, phylogenetic relationships, conserved motifs, protein structures, collinearity, spatiotemporal RNA-seq expression, GO enrichment, and expression profiling under six HM stresses (Mn2+, Fe2+, Zn2+, Cd2+, Sb3+, and Pb2+) were carried out. According to the findings of physicochemical characteristics, phylogenetic tree, and collinearity, the allopolyploid B. juncea's MTP genes were inherited from its progenitors, B. rapa and B. nigra, with minimal gene loss during polyploidization. Members of the BjMTP family exhibited conserved motifs, promoter elements, and expression patterns across subgroups, consistent with the seven evolutionary branches (G1, G4-G9, and G12) of the MTPs. Further, spatiotemporal expression profiling under HM stresses successfully identified specific genes and crucial cis-regulatory elements associated with the response of BjMTPs to HM stresses. These findings may contribute to the genetic improvement of B. juncea for enhanced HM tolerance, facilitating the remediation of HM-contaminated areas.

Prochloraz induced alterations in the expression of mRNA in the reproductive system of male offspring mice.

Prochloraz is a widely used fungicide worldwide. It is classified as an endocrine disrupting pesticide that affects the reproductive system. This study aimed to examine the impact of exposure to prochloraz of male mice on the reproductive system of their offspring male mice. Male father mice were intragastrically administered different dosages of prochloraz (group MA: 0 mg/kg/day; MB: 53.33 mg/kg/day; MD:160 mg/kg/day). Then, the testicular average weight of male offspring in the dose groups was found to be significantly lower than those in the control group (MB:0.312g, MD:0.294g, and MA:0.355 g; P < 0.05). Additionally, the testicular coefficient index in the MB and MD groups was also lower than that of the control group. Secondly,we observed that there were significantly different expressed genes clustered in groups B and D, in contrast to the control. Finally, the findings demonstrated a significant alteration in the response of male mice reproductive relative genes to prochloraz invasion. Two genes (Mt-nd6 and Slc12a4) were found to be involved in the regulation of sperm mitochondria function and six genes (Greb1, Esrrb, Catsperb, Mospd2, Sohlh1 and Specc1) were closely linked to sperm functions and estrogen response. The study revealed a significant impact of prochloraz on the reproductive system of male mice, thereby supporting further investigation into the reproductive toxicological effects of the drug.

Insulin-transferrin-selenium (ITS) improves maturation of porcine oocytes in vitro.

The objective of this study was to determine if insulin-transferrin-selenium (ITS) promoted a nuclear and cytoplasmic maturation of porcine oocytes that better supports subsequent embryonic development. The rate of oocyte in vitro maturation (IVM) in an experimental group treated with hormones for 42 h was significantly increased compared with that in a control group without hormone treatment (47.8% vs. 11.7%, respectively, p < 0.05). Following reduction of the hormone treatment period from 42 h to 21 h, which included both the first 21 h period of hormones treatment (45.4%) and the second 21 h period of hormone treatment (44.8%), the rate of oocyte IVM was still higher than that of the control group (p < 0.05). To improve porcine oocyte nuclear maturation, 1% ITS was added to medium supplemented with hormones. The rate of nuclear maturation in the ITS-treated group was significantly higher than in the ITS-untreated group (78.6% vs. 54.4%, respectively, p < 0.05). ITS treatment also significantly reduced the per cent of oocytes with type I and type III cortical granule (CG) distribution, respectively, and significantly increased the per cent of oocytes with type II CG distribution (85.3%). These observations indicated that the synchronization rates of nuclear and ooplasmic maturation reached 67.04% (78.56 × 85.33%). In conclusion, the combination of modified Tissue Culture Medium-199 (mM199) + 10 ng/ml epidermal growth factor (EGF) + 10 IU/ml pregnant mare serum gonadotrophin (PMSG) + 10 IU/ml human chorion gonadotrophin (hCG) + 2.5 IU/ml follicle stimulating hormone (FSH) + 1% ITS is suitable for culturing porcine oocytes in vitro, and effectively enhances porcine oocyte nuclear and cytoplasmic maturation.

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Old trees are critical components of ecosystems, with important ecological function and high genetic diversity. To strengthen the protection and management of old trees, we analyzed the distribution, survival and protection status of old trees and their threatened factors in China. The results showed there were a total of 10.66 million old trees in China. The Inner Mongolia Autonomous Region and Yunnan Province had more than one million trees, respectively. For 440000 old trees in 102 counties, 94.3% grew normally, 5.5% in a weak or endangered status, and 0.2% had been dead. The main factors threatened to old trees included natural disasters (e.g., elevated temperature, drought, fire), urbanization, land use, pests and diseases, and cutting and stealing. Among those factors, damage from pests and diseases was the most serious, which was found in 83 counties (81.4%). The second important threatened factor was natural disasters, which occurred in 68 regions (66.7%). In addition, most of the old trees (around 89%) grew in remote countryside, lacking of enough protection. Modern technologies should be used to protect old trees, such as using unmanned aerial vehicles to monitor the growth status of old trees, strengthening pest and disease control, and avoiding natural disasters. Establishing a database of old tree resources is important to update and share information timely to avoid stealing and felling old trees.

The expression of small RNAs in exosomes of follicular fluid altered in human polycystic ovarian syndrome.

Polycystic ovary syndrome (PCOS) can cause reproductive disorders that may affect oocyte quality from punctured follicles in human follicular fluid (HFF). The non-coding RNA family includes micro RNA (miRNA), piwi-interacting RNA (piRNA) and transfer RNA (tRNA); these non-coding RNA transcripts play diverse functions and are implicated in a variety of diseases and health conditions, including infertility. In this study, to explore the role of HFF exosomes in PCOS, we extracted and sequenced RNA from HFF exosomes of PCOS patients and compared the analysis results with those of non-PCOS control group. The HFF exosomes were successfully isolated and characterized in a variety of ways. The sequencing results of the HFF exosomal RNA showed that about 6.6% of valid reads in the PCOS group and 8.6% in the non-PCOS group were successfully mapped to the human RNA database. Using a hierarchical clustering method, we found there were ten small RNA sequences whose expression was significantly different between the PCOS and non-PCOS groups. We chose six of them to predict target genes of interest for further GO analysis, and pathway analysis showed that the target genes are mainly involved in biosynthesis of amino acids, glycine, serine and glycosaminoglycan, as well as threonine metabolism. Therefore, the small RNA sequences contained in HFF EXs may play a key role in the mechanism that drives PCOS pathogenesis, and thereby can act as molecular biomarkers for PCOS diagnosis in the future.

Porcine induced pluripotent stem cells require LIF and maintain their developmental potential in early stage of embryos.

Porcine induced pluripotent stem (piPS) cell lines have been generated recently by using a cocktail of defined transcription factors, however, the features of authentic piPS cells have not been agreed upon and most of published iPS clones did not meet the stringent requirements of pluripotency. Here, we report the generation of piPS cells from fibroblasts using retrovirus carrying four mouse transcription factors (mOct4, mSox2, mKlf4 and mc-Myc, 4F). Multiple LIF-dependent piPS cell lines were generated and these cells showed the morphology similar to mouse embryonic stem cells and other pluripotent stem cells. In addition to the routine characterization, piPS cells were injected into porcine pre-compacted embryos to generate chimera embryos and nuclear transfer (NT) embryos. The results showed that piPS cells retain the ability to integrate into inner and outer layers of the blastocysts, and support the NT embryos development to blastocysts. The generations of chimera embryos and NT embryos derived from piPS clones are a practical means to determine the quality of iPS cells ex vivo.

FSH is superior to eCG for promoting ovarian response in Chinese Bamei gilts.

The Bamei gilt is a Chinese native breed located in northwest China, which adapts to the extremely dry and cold environment and is distinguished for its excellent reproductive and maternal characters. To ensure sufficient numbers of embryos for transgenic and nuclear transfer research, hormonal induction of gilt estrus and superovulation may be necessary. The objective of this study was to compare the superovulation effects of equine chorionic gonadotropin (eCG, Group A) and FSH (Groups B-D) in Chinese Bamei gilts. The results show that though eCG could produce more corpora lutea (CL, 14.3) than the control (CL, 9.2), and the FSH treatments had significantly increased the number of CL compared with the eCG treatment. Within the different FSH protocols, the numbers of CL were significantly greater in Groups B (CL, 77.8) and C (CL, 66.8) than in Group D (CL, 42.7), however, ovarian cysts were observed in Groups B and C, but not in Group D. These data suggest that Group D (280 IU FSH) is a suitable protocol to facilitate the development of ovarian follicles and increase the number of useful embryos per gilt for embryos recovery. The optimal FSH protocol of superovulation in Bamei gilts appears to be: D13/100 IU, D14/80 IU, D15/60 IU, D16/40 IU plus prostaglandin (PG) 0.2mg, D17/hCG 1000 IU.