Differential microRNA expression between shoots and rhizomes in Oryza longistaminata using high-throughput RNA sequencing

AbstractPlant microRNAs (miRNAs) play important roles in biological processes such as development and stress responses. Although the diverse functions of miRNAs in model organisms have been well studied, their function in wild rice is poorly understood. In this study, high-throughput small RNA sequencing was performed to characterize tissue-specific transcriptomes in Oryza longistaminata. A total of 603 miRNAs, 380 known rice miRNAs, 72 conserved plant miRNAs, and 151 predicted novel miRNAs were identified as being expressed in aerial shoots and rhizomes. Additionally, 99 and 79 miRNAs were expressed exclusively or differentially, respectively, in the two tissues, and 144 potential targets were predicted for the differentially expressed miRNAs in the rhizomes. Functional annotation of these targets suggested that transcription factors, including squamosa promoter binding proteins and auxin response factors, function in rhizome growth and development. The expression levels of several miRNAs and target genes in the rhizomes were quantified by RT-PCR, and the results indicated the existence of complex regulatory mechanisms between the miRNAs and their targets. Eight target cleavage sites were verified by RNA ligase-mediated rapid 5′ end amplification. These results provide valuable information on the composition, expression and function of miRNAs in O. longistaminata, and will aid in understanding the molecular mechanisms of rhizome development

Cytoplasm affects grain weight and filled-grain ratio in indica rice

<p>Abstract</p> <p>Background</p> <p>Cytoplasmic effects on agronomic traits -involving cytoplasmic and nuclear genomes of either different species or different cultivars - are well documented in wheat but have seldom been demonstrated in rice (<it>Oryza sativa </it>L.). To detect cytoplasmic effects, we introgressed the nuclear genomes of three <it>indica </it>cultivars - Guichao 2, Jiangchengkugu, and Dianrui 449 - into the cytoplasms of six <it>indica </it>cultivars - Dijiaowujian, Shenglixian, Zhuzhan, Nantehao, Aizizhan, and Peta. These 18 nuclear substitution lines were evaluated during the winter season of 2005 in Sanya, Hainan, China, and during the summer season of 2006 in Kunming, Yunnan, China. The effects of 6 cytoplasm sources, 3 nucleus sources, 2 locations and their interactions were estimated for plant height, panicle length, panicle number per plant, spikelet number per panicle, grain weight, filled-grain ratio, and yield per plot.</p> <p>Results</p> <p>For five of the seven traits, analysis of variance showed that there were no significant cytoplasmic effects or interactions involving cytoplasmic effects. The effect of cytoplasm on 1000-grain weight was highly significant. Mean 1000-grain weight over the two locations in four of the six cytoplasms clustered close to the overall mean, whereas plants with Nantehao cytoplasm had a high, and those with Peta cytoplasm a low mean grain weight. There was a highly significant three-way interaction affecting filled-grain ratio. At Sanya, cytoplasms varied in very narrow ranges within nuclear backgrounds. Strong cytoplasmic effects were observed only at Kunming and in only two of the three nuclear backgrounds; in the Jianchenkugu nuclear background, there was no evidence of strong cytoplasmic effects at either location. In the Dianrui 449 and Guichao 2 nuclear background evaluated at Kunming, filled-grain ratios of the six cytoplasms showed striking rank shifts</p> <p>Conclusions</p> <p>We detected cytoplasmic variation for two agronomically important traits in <it>indica </it>rice. The cytoplasm source had a significant effect on grain weight across the two experimental locations. There was also a significant cytoplasmic effect on filled-grain ratio, but only in two of three nuclear background and at one of the two locations. The results extend our previous findings with <it>japonica </it>rice, suggesting that the selection of appropriate cytoplasmic germplasm is broadly important in rice breeding, and that cytoplasmic effects on some traits, such as filled-grain ratio, cannot be generalized; effects should be evaluated in the nuclear backgrounds of interest and at multiple locations.</p

Identification of rhizome-specific genes by genome-wide differential expression Analysis in Oryza longistaminata

<p>Abstract</p> <p>Background</p> <p>Rhizomatousness is a key component of perenniality of many grasses that contribute to competitiveness and invasiveness of many noxious grass weeds, but can potentially be used to develop perennial cereal crops for sustainable farmers in hilly areas of tropical Asia. <it>Oryza longistaminata</it>, a perennial wild rice with strong rhizomes, has been used as the model species for genetic and molecular dissection of rhizome development and in breeding efforts to transfer rhizome-related traits into annual rice species. In this study, an effort was taken to get insights into the genes and molecular mechanisms underlying the rhizomatous trait in <it>O. longistaminata </it>by comparative analysis of the genome-wide tissue-specific gene expression patterns of five different tissues of <it>O. longistaminata </it>using the Affymetrix GeneChip Rice Genome Array.</p> <p>Results</p> <p>A total of 2,566 tissue-specific genes were identified in five different tissues of <it>O. longistaminata</it>, including 58 and 61 unique genes that were specifically expressed in the rhizome tips (RT) and internodes (RI), respectively. In addition, 162 genes were up-regulated and 261 genes were down-regulated in RT compared to the shoot tips. Six distinct <it>cis</it>-regulatory elements (CGACG, GCCGCC, GAGAC, AACGG, CATGCA, and TAAAG) were found to be significantly more abundant in the promoter regions of genes differentially expressed in RT than in the promoter regions of genes uniformly expressed in all other tissues. Many of the RT and/or RI specifically or differentially expressed genes were located in the QTL regions associated with rhizome expression, rhizome abundance and rhizome growth-related traits in <it>O. longistaminata </it>and thus are good candidate genes for these QTLs.</p> <p>Conclusion</p> <p>The initiation and development of the rhizomatous trait in <it>O. longistaminata </it>are controlled by very complex gene networks involving several plant hormones and regulatory genes, different members of gene families showing tissue specificity and their regulated pathways. Auxin/IAA appears to act as a negative regulator in rhizome development, while GA acts as the activator in rhizome development. Co-localization of the genes specifically expressed in rhizome tips and rhizome internodes with the QTLs for rhizome traits identified a large set of candidate genes for rhizome initiation and development in rice for further confirmation.</p

Bacterial Effector Binding to Ribosomal Protein S3 Subverts NF-κB Function

Enteric bacterial pathogens cause food borne disease, which constitutes an enormous economic and health burden. Enterohemorrhagic Escherichia coli (EHEC) causes a severe bloody diarrhea following transmission to humans through various means, including contaminated beef and vegetable products, water, or through contact with animals. EHEC also causes a potentially fatal kidney disease (hemolytic uremic syndrome) for which there is no effective treatment or prophylaxis. EHEC and other enteric pathogens (e.g., enteropathogenic E. coli (EPEC), Salmonella, Shigella, Yersinia) utilize a type III secretion system (T3SS) to inject virulence proteins (effectors) into host cells. While it is known that T3SS effectors subvert host cell function to promote diarrheal disease and bacterial transmission, in many cases, the mechanisms by which these effectors bind to host proteins and disrupt the normal function of intestinal epithelial cells have not been completely characterized. In this study, we present evidence that the E. coli O157:H7 nleH1 and nleH2 genes encode T3SS effectors that bind to the human ribosomal protein S3 (RPS3), a subunit of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) transcriptional complexes. NleH1 and NleH2 co-localized with RPS3 in the cytoplasm, but not in cell nuclei. The N-terminal region of both NleH1 and NleH2 was required for binding to the N-terminus of RPS3. NleH1 and NleH2 are autophosphorylated Ser/Thr protein kinases, but their binding to RPS3 is independent of kinase activity. NleH1, but not NleH2, reduced the nuclear abundance of RPS3 without altering the p50 or p65 NF-κB subunits or affecting the phosphorylation state or abundance of the inhibitory NF-κB chaperone IκBα NleH1 repressed the transcription of a RPS3/NF-κB-dependent reporter plasmid, but did not inhibit the transcription of RPS3-independent reporters. In contrast, NleH2 stimulated RPS3-dependent transcription, as well as an AP-1-dependent reporter. We identified a region of NleH1 (N40-K45) that is at least partially responsible for the inhibitory activity of NleH1 toward RPS3. Deleting nleH1 from E. coli O157:H7 produced a hypervirulent phenotype in a gnotobiotic piglet model of Shiga toxin-producing E. coli infection. We suggest that NleH may disrupt host innate immune responses by binding to a cofactor of host transcriptional complexes

Potential of Core-Collapse Supernova Neutrino Detection at JUNO

JUNO is an underground neutrino observatory under construction in Jiangmen, China. It uses 20kton liquid scintillator as target, which enables it to detect supernova burst neutrinos of a large statistics for the next galactic core-collapse supernova (CCSN) and also pre-supernova neutrinos from the nearby CCSN progenitors. All flavors of supernova burst neutrinos can be detected by JUNO via several interaction channels, including inverse beta decay, elastic scattering on electron and proton, interactions on C12 nuclei, etc. This retains the possibility for JUNO to reconstruct the energy spectra of supernova burst neutrinos of all flavors. The real time monitoring systems based on FPGA and DAQ are under development in JUNO, which allow prompt alert and trigger-less data acquisition of CCSN events. The alert performances of both monitoring systems have been thoroughly studied using simulations. Moreover, once a CCSN is tagged, the system can give fast characterizations, such as directionality and light curve

Detection of the Diffuse Supernova Neutrino Background with JUNO

As an underground multi-purpose neutrino detector with 20 kton liquid scintillator, Jiangmen Underground Neutrino Observatory (JUNO) is competitive with and complementary to the water-Cherenkov detectors on the search for the diffuse supernova neutrino background (DSNB). Typical supernova models predict 2-4 events per year within the optimal observation window in the JUNO detector. The dominant background is from the neutral-current (NC) interaction of atmospheric neutrinos with 12C nuclei, which surpasses the DSNB by more than one order of magnitude. We evaluated the systematic uncertainty of NC background from the spread of a variety of data-driven models and further developed a method to determine NC background within 15\% with {\it{in}} {\it{situ}} measurements after ten years of running. Besides, the NC-like backgrounds can be effectively suppressed by the intrinsic pulse-shape discrimination (PSD) capabilities of liquid scintillators. In this talk, I will present in detail the improvements on NC background uncertainty evaluation, PSD discriminator development, and finally, the potential of DSNB sensitivity in JUNO

A Novel Technique of Arthroscopic Femoral Tunnel Placement during Medial Patellofemoral Ligament Reconstruction for Recurrent Patellar Dislocation

Recurrent patellar dislocation is a commonly encountered patellofemoral disease. Prompt surgical intervention is indicated for recurrent dislocation to restore patellofemoral stability. As one of the most preferred procedures, medial patellofemoral ligament (MPFL) reconstruction has been implemented on a large scale. Femoral tunnel placement remains a crucial technical issue during MPFL reconstruction and is critical to ensure the isometry and proper tension of the graft. Currently, visual–palpatory anatomic landmarks and fluoroscopy-guided radiographic landmarks comprise the main approaches to intraoperative femoral tunnel positioning. However, the accuracy of both methods has been questioned. This article introduces an arthroscopic femoral tunnel placement technique. Apart from traditional anteromedial and anterolateral portals, two auxiliary arthroscopic portals are specially designed. The adductor tubercle, the medial epicondyle and the posterior edge are selected as main anatomic landmarks and are directly visualized in sequence under arthroscope. The relative position between the femoral attachment of the MPFL and the three landmarks is measured on preoperative three-dimensional computed tomography, providing semi-quantified reference for intraoperative localization. This technique achieves minimally invasive tunnel placement without X-ray exposure, and especially suits obese patients for whom palpatory methods are difficult to perform

Clinical narrative competence and humanistic care ability of nurses in assisted reproductive technology: a cross-sectional study

Abstract Background Growing focus on patient-centred care emphasizes humanistic skills and clinical narrative competence in nursing, particularly in assisted reproductive nursing. However, there is limited evidence to suggest the levels of nurse’ clinical narrative competence and humanistic care ability. This study aimed to investigate the clinical narrative competence and humanistic care ability of nurse specialists in assisted reproductive technology (ART) in China. Methods This cross-sectional study included nurses who obtained the ART specialist nurse certificate after nurse training in Zhejiang province assisted reproductive technology specialist nurse training base between 2017 and 2022. A demographic questionnaire, the Caring Ability Inventory (CAI) and Narrative Competence Scale (NCS) were used for data collection. Multivariate linear regression analysis was used to explore risk factors. Results A total of 122 participants (120 females, with a mean age of 33.35 ± 5.00 years) were included (response rate = 82.43%). NCS score and CAI score was 143.39 ± 19.24 (range: 27–189) and 198.42 ± 19.51 (range: 37–259) among nurse specialists in assisted reproductive technology, respectively. Multivariate linear regression analysis indicated that professional title (β = 20.003, 95%CI: 3.271–36.735, P = 0.020), and the CAI (β = 0.342, 95%CI: 0.180–0.540, P < 0.001) was independently associated with NCS. Head Nurse/ Team Leader/ Clinical Faculty had significantly higher CAI score than nurse (P = 0.006). Conclusions The clinical narrative competence and caring ability of nurse specialists in assisted reproductive technology was considered sufficient. Professional titles and work position were associated with clinical narrative competence. Enhancing clinical narrative competence can be considered as an effective strategy for promoting humanistic care ability. Trial registration Not applicable