Triplex qRT-PCR with specific probe for synchronously detecting Bovine parvovirus, bovine coronavirus, bovine parainfluenza virus and its applications

Bovine parvovirus (BPV), bovine coronavirus (BCoV) and bovine parainfluenza virus (BPIV) are common etiologies causing gastrointestinal and respiratory diseases in dairy herds. However, there are few reports on the synchronous detection of BPV, BCoV and BPIV. The present article aimed to develop a quick and accurate RT-PCR assay to synchronously detect BPV, BCoV and BPIV based on their specific probes. One pair universal primers, one pair specific primers and one specific probe was designed and synthesized. After the concentrations of primer and probe and annealing temperature were strictly optimized, the specificity, sensitivity and repeatability of the established triplex probe qRT-PCR were evaluated, respectively. The results showed the recombinant plasmids of pMD18-T-BPV, pMD18-T-BCoV and pMD18-T-BPIV were 554bp, 699bp and 704bp, respectively. The optimal annealing temperature was set at 45.0°C for triplex qRT-PCR. The triplex probe qRT-PCR can only synchronously detect BPV, BCoV and BPIV. Detection sensitivities were 2.0×102, 2.0×102 and 2.0×101 copies/μL for BPV, BCoV and BPIV, being 1000-fold greater than that in the conventional PCR. Detection of clinical samples demonstrated that triplex probe qRT-PCR had a higher sensitivity and specificity. The intra-assay and inter-assay coefficient of variation were lower than 2.0%. Clinical specimens verified that the triplex qRT-PCR had a higher sensitivity and specificity than universal PCR. In conclusion, this triplex probe qRT-PCR could detect only BPV, BCoV and BPIV. Minimum detection limits were 2.0×102 copies/μL for BPV and BCoV, and 2.0×101 copies/μL for BPIV. The sensitivity of this triplex probe qRT-PCR was 1000-fold greater than that in the conventional PCR. The newly qRT-PCR could be used to monitor or differentially diagnose virus infection.

Comparison of clinical outcomes between robotic and thoracoscopic mitral valve repair

Background

To compare the clinical outcomes and hospital cost of robotic versus thoracoscopic approaches to mitral valve plasty (MVP).

Methods

We retrospectively analyzed patients who received minimal invasive MVP between 2007 January and 2020 January at our department. The basic characteristics, echocardiography, surgical data, postoperative adverse events and hospital cost of the patients were collected. The primary outcomes of this study were direct hospital cost and 30-day outcomes, including the operative time, complications, and length of hospital stay.

Results

A total of 234 patients received minimally invasive MVP by using robotic (n=121) and thoracoscopic (n=113) technique respectively. The overall 30-day mortality rate was 0.9% (n=2), with no significant difference between two groups. The cardiopulmonary bypass time and aorta clamping time in thoracoscopic group were longer than that in robotic group (153.2±25.6 vs. 123.8±34.9 min and 111.8±23.0 vs. 84.9±24.3 min, P<0.001). The intraoperative blood transfusion rate (52.2% vs. 64.5%) and ICU time (2.8±2.3 vs. 3.6±2.7 days, all P<0.05) of the thoracoscopic group were lower than those in the robotic group. The adjusted hospital and operating room cost of the thoracoscopic group were significant lower ($18,208.4±$4,429.1 vs. $35,674.3±$4,936.1 and $9,038.3±$2,171.7 vs. $18,655.1±$2,558.3, all P<0.001).

Conclusions

Both robotic and thoracoscopic approach for MVP are safe and reliable. Robotic technique has shorter operation time, while thoracoscopic technique has more advantages in blood transfusion rate, postoperative ventilation time, ICU duration and hospitalization expenses.

OsPP2C09, a negative regulatory factor in abscisic acid signalling, plays an essential role in balancing plant growth and drought tolerance in rice

Plants maintain a dynamic balance between plant growth and stress tolerance to optimise their fitness and ensure survival. Here, we investigated the roles of a clade A type 2C protein phosphatase (PP2C)-encoding gene, OsPP2C09, in regulating the trade-off between plant growth and drought tolerance in rice (Oryza sativa L.). The OsPP2C09 protein interacted with the core components of abscisic acid (ABA) signalling and showed PP2C phosphatase activity in vitro. OsPP2C09 positively affected plant growth but acted as a negative regulator of drought tolerance through ABA signalling. Transcript and protein levels of OsPP2C09 were rapidly induced by exogenous ABA treatments, which suppressed excessive ABA signalling and plant growth arrest. OsPP2C09 transcript levels in roots were much higher than those in shoots under normal conditions. After ABA, polyethylene glycol and dehydration treatments, the accumulation rate of OsPP2C09 transcripts in roots was more rapid and greater than that in shoots. This differential expression between the roots and shoots may increase the plant's root-to-shoot ratio under drought-stress conditions. This study sheds new light on the roles of OsPP2C09 in coordinating plant growth and drought tolerance. In particular, we propose that OsPP2C09-mediated ABA desensitisation contributes to root elongation under drought-stress conditions in rice.

Direct laser acceleration of electrons assisted by strong laser-driven azimuthal plasma magnetic fields

A high-intensity laser beam propagating through a dense plasma drives a strong current that robustly sustains a strong quasistatic azimuthal magnetic field. The laser field efficiently accelerates electrons in such a field that confines the transverse motion and deflects the electrons in the forward direction. Its advantage is a threshold rather than resonant behavior, accelerating electrons to high energies for sufficiently strong laser-driven currents. We study the electron dynamics via a test-electron model, specifically deriving the corresponding critical current density. We confirm the model's predictions by numerical simulations, indicating energy gains two orders of magnitude higher than achievable without the magnetic field.

COM1, a factor of alternative non-homologous end joining, lagging behind the classic non-homologous end joining pathway in rice somatic cells

The role of rice (Oryza sativa) COM1 in meiotic homologous recombination (HR) is well understood, but its part in somatic double-stranded break (DSB) repair remains unclear. Here, we show that for rice plants COM1 conferred tolerance against DNA damage caused by the chemicals bleomycin and mitomycin C, while the COM1 mutation did not compromise HR efficiencies and HR factor (RAD51 and RAD51 paralogues) localization to irradiation-induced DSBs. Similar retarded growth at the post-germination stage was observed in the com1-2 mre11 double mutant and the mre11 single mutant, while combined mutations in COM1 with the HR pathway gene (RAD51C) or classic non-homologous end joining (NHEJ) pathway genes (KU70, KU80, and LIG4) caused more phenotypic defects. In response to γ-irradiation, COM1 was loaded normally onto DSBs in the ku70 mutant, but could not be properly loaded in the MRE11^RNAi plant and in the wortmannin-treated wild-type plant. Under non-irradiated conditions, more DSB sites were occupied by factors (MRE11, COM1, and LIG4) than RAD51 paralogues (RAD51B, RAD51C, and XRCC3) in the nucleus of wild-type; protein loading of COM1 and XRCC3 was increased in the ku70 mutant. Therefore, quite differently to its role for HR in meiocytes, rice COM1 specifically acts in an alternative NHEJ pathway in somatic cells, based on the Mre11-Rad50-Nbs1 (MRN) complex and facilitated by PI3K-like kinases. NHEJ factors, not HR factors, preferentially load onto endogenous DSBs, with KU70 restricting DSB localization of COM1 and XRCC3 in plant somatic cells.

Proteome-Wide Analyses Reveal the Diverse Functions of Lysine 2-Hydroxyisobutyrylation in Oryza sativa

BACKGROUND

Lysine 2-hydroxyisobutyrylation (Khib), a newly identified post-translational modification, is known to regulate transcriptional activity in animals. However, extensive studies of the lysine 2-hydroxyisobutyrylome in plants and animals have yet to be performed.

RESULTS

In this study, using LC-MS/MS qualitative proteomics strategies, we identified 4163 Khib sites on 1596 modified proteins in rice (Oryza sativa) seedlings. Motif analysis revealed 10 conserved motifs flanking the Khib sites, and subcellular localization analysis revealed that 44% of the Khib proteins are localized in the chloroplast. Gene ontology function, KEGG pathway, and protein domain enrichment analyses revealed that Khib occurs on proteins involved in diverse biological processes and is especially enriched in carbon metabolism and photosynthesis. Among the modified proteins, 20 Khib sites were identified in histone H2A and H2B, while only one site was identified in histone H4. Protein-protein interaction (PPI) network analysis further demonstrated that Khib participates in diverse biological processes including ribosomal activity, biosynthesis of secondary metabolites, and metabolic pathways. In addition, a comparison of lysine 2-hydroxyisobutyrylation, acetylation, and crotonylation in the rice proteome showed that 45 proteins with only 26 common lysine sites are commonly modified by three PTMs. The crosstalk of modified sites and PPI among these PTMs may form a complex network with both similar and different regulatory mechanisms.

CONCLUSIONS

In summary, our study comprehensively profiles the lysine 2-hydroxyisobutyrylome in rice and provides a better understanding of its biological functions in plants.

Energy gain by laser-accelerated electrons in a strong magnetic field

This paper deals with electron acceleration by a laser pulse in a plasma with a static uniform magnetic field B_{*}. The laser pulse propagates perpendicular to the magnetic field lines with the polarization chosen such that (E_{laser}·B_{*})=0. The focus of the work is on the electrons with an appreciable initial transverse momentum that are unable to gain significant energy from the laser in the absence of the magnetic field due to strong dephasing. It is shown that the magnetic field can initiate an energy increase by rotating such an electron, so that its momentum becomes directed forward. The energy gain continues well beyond this turning point where the dephasing drops to a very small value. In contrast to the case of purely vacuum acceleration, the electron experiences a rapid energy increases with the analytically derived maximum energy gain dependent on the strength of the magnetic field and the phase velocity of the wave. The energy enhancement by the magnetic field can be useful at high laser amplitudes, a_{0}≫1, where the acceleration similar to that in the vacuum is unable to produce energetic electrons over just tens of microns. A strong magnetic field helps leverage an increase in a_{0} without a significant increase in the interaction length.

Dual-color oligo-FISH can reveal chromosomal variations and evolution in Oryza species

Fluorescence in situ hybridization using probes based on oligonucleotides (oligo-FISH) is a useful tool for chromosome identification and karyotype analysis. Here we developed two oligo-FISH probes that allow the identification of each of the 12 pairs of chromosomes in rice (Oryza sativa). These two probes comprised 25 717 (green) and 25 215 (red) oligos (45 nucleotides), respectively, and generated 26 distinct FISH signals that can be used as a barcode to uniquely label each of the 12 pairs of rice chromosomes. Standard karyotypes of rice were established using this system on both mitotic and meiotic chromosomes. Moreover, dual-color oligo-FISH was used to characterize diverse chromosomal abnormalities. Oligo-FISH analyses using these probes in various wild Oryza species revealed that chromosomes from the AA, BB or CC genomes generated specific and intense signals similar to those in rice, while chromosomes with the EE genome generated less specific signals and the FF genome gave no signal. Together, the oligo-FISH probes we established will be a powerful tool for studying chromosome variations and evolution in the genus Oryza.

TaqMan real-time PCR for detecting bovine viral diarrhea virus

The present study was aimed to establish a novel TaqMan real-time PCR (RTm-PCR) for detecting and typing bovine viral diarrhea virus (BVDV), and also to develop a diagnostic protocol which simplifies sample collection and processing. Universal primers and TaqMan-MGB probes were designed from the known sequences of conserved 5' - and 3'-untranslated regions (5'UTR, 3'UTR) of the NADL strain of BVDV. Prior to optimizing the assay, cDNAs were transcribed in vitro to make standard curves. The sensitivity, specificity and stability (reproducibility) were evaluated. The RTm-PCR was tested on the 312 feces specimens collected from persistently infected (PI) calves. The results showed the optimum conditions for RTm-PCR were 17.0 μmol/L primer, 7.5 μmol/L probe and 51.4°C annealing temperature. The established TaqMan RTm-PCR assay could specially detect BVDV without detecting any other viruses. Its detection limit was 1.55×100 copies/μL for viral RNA. It was 10000-fold higher than conventional PCR with excellent specificity and reproducibility. 312 samples were tested using this method and universal PCR from six dairy farms, respectively. Positive detections were found in 49 and 44 feces samples, respectively. The occurrence rate was 89.80%. In conclusion, the established TaqMan RTm-PCR could rapidly detect BVDV and effectively identify PI cattle. The detection limit of RTm-PCR was 1.55 copies/μL. It will be beneficial for enhancing diagnosis and therapy efficacy and reduce losses in cattle farms.

Deflection of a reflected intense circularly polarized light beam induced by asymmetric radiation pressure

A deflection effect of an intense laser beam with spin angular momentum is revealed theoretically by an analytical modeling using radiation pressure and momentum balance of laser plasma interaction in the relativistic regime as a deviation from the law of reflection. The reflected beam deflects out of the plane of incidence with a deflection angle up to several milliradians, when a nonlinear polarized laser, with the intensity I_{0}∼10^{19}W/cm^{2} and duration around tens of femtoseconds, is obliquely incident and reflected by an overdense plasma target. This effect originates from the asymmetric radiation pressure caused by spin angular momentum of the laser photons. The dependence of the deflection angle of a Gaussian-type laser on the parameters of laser pulse and plasma foil is theoretically derived, which is also confirmed by three-dimensional particle-in-cell simulations of circularly polarized laser beams with the different intensity and pulse duration.

Genome-wide Profiling of Histone Lysine Butyrylation Reveals its Role in the Positive Regulation of Gene Transcription in Rice

BACKGROUND

Histone modifications play important roles in growth and development of rice (Oryza sativa L.). Lysine butyrylation (Kbu) with a four-carbon chain is a newly-discovered histone acylation modification in rice.

MAIN BODY

In this study, we performed chromatin immunoprecipitation sequencing (ChIP-seq) analyses, the result showed that major enrichment of histone Kbu located in genebody regions of rice genome, especially in exons. The enrichment level of Kbu histone modification is positively correlated with gene expression. Furthermore, we compared Kbu with DNase-seq and other histone modifications in rice. We found that 60.06% Kub enriched region co-located with DHSs in intergenic regions. The similar profiles were detected among Kbu and several acetylation modifications such as H3K4ac, H3K9ac, and H3K23ac, indicating that Kbu modification is an active signal of transcription. Genes with both histone Kbu and one other acetylation also had significantly increased expression compared with genes with only one acetylation. Gene Ontology (GO) enrichment analysis revealed that these genes with histone Kbu can regulate multiple metabolic process in different rice varieties.

CONCLUSION

Our study showed that the lysine butyrylation modificaiton may promote gene expression as histone acetylation and will provide resources for futher studies on histone Kbu and other epigenetic modifications in plants.

Radiation reaction as an energy enhancement mechanism for laser-irradiated electrons in a strong plasma magnetic field

Conventionally, friction is understood as a mechanism depleting a physical system of energy and as an unavoidable feature of any realistic device involving moving parts. In this work, we demonstrate that this intuitive picture loses validity in nonlinear quantum electrodynamics, exemplified in a scenario where spatially random friction counter-intuitively results in a highly directional energy flow. This peculiar behavior is caused by radiation friction, i.e., the energy loss of an accelerated charge due to the emission of radiation. We demonstrate analytically and numerically how radiation friction can dramatically enhance the energy gain by electrons from a laser pulse in a strong magnetic field that naturally arises in dense laser-irradiated plasma. We find the directional energy boost to be due to the transverse electron momentum being reduced through friction whence the driving laser can accelerate the electron more efficiently. In the considered example, the energy of the laser-accelerated electrons is enhanced by orders of magnitude, which then leads to highly directional emission of gamma-rays induced by the plasma magnetic field.

Mutation of RGG2, which encodes a type B heterotrimeric G protein γ subunit, increases grain size and yield production in rice

Heterotrimeric G proteins, which consist of G_α , G_β and G_γ subunits, function as molecular switches that regulate a wide range of developmental processes in plants. In this study, we characterised the function of rice RGG2, which encodes a type B G_γ subunit, in regulating grain size and yield production. The expression levels of RGG2 were significantly higher than those of other rice G_γ -encoding genes in all tissues tested, suggesting that RGG2 plays essential roles in rice growth and development. By regulating cell expansion, overexpression of RGG2 in Nipponbare (NIP) led to reduced plant height and decreased grain size. By contrast, two mutants generated by the clustered, regularly interspaced, short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system in the Zhenshan 97 (ZS97) background, zrgg2-1 and zrgg2-2, exhibited enhanced growth, including elongated internodes, increased 1000-grain weight and plant biomass and enhanced grain yield per plant (+11.8% and 16.0%, respectively). These results demonstrate that RGG2 acts as a negative regulator of plant growth and organ size in rice. By measuring the length of the second leaf sheath after gibberellin (GA₃ ) treatment and the GA-induced α-amylase activity of seeds, we found that RGG2 is also involved in GA signalling. In summary, we propose that RGG2 may regulate grain and organ size via the GA pathway and that manipulation of RGG2 may provide a novel strategy for rice grain yield enhancement.

EDACO, a derivative of myricetin, inhibits the differentiation of Gaoyou duck embryonic osteoclasts in vitro

1. This study determined the effects of (E)-3-(2-(4-(3-(2,4-dimethoxyphenyl)acryloyl)phenoxy)ethoxy)-5,7-dimethoxy-2-(3,4,5-trimethoxyphenyl)-4H-chromen-4-one (EDACO) on the differentiation of Gaoyou duck embryonic osteoclasts cultured in vitro. 2. Bone marrow mononuclear cells (BM-MNC) were collected from 23-d-old Gaoyou duck embryos and induced by macrophage colony-stimulating factor and receptor activator of nuclear factor κB ligand in the presence of EDACO at different concentrations (i.e. 10, 20, 40, 80 and 160 µM). Tartrate-resistant acid phosphatase (TRAP) staining and resorption ability determination were conducted. 3. Results suggested that EDACO suppressed the shaping of positive multinucleated cells and the number of TRAP-positive cells in the 20, 40, 80 and 160 μM EDACO groups was significantly decreased (P < 0.05 or P < 0.01). Besides, the absorption activity of differentiated duck embryonic osteoclasts was significantly inhibited (P < 0.05) in both 80 and 160 μM EDACO groups. 4. Overall, EDACO can inhibit the differentiation of BM-MNC into mature osteoclasts in duck embryos.1.

[Rush poppers use and risks of human papillomavirus infection among men who have sex with men in Urumqi: mediation effect through high-risk sexual behaviors]

Objective: To study the prevalence of rush poppers use among men who have sex with men (MSM) in Urumqi and to analyze the mediating effect of high-risk sexual behavior between the use of rush poppers and human papillomavirus (HPV) infection. Methods: From January to June 2018, 651 MSM were recruited through network and publicity. Data was collected by using online questionnaire and anal swab were collected from them for HPV genotyping. According to Baron and Kenny's criterion, multivariate logistic regression models was used to analyze the mediation effect of high-risks sexual behaviors (multiple sexual partners, anal intercourse condom use) between rush poppers use and HPV infection. Results: A total of 651 subjects were (32.0±8.0) years old, and 174 subjects (26.7%) had ever used rush poppers in the past 6 months, while 350 subjects (46.9%) had more than 2 sexual partners and 188 subjects (28.9%) did not use anal condom. After adjusting age and marital status, rush poppers use was associated with HPV infection (OR (95%CI) was 2.34 (1.63-3.36), P<0.05), and sexual partners in the past 6 months (OR (95%CI) was 2.72 (1.89-3.93), P<0.05).After adjustment for age, marital status, sexual partners in the past 6 months, and anal condom use, rush poppers use was still associated with HPV infection (OR (95%CI) was 2.21 (1.53-3.19), P<0.05).After adjustment and adjustment of age, marital status, rush poppers use and anal sex condom use, the number of sexual partners at nearly 6 months was still associated with HPV infection (OR (95%CI) was 1.46 (1.05-2.04), P<0.05). Conclusion: Sexual partners in the past 6 months have a mediation effect between rush poppers use and HPV infection in Urumqi. For the prevention of sexually transmitted diseases, we should focus on rush poppers use.

Global Proteome Analysis Links Lysine Acetylation to Diverse Functions in Oryza Sativa

Lysine acetylation (Kac) is an important protein post-translational modification in both eukaryotes and prokaryotes. Herein, we report the results of a global proteome analysis of Kac and its diverse functions in rice (Oryza sativa). We identified 1353 Kac sites in 866 proteins in rice seedlings. A total of 11 Kac motifs are conserved, and 45% of the identified proteins are localized to the chloroplast. Among all acetylated proteins, 38 Kac sites are combined in core histones. Bioinformatics analysis revealed that Kac occurs on a diverse range of proteins involved in a wide variety of biological processes, especially photosynthesis. Protein-protein interaction networks of the identified proteins provided further evidence that Kac contributes to a wide range of regulatory functions. Furthermore, we demonstrated that the acetylation level of histone H3 (lysine 27 and 36) is increased in response to cold stress. In summary, our approach comprehensively profiles the regulatory roles of Kac in the growth and development of rice.

Creation of Electron-Positron Pairs in Photon-Photon Collisions Driven by 10-PW Laser Pulses

A novel approach is proposed to demonstrate the two-photon Breit-Wheeler process by using collimated and wide-bandwidth γ-ray pulses driven by 10-PW lasers. Theoretical calculations suggest that more than 3.2×10^{8} electron-positron pairs with a divergence angle of 7° can be created per shot, and the signal-to-noise ratio is higher than 10^{3}. The positron signal, which is roughly 100 times higher than the detection limit, can be measured by using the existing spectrometers. This approach, which could demonstrate the e^{-}e^{+} pair creation process from two photons, would provide important tests for two-photon physics and other fundamental physical theories.