Ecological characteristics of tall fescue and spatially organized communities: Their contribution to mitigating cadmium damage

The threat of cadmium (Cd) stress to agricultural soil environments, as well as their productivity attracting growing global interest. Tall fescue (Festuca arundinacea Schreb.) is a strong candidate for the remediation of heavy metals in soil. However, the joint analysis of Cd tolerance, physiological responses, and multifaceted plant microbiomes in tall fescue fields has not been extensively researched. Therefore, this study employed microbial sequencing (i.e., 16S and ITS sequencing) to investigate the differences in microbial community structure among various plant compartments of Cd-resistant tall fescue (cv. 'Arid3') and Cd-sensitive tall fescue (cv. 'Barrington'). Furthermore, we examined the mechanism of resistance to Cd by introducing three different bacteria and a fungus that were isolated from the 'Arid3' rhizosheath soil. It highlighted the potential application of enriched taxa such as Delftia, Novosphingobium, Cupriavidus and Torula in enhancing the activity of antioxidant defense systems, increasing the production of osmotic regulatory substances, and stimulating the expression of Cd-resistance genes. This ultimately promoted plant growth and enhanced phytoremediation efficiency. This study shed light on the response mechanism of the tall fescue microbiome to Cd stress and underscored the potential of tall fescue-microbe co-culture in the remediation of heavy metal-contaminated areas.

[Preliminary study on the role and mechanism of IL-6 receptor antagonists in improving post-infarction ventricular arrhythmia]

Objective: To investigate the effect of tocilizumab (TCZ) on ventricular arrhythmias (VAs) after myocardial infarction (MI) in Sprague-Dawley rats and explore its potential mechanism. Methods: The random number table method was used to divide 32 adult male Sprague-Dawley rats into 4 groups: Sham group, TCZ group, MI group and MI+TCZ group, with 8 rats in each group. The MI model was established by ligation of the left anterior descending branch of the coronary artery in the MI and MI+TCZ groups, and only sutured without ligation in the Sham and TCZ groups. TCZ was injected into the left superior cervical ganglion (SCG) of rats in the TCZ and MI+TCZ groups after successful modeling or sham operation, and the same amount of normal saline was injected in the Sham and MI groups. 24 h after successful modeling, ECG of rats in each group was recorded, heart rate variability (HRV, including low frequency power (LF), high frequency power (HF), LF/HF ratio), QT interval, QTc interval were calculated, and left ventricular effective refractory period (ERP) and VA inducibility were measured. Myocardial infarct size and tissue changes were observed with triphenyl tetrazolium chloride staining and HE staining. Real-time PCR analysis was used to detect the messager RNA (mRNA) expression of interleukin-6 (IL-6) and signal transducer and activator of transcription (STAT) 3 in SCG and potassium voltage-gated channel subfamily D member 2 (Kcnd2) in myocardial infarction periphery. The expression of c-fos in SCG was detected by immunofluorescence staining. Results: Compared with Sham group and MI+TCZ group, rats in MI group had higher LF and LF/HF ratio, longer QT interval and QTc interval, more VAs induced, lower HF and shorter ERP (P all<0.05). Triphenyl tetrazolium chloride staining and HE staining showed that rats in the Sham and TCZ groups had normal myocardial tissue structure, those in the MI group had severe myocardial injury, and those in the MI+TCZ group had less myocardial injury than those in the MI group. Real-ime PCR analysis showed that compared with Sham group and MI+TCZ group, mRNA expression levels of IL-6 and STAT3 in SCG of rats in MI group were higher, and mRNA expression level of myocardial Kcnd2 was lower (P all<0.05). Immunofluorescence staining showed that the content of c-fos in SCG of rats in MI group was higher than that of Sham group and MI+TCZ group (P all<0.05). Conclusions: TCZ may reduce neural activity of the SCG after MI by inhibiting the IL-6/STAT3 signaling pathway, thereby alleviating myocardial injury and inhibiting VAs.

[Efficacy and safety of neoadjuvant toripalimab combined with nimotuzumab and chemotherapy in patients with unresectable stage Ⅳ squamous cell carcinoma of penis]

Objective: To compare the efficacy and safety of neoadjuvant chemotherapy alone or combined with toripalimab and nimotuzumab in patients with unresectable locally advanced or metastatic squamous cell carcinoma of penis. Methods: A total of 33 patients with unresectable squamous cell carcinoma of penis undergoing neoadjuvant chemotherapy alone or combined with toripalimab and nimotuzumab at Sun Yat-sen University Cancer Center from May 2015 to June 2021 were enrolled retrospectively. All the patients were male, with a median age (M(IQR))of 49.0 (13.5) years (range: 30 to 70 years). According to the therapy protocols, patients were divided into the chemotherapy group (16 cases) and the triple combination group (17 cases). Log-rank test was used to compare the progression-free survival and overall survival. χ² test or Fisher exact method was used to compare the objective response rate, pathological down-stage rate and adverse events between these two groups. Results: The follow-up time was 28.1(19.2) months (range: 1.5 to 33.4 months). Patients of triple combination group were observed significantly longer progression-free survival (30.0 months vs. 8.2 months, χ²=3.998, P=0.046) than those of chemotherapy group. The median overall survival of the triple combination group and chemotherapy group were not reached and 15.2 months (χ²=3.298, P=0.069), respectively. Although there was no significant difference in the subsequent surgical resection rate between these two groups (12/17 vs.11/16, P=1), the objective response rate and the pathological complete response rate in triple combination group were significantly higher than in chemotherapy group (13/17 vs. 6/16, χ²=5.125, P=0.024; 6/7 vs. 0, P=0.001). The main common grade 1 to 2 adverse events in the triple combination group were alopecia (16 cases), anemia (15 cases), and nausea (14 cases). The main common grade 1 to 2 adverse events in the chemotherapy group were anemia (14 cases), alopecia (12 cases), decreased appetite (12 cases), and nausea (11 cases). The incidence of adverse events ≥grade 3 was similar in the triple combination group and chemotherapy group (8/17 vs. 6/16, χ²=0.308, P=0.579). There was no grade 3 adverse event in both groups. Conclusion: Compared with traditional chemotherapy alone, chemotherapy combined with toripalimab and nimotuzumab provides longer progression-free survival and similar toxicity for unresectable stage Ⅳ squamous cell carcinoma of penis.

Isolation and identification of plant growth-promoting rhizobacteria from tall fescue rhizosphere and their functions under salt stress

Soil salinity has become one of the major factors that threaten tall fescue growth and turf quality. Plants recruit diverse microorganisms in the rhizosphere to cope with salinity stress. In this study, 15 plant growth-promoting rhizobacteria (PGPR) were isolated from the salt-treated rhizosphere of tall fescue and were annotated to 10 genera, including Agrobacterium, Fictibacillus, Rhizobium, Bhargavaea, Microbacterium, Paenarthrobacter, Pseudarthrobacter, Bacillus, Halomonas, and Paracoccus. All strains could produce indole-3-acetic acid (IAA). Additionally, eight strains exhibited the ability to solubilize phosphate and potassium. Most strains could grow on the medium containing 600 mM NaCl, such as Bacillus zanthoxyli and Bacillus altitudinis. Furthermore, Bacillus zanthoxyli and Bacillus altitudinis were inoculated with tall fescue seeds and seedlings to determine their growth-promoting effect. The results showed that Bacillus altitudinis and mixed culture significantly increased the germination rate of tall fescue seeds. Bacillus zanthoxyli can significantly increase the tillers number and leaf width of seedlings under salt conditions. Through the synergistic effect of FaSOS1, FaHKT1, and FaHAK1 genes, Bacillus zanthoxyli helps to expel the excess Na⁺ from aboveground parts and absorb more K⁺ in roots to maintain ion homeostasis in tall fescue. Unexpectedly, we found that Bacillus altitudinis displayed an inapparent growth-promoting effect on seedlings under salt stress. Interestingly, the mixed culture of the two strains was also able to alleviate, to some extent, the effects of salt stress on tall fescue. This study provides a preliminary understanding of tall fescue rhizobacteria and highlights the role of Bacillus zanthoxyli in tall fescue growth and salt tolerance.

[The role of preventive pancreatic duct stent placement in preventing acute pancreatitis after endoscopic retrograde cholangiopancreatography]

The aim of this study was to investigate the preventive effect of pancreatic duct stent on acute pancreatitis after endoscopic retrograde cholangiopancreatography. A retrospective analysis of the case data of patients who first underwent endoscopic retrograde cholangiopancreatography for choledocholithiasis in the Beijing Friendship Hospital from January 2015 to December 2019 for 5 years. According to whether the pancreatic duct stent was indwelled during the operation, they were divided into pancreatic duct stent group (147 cases) and non-indwelling pancreatic duct stent group (192 cases). The incidence of acute pancreatitis after endoscopic retrograde cholangiopancreatography was compared between the two groups according to COTTON criteria. Independent sample t test, Pearson Chi-square test (χ²) and Fisher's exact test were used to compare groups' differences. There were 2 cases of acute pancreatitis in the pancreatic duct stent group, all of which improved after 48 hours. There were 22 cases of acute pancreatitis in the non-indwelling pancreatic duct stent group, of which 20 cases improved within 48 hours, and the other 2 cases had severe pancreatitis, which improved and discharged after 30 days of treatment. There was significant difference in the incidence of acute pancreatitis between the pancreatic duct stenting group (1.4%) and the group without placement of pancreatic duct stents (11.5%) (χ²=12.905,P<0.001). In conclusion, Pancreatic duct stent may be an effective method to prevent PEP.

[Effect of measurement sites on coronary computed tomography angiography-derived instantaneous wave-free ratio in the diagnosis of coronary stenosis ischemia]

Objective: To explore the influence of measurement sites on the diagnostic performance of coronary computed tomography angiography (CCTA) -derived instantaneous wave-free ratio (iFR_CT) for coronary stenosis ischemia. Methods: A total of 44 patients, including 27 males and 17 females aged from 44 to 83 (59±90) years, who underwent coronary computed tomography angiography (CCTA) and invasive fractional flow reserve (FFR) in the Department of Radiology, Eastern Theater Command General Hospital from February 2009 to May 2018 were retrospectively collected. Based on CCTA images, iFR_CT values at different locations (stenosis, proximal downstream of stenosis, 2 cm downstream of stenosis, 3 cm downstream of stenosis, and 4 cm downstream of stenosis) were calculated through fluid mechanics simulation. With invasive FFR≤0.80 as the reference standard, receiver operating characteristic (ROC) was used to analyze and evaluate the diagnostic performance of iFR_CT in different sites. Bland-Altman and spearman correlation coefficient were used to analyze the consistency between iFR_CT and invasive FFR. Intraclass correlation coefficient (ICC) and spearman correlation coefficient were used to test the repeatability of iFR_CT. Results: iFR_CT values at the proximal downstream of the stenosis (approximately 1 cm downstream of the stenosis) was superior to other measurement sites in the diagnosis of coronary ischemic specific stenosis. The threshold, area under the curve, sensitivity, specificity and accuracy of iFR_CT at the stenosis were 0.91, 0.87 (95%CI:0.76~0.96), 82% (95%CI:48%~97%), 76% (95%CI:57%~88%) and 77% (95%CI: 63%~87%), respectively. Bland-Altman analysis showed that the mean differences between iFR_CT and FFR at the proximal downstream of the stenosis was 0.07 (95%LoA: 0.06~0.09) and Spearman correlation coefficient was 0.53 (P<0.001). At the proximal downstream of the stenosis, the intraobserver ICC of iFR_CT was 0.92 (95%CI: 0.85 ~0.95), the correlation coefficient was 0.85 (P<0.001); the interobserver ICC was 0.84 (95%CI: 0.60~0.94), correlation coefficient was 0.75 (P<0.001), demonstrating good repeatability between iFR_CT and FFR. Conclusion: With the invasive FFR value as reference standard, iFR_CT had a high diagnostic performance in detecting myocardial ischemia and the best measurement site was the proximal downstream of the stenosis.

[Association of coronary perivascular fat attenuation index, the parameters of plaque and fractional flow reserve]

Objective: To explore the association of coronary perivascular fat attenuation index (FAI), the parameters of plaque and fractional flow reserve (FFR). Methods: A total of 113 patients (with 141 plaques) (78 males and 35 females, age from 40 to 83 years) with stable coronary artery disease were retrospectively collected from Jingling Hospital and Shanghai Sixth People's Hospital. All the patients underwent coronary CT angiography and invasive FFR examinations. The quantitative and qualitative parameters of plaque and vessel (such as the length and volume of plaque, the characteristics of plaque and high-risk plaque) and the FAI around the plaque were measured. The patients were divided into positive FAI group (n=46) and negative FAI group (n=66) according to the standard of whether the threshold of FAI≥ -70 HU. The quantitative indexes, including age, the length and volume of plaque, minimal lumen area (MLA) and FAI, as well as the qualitative indexed, including the characteristics of plaque, the number and characteristic of high-risk plaque and the number of patients and plaque with positive FFR were compared between the two groups. Further, logistic regression analysis was performed to analyze the correlation among myocardial ischemia, age, the length of plaque, minimal lumen area (MLA), FAI and so on. ROC curve was used for evaluating the performance of each parameter. Results: Compared to the negative FAI group, positive FAI group had lower MLA (2.00±1.33 mm² vs 4.13±2.41 mm², P<0.001). The proportion of patients and vessels with FFR<0.75 in positive FAI group were significantly higher than that in negative FAI group (21.3% vs 4.5%, P=0.006; 23.2% vs 8.2%, P=0.016). The FAI between high-risk plaque and non-high-risk plaque had no significant difference (21.2% vs 16.1%, P=0.451). FAI predicted myocardial ischemia (AUC=0.666, P=0.021) and significantly improved the prediction efficiency of complex model(0.915 vs 0.951,P=0.033). Conclusion: Lower MLA and higher incidence of myocardial ischemia were associated with patients with higher FAI. In addition, FAI has a certain prediction efficiency and can provide incremental value for the determination of myocardial ischemia.

Drought stress and plant ecotype drive microbiome recruitment in switchgrass rhizosheath

The rhizosheath, a layer of soil grains that adheres firmly to roots, is beneficial for plant growth and adaptation to drought environments. Switchgrass is a perennial C4 grass which can form contact rhizosheath under drought conditions. In this study, we characterized the microbiomes of four different rhizocompartments of two switchgrass ecotypes (Alamo and Kanlow) grown under drought or well-watered conditions via 16S ribosomal RNA amplicon sequencing. These four rhizocompartments, the bulk soil, rhizosheath soil, rhizoplane, and root endosphere, harbored both distinct and overlapping microbial communities. The root compartments (rhizoplane and root endosphere) displayed low-complexity communities dominated by Proteobacteria and Firmicutes. Compared to bulk soil, Cyanobacteria and Bacteroidetes were selectively enriched, while Proteobacteria and Firmicutes were selectively depleted, in rhizosheath soil. Taxa from Proteobacteria or Firmicutes were specifically selected in Alamo or Kanlow rhizosheath soil. Following drought stress, Citrobacter and Acinetobacter were further enriched in rhizosheath soil, suggesting that rhizosheath microbiome assembly is driven by drought stress. Additionally, the ecotype-specific recruitment of rhizosheath microbiome reveals their differences in drought stress responses. Collectively, these results shed light on rhizosheath microbiome recruitment in switchgrass and lay the foundation for the improvement of drought tolerance in switchgrass by regulating the rhizosheath microbiome.

Application of Hollow Fiber Ultrafiltration Technology in the Detection of Total IgE of Hemolytic Blood after Death

Abstract

Objective To investigate the treatment effect of hollow fiber ultrafiltration technology on hemolytic samples and the differences between IgE concentration and serum concentration before hemolysis in ultrafiltrate. Methods The 33 postmortem blood samples of non-frozen corpses within 72 hours after death were collected, 4 mL blood was taken from each case, among which 1 mL was centrifuged to get serum, and the remaining 3 mL blood was frozen-thawed 3-5 times to cause complete hemolysis. The 2 mL hemolytic samples were processed by hollow fiber ultrafiltration to obtain ultrafiltrate. The hemoglobin concentration in serum, complete hemolytic sample and ultrafiltrate was determined by Van-Zij solution-cyanated methemoglobin assay method, and the total IgE in serum and ultrafiltrate was determined by electrochemical luminescence method. Results The hemoglobin concentration in ultrafiltrate was significantly lower than that in complete hemolytic samples （P<0.05）. There was a good correlation between the total IgE detection values of ultrafiltrate and serum （r=0.984）. The difference between the serum and the value of IgE in ultrafiltrate after correction had no statistical significance, and the differences between the two in positive rates had no statistical significance （P>0.05）. Conclusion Ultrafiltration technology has a good treatment effect on complete hemolytic samples, and the correction value of ultrafiltrate detection is close to the serum level before hemolysis, and therefore, it can be applied to the detection of total IgE of frozen corpse hemolytic samples.

[The clinical study of ocular vestibular evoked myogenic potential on three eye positions]

Objective: To analyze the characteristics of the ocular vestibular evoked myogenic potential on three different eye positions and to explore the appropriate eye position for oVEMP. Methods: 15 patients (30 ears) with vertigo who underwent oVEMP test from December 2017 to May 2018 were selected as the patient group, including seven males and eight females, with an average age of (51±13) years. Another 22 (44 ears) healthy young people were recruited into the control group, including 10 males and 12 females, with an average age of (23±5) years. oVEMPs were measured on the following three eye positions respectively: 30 degrees straight up(upper median position),45 degrees upper right(upper right position), and 45 degrees upper left(upper left position). oVEMP elicitation rate, oVEMP latencies, amplitudes and interaural amplitude asymmetry ratio were analyzed by SPSS 23.0 statistical software. Results: There was no statistical significance (P>0.05) in the oVEMP elicitation rate, oVEMP latency, amplitude and asymmetry ratio on the three eye positions among the control group, the patient group and the overall subjects. Conclusions: The three eye positions can be used to detect oVEMP in clinic. There is no difference in the extraction rate and waveform characteristics. When one of the eye positions is difficult to gaze or not easy to obtain the coincidence curve, the other two can be used to obtain the ideal oVEMP curves as well.

Rotation control of a variable-capacitance electrostatic motor for space equivalence principle tests with rotating masses

Variable-capacitance electrostatic motors are ideal for driving the test mass in ultra-low-noise electrostatic accelerometers. Such devices are essential for testing the new equivalence principle (NEP) with rotating extended masses. However, as the air-film damping is greatly reduced by placing the sensor core assembly in a high-vacuum housing, this synchronous motor may easily fall out of step and suffer spin-up failures with traditional open-loop excitation. In this study, a synchronous electronic phase commutation scheme is proposed by sensing the three-phase position change of the rotor poles and activating the stator electrodes in careful correlation with the instantaneous rotor position. Experiments on a ground-test NEP instrument prototype show that the proposed closed-loop excitation scheme can spin-up the rotor synchronously and maintain stable constant-speed operation of this macroscale variable capacitance motor operated in a high-vacuum environment. This rotation control method is also applicable to the synchronous operation of micromachined variable-capacitance electrostatic motors.

Comparative metabolite profiling of two switchgrass ecotypes reveals differences in drought stress responses and rhizosheath weight

Rhizosheath comprises soil that adheres firmly to roots. In this study, two ecotypes of switchgrass with different rhizosheath sizes after drought stress were analyzed which showed metabolic differences under drought conditions. The rhizosheath comprises soil that adheres firmly to roots by a combination of root hairs and mucilage and may aid in root growth under soil drying. The aim of this work is to reveal the potential metabolites involved in rhizosheath formation under drought stress conditions. Panicum virgatum L. (switchgrass), which belongs to the Poaceae family, is an important biofuel and fodder crop in drought areas. Five switchgrass ecotypes (cv. Alamo, cv. Blackwake, cv. Summer, cv. Cave-in-Rock and cv. Kanlow) have a broad range of rhizosheath weight under drought conditions. For two selected ecotypes with contrast rhizosheath weight (cv. Alamo and cv. Kanlow), root hair length and density, lateral root number, root morphological parameters were measured, and real-time qRT-PCR was performed. Gas chromatography mass spectrophotometry (GC-MS) was used to determine the primary metabolites in the shoots and roots of selected ecotypes under drought stress conditions. The change trends of root hair length and density, lateral root number and related gene expression were consistent with rhizosheath weight in Alamo and Kanlow under drought and watered conditions. For root morphological parameters, Alamo grew deeper than Kanlow, while Kanlow exhibited higher values for other parameters. In this study, the levels of amino acids, sugars and organic acids were significantly changed in response to drought stress in two switchgrass ecotypes. Several metabolites including amino acids (arginine, isoleucine, methionine and cysteine) and sugars (kestose, raffinose, fructose, fucose, sorbose and xylose) in the large soil-sheathed roots of Alamo and Kanlow were significantly increased compared to small or no soil-sheathed roots of Alamo and Kanlow. Difference in rhizosheath size is reflected in the plant internal metabolites under drought stress conditions. Additionally, our results highlight the importance of using metabolite profiling and provide a better understanding of rhizosheath formation at the cellular level.

Identification, evolution and alternative splicing profile analysis of the splicing factor 30 (SPF30) in plant species

The work offers a comprehensive evaluation on the phylogenetics and conservation of splicing patterns of the plant SPF30 splicing factor gene family. In eukaryotes, one pre-mRNA can generate multiple mRNA transcripts by alternative splicing (AS), which expands transcriptome and proteome diversity. Splicing factor 30 (SPF30), also known as survival motor neuron domain containing protein 1 (SMNDC1), is a spliceosomal protein that plays an essential role in spliceosomal assembly. Although SPF30 genes have been well characterised in human and yeast, little is known about their homologues in plants. Here, we report the genome-wide identification and phylogenetic analysis of SPF30 genes in the plant kingdom. In total, 82 SPF30 genes were found in 64 plant species from algae to land plants. Alternative transcripts were found in many SPF30 genes and splicing profile analysis revealed that the second intron in SPF30 genome is frequently associated with AS events and contributed to the birth of novel exons in a few SPF30 members. In addition, different conserved sequences were observed at these putative splice sites among moss, monocots and dicots, respectively. Our findings will facilitate further functional characterization of plant SPF30 genes as putative splicing factors.

Rhizosheath formation and involvement in foxtail millet (Setaria italica) root growth under drought stress

The rhizosheath, a layer of soil particles that adheres firmly to the root surface by a combination of root hairs and mucilage, may improve tolerance to drought stress. Setaria italica (L.) P. Beauv. (foxtail millet), a member of the Poaceae family, is an important food and fodder crop in arid regions and forms a larger rhizosheath under drought conditions. Rhizosheath formation under drought conditions has been studied, but the regulation of root hair growth and rhizosheath size in response to soil moisture remains unclear. To address this question, in this study we monitored root hair growth and rhizosheath development in response to a gradual decline in soil moisture. Here, we determined that a soil moisture level of 10%-14% (w/w) stimulated greater rhizosheath production compared to other soil moisture levels. Root hair density and length also increased at this soil moisture level, which was validated by measurement of the expression of root hair-related genes. These findings contribute to our understanding of rhizosheath formation in response to soil water stress.

Effects of IBDV infection on expression of ghrelin and ghrelin-related genes in chicken

Ghrelin is a peptide hormone that plays a modulatory role in the immune system. Studies have demonstrated that mammal ghrelin level is influenced by pathological status. However, it has not been reported whether chicken ghrelin level changes during pathogen infection. This study was designed to investigate changes of ghrelin levels in chickens infected with infectious bursal disease virus (IBDV) and to explore the relationship between ghrelin changes and bursal damage, and inflammatory cells infiltration induced by IBDV. The results showed that (1) plasma ghrelin concentration increased after IBDV infection. It reached a peak at 10443.6 ± 2612.9 pg/mL on 2 dpi, which was about 100-fold as high as that of the control. Then it decreased sharply on 3 dpi, which was only 31.7% as that of 2 dpi, and remained stable until 5 dpi. Meanwhile, ghrelin and ghrelin-related gene, ghrelin-o-acyltransferase (GOAT), and growth hormone secretagogue receptor (GHSR) mRNA expression levels in bursa were also increased after IBDV infection, and reached the peak on 2 dpi at 149, 28.8, and 117.2-fold higher than that of the control, respectively. Then they decreased and remained at a higher status. Correlation analysis showed that plasma ghrelin concentration and ghrelin, GOAT, and GHSR mRNA expressions in bursa were strongly associated with IBDV VP2 mRNA expression in bursa. (2) The damage of bursa was the most severe on 5 dpi with a histopathological score of 12. It had no direct correlation with plasma ghrelin level and ghrelin, GOAT, and GHSR mRNA expressions in bursa. However, the number of inflammatory cells infiltrating into bursa, which was the highest on 2 and 3 dpi, showed significant a positive correlation with the ghrelin and GHSR mRNA expression. Presumably chicken ghrelin may function as an anti-inflammatory factor. In conclusion, IBDV infection upregulates the expression of ghrelin and ghrelin-related gene in chickens, and chicken ghrelin may play an important regulatory role during pathogen infection.

Alternative splicing and translation play important roles in hypoxic germination in rice

Post-transcriptional mechanisms (PTMs), including alternative splicing (AS) and alternative translation initiation (ATI), may explain the diversity of proteins involved in plant development and stress responses. Transcriptional regulation is important during the hypoxic germination of rice seeds, but the potential roles of PTMs in this process have not been characterized. We used a combination of proteomics and RNA sequencing to discover how AS and ATI contribute to plant responses to hypoxia. In total, 10 253 intron-containing genes were identified. Of these, ~1741 differentially expressed AS (DAS) events from 811 genes were identified in hypoxia-treated seeds compared with controls. Over 95% of these were not present in the list of differentially expressed genes. In particular, regulatory pathways such as the spliceosome, ribosome, endoplasmic reticulum protein processing and export, proteasome, phagosome, oxidative phosphorylation, and mRNA surveillance showed substantial AS changes under hypoxia, suggesting that AS responses are largely independent of transcriptional regulation. Considerable AS changes were identified, including the preferential usage of some non-conventional splice sites and enrichment of splicing factors in the DAS data sets. Taken together, these results not only demonstrate that AS and ATI function during hypoxic germination but they have also allowed the identification of numerous novel proteins/peptides produced via ATI.

Modeling and compensation of cross-axis coupling in an electrostatic accelerometer for testing the equivalence principle

Electrostatic accelerometers have extremely high sensitivity and are ideal scientific instruments for measuring very weak acceleration. In particular, a single-sensitive-axis electrostatic accelerometer can be used for testing the equivalence principle in space. Sensitive-axis capacitances formed by axial electrodes and a cylindrical proof mass vary with the axial motion of the mass and are also affected by radial motion, which results in cross-axis coupling disturbances. A quantitative model is built to analyze the cross-axis coupling effect on the sensitive axis from the radial suspension loop, including a nonlinear model for large radial motion and a linear model for small radial motion. Frequency response simulation shows that the cross-axis coupling effect for a small signal case arises mostly in the high-frequency range. Experiments are carried out with a ground-based electrostatic accelerometer made of a single, non-rotating test cylinder, and in this case, the experimental results are utilized to verify the mathematical model. Cross-axis coupling for small signal perturbations is virtually removed if the equilibrium position of the proof mass is calibrated to the null position of the sensor cage. In addition, data post-processing can further attenuate the cross-axis coupling disturbances when dealing with large radial motion. The cross-axis coupling disturbances on both the position and the acceleration measurement signals in the sensitive axis are mostly removed in ground-based experiments. The proposed model and compensation can be extended to space equivalence principle instruments and other electrostatic accelerometers with a cylindrical proof mass.

Comparative performance of the BGISEQ-500 and Illumina HiSeq4000 sequencing platforms for transcriptome analysis in plants

BACKGROUND

The next-generation sequencing (NGS) technology has greatly facilitated genomic and transcriptomic studies, contributing significantly in expanding the current knowledge on genome and transcriptome. However, the continually evolving variety of sequencing platforms, protocols and analytical pipelines has led the research community to focus on cross-platform evaluation and standardization. As a NGS pioneer in China, the Beijing Genomics Institute (BGI) has announced its own NGS platform designated as BGISEQ-500, since 2016. The capability of this platform in large-scale DNA sequencing and small RNA analysis has been already evaluated. However, the comparative performance of BGISEQ-500 platform in transcriptome analysis remains yet to be elucidated. The Illumina series, a leading sequencing platform in China's sequencing market, would be a preferable reference to evaluate new platforms.

METHODS

To this end, we describe a cross-platform comparative study between BGISEQ-500 and Illumina HiSeq4000 for analysis of Arabidopsis thaliana WT (Col 0) transcriptome. The key parameters in RNA sequencing and transcriptomic data processing were assessed in biological replicate experiments, using aforesaid platforms.

RESULTS

The results from the two platforms BGISEQ-500 and Illumina HiSeq4000 shared high concordance in both inter- (correlation, 0.88-0.93) and intra-platform (correlation, 0.95-0.98) comparison for gene quantification, identification of differentially expressed genes and alternative splicing events. However, the two platforms yielded highly variable interpretation results for single nucleotide polymorphism and insertion-deletion analysis.

CONCLUSION

The present case study provides a comprehensive reference dataset to validate the capability of BGISEQ-500 enabling it to be established as a competitive and reliable platform in plant transcriptome analysis.

Natural variation in the promoter of rice calcineurin B-like protein10 (OsCBL10) affects flooding tolerance during seed germination among rice subspecies

Rice (Oryza sativa L.) has two ecotypes, upland and lowland rice, that have been observed to show different tolerance levels under flooding stress. In this study, two rice cultivars, upland (Up221, flooding-intolerant) and lowland (Low88, flooding-tolerant), were initially used to study their molecular mechanisms in response to flooding germination. We observed that variations in the OsCBL10 promoter sequences in these two cultivars might contribute to this divergence in flooding tolerance. Further analysis using another eight rice cultivars revealed that the OsCBL10 promoter could be classified as either a flooding-tolerant type (T-type) or a flooding-intolerant type (I-type). The OsCBL10 T-type promoter only existed in japonica lowland cultivars, whereas the OsCBL10 I-type promoter existed in japonica upland, indica upland and indica lowland cultivars. Flooding-tolerant rice cultivars containing the OsCBL10 T-type promoter have shown lower Ca²⁺ flow and higher α-amylase activities in comparison to those in flooding-intolerant cultivars. Furthermore, the OsCBL10 overexpression lines were sensitive to both flooding and hypoxic treatments during rice germination with enhanced Ca²⁺ flow in comparison to wild-type. Subsequent findings also indicate that OsCBL10 may affect OsCIPK15 protein abundance and its downstream pathways. In summary, our results suggest that the adaptation to flooding stress during rice germination is associated with two different OsCBL10 promoters, which in turn affect OsCBL10 expression in different cultivars and negatively affect OsCIPK15 protein accumulation and its downstream cascade.

A connection between the maximum displacements of rogue waves and the dynamics of poles in the complex plane

Rogue waves of evolution systems are displacements which are localized in both space and time. The locations of the points of maximum displacements of the wave profiles may correlate with the trajectories of the poles of the exact solutions from the perspective of complex variables through analytic continuation. More precisely, the location of the maximum height of the rogue wave in laboratory coordinates (real space and time) is conjectured to be equal to the real part of the pole of the exact solution, if the spatial coordinate is allowed to be complex. This feature can be verified readily for the Peregrine breather (lowest order rogue wave) of the nonlinear Schrödinger equation. This connection is further demonstrated numerically here for more complicated scenarios, namely the second order rogue wave of the Boussinesq equation (for bidirectional long waves in shallow water), an asymmetric second order rogue wave for the nonlinear Schrödinger equation (as evolution system for slowly varying wave packets), and a symmetric second order rogue wave of coupled Schrödinger systems. Furthermore, the maximum displacements in physical space occur at a time instant where the trajectories of the poles in the complex plane reverse directions. This property is conjectured to hold for many other systems, and will help to determine the maximum amplitudes of rogue waves.

Proteogenomic analysis reveals alternative splicing and translation as part of the abscisic acid response in Arabidopsis seedlings

In eukaryotes, mechanisms such as alternative splicing (AS) and alternative translation initiation (ATI) contribute to organismal protein diversity. Specifically, splicing factors play crucial roles in responses to environment and development cues; however, the underlying mechanisms are not well investigated in plants. Here, we report the parallel employment of short-read RNA sequencing, single molecule long-read sequencing and proteomic identification to unravel AS isoforms and previously unannotated proteins in response to abscisic acid (ABA) treatment. Combining the data from the two sequencing methods, approximately 83.4% of intron-containing genes were alternatively spliced. Two AS types, which are referred to as alternative first exon (AFE) and alternative last exon (ALE), were more abundant than intron retention (IR); however, by contrast to AS events detected under normal conditions, differentially expressed AS isoforms were more likely to be translated. ABA extensively affects the AS pattern, indicated by the increasing number of non-conventional splicing sites. This work also identified thousands of unannotated peptides and proteins by ATI based on mass spectrometry and a virtual peptide library deduced from both strands of coding regions within the Arabidopsis genome. The results enhance our understanding of AS and alternative translation mechanisms under normal conditions, and in response to ABA treatment.

Mechanical complications of central venous catheterisation in trauma patients

INTRODUCTION Central venous catheterisation (CVC) is a commonly performed procedure in a wide variety of hospital settings and is associated with appreciable morbidity. There is a paucity of literature focusing on mechanical complications specifically in the trauma setting. The aim of our study was to determine the spectrum of mechanical complications in a high-volume trauma centre in a developing world setting where ultrasound guidance was not available. METHODS A retrospective study was performed analysing data from a four-year period at the Pietermaritzburg Metropolitan Trauma Service in South Africa. RESULTS A total of 178 mechanical complications (18%) occurred in 1,015 patients undergoing CVC: 117 pneumothoraces, 25 malpositions, 18 catheter dislodgements, 14 arterial cannulations, one air embolism, one chylothorax, one pleural cannulation and one retained guide-wire. The internal jugular vein (IJV) approach was associated with a higher overall complication rate than the subclavian vein (SCV) approach (24% vs. 13%, p<0.001). Pneumothorax (73% vs. 57%, p<0.001) and arterial cannulation (15% vs. 0%, p<0.001) were more common with the IJV. Catheter dislodgement (21% vs. 0%, p<0.001) was more common with the SCV. Junior doctors performed 66% of the CVCs and this was associated with a significantly higher complication rate (20% vs. 12%, p<0.001). CONCLUSIONS CVC carries appreciable morbidity, with pneumothorax being the most frequent mechanical complication. The SCV was the most commonly used approach at our institution. The majority of CVCs were performed by junior doctors and this was associated with a considerable complication rate.

A Phylogenetically Informed Comparison of GH1 Hydrolases between Arabidopsis and Rice Response to Stressors

Glycoside hydrolases Family 1 (GH1) comprises enzymes that can hydrolyze β-O-glycosidic bond from a carbohydrate moiety. The plant GH1 hydrolases participate in a number of developmental processes and stress responses, including cell wall modification, plant hormone activation or deactivation and herbivore resistance. A large number of members has been observed in this family, suggesting their potential redundant functions in various biological processes. In this study, we have used 304 sequences of plant GH1 hydrolases to study the evolution of this gene family in plant lineage. Gene duplication was found to be a common phenomenon in this gene family. Although many members of GH1 hydrolases showed a high degree of similarity in Arabidopsis and rice, they showed substantial tissue specificity and differential responses to various stress treatments. This differential regulation implies each enzyme may play a distinct role in plants. Furthermore, some of salt-responsive Arabidopsis GH1 hydrolases were selected to test their genetic involvement in salt responses. The knockout mutants of AtBGLU1 and AtBGLU19 were observed to be less-sensitive during NaCl treatment in comparison to the wild type seedlings, indicating their participation in salt stress response. In summary, Arabidopsis and rice GH1 glycoside hydrolases showed distinct features in their evolutionary path, transcriptional regulation and genetic functions.

SWATH-MS Quantitative Analysis of Proteins in the Rice Inferior and Superior Spikelets during Grain Filling

Modern rice cultivars have large panicle but their yield potential is often not fully achieved due to poor grain-filling of late-flowering inferior spikelets (IS). Our earlier work suggested a broad transcriptional reprogramming during grain filling and showed a difference in gene expression between IS and earlier-flowering superior spikelets (SS). However, the links between the abundances of transcripts and their corresponding proteins are unclear. In this study, a SWATH-MS (sequential window acquisition of all theoretical spectra-mass spectrometry) -based quantitative proteomic analysis has been applied to investigate SS and IS proteomes. A total of 304 proteins of widely differing functionality were observed to be differentially expressed between IS and SS. Detailed gene ontology analysis indicated that several biological processes including photosynthesis, protein metabolism, and energy metabolism are differentially regulated. Further correlation analysis revealed that abundances of most of the differentially expressed proteins are not correlated to the respective transcript levels, indicating that an extra layer of gene regulation which may exist during rice grain filling. Our findings raised an intriguing possibility that these candidate proteins may be crucial in determining the poor grain-filling of IS. Therefore, we hypothesize that the regulation of proteome changes not only occurs at the transcriptional, but also at the post-transcriptional level, during grain filling in rice.