Efficient isolation of high quality RNA from tropical palms for RNA-seq analysis

Currently, RNA-seq as a high throughput technology is being widely applied to various species to elucidate the complexity of the transcriptome and to discover large number of novel genes. However, the technology has had poor success in elucidating the transcriptome of tropical palms, as it is difficult to isolate high quality RNA from tropical palm tissues due to their high polysaccharide and polyphenol content. Here, we developed an RNA-isolation protocol for tropical palms, the MRIP method (Methods for RNA Isolation from Palms). The integrity of the RNA molecules extracted using this protocol was determined to be of high quality by means of gel electrophoresis and Agilent 2100 Bioanalyzer microfluidic electrophoresis chip examination with a RIN (RNA Integrity Number) value of more than 9, indicating that the mRNAs were of good integrity. Subsequently the isolated RNA was used for transcription analysis without further purification. With Illumina sequencing, we obtained 54.9 million short reads and then conducted de novo assembly to gain 57,304 unigenes with an average length of 752 base pairs. Moreover, the RNA isolated with this protocol was also successfully used for real-time RT-PCR. These results suggested that the RNA isolated was suitable for Illumina RNA sequencing and quantitative real-time RT-PCR. Furthermore, this method was also successful in isolating total RNA from the leaves of various Palmaceae species

Areca palm velarivirus 1 infection caused disassembly of chloroplast and reduction of photosynthesis in areca palm

The expansion of betel palm cultivation is driven by rising demand for betel nut, yet this growth is accompanied by challenges such as decreased agricultural biodiversity and the spread of infectious pathogens. Among these, Yellow Leaf Disease (YLD) emerges as a prominent threat to betel palm plantation. Areca Palm Velarivirus 1 (APV1) has been identified as a primary causative agent of YLD, precipitating leaf yellowing, stunted growth, and diminished yield. However, the precise mechanisms underlying APV1-induced damage remain elusive. Our study elucidates that APV1 infiltrates chloroplasts, instigating severe damage and consequential reductions in chlorophyll a/b and carotene levels, alongside notable declines in photosynthetic efficiency. Moreover, APV1 infection exerts broad regulatory effects on gene expression, particularly suppressing key genes implicated in chloroplast function and photosynthesis. These disruptions correlate with growth retardation, yield diminishment, and compromised nut quality. Intriguingly, the paradoxical destruction of the host's photosynthetic machinery by APV1 prompts inquiry into its evolutionary rationale, given the virus's dependence on host resources for replication and proliferation. Our findings reveal that APV1-induced leaf yellowing acts as a beacon for transmission vectors, hinting at a nuanced “host-pathogen-vector co-evolutionary” dynamic

Surface electromyography characteristics of patients with anterior cruciate ligament injury in different rehabilitation phases

Background: Anterior cruciate ligament reconstruction (ACLR) is a common treatment for anterior cruciate ligament (ACL) injury. However, after ACLR, a significant proportion of patients do not return to pre-injury levels. Research on muscle function during movement has important implications in rehabilitation.Methods: Sixty patients with unilateral ACL injury were recruited for this study and assigned into three groups: group A, individuals with an ACL injury before 6 months; group B, individuals with ACLR from 6 months to 1 year; and group C, individuals with ACLR 1 year later. Surface electromyography (SEMG) signals were collected from the bilateral rectus femoris (RF), vastus medialis (VM), vastus lateralis (VL), biceps femoris (BF), and semitendinosus (ST). The tasks performed during the experiment included straight leg raising (SLR) training at 30°, SLR training at 60°, ankle dorsiflexion, walking, and fast walking.Results: In the maximum muscle strength test, the affected side of the BF in group A (199.4 ± 177.12) was significantly larger than in group B (53.91 ± 36.61, p = 0.02) and group C (75.08 ± 59.7, p = 0.023). In the walking test, the contralateral side of the RF in group B (347.53 ± 518.88) was significantly greater than that in group C (139.28 ± 173.78, p = 0.029). In the SLR training (60°) test, the contralateral side of the RF in group C (165.37 ± 183.06) was significantly larger than that in group A (115.09 ± 62.47, p = 0.023) and smaller than that in group B (226.21 ± 237.17, p = 0.046); In the ankle dorsiflexion training test, the contralateral side of the RF in group B (80.37 ± 87.9) was significantly larger than that in group C (45.61 ± 37.93, p = 0.046).Conclusion: This study showed the EMG characteristics of patients with ACL injury helped to determine which muscle requires more training and which exercise model would be best suited for intervention

Acidification oxidation reagent system optimization on coal seams and stimulation effect evaluation

China has abundant coalbed methane (CBM) resources, and most of them are low-permeability and tight reservoirs, with generally low production rate and small recovery factor. Existing technologies face great challenges to meet the demand on CBM in China. It is desirable to develop new methods to improve the production rate and enhance recovery factor. In addition to physical stimulation methods such as hydraulic fracturing and open-hole cave completion, the use of chemical methods to improve physical properties of coal reservoirs has also been a hot research topic in recent years. Coal reservoir acidification and oxidation technology can promote desorption of gas and enlarge permeability of reservoir. But for different coal rank coal reservoirs, the acidification and oxidation agents need to be optimized and their performance evaluated. Laboratory experiments are conducted to compare and analyze the physical properties coal samples from Baode, Mu’ai, and Xinjiang blocks, including coal rank, texture, macroscopic characteristics, quality, porosity, permeability, element, and mineral composition. The optimal concentration of hydrochloric acid is determined through pre-dissolution experiment of coal powder in acid solution. Then a five-factor and three-level orthogonal experiment for acid solution optimization is designed and performed by using Design-Expert software, which identifies the sensitive factors affecting the dissolution. For the coal samples in Baode, Mu’ai, and Xinjiang blocks, the oxidant types and the corresponding acidification and oxidation agent systems are optimized. Applying these acidification and oxidation agent systems to coal samples from Baode, Mu’ai, and Xinjiang blocks, the change of porosity, permeability, and wettability are compared and analyzed. Finally, through numerical simulation, the gas production is predicted for acidification and oxidation in typical well group in Block Mu’ai. Results show that the acid solution has the best dissolution at a concentration of hydrochloric acid of 3 mol/L to 4 mol/L; Top factors played in the experiment are soaking time, acid type, soaking temperature, coal sample type, and acid concentration, in descending order of importance; The optimal oxidant is a hydrogen peroxide solution with a concentration of 3%; the mixed acidification oxidant formula in Baode block is 10% HCl + 2% CH3COOH + 2% HF + 3% H2O2; The optimal mixed acidification oxidant formula in Mu’ai block is 8% HCl + 2% CH3COOH + 4% HF + 3% H2O2; the optimal mixed acidification oxidant formula in Xinjiang block is 12% HCl + 1% CH3COOH + 1% HF + 3% H2O2; The higher the coal rank, the greater the HF content in the optimal acidification oxidant system. Both acidification and oxidation improve the porosity and permeability of coal samples to some extent, and the improvement in low-rank coal is more significant than that in high-rank coal. Acidification and oxidation have different effects on the wettability of coal: Acidification increases the hydrophilicity of coal, whereas oxidation reduce the hydrophilicity of coal; and the hydrophilicity of coal samples treated by the optimized acidification and oxidation system is weakened. Reservoir simulation results show that acidification and oxidation lead to a recovery factor of 64.64% after 10 years of production, which is 19.72% higher than that without acidification and oxidation. The advantage of acidification and oxidation is 0.97% after 18 years of production. However, the acidification and oxidation saved 8 years of production time to achieve a close final recovery factor, which greatly reduces the operating costs. The optimized acidizing oxidation agent systems for CBM reservoirs with low, medium, and high ranks improved the desorption and permeability of the target reservoirs, and increase well production and recovery factor. This research provides technical support for stimulation practices of CBM reservoirs in the aforementioned blocks in China, as well as similar coal reservoirs in the world

Efficacy of transcranial direct current stimulation for improving postoperative quality of recovery in elderly patients undergoing lower limb major arthroplasty: a randomized controlled substudy

BackgroundPrevious studies have demonstrated improvements in motor, behavioral, and emotional areas following transcranial direct current stimulation (tDCS), but no published studies have reported the efficacy of tDCS on postoperative recovery quality in patients undergoing lower limb major arthroplasty. We hypothesized that tDCS might improve postoperative recovery quality in elderly patients undergoing lower limb major arthroplasty.MethodsNinety-six patients (≥65 years) undergoing total hip arthroplasty (THA) or total knee arthroplasty (TKA) were randomized to receive 2 mA tDCS for 20 min active-tDCS or sham-tDCS. The primary outcome was the 15-item quality of recovery (QoR-15) score on postoperative day one (Т2). Secondary outcomes included the QoR-15 scores at the 2nd hour (T1), the 1st month (Т3), and the 3rd month (Т4) postoperatively, numeric rating scale scores, and fatigue severity scale scores.ResultsNinety-six elderly patients (mean age, 71 years; 68.7% woman) were analyzed. Higher QoR-15 scores were found in the active-tDCS group at T2 (123.0 [114.3, 127.0] vs. 109.0 [99.3, 115.3]; median difference, 13.0; 95% CI, 8.0 to 17.0; p < 0.001). QoR-15 scores in the active-tDCS group were higher at T1 (p < 0.001), T3 (p = 0.001), and T4 (p = 0.001). The pain scores in the active-tDCS group were lower (p < 0.001 at motion; p < 0.001 at rest). The fatigue degree scores were lower in the active-tDCS group at T1 and T2 (p < 0.001 for each).ConclusiontDCS may help improve the quality of early recovery in elderly patients undergoing lower limb major arthroplasty.Clinical trial registrationThe trial was registered at the China Clinical Trial Center (ChiCTR2200057777, https://www.chictr.org.cn/showproj.html?proj=162744)

Genetic Variation of the Human α-2-Heremans-Schmid Glycoprotein (AHSG) Gene Associated with the Risk of SARS-CoV Infection

Genetic background may play an important role in the process of SARS-CoV infection and SARS development. We found several proteins that could interact with the nucleocapsid protein of the SARS coronavirus (SARS-CoV). α-2-Heremans-Schmid Glycoprotein (AHSG), which is required for macrophage deactivation by endogenous cations, is associated with inflammatory regulation. Cytochrome P450 Family 3A (CYP4F3A) is an ω-oxidase that inactivates Leukotriene B4 (LTB4) in human neutrophils and the liver. We investigated the association between the polymorphisms of these two inflammation-associated genes and SARS development. The linkage disequilibrium (LD) maps of these two genes were built with Haploview using data on CHB+JPT (version 2) from the HapMap. A total of ten tag SNPs were selected and genotyped. In the Guangzhou cohort study, after adjusting for age and sex, two AHSG SNPs and one CYP4F3 SNP were found to be associated with SARS susceptibility: rs2248690 (adjusted odds ratio [AOR] 2.42; 95% confidence interval [CI] 1.30-4.51); rs4917 (AOR 1.84; 95% CI 1.02-3.34); and rs3794987 (AOR 2.01; 95% CI 1.10–3.68). To further validate the association, the ten tag SNPs were genotyped in the Beijing cohort. After adjusting for age and sex, only rs2248690 (AOR, 1.63; 95% CI, 1.30–2.04) was found to be associated with SARS susceptibility. The combined analysis of the two studies confirmed tag SNP rs2248690 in AHSG as a susceptibility variant (AOR 1.70; 95% CI 1.37–2.09). The statistical analysis of the rs2248690 genotype data among the patients and healthy controls in the HCW cohort, who were all similarly exposed to the SARS virus, also supported the findings. Further, the SNP rs2248690 affected the transcriptional activity of the AHSG promoter and thus regulated the AHSG serum level. Therefore, our study has demonstrated that the AA genotype of rs2268690, which leads to a higher AHSG serum concentration, was significantly associated with protection against SARS development