Comparative analyses of chloroplast genomes from Six Rhodiola species: variable DNA markers identification and phylogenetic relationships within the genus.

BACKGROUND: As a valuable medicinal plant, Rhodiola has a very long history of folk medicine used as an important adaptogen, tonic, and hemostatic. However, our knowledge of the chloroplast genome level of Rhodiola is limited. This drawback has limited studies on the identification, evolution, genetic diversity and other relevant studies on Rhodiola. RESULTS: Six Rhodiola complete chloroplast genomes were determined and compared to another Rhodiola cp genome at the genome scale. The results revealed a cp genome with a typical quadripartite and circular structure that ranged in size from 150,771 to 151,891 base pairs. High similarity of genome organization, gene number, gene order, and GC content were found among the chloroplast genomes of Rhodiola. 186 (R. wallichiana) to 200 (R. gelida) SSRs and 144 pairs of repeats were detected in the 6 Rhodiola cp genomes. Thirteen mutational hotspots for genome divergence were determined and could be used as candidate markers for phylogenetic analyses and Rhodiola species identification. The phylogenetic relationships inferred by members of Rhodiola cluster into two clades: dioecious and hermaphrodite. Our findings are helpful for understanding Rhodiola's taxonomic, phylogenetic, and evolutionary relationships. CONCLUSIONS: Comparative analysis of chloroplast genomes of Rhodiola facilitates medicinal resource conservation, phylogenetic reconstruction and biogeographical research of Rhodiola.

Spatial variability of microplastic pollution on surface of rivers in a mountain-plain transitional area: A case study in the Chin Ling-Wei River Plain, China.

Inland lakes and rivers are large reservoirs of microplastics. But currently, not too much research was done on microplastics of mountain rivers. The protection of water sources from microplastics is extremely significant for the safety of human drinking water. We quantified the distribution and variation of microplastics in the surface water from tributary (upstream water-source regions) to main stream (human settlements) in the Chin Ling-Wei River Plain Rivers, and assessed the pollution risk. Rivers in the Chin Ling-Wei River Plain contained various levels of microplastics (2.30-21.05 items/L), and the main stream of the river contained higher concentrations most commonly of microplastics than tributaries. The microplastics were fragments and films; they constituted 82.3% of the total abundance of microplastics. Microplastics with a particle size < 500 µm accounted for 64.3% of all the samples. As rivers flow from the mountains to the plains, the land-use types along the rivers become more multifunctional. Thus, the risk of river microplastic pollution increases sharply with distance downstream. Our research explored the microplastics pollution in the Chin Ling mountains based on topography and land-use types and thus provides a reference for further studies exploring the spatial distribution characteristics of microplastics in small-scale rivers and for pollution risk assessments.

Identification of close relationship between large-scale circulation patterns and ozone-precursor sensitivity in the Pearl River Delta, China.

To curb the continuous deterioration of ozone (O3) pollution in China, identifying the O3-precursor sensitivity (OPS) and its driving factors is a prerequisite for formulating effective O3 pollution control measures. Traditional OPS identification methods have limitations in terms of spatiotemporal representation and timeliness; therefore, they are not appropriate for making OPS forecasts for O3 contingency control. OPS is not only influenced by local precursor emissions but is also closely related to meteorological conditions governed by large-scale circulation (LSC). In this study, a localized three-dimensional numerical modeling system was used to investigate the relationship between LSC and OPS in the Pearl River Delta (PRD) of China during September 2017, a month with continuous O3 pollution. Our results highlighted that there was a close relationship between LSC and OPS over the PRD, and the four dominant LSC patterns corresponded well to the NOx-limited, NOx-limited, VOC-limited, and transitional regimes, respectively. The clear linkage between LSC and OPS was mainly driven by the spatial heterogeneity of NOx and VOC emissions within and beyond the PRD along the prevailing winds under different LSC patterns. A conceptual model was developed to highlight the intrinsic causality between the LSC and OPS. Because current technology can accurately forecast LSC 48-72 h in advance, the LSC-based OPS forecast method provided us with a novel approach to guide contingency control and management measures to reduce peak O3 at a regional scale.

[Novel compound heterozygous SCN9A variations causing congenital insensitivity to pain in a patient].

OBJECTIVE: To explore the genetic basis for a child featuring congenital insensitivity to pain (CIP). METHODS: Targeted capture and next generation sequencing (NGS) was carried out for the proband. Suspected pathogenic variants were confirmed by Sanger sequencing of the proband and his parents. RESULTS: The proband was found to harbor compound heterozygous variants of SCN9A gene, namely c.1598delA (p.N533Ifs*31) and c.295_296delCGinsAT (p.R99I), which were respectively inherited from his father and mother. Both variants were predicted to be pathogenic, and neither was reported previously. CONCLUSION: The compound heterozygous variants of the SCN9A gene probably underlay the CIP in this child. Above finding has enabled genetic counseling for this family.

[Genetic testing of a Chinese pedigree affected with non-syndromic autosomal dominant deafness 15].

OBJECTIVE: To explore the genetic basis of a Chinese pedigree affected with progressive non-syndromic sensorineural hearing loss. METHODS: High-throughput DNA sequencing was carried out to analyze 415 genes associated with hereditary deafness in the proband. Sanger sequencing was carried out to verify the suspected variants among her family members. RESULTS: The proband was found to carry a heterozygous c.842T>A (p.Ile281Asn) variant of the POU4F3 gene. The same variant was found among all other patients from the pedigree including the proband's mother, brother, aunt and maternal grandfather, but not among those with normal hearing. Based on the standards and guidelines of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology, the c.842T>A(p.Ile281Asn) variant of the POU4F3 gene was predicted as likely pathogenic (PM2+PM5+PP1+PP3+PP4). CONCLUSION: A Chinese pedigree affected by a rare type autosomal dominant deafness-15 (DFNA15) due to a novel c.842T>A (p.Ile281Asn) variant of the POU4F3 gene was identified. The result has facilitated genetic counseling and risk assessment for the pedigree.

[Genetic diagnosis of a pedigree affected with Usher syndrome type 1D/F].

OBJECTIVE: To explore the genetic basis for a pedigree affected with congenital sensorineural deafness. METHODS: High-throughput sequencing was carried out to analyze the coding regions of 415 genes associated with hereditary deafness in the proband. Suspected variants were verified by PCR amplification and Sanger sequencing of her parents and sister. RESULTS: The proband was found to have carried a heterozygous c.5131G>A (p.Val1711Ile) variant of the CDH23 gene and a heterozygous c.2884C>T(p.Arg962Cys) variant of the PCDH15 gene, which were respectively inherited from her mother and father. Her sister (with normal hearing) was also heterozygous for the c.5131G>A (p.Val1711Ile) variant of the CDH23 gene but not the c.2884C>T (p.Arg962Cys) variant of the PCDH15 gene. Based on the guidelines of the American College of Medical Genetics and Genomics, both variants were predicted to be likely pathogenic (PS1+PM2+PP3+PP4). CONCLUSION: The c.5131G>A (p.Val1711Ile) variant of the CDH23 gene and c.2884C>T (p.Arg962Cys) variant of the PCDH15 gene probably underlay the pathogenesis of Usher syndrome type 1D/F in this pedigree.

Emission source-based ozone isopleth and isosurface diagrams and their significance in ozone pollution control strategies.

In the past decade, ozone (O3) pollution has been continuously worsening in most developing countries. The accurate identification of the nonlinear relationship between O3 and its precursors is a prerequisite for formulating effective O3 control measures. At present, precursor-based O3 isopleth diagrams are widely used to infer O3 control strategy at a particular location. However, there is frequently a large gap between the O3-precursor nonlinearity delineated by the O3 isopleths and the emission source control measures to reduce O3 levels. Consequently, we developed an emission source-based O3 isopleth diagram that directly illustrates the O3 level changes in response to synergistic control on two types of emission sources using a validated numerical modeling system and the latest regional emission inventory. Isopleths can be further upgraded to isosurfaces when co-control on three types of emission sources is investigated. Using Guangzhou and Foshan as examples, we demonstrate that similar precursor-based O3 isopleths can be associated with significantly different emission source co-control strategies. In Guangzhou, controlling solvent use emissions was the most effective approach to reduce peak O3 levels. In Foshan, co-control of on-road mobile, solvent use, and fixed combustion sources with a ratio of 3:1:2 or 3:1:3 was best to effectively reduce the peak O3 levels below 145 ppbv. This study underscores the importance of using emission source-based O3 isopleths and isosurface diagrams to guide a precursor emission control strategy that can effectively reduce the peak O3 levels in a particular area.

Identification of close relationship between atmospheric oxidation and ozone formation regimes in a photochemically active region.

Understanding ozone (O3) formation regime is a prerequisite in formulating an effective O3 pollution control strategy. Photochemical indicator is a simple and direct method in identifying O3 formation regimes. Most used indicators are derived from observations, whereas the role of atmospheric oxidation is not in consideration, which is the core driver of O3 formation. Thus, it may impact accuracy in signaling O3 formation regimes. In this study, an advanced three-dimensional numerical modeling system was used to investigate the relationship between atmospheric oxidation and O3 formation regimes during a long-lasting O3 exceedance event in September 2017 over the Pearl River Delta (PRD) of China. We discovered a clear relationship between atmospheric oxidative capacity and O3 formation regime. Over eastern PRD, O3 formation was mainly in a NOx-limited regime when HO2/OH ratio was higher than 11, while in a VOC-limited regime when the ratio was lower than 9.5. Over central and western PRD, an HO2/OH ratio higher than 5 and lower than 2 was indicative of NOx-limited and VOC-limited regime, respectively. Physical contribution, including horizontal transport and vertical transport, may pose uncertainties on the indication of O3 formation regime by HO2/OH ratio. In comparison with other commonly used photochemical indicators, HO2/OH ratio had the best performance in differentiating O3 formation regimes. This study highlighted the necessities in using an atmospheric oxidative capacity-based indicator to infer O3 formation regime, and underscored the importance of characterizing behaviors of radicals to gain insight in atmospheric processes leading to O3 pollution over a photochemically active region.

[Genetic analysis of five pedigrees affected with multiple osteochondromas].

OBJECTIVE: To detect variants of EXT1 and EXT2 genes among five pedigrees affected with multiple osteochondromas and provide prenatal diagnosis for the families based on the results. METHODS: The EXT1 and EXT2 genes of the probands were analyzed by targeted next generation sequencing (NGS). Suspected pathological variants were validated by Sanger sequencing in the probands, their family members and 200 unrelated healthy controls. Multiple ligation-dependent probe amplification (MLPA) was used to confirm the presence of gross deletions. Prenatal diagnosis was provided for 2 couples carrying pathogenic or likely pathogenic variants. RESULTS: Five variants were detected in the pedigrees, which included EXT1 exon 2-3 deletion, c.1468dupC (p.Leu490ProfsX31), c.2084delC (p.Pro695LeufsX11), and EXT2 c.187delT (p.Phe63SerfsX29) and c.1362T>G (p.Tyr454X). Among these, EXT1 exon 2-3 deletion, c.2084delC (p.Pro695LeufsX11) and EXT2 c.187delT (p.Phe63SerfsX29) were unreported previously. The three novel variants were not found among unaffected members of the pedigree and the 200 healthy controls. Upon prenatal diagnosis, the two fetuses were found to carry the same variants of the the probands. CONCLUSION: Pathological variants of the EXT1 and EXT2 genes probably underlie the multiple osteochondromas among the 5 pedigrees. Prenatal diagnosis based on the results can effectively reduce the birth of further offspring affected with the disease.

Sliding Mode Observer-Based Current Sensor Fault Reconstruction and Unknown Load Disturbance Estimation for PMSM Driven System.

This paper proposes a new scheme of reconstructing current sensor faults and estimating unknown load disturbance for a permanent magnet synchronous motor (PMSM)-driven system. First, the original PMSM system is transformed into two subsystems; the first subsystem has unknown system load disturbances, which are unrelated to sensor faults, and the second subsystem has sensor faults, but is free from unknown load disturbances. Introducing a new state variable, the augmented subsystem that has sensor faults can be transformed into having actuator faults. Second, two sliding mode observers (SMOs) are designed: the unknown load disturbance is estimated by the first SMO in the subsystem, which has unknown load disturbance, and the sensor faults can be reconstructed using the second SMO in the augmented subsystem, which has sensor faults. The gains of the proposed SMOs and their stability analysis are developed via the solution of linear matrix inequality (LMI). Finally, the effectiveness of the proposed scheme was verified by simulations and experiments. The results demonstrate that the proposed scheme can reconstruct current sensor faults and estimate unknown load disturbance for the PMSM-driven system.

[Mutational analysis and prenatal diagnosis of COL1A1 and COL1A2 genes in four Chinese families affected with osteogenesis imperfecta].

OBJECTIVE: To detect potential mutations of COL1A1 and COL1A2 genes in four Chinese pedigrees affected with osteogenesis imperfecta (OI) and provide prenatal diagnosis for a fetus at 18th gestational week. METHODS: All coding regions and exon/intron boundaries of the COL1A1 and COL1A2 genes were analyzed with targeted next-generation sequencing (NGS). Suspected mutations were confirmed with Sanger sequencing in the probands, unaffected relatives and 200 unrelated healthy individuals. Prenatal diagnosis for a high-risk fetus was carried out through Sanger sequencing. RESULTS: The probands of families 1 and 2 have respectively carried a c.760G>A (p.Gly254Arg) and a c.608G>T (p.Gly203Val) mutation of the COL1A1 gene. For family 3, the proband and his daughter have carried a novel c.299-1G>C splicing mutation of the COL1A1 gene. The same mutation was not found in the fetus of this family. For family 4, the proband has carried a novel c.1990G>C (p.Gly664Arg) mutation of the COL1A2 gene. The four mutations were not found in the unaffected relatives and 200 unrelated healthy individuals. CONCLUSION: The mutations of the COL1A1 and COL1A2 genes probably underlie the disease in the four families. NGS combined with Sanger sequencing can provide an effective and accurate method for their genetic and prenatal diagnosis.

Current Sensor Fault Diagnosis Based on a Sliding Mode Observer for PMSM Driven Systems.

This paper proposes a current sensor fault detection method based on a sliding mode observer for the torque closed-loop control system of interior permanent magnet synchronous motors. First, a sliding mode observer based on the extended flux linkage is built to simplify the motor model, which effectively eliminates the phenomenon of salient poles and the dependence on the direct axis inductance parameter, and can also be used for real-time calculation of feedback torque. Then a sliding mode current observer is constructed in αß coordinates to generate the fault residuals of the phase current sensors. The method can accurately identify abrupt gain faults and slow-variation offset faults in real time in faulty sensors, and the generated residuals of the designed fault detection system are not affected by the unknown input, the structure of the observer, and the theoretical derivation and the stability proof process are concise and simple. The RT-LAB real-time simulation is used to build a simulation model of the hardware in the loop. The simulation and experimental results demonstrate the feasibility and effectiveness of the proposed method.

Online fault detection of permanent magnet demagnetization for IPMSMs by nonsingular fast terminal-sliding-mode observer.

To prevent irreversible demagnetization of a permanent magnet (PM) for interior permanent magnet synchronous motors (IPMSMs) by flux-weakening control, a robust PM flux-linkage nonsingular fast terminal-sliding-mode observer (NFTSMO) is proposed to detect demagnetization faults. First, the IPMSM mathematical model of demagnetization is presented. Second, the construction of the NFTSMO to estimate PM demagnetization faults in IPMSM is described, and a proof of observer stability is given. The fault decision criteria and fault-processing method are also presented. Finally, the proposed scheme was simulated using MATLAB/Simulink and implemented on the RT-LAB platform. A number of robustness tests have been carried out. The scheme shows good performance in spite of speed fluctuations, torque ripples and the uncertainties of stator resistance.

Molecular Docking and Molecular Dynamics Simulation of New Potential JAK3 Inhibitors.

INTRODUCTION: JAK3 kinase inhibitor has become an effective means to treat tumors and autoimmune diseases. METHOD: In this study, molecular docking and molecular dynamics simulation were used to study the theoretical interaction mechanism between 1-phenylimidazolidine-2-one molecules and JAK3 protein. RESULT: The results of molecular docking showed that the six 1-phenylimidazolidine-2-one derivatives obtained by virtual screening were bound to the ATP pocket of JAK3 kinase, which were competitive inhibitors of ATP, and were mainly bound to the pocket through hydrogen bonding and hydrophobic interaction. Further, MM/GBSA based on molecular dynamics simulation sampling was used to calculate the binding energy between six molecules and the JAK3 kinase protein. Subsequently, the binding energy was decomposed into the contribution of each amino acid residue, of which Leu905, Lys855, Asp967, Leu956, Tyr904, and Val836 were the main energy-contributing residues. Among them, the molecule numbered LCM01415405 can interact with the specific amino acid Arg911 of JAK3 kinase, suggesting that the molecule may be a selective JAK3 kinase inhibitor. The root-mean-square fluctuation (RMSF) of JAK3 kinase pocket residues during molecular dynamics simulation showed that the combination of six new potential small molecule inhibitors with JAK3 kinase could reduce the flexibility of JAK3 kinase pocket residues. CONCLUSION: These findings reveal the mechanism of 1-phenylimidazolidine-2-one derivatives on JAK3 protein and provide a relatively solid theoretical basis for the development and structural optimization of JAK3 protein inhibitors.

Identification of the roles of urban plume and local chemical production in ozone episodes observed in Long Island Sound during LISTOS 2018: Implications for ozone control strategies.

Long Island Sound (LIS) frequently experiences ozone (O3) exceedance events that surpass national ambient air quality standards (NAAQS) due to complex driving factors. The underlying mechanisms governing summertime O3 pollution are investigated through collaborative observations from lidar remote sensing and ground samplers during the 2018 LIS Tropospheric O3 Study (LISTOS). Regional transport and local chemical reactions are identified as the two key driving factors behind the observed O3 episodes in LIS. An enhanced laminar structure is observed in the O3 vertical structure in the atmospheric boundary layer (i.e., 0-2 km layer) for the case dominated by regional transport. An O3 formation regime shift is found in ozone-precursor sensitivity (OPS) for the O3 exceedance event dominated by regional transport with NOx-enriched air mass transport from the New York City (NYC) urban area to LIS. Furthermore, the Integrated Process Rate (IPR) analysis demonstrates that transport from the NYC urban area contributed 40% and 27.1% of surface O3 enhancement to the cases dominated by regional transport and local production, respectively. This study provides scientific evidence to uncovers two key processes that govern summertime O3 pollution over LIS and can help to improve emission control strategies to meet the attainment standards for ambient O3 levels over LIS and other similar coastal areas.

Model-free fast integral terminal sliding-mode control method based on improved fast terminal sliding-mode observer for PMSM with unknown disturbances.

This paper presents a novel model-free fast integral terminal sliding-mode control (MFFITSMC) method based on an improved fast terminal sliding-mode observer (IFTSMO) for permanent magnet synchronous motor (PMSM) drive system, which can effectively eliminate the impact caused by unknown disturbances, such as parameter perturbations and external disturbances. The PMSM mathematical model with unknown disturbances is first established, and the ultra-local model (ULM) of the PMSM speed loop is constructed. Next, the model-free fast integral terminal sliding-mode controller is designed in the speed loop based on the ULM. Then, the IFTSMO is designed to precisely estimate the unknown term of the ULM, and the estimated unknown term is fed back to the MFFITSMC controller to perform compensation for unknown disturbances in real time. Finally, compared with the proportional-integral (PI) control method and the conventional model-free sliding-mode control (MFSMC) method, the results of simulations and experiments demonstrate that the presented MFFITSMC method reduces the dependence on the precise model and achieves the purpose of anti-disturbance control of the PMSM drive system.

Transcriptome and Metabolome Analyses of Codonopsis convolvulacea Kurz Tuber, Stem, and Leaf Reveal the Presence of Important Metabolites and Key Pathways Controlling Their Biosynthesis.

Codonopsis convolvulacea Kurz. var. vinciflora (Kom.) L.T. Shen is a member of Campanulaceae, which is used in traditional Chinese medicine. However, apart from a few Codonopsis species, no detailed knowledge is available on the metabolite composition and respective transcriptome signatures. We performed a combined transcriptome and metabolome analysis of the tuber, stem, and leaf of C. convolvulacea and found 1,144 metabolites and 231,840 unigenes in three experimental groups. The analysis revealed considerable variations in the three tissues. Tubers were rich in amino acids and derivatives, flavonoids, and organic acids, whereas the stems and leaves were rich in alkaloids and flavonoids, respectively. Transcriptome sequencing revealed candidate genes being involved in flavonoid, tryptophan, and alkaloid biosyntheses. In particular, we indicated that the variation in the isoflavone content is linked to the expressions of CHI, CYP73A, C3'H, F3H, CYP75B1, anthocyanidin synthase, and FLS. In a similar way, the levels of indole, L-tyrosine, and tryptamine were also consistent with the expressions of TDC/DDCs in the respective tissues. In addition, the expression levels of ASP5, ARO8, GOT, and AOC3 indicated that L-tryptophan is being converted to downstream metabolites. Overall, our datasets present a useful resource for future research on the uses of this medicinal plant and put forward many research questions.

Multi-factor reconciliation of discrepancies in ozone-precursor sensitivity retrieved from observation- and emission-based models.

Ground-level O3 pollution has been continuously worsening in China despite gradual improvement in other major pollutant levels. Understanding the sensitivity of O3 production to its precursors (OPS) is a prerequisite for formulating effective O3 control measures, but this has been hampered by significant discrepancies in OPS produced by traditional identification approaches using observation-based models (OBM) and emission-based models (EBM). In this study, by applying OBM and EBM in parallel within a month having significant O3 pollution in Shanghai, China, we demonstrated that a lack of carbonyl input, overestimation in NO2 monitoring data, and differences in simulation period and emission reduction area were the core factors leading to OPS discrepancies, and that a reliable OPS cannot be obtained unless these factors are reconciled. By collectively addressing these factors, the number of days with a consistent OPS from both models increased from 6-7 to 20-21 in a month, and the R value defined to quantify the discrepancy decreased by ∼55%. The contributions of these factors to OPS discrepancy differed greatly in urban and suburban settings, mainly caused by differences in pollutant emission and transport characteristics. Overall, OPS identified solely by OBM or EBM is associated with great uncertainty, while reliable OPS estimation can be achieved by a collective application of OBM and EBM with consensus on the above factors. The method demonstrated here could be applied to other photo-chemically active regions worldwide as part of efforts to address ozone pollution.

Understanding the underlying mechanisms governing the linkage between atmospheric oxidative capacity and ozone precursor sensitivity in the Yangtze River Delta, China: A multi-tool ensemble analysis.

Continued exacerbation of ozone (O3) pollution in China has driven the urgent need for an emission control strategy that efficiently reduces O3 levels. Determining O3 precursor sensitivity (OPS) and its driving factors is a prerequisite for formulating effective O3 control strategies. In this study, we proposed an atmospheric oxidative capacity-based indicator, HO2/OH, and demonstrated its effectiveness in indicating OPS over the Yangtze River Delta (YRD) of China by applying a localized comprehensive air quality model with extensions (CAMx) coupled with the Weather Research and Forecasting (WRF) model. A strong correlation was discovered between HO2/OH and OPS, and HO2/OH showed the best performance in separating NOx- and VOC-limited regimes in comparison with other commonly used indicators. A comprehensive analysis with ensemble diagnostic tools revealed the spatial heterogeneity of NOx and VOC emissions and the impact of regional transport controlling the relationship between OPS variations and the HO2/OH indicator over the YRD. The process analysis results show that days with higher contributions from horizontal advection favored OPS transitions in Shanghai, Nanjing, Hefei, Suzhou, and Wuhu, while vertical advection caused OPS transitions in Hangzhou and Ningbo. O3 source apportionment technology analysis indicated that the regional contributions from Zhejiang and Jiangsu/Anhui corresponded well to the NOx-limited and VOC-limited regimes, respectively. Our results provide a better understanding of the underlying mechanisms of the relationship between OPS and the HO2/OH indicator and can help guide contingency control measures for O3 despiking over the YRD and other photochemically active regions worldwide.

The complete chloroplast genome sequence of Rumex nepalensis Spreng.

Rumex nepalensis is a traditional Chinese herb used for detoxification, hemostasis, and anti-inflammatory. In this study, the complete chloroplast sequence of R. nepalensis was characterized from Illumina pair-end sequencing. The cpDNA was 159,044 bp in length, containing a pair of inverted repeats of 30,623 bp each separated by a large and small single copy region of 84,819 bp and 12,979 bp, respectively. The complete chloroplast genome of R. nepalensis contained 128 genes, 37 tRNA, and 8 rRNA. Phylogenetic tree demonstrated that R. nepalensis was closely related to Rumex acetosa.