Publications by authors named "Kang Du"

91 Publications

The diverse roles of cytokinins in regulating leaf development.

Hortic Res 2021 Jun 1;8(1):118. Epub 2021 Jun 1.

College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, USA.

Leaves provide energy for plants, and consequently for animals, through photosynthesis. Despite their important functions, plant leaf developmental processes and their underlying mechanisms have not been well characterized. Here, we provide a holistic description of leaf developmental processes that is centered on cytokinins and their signaling functions. Cytokinins maintain the growth potential (pluripotency) of shoot apical meristems, which provide stem cells for the generation of leaf primordia during the initial stage of leaf formation; cytokinins and auxins, as well as their interaction, determine the phyllotaxis pattern. The activities of cytokinins in various regions of the leaf, especially at the margins, collectively determine the final leaf morphology (e.g., simple or compound). The area of a leaf is generally determined by the number and size of the cells in the leaf. Cytokinins promote cell division and increase cell expansion during the proliferation and expansion stages of leaf cell development, respectively. During leaf senescence, cytokinins reduce sugar accumulation, increase chlorophyll synthesis, and prolong the leaf photosynthetic period. We also briefly describe the roles of other hormones, including auxin and ethylene, during the whole leaf developmental process. In this study, we review the regulatory roles of cytokinins in various leaf developmental stages, with a focus on cytokinin metabolism and signal transduction processes, in order to shed light on the molecular mechanisms underlying leaf development.
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http://dx.doi.org/10.1038/s41438-021-00558-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8167137PMC
June 2021

Transcriptome comparison of different ploidy reveals the mechanism of photosynthetic efficiency superiority of triploid poplar.

Genomics 2021 May 19;113(4):2211-2220. Epub 2021 May 19.

Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, PR China; National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, PR China; Key Laboratory for Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China. Electronic address:

Triploid poplars have obvious growth advantages, especially in leaf development and photosynthetic characteristics, but the molecular mechanism has not been revealed yet. In order to better understand the regulation mechanisms of leaf and chlorophyll development in the triploid poplars, we combined the leaf phenotypic data with the transcriptomic data of the 5th, 10th, and 25th leaves from triploid and diploid poplars, using weighted gene co-expression network analysis (WGCNA), and revealed that PpnGRF5-1 had a strong correlation with leaf development and net photosynthetic rate (Pn). PpnGRF5-1 overexpression transgenic plants showed that the leaf area, Pn, and chlorophyll concentration were significantly increased. Transcriptomic data analysis of the third leaf from PpnGRF5-1 overexpression transgenic plants showed that PpnGRF5-1 could up-regulate the expression levels of chlorophyll synthesis genes and down-regulate the transcription of chlorophyll degradation enzymes. Overall, our studies have greatly expanded our understanding of the molecular mechanisms regulating triploid growth dominance.
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http://dx.doi.org/10.1016/j.ygeno.2021.05.009DOI Listing
May 2021

Procalcitonin measurement using antibody-conjugated fluorescent microspheres distinguishes atypical bacterial meningitis from viral encephalitis in children.

Anal Biochem 2021 Apr 27;626:114219. Epub 2021 Apr 27.

School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, China. Electronic address:

Examination of cerebrospinal fluid in atypical bacterial meningitis (ABM) is similar to that of viral encephalitis (VE), so ABM can easily be misdiagnosed as VE, which can delay diagnosis and treatment. We developed a simple, rapid hand-held lateral flow immunoassay detection system based on fluorescent microspheres (FMS) for procalcitonin (PCT) detection, which provides an indicator to differentiate between ABM and VE. With this novel method, the antigen-antibody reaction systems involve different species, making the test strips more stable than those utilizing one species. The strips exhibited a wide dynamic range (0.04-50 ng/mL) and good sensitivity (0.03 ng/mL). The function of PCT in the identification of ABM and VE in children was further studied. A significant difference in PCT levels was observed between the ABM and VE groups (P = 0.00) and between the ABM and the normal control groups (P = 0.00). PCT levels were not significantly different between the VE and normal control groups (P = 0.30). The area under the receiver operating characteristic curve of PCT for the diagnosis of ABM was 0.95. These findings collectively indicate the usefulness of the PCT detection method based on FMS for clinically differentiating between ABM and VE.
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http://dx.doi.org/10.1016/j.ab.2021.114219DOI Listing
April 2021

Effects of Vision Health Education and Free Eyeglasses on Knowledge of Vision and Usage of Spectacles Among Primary School Students: Evidence from Gansu and Shaanxi Provinces in China.

Risk Manag Healthc Policy 2021 9;14:1449-1464. Epub 2021 Apr 9.

Zhongshan Ophthalmic Center, State Key Laboratory of Ophthalmology, Sun Yat-Sen University, Guangzhou, People's Republic of China.

Background: In rural China, children's vision problems are very common, with many who would benefit from refractive correction not getting the care they need. This study examines whether a health information campaign that involves vision health education and a free trial of health product with free eyeglasses is effective at raising students' awareness of myopia and promoting students' eyeglasses usage.

Methods: We conducted an in-the-field randomized controlled experiment of a program providing vision health education and subsidized free eyeglasses to myopic children from 168 primary schools in rural Northwestern China in 2012.

Results: A total of 2189 students, mean age 10.5 years (49.3% male), participated in the baseline survey. At the baseline, the average correct response rate for visual knowledge among the sample students was 30.1%, and only 15% who needed eyeglasses used them. Seven months after intervention, the average correct response rate for vision knowledge were 48.5% and 48.3% in the education group and the education plus free eyeglasses group respectively, significantly higher than that of the control group. The rate of eyeglasses usage was 36% and 43% in the free eyeglasses group and the education plus free eyeglasses group respectively, significantly higher than that of the control group. The rate of eyeglasses compliance in the free eyeglasses group and the education plus free eyeglasses group was 19% and 26%, which also were significantly higher than the control group.

Conclusion: The information campaign combined with subsidized eyeglasses had a better effect both on vision knowledge and eyeglasses usage. The information campaign improved knowledge by providing the right information, and free eyeglasses changed the perceived utility and experience by the students using the product and getting benefits. Information and the free eyeglasses (subsidized) are complements.
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http://dx.doi.org/10.2147/RMHP.S297265DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8044073PMC
April 2021

Development and operation of a digital platform for sharing pathology image data.

BMC Med Inform Decis Mak 2021 04 3;21(1):114. Epub 2021 Apr 3.

Department of Biomedical Engineering, College of Medicine, Seoul National University, Seoul, Republic of Korea.

Background: Artificial intelligence (AI) research is highly dependent on the nature of the data available. With the steady increase of AI applications in the medical field, the demand for quality medical data is increasing significantly. We here describe the development of a platform for providing and sharing digital pathology data to AI researchers, and highlight challenges to overcome in operating a sustainable platform in conjunction with pathologists.

Methods: Over 3000 pathological slides from five organs (liver, colon, prostate, pancreas and biliary tract, and kidney) in histologically confirmed tumor cases by pathology departments at three hospitals were selected for the dataset. After digitalizing the slides, tumor areas were annotated and overlaid onto the images by pathologists as the ground truth for AI training. To reduce the pathologists' workload, AI-assisted annotation was established in collaboration with university AI teams.

Results: A web-based data sharing platform was developed to share massive pathological image data in 2019. This platform includes 3100 images, and 5 pre-processing algorithms for AI researchers to easily load images into their learning models.

Discussion: Due to different regulations among countries for privacy protection, when releasing internationally shared learning platforms, it is considered to be most prudent to obtain consent from patients during data acquisition.

Conclusions: Despite limitations encountered during platform development and model training, the present medical image sharing platform can steadily fulfill the high demand of AI developers for quality data. This study is expected to help other researchers intending to generate similar platforms that are more effective and accessible in the future.
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http://dx.doi.org/10.1186/s12911-021-01466-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8019341PMC
April 2021

Hereditary transthyretin amyloidosis in mainland China: a unicentric retrospective study.

Ann Clin Transl Neurol 2021 04 19;8(4):831-841. Epub 2021 Mar 19.

Department of Neurology, Peking University First Hospital, 8 Xishiku Street, Xicheng District, Beijing, 100034, China.

Objective: This study aims to report the genotypes and phenotypes of hereditary transthyretin amyloidosis (ATTR) in a large Chinese cohort, yet the clinical and genetic profiles of ATTR remain elusive in mainland China.

Methods: Fifty-four patients with molecularly confirmed ATTR from 39 unrelated families were identified by sequencing the TTR gene. Sural nerve biopsies were performed in 40 of these cases. The clinical and electrophysiological data were retrospectively collected and analyzed.

Results: The male/female ratio was 42:12. The average age of patients at the onset of the disease was 47.8 ± 13.0 years. The late-onset type occurred in 29 cases (53.7%). Twenty-two probands (56.4%) had a family history with ATTR. The initial symptoms were limb paresthesia in 33 cases (61.1%), autonomic dysfunction in 15 cases (27.8%), and blurred vision in 6 cases (11.1%). A total of 22 different TTR mutations were identified, including Val30Met (25.6%) in 10 families in North China and Ala97Ser in 4 families (10.3%) in South China. Electrophysiological studies revealed general sensorimotor axonal polyneuropathy in 33/44 cases (75.0%), mixed neuropathy with axonal and demyelinating impairment features in 9/44 cases (20.5%) and isolated carpal tunnel syndrome in two cases. Sural nerve biopsies revealed positive Congo red staining in 16/40 cases (40.0%).

Conclusion: Chinese patients with ATTR exhibited heterogeneous TTR genotypes and clinical phenotypes. Val30Met remains the most common mutation type in mainland China.
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http://dx.doi.org/10.1002/acn3.51328DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8045954PMC
April 2021

Variation of homologous recombination in Populus tomentosa with different genotypes.

Yi Chuan 2021 Feb;43(2):182-193

Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China;National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China;Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing 100083, China.

Homologous recombination is an important source of biological genetic variation. Limited by detection methods, there are only a few reports on the homologous recombination in high plants and its product - heteroduplex DNA (hDNA). In the present study, applying the strategy of detecting hDNA by constructing populations from inhibited post-meiotic segregation, two hybrid triploid populations were constructed from two maternal parents inPopulus tomentosa by inhibiting post-meiotic segregation. One hundred and ten simple sequence repeat (SSR) markers were used to study the occurrence and variation of hDNA on nine chromosomes inP. tomentosa with different genotypes. The results showed that the frequencies of hDNA between two female parents inP. tomentosa ranged from 8.5% to 87.2%. The hDNA frequency was positively correlated to the distance from the centromere, but the average hDNA frequency on a chromosome had no correlation with the chromosome length. One to 3 times recombination events were detected on most chromosomes, and only a few four- or five-times recombination events were detected. The overall frequencies of hDNA on the same chromosome in two genotypic individuals were roughly similar, while the hDNA frequencies varied greatly at specific SSR loci. Compared withTacamahaca poplar hybrid,P. pseudo-simonii × P. nigra 'Zheyin3#', detection of homologous recombination times and the frequency and location of hDNA were largely different. This study is the first to describe the characteristics and variations of homologous recombination inP. tomentosa with two different genotypes, which will provide valuable insights for exploring the characteristics and variations of homologous recombination among interspecies and intraspecies in higher plant.
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http://dx.doi.org/10.16288/j.yczz.20-205DOI Listing
February 2021

Nerve Ultrasound Comparison Between Transthyretin Familial Amyloid Polyneuropathy and Chronic Inflammatory Demyelinating Polyneuropathy.

Front Neurol 2021 26;12:632096. Epub 2021 Feb 26.

Department of Neurology, Peking University First Hospital, Beijing, China.

Transthyretin familial amyloid polyneuropathy (TTR-FAP) is frequently misdiagnosed as chronic inflammatory demyelinating polyneuropathy (CIDP) because of similar phenotypes in the two diseases. This study was intended to identify the role of nerve ultrasonography in evaluating TTR-FAP and CIDP. Eighteen patients with TTR-FAP, 13 patients with CIDP, and 14 healthy controls (HC) were enrolled in this study. Consecutive ultrasonography scanning was performed in six pairs of nerves of bilateral limbs with 30 sites. The cross-sectional areas (CSAs) and CSA variability data of different groups were calculated and compared. Both TTR-FAP and CIDP showed larger CSAs at most sites of both upper and lower limbs than in HC groups. CIDP patients had larger CSAs than TTR-FAP patients at 8/15 of these sites, especially at U1-3, Sci2 sites ( < 0.01). However, the CSAs at above sites were not a credible index to differentiate TTR-FAP from CIDP with a low area under the curve (<0.8). The CSA variability of median nerves was significantly higher in CIDP than in TTR-FAP and HC groups, with high sensitivity (0.692) and specificity (0.833) to differentiate CIDP from TTR-FAP. The CSA variability of ulnar nerves was not significantly different between the three groups. For the TTR-FAP group, mean CSAs at each site were not correlated with different Coutinho stages, modified polyneuropathy disability, course of sensory motor peripheral neuropathy, Neuropathy Impairment Score, or Norfolk Quality of life-diabetic neuropathy score. The mean compound muscle action potential of ulnar nerves was negatively correlated with the mean CSAs of ulnar nerves. TTR-FAP patients had milder nerve enlargement with less variability in CSAs of median nerves than those with CIDP, suggesting that nerve ultrasound can be a potential useful auxiliary tool to help differentiate the two neuropathies.
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http://dx.doi.org/10.3389/fneur.2021.632096DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7953716PMC
February 2021

Investigations of Thermal Stability and Solid Electrolyte Interphase on NaTiO/C as a Non-carbonaceous Anode Material for Sodium Storage Using Non-flammable Ether-based Electrolyte.

ACS Appl Mater Interfaces 2021 Mar 5;13(10):11732-11740. Epub 2021 Mar 5.

Department of Mechanical Engineering, National University of Singapore, Singapore 117575, Singapore.

In order to become commercially viable, sodium-ion batteries need to deliver long cycle life with good capacity and energy density while still ensuring safety. Electrolyte plays a key role forming solid electrolyte interphase (SEI) layers at low potential, which affects the thermal stability and cycle life of the anode materials under consideration. In this study, an ether-based non-flammable electrolyte, 1 M NaBF in tetraglyme, is tested for sodium storage using a non-carbonaceous anode material NaTiO/C, and the results are compared with those obtained with the popularly used carbonate-based electrolyte, 1 M NaClO in ethylene carbonate (EC) and propylene carbonate (PC) (v/v = 1:1). The NaTiO/C Na cells using 1 M NaBF in tetraglyme show a much higher first cycle Coulombic efficiency (73%) than those using 1 M NaClO in EC/PC (33%). Thermal stability studies using differential scanning calorimetry (DSC) conclusively show that NaTiO/C electrodes cycled with 1 M NaBF in tetraglyme are more thermally stable than the one cycled with 1 M NaClO in EC/PC. Further investigations on the formation of SEI layers were performed using attenuated total reflection-Fourier transform infrared spectroscopy, field-emission scanning electron microscopy, transmission electron microscopy, energy-dispersive X-ray spectroscopy, electrochemical impedance spectroscopy, and DSC studies. These studies unambiguously demonstrate that the SEI formed on NaTiO/C using 1 M NaBF in tetraglyme is not only less resistive but also more stable than the SEI formed using 1 M NaClO in EC/PC.
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http://dx.doi.org/10.1021/acsami.0c18670DOI Listing
March 2021

RADSex: A computational workflow to study sex determination using restriction site-associated DNA sequencing data.

Mol Ecol Resour 2021 Feb 16. Epub 2021 Feb 16.

Physiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany.

The study of sex determination and sex chromosome organization in nonmodel species has long been technically challenging, but new sequencing methodologies now enable precise and high-throughput identification of sex-specific genomic sequences. In particular, restriction site-associated DNA sequencing (RAD-Seq) is being extensively applied to explore sex determination systems in many plant and animal species. However, software specifically designed to search for and visualize sex-biased markers using RAD-Seq data is lacking. Here, we present RADSex, a computational analysis workflow designed to study the genetic basis of sex determination using RAD-Seq data. RADSex is simple to use, requires few computational resources, makes no prior assumptions about the type of sex-determination system or structure of the sex locus, and offers convenient visualization through a dedicated R package. To demonstrate the functionality of RADSex, we re-analysed a published data set of Japanese medaka, Oryzias latipes, where we uncovered a previously unknown Y chromosome polymorphism. We then used RADSex to analyse new RAD-Seq data sets from 15 fish species spanning multiple taxonomic orders. We identified the sex determination system and sex-specific markers in six of these species, five of which had no known sex-markers prior to this study. We show that RADSex greatly facilitates the study of sex determination systems in nonmodel species thanks to its speed of analyses, low resource usage, ease of application and visualization options. Furthermore, our analysis of new data sets from 15 species provides new insights on sex determination in fish.
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http://dx.doi.org/10.1111/1755-0998.13360DOI Listing
February 2021

Giant lungfish genome elucidates the conquest of land by vertebrates.

Nature 2021 02 18;590(7845):284-289. Epub 2021 Jan 18.

Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany.

Lungfishes belong to lobe-fined fish (Sarcopterygii) that, in the Devonian period, 'conquered' the land and ultimately gave rise to all land vertebrates, including humans. Here we determine the chromosome-quality genome of the Australian lungfish (Neoceratodus forsteri), which is known to have the largest genome of any animal. The vast size of this genome, which is about 14× larger than that of humans, is attributable mostly to huge intergenic regions and introns with high repeat content (around 90%), the components of which resemble those of tetrapods (comprising mainly long interspersed nuclear elements) more than they do those of ray-finned fish. The lungfish genome continues to expand independently (its transposable elements are still active), through mechanisms different to those of the enormous genomes of salamanders. The 17 fully assembled lungfish macrochromosomes maintain synteny to other vertebrate chromosomes, and all microchromosomes maintain conserved ancient homology with the ancestral vertebrate karyotype. Our phylogenomic analyses confirm previous reports that lungfish occupy a key evolutionary position as the closest living relatives to tetrapods, underscoring the importance of lungfish for understanding innovations associated with terrestrialization. Lungfish preadaptations to living on land include the gain of limb-like expression in developmental genes such as hoxc13 and sall1 in their lobed fins. Increased rates of evolution and the duplication of genes associated with obligate air-breathing, such as lung surfactants and the expansion of odorant receptor gene families (which encode proteins involved in detecting airborne odours), contribute to the tetrapod-like biology of lungfishes. These findings advance our understanding of this major transition during vertebrate evolution.
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http://dx.doi.org/10.1038/s41586-021-03198-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7875771PMC
February 2021

Growth-regulating factor 5 (GRF5)-mediated gene regulatory network promotes leaf growth and expansion in poplar.

New Phytol 2021 04 14;230(2):612-628. Epub 2021 Feb 14.

College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA.

Although polyploid plants have larger leaves than their diploid counterparts, the molecular mechanisms underlying this difference (or trait) remain elusive. Differentially expressed genes (DEGs) between triploid and full-sib diploid poplar trees were identified from two transcriptomic data sets followed by a gene association study among DEGs to identify key leaf growth regulators. Yeast one-hybrid system, electrophoretic mobility shift assay, and dual-luciferase assay were employed to substantiate that PpnGRF5-1 directly regulated PpnCKX1. The interactions between PpnGRF5-1 and growth-regulating factor (GRF)-interacting factors (GIFs) were experimentally validated and a multilayered hierarchical regulatory network (ML-hGRN)-mediated by PpnGRF5-1 was constructed with top-down graphic Gaussian model (GGM) algorithm by combining RNA-sequencing data from its overexpression lines and DAP-sequencing data. PpnGRF5-1 is a negative regulator of PpnCKX1. Overexpression of PpnGRF5-1 in diploid transgenic lines resulted in larger leaves resembling those of triploids, and significantly increased zeatin and isopentenyladenine in the apical buds and third leaves. PpnGRF5-1 also interacted with GIFs to increase its regulatory diversity and capacity. An ML-hGRN-mediated by PpnGRF5-1 was obtained and could largely elucidate larger leaves. PpnGRF5-1 and the ML-hGRN-mediated by PpnGRF5-1 were underlying the leaf growth and development.
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http://dx.doi.org/10.1111/nph.17179DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8048564PMC
April 2021

Foundation and Clinical Evaluation of a New Method for Detecting SARS-CoV-2 Antigen by Fluorescent Microsphere Immunochromatography.

Front Cell Infect Microbiol 2020 30;10:553837. Epub 2020 Nov 30.

Translational Medicine Research Center, Key Laboratory of Ministry of Industry and Information Technology of Biomedical Engineering and Translational Medicine, Chinese PLA General Hospital, Beijing, China.

Purpose: To develop a rapid detection reagent for SARS-CoV-2 antigen for the auxiliary diagnosis of new coronary pneumonia (COVID-19), and perform the methodological evaluation and clinical evaluation of the reagent.

Method: SARS-CoV-2 N-protein test strip was created by combining fluorescent microsphere labeling technology and immunochromatographic technology, based on the principle of double antibody sandwich. Then we evaluated the analytical capability and clinical application of the strips.

Result: The limit of detection of the strips for recombinant N protein was 100 ng/ml and for activated SARS -CoV-2 virus was 1 × 10 TCID/ml. The strips also have high analytical specificity and anti-interference capability. According to the predetermined cut-off value, the specificity of the test strip in healthy controls and patients with other respiratory disease was 100.00 and 97.29%, the sensitivity in COVID-19 cases at progress stage and cured stage was 67.15 and 7.02%. The positive percentage agreement and negative percentage agreement of antigen strip to RNA test were 83.16 and 94.45%.

Conclusion: SARS-CoV-2 fluorescence immunochromatographic test strip can achieve fast, sensitive and accurate detection, which can meet the clinical requirements for rapid detection of viruses on the spot.
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http://dx.doi.org/10.3389/fcimb.2020.553837DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7734310PMC
December 2020

High-quality de novo assembly of the Eucommia ulmoides haploid genome provides new insights into evolution and rubber biosynthesis.

Hortic Res 2020 Nov 1;7(1):183. Epub 2020 Nov 1.

Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, 100083, Beijing, People's Republic of China.

We report the acquisition of a high-quality haploid chromosome-scale genome assembly for the first time in a tree species, Eucommia ulmoides, which is known for its rubber biosynthesis and medicinal applications. The assembly was obtained by applying PacBio and Hi-C technologies to a haploid that we specifically generated. Compared to the initial genome release, this one has significantly improved assembly quality. The scaffold N50 (53.15 MB) increased 28-fold, and the repetitive sequence content (520 Mb) increased by 158.24 Mb, whereas the number of gaps decreased from 104,772 to 128. A total of 92.87% of the 26,001 predicted protein-coding genes identified with multiple strategies were anchored to the 17 chromosomes. A new whole-genome duplication event was superimposed on the earlier γ paleohexaploidization event, and the expansion of long terminal repeats contributed greatly to the evolution of the genome. The more primitive rubber biosynthesis of this species, as opposed to that in Hevea brasiliensis, relies on the methylerythritol-phosphate pathway rather than the mevalonate pathway to synthesize isoprenyl diphosphate, as the MEP pathway operates predominantly in trans-polyisoprene-containing leaves and central peels. Chlorogenic acid biosynthesis pathway enzymes were preferentially expressed in leaves rather than in bark. This assembly with higher sequence contiguity can foster not only studies on genome structure and evolution, gene mapping, epigenetic analysis and functional genomics but also efforts to improve E. ulmoides for industrial and medical uses through genetic engineering.
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http://dx.doi.org/10.1038/s41438-020-00406-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7603500PMC
November 2020

The Developmental and Genetic Architecture of the Sexually Selected Male Ornament of Swordtails.

Curr Biol 2021 Mar 3;31(5):911-922.e4. Epub 2020 Dec 3.

Institute of Neuroscience, University of Oregon, Eugene, OR 97401, USA. Electronic address:

Sexual selection results in sex-specific characters like the conspicuously pigmented extension of the ventral tip of the caudal fin-the "sword"-in males of several species of Xiphophorus fishes. To uncover the genetic architecture underlying sword formation and to identify genes that are associated with its development, we characterized the sword transcriptional profile and combined it with genetic mapping approaches. Results showed that the male ornament of swordtails develops from a sexually non-dimorphic prepattern of transcription factors in the caudal fin. Among genes that constitute the exclusive sword transcriptome and are located in the genomic region associated with this trait we identify the potassium channel, Kcnh8, as a sword development gene. In addition to its neural function kcnh8 performs a known role in fin growth. These findings indicate that during evolution of swordtails a brain gene has been co-opted for an additional novel function in establishing a male ornament.
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http://dx.doi.org/10.1016/j.cub.2020.11.028DOI Listing
March 2021

Visual Detection of Alpha Toxin by Combining Nanometer Microspheres with Smart Phones.

Microorganisms 2020 Nov 26;8(12). Epub 2020 Nov 26.

School of Life Sciences, Tianjin University, Tianjin 300072, China.

α toxin (CPA) is an important virulence factor that causes livestock hemorrhagic enteritis and food poisoning by contaminated meat products. In this study, the nano-silica microspheres combined with smartphone image processing technology was developed to realize real-time CPA detection. First, the N-terminal and C-terminal domain of the CPA toxin (CPA and CPA) and their anti-sera were prepared. The silica microspheres coupled with the antibody of CPA was prepared to capture the toxin that existed in the detection sample and the fluorescent-labeled antibody of CPA was incubated. Moreover, the fluorescent pictures of gray value were performed in a cell phone app, corresponding to toxin concentration. The new assay takes 90 min to perform and can detect CPA as little as 32.8 ng/mL. Our results showed a sensitive, stable, and convenient CPA detection system, which provides a novel detection method of native CPA in foods.
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http://dx.doi.org/10.3390/microorganisms8121865DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7761010PMC
November 2020

Whole genome sequencing of silver carp (Hypophthalmichthys molitrix) and bighead carp (Hypophthalmichthys nobilis) provide novel insights into their evolution and speciation.

Mol Ecol Resour 2021 Apr 26;21(3):912-923. Epub 2020 Dec 26.

The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.

The edible silver carp (Hypophthalmichthys molitrix) and bighead carp (H. nobilis), which are two of the "Four Domesticated Fish" of China, are cultivated intensively worldwide. Here, we constructed 837- and 845-Mb draft genome assemblies for the silver carp and the bighead carp, respectively, including 24,571 and 24,229 annotated protein-coding genes. Genetic maps, anchoring 71.7% and 83.8% of all scaffolds, were obtained for the silver and bighead carp, respectively. Phylogenetic analysis showed that the bighead carp formed a clade with the silver carp, with an estimated divergence time of 3.6 million years ago; the time of divergence between the silver carp and zebrafish was 50.7 million years ago. An East Asian cyprinid genome-specific chromosome fusion took place ~9.2 million years after this clade diverged from the clade containing the common carp and Sinocyclocheilus. KEGG and GO analyses indicated that the expanded gene families in the silver and bighead carp were associated with diseases, the immune system and environmental adaptations. Genomic regions differentiating the silver and bighead carp populations were detected based on the whole-genome sequences of 42 individuals. Genes associated with the divergent regions were associated with reproductive system development and the development of primary female sexual characteristics. Thus, our results provided a novel systematic genomic analysis of the East Asian cyprinids, as well as the evolution and speciation of the silver carp and bighead carp.
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http://dx.doi.org/10.1111/1755-0998.13297DOI Listing
April 2021

Does Performing the Chinese Eye Exercises Help Protect Children's Vision? - New Evidence from Primary Schools in Rural Northwestern China.

Risk Manag Healthc Policy 2020 3;13:2425-2438. Epub 2020 Nov 3.

Center for Experimental Economics in Education, Shaanxi Normal University, Xi'an, People's Republic of China.

Background: The high prevalence of myopia among school-age children in China has raised serious concerns about protecting Chinese students' vision. While the regular performance of the Chinese eye exercises has been adopted as a preventive approach in China since the mid-1960s, these exercises' effectiveness at protecting students' vision has remained largely unknown. This study attempts to provide new evidence of the impact of regularly performing the exercises on Chinese students' visual outcomes, based on a large-scale dataset.

Methods: A school-based survey was conducted among 9842 randomly selected students (fourth graders) from 252 primary schools in rural Northwestern China in 2012. To address potential estimation bias, we adopted both an instrumental variable (IV) approach and a bivariate-probit model to estimate the impacts on students' visual acuity and the incidences of visual impairment and myopia.

Results: Both IV and bivariate-probit estimates reveal a detrimental impact of regularly performing the Chinese eye exercises on students' vision. Compared with students who did not regularly perform the exercises, those who did were 6.2 percentage points more likely to have impaired vision and 7.6 percentage points more likely to be myopic. The estimates are robust to different estimation strategies, various specifications, and the majority of subsamples.

Conclusion: Under the assumption that the correct performance of the Chinese eye exercises would not undermine students' vision, our findings suggest that the commonly-observed incorrect performance of these exercises among Chinese students imposes non-trivial threats to their vision health.
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http://dx.doi.org/10.2147/RMHP.S277917DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7650230PMC
November 2020

Sural biopsy to detect the axonal cytoskeleton defects in -related Charcot-Marie-Tooth disease type 2.

Clin Neuropathol 2021 May-Jun;40(3):142-149

Kinesins are microtubule-associated motor proteins involved in in regulating microtubule dynamics in neuronal and non-neuronal cells. However, the axonal cytoskeleton-related pathological changes in peripheral nerve have never been described in patients with mutation. This study aims to report sural biopsy to detect axonal cytoskeleton abnormalities in a patient with -related Charcot-Marie-Tooth disease type 2 (CMT2). We screened for the variants of CMT or related pathogenic genes using next-generation sequencing in a Chinese family with CMT2. The proband was a 13-year-old girl who presented with severe weakness and wasting of distal muscles of limbs starting at early childhood. The disease rapidly progressed, and the girl lost ambulation. Her mother showed absence of deep tendon reflexes in the lower limbs. Nerve conduction studies disclosed a more pronounced axonal sensory-motor neuropathy in the proband. The girl and her mother had a heterozygous p.E755K mutation of the gene, which was previously reported only in hereditary spastic paraplegia and amyotrophic lateral sclerosis. Sural biopsy revealed loss of both myelinated and unmyelinated nerve fibers. Closely packed, irregularly oriented neurofilaments were observed in axons of unmyelinated nerve fibers. Another important finding was ubiquitous presence of elongated mitochondria with vacuole in the myelinated and unmyelinated axons. This study suggested the p.E755K mutation of was a cause of early-onset CMT2 with defective axonal transport, and emphasized sural biopsy could be an important tool to detect axonal cytoskeleton defects in related CMT2.
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http://dx.doi.org/10.5414/NP301323DOI Listing
April 2021

Construction of a breeding parent population of Populus tomentosa based on SSR genetic distance analysis.

Sci Rep 2020 10 29;10(1):18573. Epub 2020 Oct 29.

Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.

Parent selection is the core of hybrid breeding. The breeding strategy involving the parental identification of superior open-pollinated progeny of Populous tomentosa germplasm resources can significantly improve the efficiency of parental matching. However, due to some factors such as loose powdering time and pollen competitiveness, the offspring derived from open-pollination families which do not undergo completely random mating. Although hybrid combinations based on the male identification method have a high combining ability, this method cannot easily cover the mating combinations of all male and female specimens in the germplasm bank. In addition, the performance of superior plants in open-pollinated families also affects the selection result. If the trait performance value is higher than the population average, then the special combining ability of the reconstructed hybrid combination may be overestimated. Obtaining a solution to the above problems is of great significance for improving the efficiency and accuracy of selecting hybrid parents of P. tomentosa. In this study, 24 pairs of SSR (Simple Sequence Repeats) molecular markers were used to analyze the genetic differentiation of P. tomentosa germplasm resources. The results showed that the genetic variation of the P. tomentosa population was derived from individuals within the provenance, indicating that high genetic diversity is preserved in provenances. The correlation analysis showed that there was a significant positive correlation between the special combining ability of planting height and diameter at breast height (dbh) of the 34 full-sib progeny population and the genetic distance between the parents. Then, the genetic distance between 18 female plants with high fertility and 68 male plants with large pollen quantity was analyzed using this correlation. Fifteen female parents and 12 male parents were screened out, and 52 hybrid combinations with high specific combining ability for growth traits were predicted. Furthermore, for the male parent identification of superior individual plants, we constructed the breeding parent population including 10 female parents and 5 male parents, generating 14 hybrid combinations with potentially high combining ability. The results of the hybridization test showed that the specific combining ability of plant height and dbh was significantly higher than the controlled pollination. Moreover, genetic distance and paternal identification can be used to rapidly and efficiently construct hybrid parent combinations and breeding parent populations.
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http://dx.doi.org/10.1038/s41598-020-74941-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7596703PMC
October 2020

Ratiometric electrochemical immunosensor for the detection of procalcitonin based on the ratios of SiO-Fc-COOH-Au and UiO-66-TB complexes.

Biosens Bioelectron 2021 Jan 10;171:112713. Epub 2020 Oct 10.

Collaborative Innovation Center for Green Chemical Manufacturing and Accurate Detection, Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, PR China.

Procalcitonin (PCT) as a disease marker is of great significance in the early diagnosis of septicemia and pyemia. Biosensor have good prospects for analysis and detection of disease markers, but developing highly sensitive detection methods for detecting PCT remains a daunting task. In this paper, we develop a ratiometric electrochemical immunosensor with Au NPs modified SiO-Fc-COOH complex as matrix and UiO-66 loaded with Toluidine blue (TB) as a marker for quantitative detection of procalcitonin (PCT). The SiO modified by APTES not only has a large specific surface area but also contains abundant amino groups, which can be connected to the electrochemical probe of ferrocenecarboxylic acid (Fc-COOH). UiO-66 has the advantages of large specific surface area, high porosity and adjustable structure, which can adsorb toluidine blue electrochemical probe through electrostatic attraction. Measurement and analysis of the prepared immunosensor by Differential Pulse Voltammetry (DPV) show that the oxidation peak currents of Fc-COOH and TB appear at potentials of 0.30 V and -0.30 V respectively. As the PCT concentration increases, the oxidation peak current of TB increases and the oxidation peak current of Fc-COOH decreases. The ratios (ΔI=ΔI/ΔI) between the double signals could show a certain linear relationship with the concentration of the PCT within a certain range. Under optimal conditions, the linear range of detection obtained by the immunosensor was 1 pg/mL-100 ng/mL and the detection limit was 0.3 pg/mL. In this work, the developed ratiometric electrochemical immunosensor not only provides a simple, reliable and sensitive strategy for quantitative detection of PCT but also provides a useful method for clinical detection of other disease markers.
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http://dx.doi.org/10.1016/j.bios.2020.112713DOI Listing
January 2021

Long-term clinical outcomes of endoscopic submucosal dissection for colorectal neoplasia with or without the hybrid technique.

Colorectal Dis 2020 12 29;22(12):2008-2017. Epub 2020 Sep 29.

Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.

Aim: The main aim of this study was to compare the long-term outcome of a conventional colorectal endoscopic submucosal dissection (ESD) in which submucosal dissection was continued throughout until the completion of resection (ESD-T) to hybrid endoscopic submucosal dissection (ESD-H) in the colorectum.

Method: Medical records of 836 colorectal neoplasia patients treated by ESD-T or ESD-H were reviewed. ESD-H was defined as colorectal ESD with additional snaring in the final stage of the procedure. Primary outcomes were the overall and metastatic recurrence rates. Secondary outcomes were short-term outcomes such as the en bloc resection rate, procedure time and adverse events.

Results: The overall recurrence rate was higher in the ESD-H than in the ESD-T group (5.7% vs 0.7%, P = 0.001). The metastatic recurrence rate showed no significant difference between these groups (1.4% vs 1.4%, P = 1.000). Multivariate analysis revealed that a failed en bloc resection (hazard ratio 24.097; 95% CI 5.446-106.237; P < 0.001) and larger tumour size (hazard ratio 1.042; 95% CI 1.014-1.070; P = 0.003) were independently associated with overall recurrence. The ESD-H group showed a lower en bloc resection rate (56.8% vs 96.5%, P < 0.001), shorter procedure time (45.6 vs 54.3 min, P < 0.001) and higher perforation rate (10.3% vs 6.0%, P = 0.029).

Conclusion: Although long-term outcomes in terms of overall recurrence are inferior following ESD-H, a failed en bloc resection and large tumour size are the only independent risk factors for recurrence. Further investigations are warranted to improve the long-term outcomes of ESD-H.
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http://dx.doi.org/10.1111/codi.15339DOI Listing
December 2020

Paramagnetic Shifts and Guest Exchange Kinetics in CoFe Metal-Organic Capsules.

Inorg Chem 2020 Sep 27;59(17):12758-12767. Epub 2020 Aug 27.

Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States.

We investigate the magnetic resonance properties and exchange kinetics of guest molecules in a series of hetero-bimetallic capsules, [CoFeL] ( = 1-3), where L = 4,4'-bis[(2-pyridinylmethylene)amino]-[1,1'-biphenyl]-2,2'-disulfonate. H bond networks between capsule sulfonates and guanidinium cations promote the crystallization of [CoFeL]. The following four isostructural crystals are reported: two guest-free forms, (C(NH))[CoFeL]·69HO () and (C(NH))[CoFeL]·73HO (), and two Xe- and CFCl-encapsulated forms, (C(NH))[(Xe)CoFeL]·69HO () and (C(NH))[(CFCl)CoFeL]·73HO (), respectively. Structural analyses reveal that Xe induces negligible structural changes in , while the angles between neighboring phenyl groups expand by ca. 3° to accommodate the much larger guest, CFCl, in . These guest-encapsulated [CoFeL] molecules reveal Xe and F chemical shift changes of ca. -22 and -10 ppm at 298 K, respectively, per substitution of low-spin Fe by high-spin Co. Likewise, the temperature dependence of the Xe and F NMR resonances increases by 0.1 and 0.06 ppm/K, respectively, with each additional paramagnetic Co center. The optimal temperature for hyperpolarized (hp) Xe chemical exchange saturation transfer (hyper-CEST) with [CoFeL] capsules was found to be inversely proportional to the number of Co centers, , which is consistent with the Xe chemical exchange accelerating as the portals expand. The systematic study was facilitated by the tunability of the [ML] capsules, further highlighting these metal-organic systems for developing responsive sensors with highly shifted Xe resonances.
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http://dx.doi.org/10.1021/acs.inorgchem.0c01816DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7649716PMC
September 2020

Synthesis of Anhydroryanodol.

J Am Chem Soc 2020 07 7;142(30):12937-12941. Epub 2020 Jul 7.

Department of Chemistry, Burke Laboratory, Dartmouth College, Hanover, New Hampshire 03755, United States.

A stereoselective entry to ryanoids is described that culminates in the synthesis of anhydroryanodol and thus the formal total synthesis of ryanodol. The pathway described features an annulation reaction conceived to address the uniquely complex and highly oxygenated polycyclic skeleton common to members of this natural product class. It is demonstrated that metallacycle-mediated intramolecular coupling of an alkyne and a 1,3-diketone can proceed with a highly functionalized enyne and with outstanding levels of stereoselection. Furthermore, the first application of this technology in natural product synthesis is demonstrated here. More broadly, the advances described demonstrate the value that programs in natural product total synthesis have in advancing organic chemistry, here through the design and realization of an annulation reaction that accomplishes what previously established reactions do not.
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http://dx.doi.org/10.1021/jacs.0c05766DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7477650PMC
July 2020

Melanocortin 4 receptor signaling and puberty onset regulation in Xiphophorus swordtails.

Gen Comp Endocrinol 2020 09 26;295:113521. Epub 2020 May 26.

Physiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany; Developmental Biochemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany; The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, USA. Electronic address:

Fish of the genus Xiphophorus provide a prominent example of genetic control of male body size and reproductive tactics. In X.nigrensis and X.multilineatus, puberty onset and body length are determined by melanocortin 4 receptor (Mc4r) allelic and copy number variations which were proposed to fine-tune the signaling output of the system. Accessory protein Mrap2 is required for growth across species by affecting Mc4r signaling. The molecular mechanism how Mc4r signaling controls puberty regulation in Xiphophorus and whether the interaction with Mrap2 is also involved was so far unclear. Hence, we examined Mc4r and Mrap2 in X.nigrensis and X.multilineatus, in comparison to a more distantly related species, X.hellerii. mc4r and mrap2 transcripts co-localized in the hypothalamus and preoptic regions in large males, small males and females of X.nigrensis, with similar signal strength for mrap2 but higher expression of mc4r in large males. This overexpression is constituted by wild-type and one subtype of mutant alleles. In vitro studies revealed that Mrap2 co-expressed with Mc4r increased cAMP production but did not change EC50. Cells co-expressing the wild-type and one mutant allele showed lower cAMP signaling than Mc4r wild-type cells. This indicates a role of Mc4r alleles, but not Mrap2, in puberty signaling. Different from X.nigrensis and X.multilineatus, X.hellerii has only wild-type alleles, but also shows a puberty onset and body length polymorphism, despite the absence of mutant alleles. Like in the two other species, mc4r and mrap2 transcripts colocalized and mc4r is expressed at substantially higher levels in large males. This demonstrates that puberty and growth regulation mechanism may not be identical even within same genus.
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http://dx.doi.org/10.1016/j.ygcen.2020.113521DOI Listing
September 2020

Natural hybridization reveals incompatible alleles that cause melanoma in swordtail fish.

Science 2020 05;368(6492):731-736

Department of Biology, Stanford University and Howard Hughes Medical Institute, Stanford, CA, USA.

The establishment of reproductive barriers between populations can fuel the evolution of new species. A genetic framework for this process posits that "incompatible" interactions between genes can evolve that result in reduced survival or reproduction in hybrids. However, progress has been slow in identifying individual genes that underlie hybrid incompatibilities. We used a combination of approaches to map the genes that drive the development of an incompatibility that causes melanoma in swordtail fish hybrids. One of the genes involved in this incompatibility also causes melanoma in hybrids between distantly related species. Moreover, this melanoma reduces survival in the wild, likely because of progressive degradation of the fin. This work identifies genes underlying a vertebrate hybrid incompatibility and provides a glimpse into the action of these genes in natural hybrid populations.
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http://dx.doi.org/10.1126/science.aba5216DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8074799PMC
May 2020

Plasmonic color filter based on a hetero-metal-insulator-metal grating.

Appl Opt 2020 May;59(14):4432-4436

Plasmonic color filters are expected to be candidates for application to complementary metal-oxide-semiconductor (CMOS) image sensor arrays with reduced pixel size, owing to the subwavelength mode volume of plasmons. Designs of metallic gratings based on the guided-mode resonance effect suffer from the sideband transmission issue due to high-order diffraction. Here, we propose a plasmonic color filter structure based on a hetero-metal-insulator-metal grating. The guided mode, in resonance with the second-order diffraction, is highly attenuated by the forbidden band, such that the sideband transmission can be suppressed. As calculated by using the transfer matrix method and the finite-difference time-domain method, the Al-ZnO-Ag waveguide-based structure presents a color filter characteristic with the peak transmittance greater than 70% and the peak wavelength tunable in the visible light band. It may find application in displays, image sensors, and biomedical imaging technologies.
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http://dx.doi.org/10.1364/AO.391976DOI Listing
May 2020

Molecular Mechanism of Vegetative Growth Advantage in Allotriploid .

Int J Mol Sci 2020 Jan 10;21(2). Epub 2020 Jan 10.

Beijing Advanced Innovation Center for Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Haidian District, Beijing 100083, China.

Allotriploid poplar has a prominent vegetative growth advantage that impacts dramatically on lumber yield. The growth regulation is complex which involves abundant genes, metabolic and signaling pathways, while the information about the functional control process is very little. We used high-throughput sequencing and physiological index measurement to obtain a global overview of differences between allotriploid and diploid . The genes related to plant growth advantage show a higher expression compared to diploid, and most of them are revolved around hormones, photosynthesis and product accumulation. Thus, allotriploid showed more efficient photosynthesis, carbon fixation, sucrose and starch synthesis, and metabolism as well as augmented biosynthesis of auxin, cytokinin, and gibberellin. These data enable the connection of metabolic processes, signaling pathways, and specific gene activity, which will underpin the development of network models to elucidate the process of triploid advantage growth.
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http://dx.doi.org/10.3390/ijms21020441DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7014019PMC
January 2020

Chemical profiling and marker characterization of Huangqin decoction prepared with three types of peony root by liquid chromatography with electrospray ionization mass spectrometry.

J Sep Sci 2020 Jul 5;43(13):2558-2570. Epub 2020 May 5.

The MOE key laboratory of Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, P. R. China.

Clarification of the quality and biological effect equivalence of traditional Chinese medicines containing multi-origin species is essential to improve their current quality standards, and also is the core problem to clarify the origins of single herbs with multi-species in Chinese formulas that will guarantee their clinical application. Huangqin decoction is the typical one of multi-origin formulas frequently used in traditional Chinese medicine and Kampo medicine. An ultra high performance liquid chromatography with electrospray ionization-tandem mass spectrometry was developed for chemical profiling and marker quantification of Huangqin decoction prepared with two different original types of peony root, white and red peony root. Forty-seven main peaks in chemical profiling of Huangqin decoction prepared with white and red peony root were identified: nine were from peony root, 20 from baical skullcap root, 17 from licorice root, and one from jujubae fruit. The markers characteristics of the respective types of peony root in Huangqin decoction differ from that in single herbs, especially in terms of monoterpenoids and hydrolysable tannins. Subsequently, 17 representative markers in Huangqin decoction prepared with three types of peony root and their chemical characteristics and content distribution were carried out.
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http://dx.doi.org/10.1002/jssc.201901305DOI Listing
July 2020

The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization.

Nat Ecol Evol 2020 06 30;4(6):841-852. Epub 2020 Mar 30.

Developmental Biochemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany.

Sturgeons seem to be frozen in time. The archaic characteristics of this ancient fish lineage place it in a key phylogenetic position at the base of the ~30,000 modern teleost fish species. Moreover, sturgeons are notoriously polyploid, providing unique opportunities to investigate the evolution of polyploid genomes. We assembled a high-quality chromosome-level reference genome for the sterlet, Acipenser ruthenus. Our analysis revealed a very low protein evolution rate that is at least as slow as in other deep branches of the vertebrate tree, such as that of the coelacanth. We uncovered a whole-genome duplication that occurred in the Jurassic, early in the evolution of the entire sturgeon lineage. Following this polyploidization, the rediploidization of the genome included the loss of whole chromosomes in a segmental deduplication process. While known adaptive processes helped conserve a high degree of structural and functional tetraploidy over more than 180 million years, the reduction of redundancy of the polyploid genome seems to have been remarkably random.
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http://dx.doi.org/10.1038/s41559-020-1166-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7269910PMC
June 2020