The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

Coffea arabica, an allotetraploid hybrid of Coffea eugenioides and Coffea canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000-610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred ~30.5 thousand years ago, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica.

Clinical value of GRACE score combined with DFR in predicting short-term prognosis of patients undergoing early PCI after thrombolysis for acute myocardial infarction

OBJECTIVE

The aim of the study was to investigate the clinical value of the Global Registry of Arterial Events in Acute Coronary Syndromes (GRACE) score combined with the D-dimer/fibrinogen ratio (DFR) in predicting the short-term prognosis of patients undergoing percutaneous coronary intervention (PCI) early after thrombolysis for acute myocardial infarction (AMI).

PATIENTS AND METHODS

A total of 102 patients who underwent PCI early after thrombolysis for AMI during April 2020 to January 2022 in our hospital were picked as study subjects. These subjects were assigned as the good prognosis group (without adverse cardiovascular events) and poor prognosis group (with adverse cardiovascular events) according to whether adverse cardiovascular events occurred during hospitalization and follow-up. Changes in GRACE scores and DFR levels in patients with different prognoses were analyzed. The GRACE score and DFR level of patients with different prognosis were analyzed. The clinic pathological characteristics were collected, and the risk factors for poor prognosis of AMI patients were analyzed by logistic risk regression; ROC curve was used to analyze the prognostic value of GRACE score combined with DFR in early PCI patients after AMI thrombolysis.

RESULTS

Compared with the good prognosis group, the GRACE score and DFR level in the poor prognosis group were much higher (p<0.001). Significant differences existed in blood pressure, ejection fraction, number of diseased branches, and Killip grading between the patients with good prognosis and those with poor prognosis (p<0.05). There existed no significant difference in clinical medication between the patients with good prognosis and those with poor prognosis (p>0.05). Logistic multivariate analysis indicated that GRACE score, DFR, ejection fraction, number of lesion branches, and Killip grade were all risk factors influencing the prognosis of patients undergoing early PCI after thrombolysis in AMI (p<0.05). The ROC curve was established and the area under the curve (AUC) of GRACE score, DFR, and combined detection were 0.815, 0.783, and 0.894, respectively, and the sensitivity and specificity were 80.24%, 60.42%, 83.71%, 66.78%, 91.42% and 77.83%, respectively. The AUC, sensitivity, and specificity of combined detection were higher than those of the two alone and had a higher predictive value for the short-term prognosis of patients.

CONCLUSIONS

The GRACE score combined with DFR was of great value in diagnosing the short-term prognosis of patients undergoing PCI early after thrombolysis for AMI. Furthermore, the GRACE score, DFR, ejection fraction, number of lesion branches, and Killip classification were all important factors influencing the short-term prognosis of patients, which were of great significance in determining the prognosis of patients.

A clinical randomized controlled trial: moxibustion at Laogong interval with Panax notoginseng promoted the maturation of arteriovenous fistulae

BACKGROUND

We aim to study the clinical effect of moxibustion at Laogong interval with Panax notoginseng on the short-term maturation and long-term patency of arteriovenous fistula.

METHODS

Seventy-four pre-dialysis uremic patients who received distal forearm radial-cephalic fistula creations were enrolled in this study and randomly assigned to the control group and experimental group. After arteriovenous fistula creations, the control group underwent handgrip exercise, and the experimental group received moxibustion at Laogong acupoint interval with Panax notoginseng. Both groups received a 12-week treatment and were followed up for 24 weeks in all at the following time points: before creations and 2, 4, 8, 12, 24 weeks after creations. The diameter of anastomosis, the diameter and outflow of draining-veins 5 cm above anastomosis, the diameter and outflow of brachial arteries evaluated the maturation and patency of arteriovenous fistula. Enzyme linked immunosorbent assay determined serum levels of endothelin and nitric oxide.

RESULTS

The maturity rate in the experimental group was significantly higher than that in the control group at 4 weeks after arteriovenous fistula creations (P = 0.048). The diameter of anastomosis, the diameter of draining veins, and the blood flow of draining veins increased in both groups during the whole 24 weeks. The diameter and blood flow of brachial arteries ascended in both groups during the previous 12 weeks. Compared with the control group, moxibustion at Laogong interval with Panax notoginseng significantly improved the value of the diameter of draining-veins (P = 0.016), the blood flow of draining-veins (P = 0.015), the diameter of brachial arteries (P < 0.001), and the blood flow of brachial arteries (P = 0. 012) at 2 weeks, and enhanced the blood flow of draining-veins (P = 0.029) and brachial arteries (P < 0.001) at 12 weeks. Serum levels of endothelin were significantly lower (P = 0.047), and serum levels of nitric oxide were markedly higher (P < 0.001) in the experimental group than that in the control group at 2 weeks after creations.

CONCLUSIONS

Moxibustion at Laogong interval with Panax notoginseng was non-invasive and promoted the maturation of arteriovenous fistula at 4 weeks after creations. However, its long-term beneficial effect on patency at 24 weeks after creations was not significant. Trial registration Chinese Clinical Trial Registry, No. ChiCTR1900024042. Registered, http://www.chictr.org.cn/index.aspx.

Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars

Lychee is an exotic tropical fruit with a distinct flavor. The genome of cultivar ‘Feizixiao’ was assembled into 15 pseudochromosomes, totaling ~470 Mb. High heterozygosity (2.27%) resulted in two complete haplotypic assemblies. A total of 13,517 allelic genes (42.4%) were differentially expressed in diverse tissues. Analyses of 72 resequenced lychee accessions revealed two independent domestication events. The extremely early maturing cultivars preferentially aligned to one haplotype were domesticated from a wild population in Yunnan, whereas the late-maturing cultivars that mapped mostly to the second haplotype were domesticated independently from a wild population in Hainan. Early maturing cultivars were probably developed in Guangdong via hybridization between extremely early maturing cultivar and late-maturing cultivar individuals. Variable deletions of a 3.7 kb region encompassed by a pair of CONSTANS-like genes probably regulate fruit maturation differences among lychee cultivars. These genomic resources provide insights into the natural history of lychee domestication and will accelerate the improvement of lychee and related crops.

Two divergent haplotypes from a highly heterozygous lychee genome of the cultivar ‘Feizixiao’ and resequencing of 72 lychee accessions provide insights into the genome evolution and domestication history of lychee.

Chromosome-Level Genome Assembly of Chinese Sucker (Myxocyprinus asiaticus) Reveals Strongly Conserved Synteny Following a Catostomid-Specific Whole-Genome Duplication

Fishes of the family Catostomidae (“suckers”; Teleostei: Cypriniformes) are hypothesized to have undergone an allopolyploidy event approximately 60 Ma. However, genomic evidence has previously been unavailable to assess this hypothesis. We sequenced and assembled the first chromosome-level catostomid genome, Chinese sucker (Myxocyprinus asiaticus), and present clear evidence of a catostomid-specific whole-genome duplication (WGD) event (“Cat-4R”). Our results reveal remarkably strong, conserved synteny since this duplication event, as well as between Myxocyprinus and an unduplicated outgroup, zebrafish (Danio rerio). Gene content and repetitive elements are also approximately evenly distributed across homeologous chromosomes, suggesting that both subgenomes retain some function, with no obvious bias in gene fractionation or subgenome dominance. The Cat-4R duplication provides another independent example of genome evolution following WGD in animals, in this case at the extreme end of conserved genome architecture over at least 25.2 Myr since the duplication. The M. asiaticus genome is a useful resource for researchers interested in understanding genome evolution following WGD in animals.

Atypical DNA methylation, sRNA-size distribution, and female gametogenesis in Utricularia gibba

The most studied DNA methylation pathway in plants is the RNA Directed DNA Methylation (RdDM), a conserved mechanism that involves the role of noncoding RNAs to control the expansion of the noncoding genome. Genome-wide DNA methylation levels have been reported to correlate with genome size. However, little is known about the catalog of noncoding RNAs and the impact on DNA methylation in small plant genomes with reduced noncoding regions. Because of the small length of intergenic regions in the compact genome of the carnivorous plant Utricularia gibba, we investigated its repertoire of noncoding RNA and DNA methylation landscape. Here, we report that, compared to other angiosperms, U. gibba has an unusual distribution of small RNAs and reduced global DNA methylation levels. DNA methylation was determined using a novel strategy based on long-read DNA sequencing with the Pacific Bioscience platform and confirmed by whole-genome bisulfite sequencing. Moreover, some key genes involved in the RdDM pathway may not represented by compensatory paralogs or comprise truncated proteins, for example, U. gibba DICER-LIKE 3 (DCL3), encoding a DICER endonuclease that produces 24-nt small-interfering RNAs, has lost key domains required for complete function. Our results unveil that a truncated DCL3 correlates with a decreased proportion of 24-nt small-interfering RNAs, low DNA methylation levels, and developmental abnormalities during female gametogenesis in U. gibba. Alterations in female gametogenesis are reminiscent of RdDM mutant phenotypes in Arabidopsis thaliana. It would be interesting to further study the biological implications of the DCL3 truncation in U. gibba, as it could represent an initial step in the evolution of RdDM pathway in compact genomes.

The cross-polarization scattering system for the magnetic fluctuation measurement in the Experimental Advanced Superconducting Tokamak

The cross-polarization scattering (CPS) system for magnetic fluctuation measurements in the Experimental Advanced Superconducting Tokamak (EAST) has been designed and installed. Different from the Doppler reflectometer (DR) system, the CPS system detects the perpendicular polarization of the electromagnetic wave induced by magnetic fluctuations B̃. The CPS system in the EAST has been developed from the existing Doppler reflectometer system, and they are integrated together for simultaneous measurement of magnetic and density fluctuations. Ray-tracing simulations are used to calculate the scattering locations and the wavenumber coverage of the magnetic fluctuation for CPS. In the experiments, the CPS and DR system data were different in Doppler shift, amplitude, and spectrum broadening. In this article, the hardware design, the ray tracing, and the preliminary results of the system in the EAST are presented.

The clinical value of the combined detection of sEGFR, CA125 and HE4 for epithelial ovarian cancer diagnosis

OBJECTIVE

This study aims to investigate the clinical value of combined detection of serum soluble epidermal growth factor receptor (sEGFR), cancer antigen 125 (CA125), and human epididymis protein 4 (HE4) in the diagnosis of epithelial ovarian cancer (EOC).

PATIENTS AND METHODS

From December 2017 to October 2018, the serum samples were obtained from the Affiliated Hospital of Xuzhou Medical University, with 30 patients as EOC group, 30 patients with benign ovarian neoplasms as benign group, and 17 healthy subjects as healthy group. Besides, among 30 EOC patients, 9 serum samples were obtained from pre-operative and post-operative EOC patients. The levels of serum sEGFR were detected by enzyme-linked immunosorbent assay (ELISA), while CA125 and HE4 were detected by enhanced chemiluminescence immunoassay (ECLIA). The diagnostic value was evaluated by receiver operating characteristic (ROC) curve analysis.

RESULTS

The levels of serum sEGFR, CA125, and HE4 in EOC group were significantly higher than those in benign group (p<0.05) and healthy group (p<0.05). When using a single tumor marker, the CA125 shows the highest sensitivity (93.30%) and HE4 shows the highest specificity (97.87%). The specificity of combined detection of serum sEGFR, CA125, and HE4 was 100%, which was significantly higher than that using a single tumor marker. The area under the ROC curve (AUC) of combined detection of serum sEGFR, CA125, and HE4 (0.965) was much higher than that of the single detection and higher than that of combined detection of CA125 and HE4 (0.940). Moreover, the level of serum sEGFR in post-operative EOC group was significantly lower than that in the corresponding pre-operative EOC group (p<0.05).

CONCLUSIONS

Our study shows that combined detection of serum sEGFR, CA125, and HE4 increases the specificity and efficiency in EOC diagnosis, indicating that sEGFR could be a potential biomarker for the diagnosis and prognosis of EOC.

TCP and MADS-Box Transcription Factor Networks Regulate Heteromorphic Flower Type Identity in Gerbera hybrida

The large sunflower family, Asteraceae, is characterized by compressed, flower-like inflorescences that may bear phenotypically distinct flower types. The CYCLOIDEA (CYC)/TEOSINTE BRANCHED1-like transcription factors (TFs) belonging to the TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) protein family are known to regulate bilateral symmetry in single flowers. In Asteraceae, they function at the inflorescence level, and were recruited to define differential flower type identities. Here, we identified upstream regulators of GhCYC3, a gene that specifies ray flower identity at the flower head margin in the model plant Gerbera hybrida We discovered a previously unidentified expression domain and functional role for the paralogous CINCINNATA-like TCP proteins. They function upstream of GhCYC3 and affect the developmental delay of marginal ray primordia during their early ontogeny. At the level of single flowers, the Asteraceae CYC genes show a unique function in regulating the elongation of showy ventral ligules that play a major role in pollinator attraction. We discovered that during ligule development, the E class MADS-box TF GRCD5 activates GhCYC3 expression. We propose that the C class MADS-box TF GAGA1 contributes to stamen development upstream of GhCYC3 Our data demonstrate how interactions among and between the conserved floral regulators, TCP and MADS-box TFs, contribute to the evolution of the elaborate inflorescence architecture of Asteraceae.

Attenuation of a virulent swine acute diarrhea syndrome coronavirus strain via cell culture passage

Swine acute diarrhea syndrome coronavirus (SADS-CoV) is a newly identified enteric alphacoronavirus that causes fatal diarrhea in newborn piglets in China. Here, we propagated a virulent strain SADS-CoV/CN/GDWT/2017 in Vero cells for up to 83 passages. Four strains of SADS-CoV/GDWT-P7, -P18, -P48 and -P83 were isolated and characterized. Sequence alignments showed that these four novel strains exhibited 16 nucleotide mutations and resultant 10 amino acid substitutions in open reading frame 1a/1b, spike, NS3a, envelope, membrane and nucleocapsid proteins. Furthermore, a 58-bp deletion in NS7a/7b was found in P48 and P83 strains, which led to the loss of NS7b and 38 amino acid changes of NS7a. Pig infection studies showed that the P7 strain caused typical watery diarrhea, while the P83 strain induced none-to-mild, delayed and transient diarrhea. This is the first report on cell adaption of a virulent SADS-CoV strain, which gives information on the potential virulence determinants of SADS-CoV.

Five-channel tunable W-band Doppler backscattering system in the experimental advanced superconducting tokamak

A 5-channel Doppler backscattering system has been designed and installed in the Experimental Advanced Superconducting Tokamak (EAST). Through an I/Q-type double sideband modulator and a frequency multiplier, an array of finely spaced (Δf = 400 MHz) frequencies that span 1.6 GHz has been created. The center of the array bandwidth is tunable within the range of 75-97.8 GHz, which covers most of the W band (75-110 GHz). The incident angle can be adjusted from -4° to 12°, and the wavenumber range is 4-15 cm^-1 with a wavenumber resolution of Δk/k ≤ 0.35. Ray tracing is used to calculate the scattering location and the scattering wavenumber. This article details the hardware design, the ray tracing, and the preliminary experimental results from EAST plasmas.

Altered Gene Regulatory Networks Are Associated With the Transition From C3 to Crassulacean Acid Metabolism in Erycina (Oncidiinae: Orchidaceae)

Crassulacean acid metabolism (CAM) photosynthesis is a modification of the core C3 photosynthetic pathway that improves the ability of plants to assimilate carbon in water-limited environments. CAM plants fix CO2 mostly at night, when transpiration rates are low. All of the CAM pathway genes exist in ancestral C3 species, but the timing and magnitude of expression are greatly altered between C3 and CAM species. Understanding these regulatory changes is key to elucidating the mechanism by which CAM evolved from C3. Here, we use two closely related species in the Orchidaceae, Erycina pusilla (CAM) and Erycina crista-galli (C3), to conduct comparative transcriptomic analyses across multiple time points. Clustering of genes with expression variation across the diel cycle revealed some canonical CAM pathway genes similarly expressed in both species, regardless of photosynthetic pathway. However, gene network construction indicated that 149 gene families had significant differences in network connectivity and were further explored for these functional enrichments. Genes involved in light sensing and ABA signaling were some of the most differently connected genes between the C3 and CAM Erycina species, in agreement with the contrasting diel patterns of stomatal conductance in C3 and CAM plants. Our results suggest changes to transcriptional cascades are important for the transition from C3 to CAM photosynthesis in Erycina.

A novel, tunable, multimodal microwave system for microwave reflectometry system

Based on a new technique, a tunable, multi-channel system that covers the Q-band (33-55 GHz) is presented in this article. It has a potential use of the Doppler backscattering system diagnostic that can measure the turbulence radial correlation and the perpendicular velocity of turbulence by changing the incident angle. The system consists primarily of a double-sideband (DSB) modulation and a multiplier, which creates four probing frequencies. The probing frequency enables the simultaneous analysis of the density fluctuations and flows at four distinct radial regions in tokamak plasma. The amplitude of the probing frequency can be adjusted by the initial phase of the intermediate frequency (IF) input from the double-sideband, and the typical flatness is less than 10 dB. The system was tested in the lab with a rotating grating, and the results show that the system can operate in the frequency range of 33-55 GHz with a Q-band multitude and that the power of each channel can be adjusted by the phase of the IF input of DSB.

Influence of neutral beam attenuation on beam emission spectroscopy and charge exchange recombination spectroscopy

Neutral beam attenuation is simulated by means of consulting the ADAS (Atomic Data and Analysis Structure) database based on experimentally diagnosed radial plasma density and electron temperature profiles on the Experimental Advanced Superconducting Tokamak (EAST). Two-dimensional distributions of beam emission and charge exchange recombination photon flux are simulated, taking neutral beam attenuation into account, together with comparison with experimental results of Beam Emission Spectroscopy (BES) and Charge eXchange Recombination Spectroscopy (CXRS). A photon number which is over 10¹⁴ promises a sufficient photon flux for typical detectors of BES, CXRS, and UltraFast-CXRS (UF-CXRS) diagnostics. Evidence shows that the ADAS database overvalues neutral beam injection effective stopping coefficient on the EAST tokamak. The joint diagnostic of BES and UF-CXRS which is under development to measure plasma pressure with a high temporal resolution of 1 μs will have strong signals in a radial range of 0.6 < ρ < 0.8. The steep gradients of plasma density and C⁶⁺ density at ρ ∼ 1 bring great difficulty to edge plasma investigation by this joint diagnostic.

Evolutionary history of enigmatic bears in the Tibetan Plateau-Himalaya region and the identity of the yeti

Although anecdotally associated with local bears (Ursus arctos and U. thibetanus), the exact identity of ‘hominid’-like creatures important to folklore and mythology in the Tibetan Plateau–Himalaya region is still surrounded by mystery. Recently, two purported yeti samples from the Himalayas showed genetic affinity with an ancient polar bear, suggesting they may be from previously unrecognized, possibly hybrid, bear species, but this preliminary finding has been under question. We conducted a comprehensive genetic survey of field-collected and museum specimens to explore their identity and ultimately infer the evolutionary history of bears in the region. Phylogenetic analyses of mitochondrial DNA sequences determined clade affinities of the purported yeti samples in this study, strongly supporting the biological basis of the yeti legend to be local, extant bears. Complete mitochondrial genomes were assembled for Himalayan brown bear (U. a. isabellinus) and black bear (U. t. laniger) for the first time. Our results demonstrate that the Himalayan brown bear is one of the first-branching clades within the brown bear lineage, while Tibetan brown bears diverged much later. The estimated times of divergence of the Tibetan Plateau and Himalayan bear lineages overlap with Middle to Late Pleistocene glaciation events, suggesting that extant bears in the region are likely descendants of populations that survived in local refugia during the Pleistocene glaciations.

Molecular mechanism of Wnt signal pathway in multiple myeloma cell line H929 cell autophagy

OBJECTIVE

Pathogenic mechanism of multiple myeloma is still unclear yet. Abnormality in cell autophagy is closely correlated with various orthopedic diseases especially multiple myeloma. Therefore, this study investigated the mechanism of cell autophagy abnormality in multiple myeloma occurrence and clinical implications.

MATERIALS AND METHODS

Using multiple myeloma cell line H929 as the model, cells were treated with UV irradiation. Western blot was used to measure the autophagy of H929 cell, expression level of autophagy molecules and activation of autophagy signal pathway such as Wnt. Using autophagy activator, H929 cell autophagy was potentiated, followed by quantification of autophagy molecular expression and signal pathway such as Wnt activation. Agonist or antagonist of Wnt signal pathway was used to treat H929 cells followed by measuring autophagy molecules and Wnt pathway activation. The correlation between Wnt signal pathway or cell autophagy and occurrence of multiple myeloma was analyzed.

RESULTS

UV irradiation treatment on multiple myeloma cell line H929 induced autophagy and Wnt signal pathway activation. The inhibitor of Wnt signal pathway suppressed UV-induced H929 cell autophagy. However, over-expression of Wnt signal pathway enhanced UV-mediated autophagy of H929 cells. The condition of Wnt activation and autophagy level were positively correlated.

CONCLUSIONS

UV irradiation can induce autophagy of multiple myeloma cells, suggesting that management of cell autophagy might be one possible treatment for multiple myeloma.

Myocardial late gadolinium enhancement: a head-to-head comparison of motion-corrected balanced steady-state free precession with segmented turbo fast low angle shot

AIM

To evaluate the image quality and diagnostic agreement with a head-to-head comparison of late gadolinium enhancement (LGE) images acquired by the motion-corrected (MOCO) balanced steady-state free precession (bSSFP) phase sensitivity inversion recovery (PSIR) and conventional segmented fast low angle shot (FLASH) PSIR methods^15,16 in a patient cohort with a wide spectrum of cardiovascular disease.

MATERIALS AND METHODS

In 59 consecutive patients, signal-to-noise ratios (SNRs), contrast-to-noise ratios (CNRs) of the normal myocardium (NM), LGE, and blood pool (BP) were pair-wise compared between the two different sequences. A further semi-qualitative score system (graded 1 -4) was used to compare the overall image quality (OIQ). The diagnostic agreement of the two techniques were evaluated by both transmural severity and absolutely quantitative size of LGE.

RESULTS

The SNRs of the NM, LGE, and BP of MOCO bSSFP were 4.8±3.4, 53.6±35.6 and 43.2±29.3, compared with 3.9±3.6 (p=0.126), 27.7±18.5 (p<0.001) and 24.3±13.4 (p<0.001) of FLASH LGE, respectively. The CNRs of LGE to NM, LGE to BP, and BP to NM were 48.3±33.1 versus 23.8±16.7 (p<0.001), 6.5±21.6 versus 3.8±10.8 (p<0.001), and 38.3±27.2 versus 20.3±10.7 (p=0.448), respectively. The OIQ of MOCO bSSFP was higher than that of segmented FLASH (median 4 versus median 3, p<0.001). For quantification of LGE size, there is good agreement and high correlation (r=0.992, p<0.001) between the two methods.

CONCLUSIONS

MOCO bSSFP is a feasible, robust sequence for LGE imaging, especially for patients with arrhythmia and those incapable of breath-holding due to severe heart failure.