[Analysis of the clinical characteristics of acute myeloid leukemia related to the treatment of hematological and solid tumors]

Objective: To compare and analyze the clinical characteristics of acute myeloid leukemia (AML) related to the treatment of hematological tumors and solid tumors. Methods: The laboratory and clinical data of 41 patients with treatment-related AML (t-AML) in the Department of Hematology, Henan Cancer Hospital from January 2014 to December 2021 were retrospectively analyzed, and they were divided into hematological tumor group and solid tumor group. Survival analysis was performed using the Kaplan-Meier method and Log rank test. Results: The median interval from the first tumor diagnosis to t-AML in 41 patients was 21.0 (16.5-46.0) months; 24 (58.5%) had abnormal expression of lymphoid antigen, 28 (68.3%) had abnormal karyotype, 18 cases (43.9%) were positive for fusion gene, and 28 cases (68.3%) were positive for gene mutation; the median recurrence-free survival (RFS) was 11.0 months, and the median overall survival (OS) was 11.5 months. The proportion of acute promyelocytic leukemia ([APL], 0.0, 0/13), complete response ([CR],18.2%, 2/11), median OS (4.5 months) and median RFS (2.5 months) of t-AML patients in the hematological tumor group were significantly lower than those in the solid tumor group (35.7%, 10/28; 68.0%, 17/25; not reach; not reach), but the proportion of M4 /M5 (93.2%,12/13) was significantly higher than that in the solid tumor group (53.6%,15/18; all P values<0.05). Through subgroup analysis, the proportion of patients with positive PML-RARa and good prognosis karyotypes in the solid tumor group (35.7%, 10/28; 46.4%, 13/28) was significantly higher than that in the hematological tumor group (0.0, 0/13; 0.0, 0/13; P<0.05), while the proportion of patients with intermediate karyotypes (42.9%, 12/28) was significantly lower than that in the hematological tumor group (84.6%, 11/13; P<0.05), the difference was statistically significant. The CR rate (90.0%, 9/10), median OS (not reach) and median RFS (not reach) in the t-APL group were higher than those in the t-AML (without t-APL) group (38.5%, 10/26; 6 months; 8 months; P<0.05). After excluding the effect of t-APL patients, there was no significant difference in the CR rate, median OS and median RFS between the solid tumor group (8; 9 months; not reach) and the hematological tumor group (2; 4 months; 2 months; P>0.05). Univariate analysis showed that the primary tumor belongs to hematological tumor was a common risk factor for OS and RFS in t-AML patients (P<0.10). Conclusions: Compared with patients with t-AML secondary to solid tumors, patients with t-AML secondary to hematological tumors have poorer treatment effects and poorer prognosis. After excluding the effect of t-APL patients, there are no significant differences in the treatment efficacy and prognosis between the two types of t-AML patients.

[Femtosecond laser assisted cataract surgery in a complicated cataract patient with reverse implantable collamer len: a case report]

The patient is a 33-year-old female who, 11 years ago, underwent bilateral posterior chamber phakic intraocular lens (pIOL) implantation due to myopia. She presented with a 2-year history of declining vision in her right eye and sought medical attention. She received femtosecond laser-assisted cataract surgery combined with pIOL extraction. Anterior segment optical coherence tomography and ultrasound biomicroscopy both showed an inverted pIOL in the right eye. Good visual results were achieved, and there were no complications during the six-month follow-up.

Genome resources for the elite bread wheat cultivar Aikang 58 and mining of elite homeologous haplotypes for accelerating wheat improvement

Despite recent progress in crop genomics studies, the genomic changes brought about by modern breeding selection are still poorly understood, thus hampering genomics-assisted breeding, especially in polyploid crops with compound genomes such as common wheat (Triticum aestivum). In this work, we constructed genome resources for the modern elite common wheat variety Aikang 58 (AK58). Comparative genomics between AK58 and the landrace cultivar Chinese Spring (CS) shed light on genomic changes that occurred through recent varietal improvement. We also explored subgenome diploidization and divergence in common wheat and developed a homoeologous locus-based genome-wide association study (HGWAS) approach, which was more effective than single homoeolog-based GWAS in unraveling agronomic trait-associated loci. A total of 123 major HGWAS loci were detected using a genetic population derived from AK58 and CS. Elite homoeologous haplotypes (HHs), formed by combinations of subgenomic homoeologs of the associated loci, were found in both parents and progeny, and many could substantially improve wheat yield and related traits. We built a website where users can download genome assembly sequence and annotation data for AK58, perform blast analysis, and run JBrowse. Our work enriches genome resources for wheat, provides new insights into genomic changes during modern wheat improvement, and suggests that efficient mining of elite HHs can make a substantial contribution to genomics-assisted breeding in common wheat and other polyploid crops.

A transcriptional atlas identifies key regulators and networks for the development of spike tissues in barley

Grain number and size determine grain yield in crops and are closely associated with spikelet fertility and grain filling in barley (Hordeum vulgare). Abortion of spikelet primordia within individual barley spikes causes a 30%-50% loss in the potential number of grains during development from the awn primordium stage to the tipping stage, after that grain filling is the primary factor regulating grain size. To identify transcriptional signatures associated with spike development, we use a six-rowed barley cultivar (Morex) to develop a spatiotemporal transcriptome atlas containing 255 samples covering 17 stages and 5 positions along the spike. We identify several fundamental regulatory networks, in addition to key regulators of spike development and morphology. Specifically, we show HvGELP96, encoding a GDSL domain-containing protein, as a regulator of spikelet fertility and grain number. Our transcriptional atlas offers a powerful resource to answer fundamental questions in spikelet development and degeneration in barley.

Gene duplications facilitate C4-CAM compatibility in common purslane

Common purslane (Portulaca oleracea) integrates both C4 and crassulacean acid metabolism (CAM) photosynthesis pathways and is a promising model plant to explore C4-CAM plasticity. Here, we report a high-quality chromosome-level genome of nicotinamide adenine dinucleotide (NAD)-malic enzyme (ME) subtype common purslane that provides evidence for 2 rounds of whole-genome duplication (WGD) with an ancient WGD (P-β) in the common ancestor to Portulacaceae and Cactaceae around 66.30 million years ago (Mya) and another (Po-α) specific to common purslane lineage around 7.74 Mya. A larger number of gene copies encoding key enzymes/transporters involved in C4 and CAM pathways were detected in common purslane than in related species. Phylogeny, conserved functional site, and collinearity analyses revealed that the Po-α WGD produced the phosphoenolpyruvate carboxylase-encoded gene copies used for photosynthesis in common purslane, while the P-β WGD event produced 2 ancestral genes of functionally differentiated (C4- and CAM-specific) beta carbonic anhydrases involved in the C4 + CAM pathways. Additionally, cis-element enrichment analysis in the promoters showed that CAM-specific genes have recruited both evening and midnight circadian elements as well as the Abscisic acid (ABA)-independent regulatory module mediated by ethylene-response factor cis-elements. Overall, this study provides insights into the origin and evolutionary process of C4 and CAM pathways in common purslane, as well as potential targets for engineering crops by integrating C4 or CAM metabolism.

[The predictive values of platelet mitochondrial mass and quantity during the perioperative period in elderly patients on the occurrence of postoperative delirium]

Objective: To investigate the changes of platelet mitochondrial mass and quantity during perioperative period in elderly patients, and assess their predictive values on the occurrence of postoperative delirium (POD). Methods: In this prospective study, 162 elderly patients scheduled for abdominal surgery under general anesthesia were enrolled from November 2021 to January 2022 in Nanjing Drum Tower Hospital Affiliated to Nanjing University Medical School. Among them, 20 patients [10 males, 10 females, aged (71.4±6.8) years] developed POD within 3 days after surgery (POD group), and another 20 patients[12 males, 8 females, aged (67.7±5.3) years] who did not develope POD were selected as controls (control group) using propensity score matching method. Blood samples were collected preoperatively, at the end of surgery and on the first postoperative day. Platelets were extracted and mitochondrial mass was detected with flow cytometry. Transmission electron microscopy was used to determine mitochondrial quantity. The receiver operating characteristic (ROC) curve was drawn to analyze the value of mitochondrial mass and quantity in predicting the occurrence of POD. Results: The mean fluorescence intensities of platelet mitochondrial mass were 193±46, 236±61, 264±53 preoperatively, at the end of surgery and on the first postoperative day in the POD group, respectively. The corresponding values were 209±61, 191±67 and 201±56 in the control group. The platelet mitochondrial mass of patients in the POD group was significantly increased on the first postoperative day compared to preoperative levels (P<0.001). In contrast, there was no significant difference in the control group (P=0.410). Patients in the POD group had higher platelet mitochondrial mass than patients in the control group on the first postoperative day(P=0.002). Meanwhile, platelets from patients in the POD group showed significantly higher number of mitochondria than platelets from patients in the control group [3 (2, 4) vs 2 (1, 2), P<0.001]. According to the ROC curve of platelet on the first postoperative day, at a mitochondrial mass cut-off value of>275.35, the sensitivity, specificity and area under the ROC curve to detect the occurrence of POD were 55%, 90% and 0.800 (95%CI: 0.666-0.934, P<0.001). At a mitochondrial quantity cut-off value of>2, the sensitivity, specificity and area under the ROC curve to detect the occurrence of POD were 53%, 78% and 0.680 (95%CI: 0.584-0.776, P<0.001). Conclusions: Patients who developed POD show higher platelet mitochondrial mass after surgery compared to preoperative levels. The mitochondrial mass of platelets on the first postoperative day has good predictive value on the occurrence of POD.

[Analysis of the prognosis and survival of patients with acute-on-chronic liver failure]

Objective: To explore the influencing factors and the impact of artificial liver treatment on the prognosis and survival of patients with acute-on-chronic liver failure (ACLF). Methods: Clinical data from 201 cases with ACLF from January 2016 to December 2019 was retrospectively analyzed. The survival rate was calculated by the Kaplan-Meier method, the log-rank test of univariate analysis, and the multivariate analysis of the stepwise Cox regression forward method. Results: The median survival time of patients was 6 months, and the survival rates at 6, 9, and 12 months were 51.2%, 38.3%, and 29.9%, respectively. In univariate analysis, age, presence or absence of hypertension and upper gastrointestinal bleeding, treatment method, model for end-stage liver disease (MELD) score, and cholinesterase were associated with prognosis (P < 0.05). Multivariate regression analysis results showed that MELD score was the main factor affecting the 1-year prognosis of ACLF patients (P = 0.002). Artificial liver treatment was beneficial for the 1-year prognosis of ACLF patients aged < 50 years or with a MELD score of ≥20 (P < 0.05 ). The relative risk ratio (RR) of mortality was 2.55 times higher in patients with advanced age (≥50 years old) than that of younger patients (P < 0.001). Regression analysis was performed using age as a stratification factor, and upper gastrointestinal bleeding was related to the prognosis of younger patients, while choline esterase was related to the prognosis of advanced age. Regression analysis after stratified MELD score showed that age and hypertension were related to the prognosis of patients with MELD score < 20, and treatment method and age were related to the prognosis of patients with MELD score≥20. Conclusion: Artificial liver treatment is beneficial for the 1-year prognosis of ACLF patients. Age, MELD score, hypertension, and upper gastrointestinal bleeding are independent risk factors affecting the prognosis of ACLF patients.

Identification of errors in draft genome assemblies at single-nucleotide resolution for quality assessment and improvement

Assembly of a high-quality genome is important for downstream comparative and functional genomic studies. However, most tools for genome assembly assessment only give qualitative reports, which do not pinpoint assembly errors at specific regions. Here, we develop a new reference-free tool, Clipping information for Revealing Assembly Quality (CRAQ), which maps raw reads back to assembled sequences to identify regional and structural assembly errors based on effective clipped alignment information. Error counts are transformed into corresponding assembly evaluation indexes to reflect the assembly quality at single-nucleotide resolution. Notably, CRAQ distinguishes assembly errors from heterozygous sites or structural differences between haplotypes. This tool can clearly indicate low-quality regions and potential structural error breakpoints; thus, it can identify misjoined regions that should be split for further scaffold building and improvement of the assembly. We have benchmarked CRAQ on multiple genomes assembled using different strategies, and demonstrated the misjoin correction for improving the constructed pseudomolecules.

[A case of left pulmonary artery sling combined with congenital tracheal stenosis in an adult]

Pulmonary artery sling in adults is a rare congenital vascular malformation usually accompanied by tracheal and bronchial stenosis. Due to its high mortality risk and relatively poor prognosis, it has rarely been reported in adults. We reported a middle-aged patient who presented with shortness of breath, predominantly after activity, since childhood. He was diagnosed with "tracheal stenosis" in another hospital and received symptomatic treatment. The diagnosis of left pulmonary artery sling with congenital tracheal stenosis was confirmed by multi-slice spiral CT (MSCT), airway examination with flexible bronchoscope and 3D image post-processing system. Data from this case and the related literatures have been summarized and analyzed. This will help clinicians to improve their level of diagnosis and treatment.

Pangenome-based trajectories of intracellular gene transfers in Poaceae unveil high cumulation in Triticeae

Intracellular gene transfers (IGTs) between the nucleus and organelles, including plastids and mitochondria, constantly reshape the nuclear genome during evolution. Despite the substantial contribution of IGTs to genome variation, the dynamic trajectories of IGTs at the pangenomic level remain elusive. Here, we developed an approach, IGTminer, that maps the evolutionary trajectories of IGTs using collinearity and gene reannotation across multiple genome assemblies. We applied IGTminer to create a nuclear organellar gene (NOG) map across 67 genomes covering 15 Poaceae species, including important crops. The resulting NOGs were verified by experiments and sequencing data sets. Our analysis revealed that most NOGs were recently transferred and lineage specific and that Triticeae species tended to have more NOGs than other Poaceae species. Wheat (Triticum aestivum) had a higher retention rate of NOGs than maize (Zea mays) and rice (Oryza sativa), and the retained NOGs were likely involved in photosynthesis and translation pathways. Large numbers of NOG clusters were aggregated in hexaploid wheat during 2 rounds of polyploidization, contributing to the genetic diversity among modern wheat accessions. We implemented an interactive web server to facilitate the exploration of NOGs in Poaceae. In summary, this study provides resources and insights into the roles of IGTs in shaping interspecies and intraspecies genome variation and driving plant genome evolution.

Comparative genomics reveals a unique nitrogen-carbon balance system in Asteraceae

The Asteraceae (daisy family) is one of the largest families of plants. The genetic basis for its high biodiversity and excellent adaptability has not been elucidated. Here, we compare the genomes of 29 terrestrial plant species, including two de novo chromosome-scale genome assemblies for stem lettuce, a member of Asteraceae, and Scaevola taccada, a member of Goodeniaceae that is one of the closest outgroups of Asteraceae. We show that Asteraceae originated ~80 million years ago and experienced repeated paleopolyploidization. PII, the universal regulator of nitrogen-carbon (N-C) assimilation present in almost all domains of life, has conspicuously lost across Asteraceae. Meanwhile, Asteraceae has stepwise upgraded the N-C balance system via paleopolyploidization and tandem duplications of key metabolic genes, resulting in enhanced nitrogen uptake and fatty acid biosynthesis. In addition to suggesting a molecular basis for their ecological success, the unique N-C balance system reported for Asteraceae offers a potential crop improvement strategy.

[Analysis of the characteristics of viral infections in children with diarrhea in Beijing from 2018 to 2022]

Objective: To explore the characteristics of viral infections in children with diarrhea in Beijing from 2018 to 2022. Methods: Real-time PCR and enzyme-linked immunosorbent assay were used to detect viral nucleic acid of Norovirus (NoV), Sappovirus (SaV), Astrovirus (AstV), Enteric Adenovirus (AdV) or antigen of Rotavirus (RV) in 748 stool samples collected from Beijing Capital Institute of Pediatrics from January 2018 to December 2021. Subsequently, the reverse transcription PCR or PCR method was used to amplify the target gene of the positive samples after the initial screening, followed by sequencing, genotyping and evolution analysis, so as to obtain the characteristics of these viruses. Phylogenetic analysis was performed using Mega 6.0. Results: From 2018 to 2021, the overall detection rate of the above five common viruses was 37.6%(281/748)in children under 5 years old in Beijing. NoV, Enteric AdV and RV were still the top three diarrhea-related viruses, followed by AstV and SaV, accounting for 41.6%, 29.2%, 27.8%, 8.9% and 7.5%, respectively. The detection rate of co-infections with two or three diarrhea-related viruses was 4.7% (35/748). From the perspective of annual distribution, the detection rate of Enteric AdV was the highest in 2021, while NoV was predominant in the other 4 years. From the perspective of genetic characteristics, NoV was predominant by GII.4, and after the first detection of GII.4[P16] in 2020, it occupied the first two gene groups together with GII.4[P31]. Although the predominant RV was G9P[8], the rare epidemic strain G8P[8] was first detected in 2021. The predominant genotypes of Enteric AdV and AstV were Ad41 and HAstV-1. SaV was sporadic spread with a low detection rate. Conclusion: Among the diarrhea-related viruses infected children under 5 years of age in Beijing, the predominant strains of NoV and RV have changed and new sub-genotypes have been detected for the first time, while the predominant strains of AstV and Enteric AdV are relatively stable.

The Sapria himalayana genome provides new insights into the lifestyle of endoparasitic plants

BACKGROUND

Sapria himalayana (Rafflesiaceae) is an endoparasitic plant characterized by a greatly reduced vegetative body and giant flowers; however, the mechanisms underlying its special lifestyle and greatly altered plant form remain unknown. To illustrate the evolution and adaptation of S. himalayasna, we report its de novo assembled genome and key insights into the molecular basis of its floral development, flowering time, fatty acid biosynthesis, and defense responses.

RESULTS

The genome of S. himalayana is ~ 1.92 Gb with 13,670 protein-coding genes, indicating remarkable gene loss (~ 54%), especially genes involved in photosynthesis, plant body, nutrients, and defense response. Genes specifying floral organ identity and controlling organ size were identified in S. himalayana and Rafflesia cantleyi, and showed analogous spatiotemporal expression patterns in both plant species. Although the plastid genome had been lost, plastids likely biosynthesize essential fatty acids and amino acids (aromatic amino acids and lysine). A set of credible and functional horizontal gene transfer (HGT) events (involving genes and mRNAs) were identified in the nuclear and mitochondrial genomes of S. himalayana, most of which were under purifying selection. Convergent HGTs in Cuscuta, Orobanchaceae, and S. himalayana were mainly expressed at the parasite-host interface. Together, these results suggest that HGTs act as a bridge between the parasite and host, assisting the parasite in acquiring nutrients from the host.

CONCLUSIONS

Our results provide new insights into the flower development process and endoparasitic lifestyle of Rafflesiaceae plants. The amount of gene loss in S. himalayana is consistent with the degree of reduction in its body plan. HGT events are common among endoparasites and play an important role in their lifestyle adaptation.

[Efficacy and prognostic factors of allogeneic hematopoietic stem cell transplantation treatment for T lymphoblastic leukemia/lymphoma]

Objective: To analyze the efficacy and prognostic factors of allogeneic hematopoietic stem cell transplantation (allo-HSCT) for treating T lymphoblastic leukemia/lymphoma (T-ALL/LBL) . Methods: This study retrospectively evaluated 119 adolescent and adult patients with T-ALL/LBL from January 2006 to January 2020 at Peking University Third Hospital and Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences. Patients were divided into chemotherapy-only, chemotherapy followed by allo-HSCT, and chemotherapy followed by autologous hematopoietic stem cell transplantation (auto-HSCT) groups according to the consolidation regimen, and the 5-year overall survival (OS) and progression-free survival (PFS) rates of each group were compared. Results: Among 113 patients with effective follow-up, 96 (84.9%) patients achieved overall response (ORR), with 79 (69.9%) having complete response (CR) and 17 (15.0%) having partial response (PR), until July 2022. The analysis of the 96 ORR population revealed that patients without transplantation demonstrated poorer outcomes compared with the allo-HSCT group (5-year OS: 11.4% vs 55.6%, P=0.001; 5-year PFS: 8.9% vs 54.2%, P<0.001). No difference was found in 5-year OS and 5-year PFS between the allo-HSCT and auto-HSCT groups (P=0.271, P=0.197). The same results were achieved in the CR population. Allo-HSCT got better 5-year OS (37.5% vs 0) for the 17 PR cases (P=0.064). Different donor sources did not affect 5-year OS, with sibling of 61.1% vs hap-haploidentical of 63.6% vs unrelated donor of 50.0% (P>0.05). No significant difference was found in the treatment response in the early T-cell precursor acute lymphoblastic leukemia/lymphoma (ETP) and non-ETP populations. The ETP group demonstrated lower 5-year OS compared with the non-ETP group in the chemotherapy alone group (0 vs 12.6%, P=0.045), whereas no significant difference was found between the ETP and non-ETP groups in the allo-HSCT group (75.0% vs 62.9%, P=0.852). Multivariate analysis revealed that high serum lactate dehydrogenase level, without transplantation, and no CR after chemotherapy induction were independently associated with inferior outcomes (P<0.05) . Conclusion: Allo-HSCT could be an effective consolidation therapy for adult and adolescent patients with T-ALL/LBL. Different donor sources did not affect survival. Allo-HSCT may overcome the adverse influence of ETP-ALL/LBL on OS.

A chromosome-scale genome assembly of Artemisia argyi reveals unbiased subgenome evolution and key contributions of gene duplication to volatile terpenoid diversity

Artemisia argyi Lévl. et Vant., a perennial Artemisia herb with an intense fragrance, is widely used in traditional medicine in China and many other Asian countries. Here, we present a chromosome-scale genome assembly of A. argyi comprising 3.89 Gb assembled into 17 pseudochromosomes. Phylogenetic and comparative genomic analyses revealed that A. argyi underwent a recent lineage-specific whole-genome duplication (WGD) event after divergence from Artemisia annua, resulting in two subgenomes. We deciphered the diploid ancestral genome of A. argyi, and unbiased subgenome evolution was observed. The recent WGD led to a large number of duplicated genes in the A. argyi genome. Expansion of the terpene synthase (TPS) gene family through various types of gene duplication may have greatly contributed to the diversity of volatile terpenoids in A. argyi. In particular, we identified a typical germacrene D synthase gene cluster within the expanded TPS gene family. The entire biosynthetic pathways of germacrenes, (+)-borneol, and (+)-camphor were elucidated in A. argyi. In addition, partial deletion of the amorpha-4,11-diene synthase (ADS) gene and loss of function of ADS homologs may have resulted in the lack of artemisinin production in A. argyi. Our study provides new insights into the genome evolution of Artemisia and lays a foundation for further improvement of the quality of this important medicinal plant.

WheatCENet: A Database for Comparative Co-expression Networks Analysis of Allohexaploid Wheat and Its Progenitors

Genetic and epigenetic changes after polyploidization events could result in variable gene expression and modified regulatory networks. Here, using large-scale transcriptome data, we constructed co-expression networks for diploid, tetraploid, and hexaploid wheat species, and built a platform for comparing co-expression networks of allohexaploid wheat and its progenitors, named WheatCENet. WheatCENet is a platform for searching and comparing specific functional co-expression networks, as well as identifying the related functions of the genes clustered therein. Functional annotations like pathways, gene families, protein-protein interactions, microRNAs (miRNAs), and several lines of epigenome data are integrated into this platform, and Gene Ontology (GO) annotation, gene set enrichment analysis (GSEA), motif identification, and other useful tools are also included. Using WheatCENet, we found that the network of WHEAT ABERRANT PANICLE ORGANIZATION 1 (WAPO1) has more co-expressed genes related to spike development in hexaploid wheat than its progenitors. We also found a novel motif of CCWWWWWWGG (CArG) specifically in the promoter region of WAPO-A1, suggesting that neofunctionalization of the WAPO-A1 gene affects spikelet development in hexaploid wheat. WheatCENet is useful for investigating co-expression networks and conducting other analyses, and thus facilitates comparative and functional genomic studies in wheat. WheatCENet is freely available at http://bioinformatics.cpolar.cn/WheatCENet and http://bioinformatics.cau.edu.cn/WheatCENet.

De novo Assembly and Comparative Analyses of Mitochondrial Genomes in Piperales

The mitochondrial genome of Liriodendron tulipifera exhibits many ancestral angiosperm features and a remarkably slow evolutionary rate, while mitochondrial genomes of other magnoliids remain yet to be characterized. We assembled nine new mitochondrial genomes, representing all genera of perianth-bearing Piperales, as well as for a member of the sister clade: three complete or nearly complete mitochondrial genomes from Aristolochiaceae and six additional draft assemblies including Thottea, Asaraceae, Lactoridaceae, and Hydnoraceae. For comparative purpose, a complete mitochondrial genome was assembled for Saururus, a member of the perianth-less Piperales. The average number of short repeats (50-99 bp) was much larger in genus Aristolochia than in other angiosperm mitochondrial genomes, and approximately 30% of repeats (<350 bp) were found to have the capacity to mediate recombination. We found mitochondrial genomes in perianth-bearing Piperales comprising conserved repertories of protein-coding genes and rRNAs but variable copy numbers of tRNA genes. We identified several shifts from cis- to trans-splicing of the Group II introns of nad1i728, cox2i373, and nad7i209. Two short regions of the cox1 and atp8 genes were likely derived from independent horizontal gene transfer events in perianth-bearing Piperales. We found biased enrichment of specific substitution types in different lineages of magnoliids and the Aristolochiaceae family showed the highest ratio of A:T > T:A substitutions of all other investigated angiosperm groups. Our study reports the first mitochondrial genomes for Piperales and uses this new information for a better understanding of the evolutionary patterns of magnoliids and angiosperms in general.

Artificial Intelligence-Assisted Evaluation of the Spatial Relationship between Brain Arteriovenous Malformations and the Corticospinal Tract to Predict Postsurgical Motor Defects

BACKGROUND AND PURPOSE

Preoperative evaluation of brain AVMs is crucial for the selection of surgical candidates. Our goal was to use artificial intelligence to predict postsurgical motor defects in patients with brain AVMs involving motor-related areas.

MATERIALS AND METHODS

Eighty-three patients who underwent microsurgical resection of brain AVMs involving motor-related areas were retrospectively reviewed. Four artificial intelligence-based indicators were calculated with artificial intelligence on TOF-MRA and DTI, including FN5mm/50mm (the proportion of fiber numbers within 5-50mm from the lesion border), FN10mm/50mm (the same but within 10-50mm), FP5mm/50mm (the proportion of fiber voxel points within 5-50mm from the lesion border), and FP10mm/50mm (the same but within 10-50mm). The association between the variables and long-term postsurgical motor defects was analyzed using univariate and multivariate analyses. Least absolute shrinkage and selection operator regression with the Pearson correlation coefficient was used to select the optimal features to develop the machine learning model to predict postsurgical motor defects. The area under the curve was calculated to evaluate the predictive performance.

RESULTS

In patients with and without postsurgical motor defects, the mean FN5mm/50mm, FN10mm/50mm, FP5mm/50mm, and FP10mm/50mm were 0.24 (SD, 0.24) and 0.03 (SD, 0.06), 0.37 (SD, 0.27) and 0.06 (SD, 0.08), 0.06 (SD, 0.10) and 0.01 (SD, 0.02), and 0.10 (SD, 0.12) and 0.02 (SD, 0.05), respectively. Univariate and multivariate logistic analyses identified FN10mm/50mm as an independent risk factor for long-term postsurgical motor defects (P = .002). FN10mm/50mm achieved a mean area under the curve of 0.86 (SD, 0.08). The mean area under the curve of the machine learning model consisting of FN10mm/50mm, diffuseness, and the Spetzler-Martin score was 0.88 (SD, 0.07).

CONCLUSIONS

The artificial intelligence-based indicator, FN10mm/50mm, can reflect the lesion-fiber spatial relationship and act as a dominant predictor for postsurgical motor defects in patients with brain AVMs involving motor-related areas.

TRAF3IP2-IL-17 Axis Strengthens the Gingival Defense against Pathogens

Recent genome-wide association studies have suggested novel risk loci associated with periodontitis, which is initiated by dysbiosis in subgingival plaque and leads to destruction of teeth-supporting structures. One such genetic locus was the tumor necrosis factor receptor-associated factor 3 interacting protein 2 (TRAF3IP2), a gene encoding the gate-keeping interleukin (IL)-17 receptor adaptor. In this study, we first determined that carriers of the lead exonic variant rs13190932 within the TRAF3IP2 locus combined with a high plaque microbial burden was associated with more severe periodontitis than noncarriers. We then demonstrated that TRAF3IP2 is essential in the IL-17-mediated CCL2 and IL-8 chemokine production in primary gingival epithelial cells. Further analysis suggested that rs13190932 may serve a surrogate variant for a genuine loss-of-function variant rs33980500 within the same gene. Traf3ip2 null mice (Traf3ip2^-/-) were more susceptible than wild-type (WT) mice to the Porphyromonas gingivalis-induced periodontal alveolar bone loss. Such bone loss was associated with a delayed P. gingivalis clearance and an attenuated neutrophil recruitment in the gingiva of Traf3ip2^-/- mice. Transcriptomic data showed decreased expression of antimicrobial genes, including Lcn2, S100a8, and Defb1, in the Traf3ip2^-/- mouse gingiva in comparison to WT mice prior to or upon P. gingivalis oral challenge. Further 16S ribosomal RNA sequencing analysis identified a distinct microbial community in the Traf3ip2^-/- mouse oral plaque, which was featured by a reduced microbial diversity and an overabundance of Streptococcus genus bacteria. More P. gingivalis was observed in the Traf3ip2^-/- mouse gingiva than WT control animals in a ligature-promoted P. gingivalis invasion model. In agreement, neutrophil depletion resulted in more local gingival tissue invasion by P. gingivalis. Thus, we identified a homeostatic IL-17-TRAF3IP2-neutrophil axis underpinning host defense against a keystone periodontal pathogen.

Efficient and fabrication error tolerant grating couplers on the InP membrane on silicon platform

In order to couple light between photonic integrated circuits and optical fibers, grating couplers are commonly employed. This paper describes the design and fabrication of deep and shallow-etched grating couplers with a metal back-reflector with record low insertion losses in InP-based platforms. The measured insertion losses for deep and shallow-etched gratings are 2.4 and 2.6 dB, respectively. Additionally, fabrication error tolerances in shallow etched grating couplers have been examined experimentally, which showed high tolerance of this structure toward the grating period and fill factor.

Reducing temperature sensitivity of gas measurement using chirped-modulated photoacoustic spectroscopy

Resonance frequency drift caused by a change in temperature greatly limits the application of high-Q resonators with high temperature sensitivity in photoacoustic (PA) gas detection systems. In this work, a chirp-wavelength combined modulation method was designed by incorporating a real-time frequency scanning in wavelength-modulated PA spectroscopy to reduce the influence of temperature changes on measurement. Theoretical analysis shows that the chirp rate depends on the precision requirements and the cutoff frequency of the cascaded low-pass filter. Trace acetylene measurement experiment at varying temperature verified that the proposed method can significantly reduce the temperature sensitivity within a preset temperature range. Thus, this method can effectively reduce the temperature sensitivity of a high-Q resonator for improving the measurement accuracy and detection limit in trace gas detection.

[Efficacy and safety of modified hemophagocytic lymphohistiocytosis 04 regimen in Beijing Children's Hospital]

Objective: To evaluate the efficacy and safety of Beijing Children's Hospital (BCH) modified hemophagocytic lymphohistiocytosis (HLH) 04 regimen in the treatment of childhood HLH. Methods: A retrospective cohort study was conducted. From January 2016 to December 2017, 110 children with HLH who were treated with the modified HLH-04 regimen (replacing dexamethasone with methylprednisolone during the induction period, reducing the dose and frequency of etoposide, and not using cyclosporine except for autoimmune-related HLH) at the Hematology Oncology Center of Beijing Children's Hospital were selected as the modified group, while 102 children treated with the standard HLH-04 regimen from January 2012 to December 2015 were selected as the control group. The early remission rate, survival rate and adverse reactions of two groups were compared. Rank sum test and chi square test were used for comparison between groups. Results: The age of onset in the modified group was 1.9 (1.1, 3.5) years, with 65 males and 45 females. The age of onset in the control group was 2.0 (1.2, 4.6) years, with 47 males and 55 females. No significant difference was found in age and gender between 2 groups (both P>0.05). Except for fibrinogen (1.3 (1.0, 1.7) vs. 1.1 (0.8, 1.4) g/L, Z=-2.67, P=0.008) and natural killer cell activity (13.9 (13.4, 16.3) % vs.14.9 (12.0, 16.1) %, Z=-2.34, P=0.028), there were no statistically significant differences in etiology, disease duration, first clinical presentation, or laboratory tests between 2 groups (all P>0.05). At 2 months and 3 years, there were no statistically significant differences in overall survival between 2 groups (84.5% (93/110) vs.76.5% (78/102), 78.2% (86/110) vs. 67.6% (69/102), χ²=2.28, 3.07, P=0.131, 0.080). The first 3 weeks were the most common time for bone marrow suppression in the modified group, with a lower incidence than in the control group (47.3% (52/110) vs. 62.7% (64/102), χ²=5.11, P=0.024). The modified group had a lower rate of fungal infections than the control group (3.6% (4/110) vs. 13.7% (14/102), χ²=6.93, P=0.008). Compared with the control group, fewer children in the modified group died as a result of side effects from chemotherapy (8.0% (2/25) vs.30.3% (10/33), χ²=4.31, P=0.038). Conclusion: The BCH modified HLH-04 regimen reduced the intensity of chemotherapy, with overall efficacy no worse than the standard HLH-04 regimen, and significantly reduced the rate of chemotherapy-related myelosuppression, fungal infection and mortality.

Chromosome-level and haplotype-resolved genome provides insight into the tetraploid hybrid origin of patchouli

Patchouli (Pogostemon cablin (Blanco) Benth.), a member of the Lamiaceae family, is an important aromatic plant that has been widely used in medicine and perfumery. Here, we report a 1.94 Gb chromosome-scale assembly of the patchouli genome (contig N50 = 7.97 Mb). The gene annotation reveals that tandem duplication of sesquiterpene biosynthetic genes may be a major contributor to the biosynthesis of patchouli bioactivity components. We further phase the genome into two distinct subgenomes (A and B), and identify a chromosome substitution event that have occurred between them. Further investigations show that a burst of universal LTR-RTs in the A subgenome lead to the divergence between two subgenomes. However, no significant subgenome dominance is detected. Finally, we track the evolutionary scenario of patchouli including whole genome tetraploidization, subgenome divergency, hybridization, and chromosome substitution, which are the key forces to determine the complexity of patchouli genome. Our work sheds light on the evolutionary history of patchouli and offers unprecedented genomic resources for fundamental patchouli research and elite germplasm development.

The ploidy level of patchouli, an aromatic plant in the Lamiaceae family, remain unclear. Here, the authors assemble a chromosome-level and haplotype-resolved genome for patchouli and reveal that it is tetraploid hybrid as well as compensated aneuploidy.

The Gastrodia menghaiensis (Orchidaceae) genome provides new insights of orchid mycorrhizal interactions

BACKGROUND

To illustrate the molecular mechanism of mycoheterotrophic interactions between orchids and fungi, we assembled chromosome-level reference genome of Gastrodia menghaiensis (Orchidaceae) and analyzed the genomes of two species of Gastrodia.

RESULTS

Our analyses indicated that the genomes of Gastrodia are globally diminished in comparison to autotrophic orchids, even compared to Cuscuta (a plant parasite). Genes involved in arbuscular mycorrhizae colonization were found in genomes of Gastrodia, and many of the genes involved biological interaction between Gatrodia and symbiotic microbionts are more numerous than in photosynthetic orchids. The highly expressed genes for fatty acid and ammonium root transporters suggest that fungi receive material from orchids, although most raw materials flow from the fungi. Many nuclear genes (e.g. biosynthesis of aromatic amino acid L-tryptophan) supporting plastid functions are expanded compared to photosynthetic orchids, an indication of the importance of plastids even in totally mycoheterotrophic species.

CONCLUSION

Gastrodia menghaiensis has the smallest proteome thus far among angiosperms. Many of the genes involved biological interaction between Gatrodia and symbiotic microbionts are more numerous than in photosynthetic orchids.

Genomes shed light on the evolution of Begonia, a mega-diverse genus

Clarifying the evolutionary processes underlying species diversification and adaptation is a key focus of evolutionary biology. Begonia (Begoniaceae) is one of the most species-rich angiosperm genera with c. 2000 species, most of which are shade-adapted. Here, we present chromosome-scale genome assemblies for four species of Begonia (B. loranthoides, B. masoniana, B. darthvaderiana and B. peltatifolia), and whole genome shotgun data for an additional 74 Begonia representatives to investigate lineage evolution and shade adaptation of the genus. The four genome assemblies range in size from 331.75 Mb (B. peltatifolia) to 799.83 Mb (B. masoniana), and harbor 22 059-23 444 protein-coding genes. Synteny analysis revealed a lineage-specific whole-genome duplication (WGD) that occurred just before the diversification of Begonia. Functional enrichment of gene families retained after WGD highlights the significance of modified carbohydrate metabolism and photosynthesis possibly linked to shade adaptation in the genus, which is further supported by expansions of gene families involved in light perception and harvesting. Phylogenomic reconstructions and genomics studies indicate that genomic introgression has also played a role in the evolution of Begonia. Overall, this study provides valuable genomic resources for Begonia and suggests potential drivers underlying the diversity and adaptive evolution of this mega-diverse clade.

The Cycas genome and the early evolution of seed plants

Cycads represent one of the most ancient lineages of living seed plants. Identifying genomic features uniquely shared by cycads and other extant seed plants, but not non-seed-producing plants, may shed light on the origin of key innovations, as well as the early diversification of seed plants. Here, we report the 10.5-Gb reference genome of Cycas panzhihuaensis, complemented by the transcriptomes of 339 cycad species. Nuclear and plastid phylogenomic analyses strongly suggest that cycads and Ginkgo form a clade sister to all other living gymnosperms, in contrast to mitochondrial data, which place cycads alone in this position. We found evidence for an ancient whole-genome duplication in the common ancestor of extant gymnosperms. The Cycas genome contains four homologues of the fitD gene family that were likely acquired via horizontal gene transfer from fungi, and these genes confer herbivore resistance in cycads. The male-specific region of the Y chromosome of C. panzhihuaensis contains a MADS-box transcription factor expressed exclusively in male cones that is similar to a system reported in Ginkgo, suggesting that a sex determination mechanism controlled by MADS-box genes may have originated in the common ancestor of cycads and Ginkgo. The C. panzhihuaensis genome provides an important new resource of broad utility for biologists.

A recent burst of gene duplications in Triticeae

Gene duplication provides raw genetic materials for evolution and potentially novel genes for crop improvement. The two seminal genomic studies of Aegilops tauschii both mentioned the large number of genes independently duplicated in recent years, but the duplication mechanism and the evolutionary significance of these gene duplicates have not yet been investigated. Here, we found that a recent burst of gene duplications (hereafter abbreviated as the RBGD) has probably occurred in all sequenced Triticeae species. Further investigations of the characteristics of the gene duplicates and their flanking sequences suggested that transposable element (TE) activity may have been involved in generating the RBGD. We also characterized the duplication timing, retention pattern, diversification, and expression of the duplicates following the evolution of Triticeae. Multiple subgenome-specific comparisons of the duplicated gene pairs clearly supported extensive differential regulation and related functional diversity among such pairs in the three subgenomes of bread wheat. Moreover, several duplicated genes from the RBGD have evolved into key factors that influence important agronomic traits of wheat. Our results provide insights into a unique source of gene duplicates in Triticeae species, which has increased the gene dosage together with the two polyploidization events in the evolutionary history of wheat.

The chrysanthemum lavandulifolium genome and the molecular mechanism underlying diverse capitulum types

Cultivated chrysanthemum (Chrysanthemum × morifolium Ramat.) is a beloved ornamental crop due to the diverse capitula types among varieties, but the molecular mechanism of capitulum development remains unclear. Here, we report a 2.60 Gb chromosome-scale reference genome of C. lavandulifolium, a wild Chrysanthemum species found in China, Korea and Japan. The evolutionary analysis of the genome revealed that only recent tandem duplications occurred in the C. lavandulifolium genome after the shared whole genome triplication (WGT) in Asteraceae. Based on the transcriptomic profiling of six important developmental stages of the radiate capitulum in C. lavandulifolium, we found genes in the MADS-box, TCP, NAC and LOB gene families that were involved in disc and ray floret primordia differentiation. Notably, NAM and LOB30 homologs were specifically expressed in the radiate capitulum, suggesting their pivotal roles in the genetic network of disc and ray floret primordia differentiation in chrysanthemum. The present study not only provides a high-quality reference genome of chrysanthemum but also provides insight into the molecular mechanism underlying the diverse capitulum types in chrysanthemum.

[Study on the genetic characteristics of enteric viral pathogens of sporadic adult diarrhea in Chaoyang district, Beijing in 2019]

Objective: To analyze the distribution and genetic characteristics of sporadic adult diarrhea virus in Chaoyang District, Beijing. Methods: Fecal samples from 177 adult patients with sporadic diarrhea were collected from 4 enteric outpatient clinics in Chaoyang District, Beijing from May to December 2019. Nucleic acid detection of Norovirus, Sappovirus, Rotavirus, Enteric Adenovirus and Astrovirus in the samples was performed by real-time quantitative PCR. The positive samples were amplified by RT-PCR/PCR and sequenced. The phylogenetic analysis was performed by neighbor-Joining (NJ) methods of Mega 6.0 software. Results: There were 60 of 177 (33.90%) adult sporadic diarrhea samples positive for enteric viral pathogens. Among them, 47 cases were infected with single virus, including 29 cases of Norovirus, 9 cases of Sappovirus, 8 cases of Astrovirus and 1 case of Enteric Adenovirus, in addition with 13 cases of multiple infections. None of rotavirus was detected. Partial sequences were successfully obtained for analysis, including 16 cases of GI Norovirus (7 subtypes and GI.3[P13] predominant), 10 cases of GII Norovirus (5 subtypes and GII.6[P7] predominant), 12 cases of Sappovirus (4 subtypes and GI.2 predominant), and 7 cases of Astrovirus (2 subtypes and AST-1 predominant). Conclusion: Norovirus, Astrovirus and Sappovirus are main pathogens among sporadic adult diarrhea in Beijing in 2019, and and different pathogenic gene subtypes show diverse characteristics.

Whole-Genome Sequencing of Acer catalpifolium Reveals Evolutionary History of Endangered Species

Acer catalpifolium is an endangered species restricted to remote localities of West China. Understanding the genomic content and evolution of A. catalpifolium is essential to conservation efforts of this rare and ecologically valuable plant. Here, we report a high-quality genome of A. catalpifolium consisting of ∼654 Mbp and ∼35,132 protein-coding genes. We detected 969 positively selected genes in two Acer genomes compared with four other eudicots, 65 of which were transcription factors. We hypothesize that these positively selected mutations in transcription factors might affect their function and thus contribute to A. catalpifolium’s decline-type population. We also identified 179 significantly expanded gene families compared with 12 other eudicots, some of which are involved in stress responses, such as the FRS–FRF family. We inferred that A. catalpifolium has experienced gene family expansions to cope with environmental stress in its evolutionary history. Finally, 109 candidate genes encoding key enzymes in the lignin biosynthesis pathway were identified in A. catalpifolium; of particular note were the large range and high copy number of cinnamyl alcohol dehydrogenase genes. The chromosome-level genome of A. catalpifolium presented here may serve as a fundamental genomic resource for better understanding endangered Acer species, informing future conservation efforts.

[Research advances on skin wounds suturing techniques and their clinical application]

Stitching skin wounds is one of the essential skills of a surgeon. Whether it is a traumatic wound or a surgical incision, choosing the most appropriate closure technique according to its characteristics is an important factor for good healing. Various skin wounds suturing techniques have been created and improved over the years, which have advantages of simple operation, precise alignment, reducing tension of the wound edges, and reducing scar formation, etc. Although these techniques provide more options for wound suture, they also put forward requirements for the judgment and operation ability of the operators. This article summarizes the advantages and disadvantages of the different skin wounds suturing techniques and their clinical application.

The Physalis floridana genome provides insights into the biochemical and morphological evolution of Physalis fruits

The fruits of Physalis (Solanaceae) have a unique structure, a lantern-like fruiting calyx known as inflated calyx syndrome (ICS) or the Chinese lantern, and are rich in steroid-related compounds. However, the genetic variations underlying the origin of these characteristic traits and diversity in Physalis remain largely unknown. Here, we present a high-quality chromosome-level reference genome assembly of Physalis floridana (~1.40 Gb in size) with a contig N50 of ~4.87 Mb. Through evolutionary genomics and experimental approaches, we found that the loss of the SEP-like MADS-box gene MBP21 subclade is likely a key mutation that, together with the previously revealed mutation affecting floral MPF2 expression, might have contributed to the origination of ICS in Physaleae, suggesting that the origination of a morphological novelty may have resulted from an evolutionary scenario in which one mutation compensated for another deleterious mutation. Moreover, the significant expansion of squalene epoxidase genes is potentially associated with the natural variation of steroid-related compounds in Physalis fruits. The results reveal the importance of gene gains (duplication) and/or subsequent losses as genetic bases of the evolution of distinct fruit traits, and the data serve as a valuable resource for the evolutionary genetics and breeding of solanaceous crops.

Insights into angiosperm evolution, floral development and chemical biosynthesis from the Aristolochia fimbriata genome

Aristolochia, a genus in the magnoliid order Piperales, has been famous for centuries for its highly specialized flowers and wide medicinal applications. Here, we present a new, high-quality genome sequence of Aristolochia fimbriata, a species that, similar to Amborella trichopoda, lacks further whole-genome duplications since the origin of extant angiosperms. As such, the A. fimbriata genome is an excellent reference for inferences of angiosperm genome evolution, enabling detection of two novel whole-genome duplications in Piperales and dating of previously reported whole-genome duplications in other magnoliids. Genomic comparisons between A. fimbriata and other angiosperms facilitated the identification of ancient genomic rearrangements suggesting the placement of magnoliids as sister to monocots, whereas phylogenetic inferences based on sequence data we compiled yielded ambiguous relationships. By identifying associated homologues and investigating their evolutionary histories and expression patterns, we revealed highly conserved floral developmental genes and their distinct downstream regulatory network that may contribute to the complex flower morphology in A. fimbriata. Finally, we elucidated the genetic basis underlying the biosynthesis of terpenoids and aristolochic acids in A. fimbriata.

A Collinearity-Incorporating Homology Inference Strategy for Connecting Emerging Assemblies in the Triticeae Tribe as a Pilot Practice in the Plant Pangenomic Era

Plant genome sequencing has dramatically increased, and some species even have multiple high-quality reference versions. Demands for clade-specific homology inference and analysis have increased in the pangenomic era. Here we present a novel method, GeneTribe (https://chenym1.github.io/genetribe/), for homology inference among genetically similar genomes that incorporates gene collinearity and shows better performance than traditional sequence-similarity-based methods in terms of accuracy and scalability. The Triticeae tribe is a typical allopolyploid-rich clade with complex species relationships that includes many important crops, such as wheat, barley, and rye. We built Triticeae-GeneTribe (http://wheat.cau.edu.cn/TGT/), a homology database, by integrating 12 Triticeae genomes and 3 outgroup model genomes and implemented versatile analysis and visualization functions. With macrocollinearity analysis, we were able to construct a refined model illustrating the structural rearrangements of the 4A-5A-7B chromosomes in wheat as two major translocation events. With collinearity analysis at both the macro- and microscale, we illustrated the complex evolutionary history of homologs of the wheat vernalization gene Vrn2, which evolved as a combined result of genome translocation, duplication, and polyploidization and gene loss events. Our work provides a useful practice for connecting emerging genome assemblies, with awareness of the extensive polyploidy in plants, and will help researchers efficiently exploit genome sequence resources.

The ancient wave of polyploidization events in flowering plants and their facilitated adaptation to environmental stress

Flowering plants, or angiosperms, consist of more than 300,000 species, far more than any other land plant lineages. The accumulated evidence indicates that multiple ancient polyploidy events occurred around 100 to 120 million years ago during the Cretaceous and drove the early diversification of four major clades of angiosperms: gamma whole-genome triplication in the common ancestor of core eudicots, tau whole-genome duplication during the early diversification of monocots, lambda whole-genome duplication during the early diversification of magnoliids, and pi whole-genome duplication in the Nymphaeales lineage. These four polyploidy events have played essential roles in the adaptive evolution and diversification of major clades of flowering plants. Here, we specifically review the current understanding of this wave of ancient whole-genome duplications and their evolutionary significance. Notably, although these ancient whole-genome duplications occurred independently, they have contributed to the expansion of many stress-related genes (e.g., heat shock transcription factors and Arabidopsis response regulators)，and these genes could have been selected for by global environmental changes in the Cretaceous. Therefore, this ancient wave of paleopolyploidy events could have significantly contributed to the adaptation of angiosperms to environmental changes, and potentially promoted the wide diversification of flowering plants.

LncRNA FAL1 promotes the development of oral squamous cell carcinoma through regulating the microRNA-761/CRKL pathway

OBJECTIVE

This study aims to elucidate the regulatory effect of long non-coding RNA (lncRNA) FAL1 on the tumorigenesis of oral squamous cell carcinoma (OSCC), and to explore its underlying mechanism.

MATERIALS AND METHODS

Quantitative Real Time-Polymerase Chain Reaction (qRT-PCR) was performed to detect the expression levels of lncRNA FAL1, microRNA-761 and CRKL in 20 pairs of OSCC tissues and adjacent normal oral tissues. Meanwhile, their expressions in OSCC cell lines were also determined by qRT-PCR. The protein expression of CRKL in OSCC tissues was detected by Western blot. The cell counting kit-8 (CCK-8) assay was performed to access the proliferation of SCC25 and HN4 cells transfected with si-FAL1. The binding conditions between lncRNA FAL1 with microRNA-761, and microRNA-761 with CRKL were tested by the Dual-Luciferase reporter gene assay. Gain-of-function experiments were conducted to determine the proliferation of OSCC cells co-transfected with si-FAL1 and microRNA-761 inhibitor. Furthermore, the proliferative potential of OSCC cells was evaluated after co-transfection of si-FAL1 and CRKL overexpression plasmid.

RESULTS

LncRNA FAL1 was highly expressed in OSCC tissues and cell lines. The proliferative capacity of OSCC cells was significantly inhibited by lncRNA FAL1 knockdown. The mRNA expression of microRNA-761 was lowly expressed in OSCC tissues and cell lines. Dual-Luciferase reporter gene assay showed that lncRNA FAL1 directly bound to microRNA-761. Meanwhile, microRNA-761 expression was negatively regulated by FAL1. CRKL was verified as the target gene of microRNA-761. Both the mRNA and protein levels of CRKL were remarkably upregulated in OSCC tissues and cell lines. CRKL expression was found to be negatively regulated by microRNA-761 in OSCC cells. Lowly expressed microRNA-761 reversed the inhibitory effect of lncRNA FAL1 knockdown on the proliferative potential of OSCC cells. In addition, the overexpression of CRKL reversed the inhibitory effect of lncRNA FAL1 down-regulation on the proliferative potential of OSCC cells as well.

CONCLUSIONS

LncRNA FAL1 is highly expressed in OSCC. Moreover, it promotes the development of OSCC by regulating CRKL expression as a sponge of microRNA-761.

A chromosome-scale reference genome of Aquilegia oxysepala var. kansuensis

The genus Aquilegia (Ranunculaceae) has been cultivated as ornamental and medicinal plants for centuries. With petal spurs of strikingly diverse size and shape, Aquilegia has also been recognized as an excellent system for evolutionary studies. Pollinator-mediated selection for longer spurs is believed to have shaped the evolution of this genus, especially the North American taxa. Recently, however, an opposite evolutionary trend was reported in an Asian lineage, where multiple origins of mini- or even nonspurred morphs have occurred. Interesting as it is, the lack of genomic resources has limited our ability to decipher the molecular and evolutionary mechanisms underlying spur reduction in this special lineage. Using long-read sequencing (PacBio Sequel), in combination with optical maps (BioNano DLS) and Hi-C, we assembled a high-quality reference genome of A. oxysepala var. kansuensis, a sister species to the nonspurred taxon. The final assembly is approximately 293.2 Mb, 94.6% (277.4 Mb) of which has been anchored to 7 pseudochromosomes. A total of 25,571 protein-coding genes were predicted, with 97.2% being functionally annotated. When comparing this genome with that of A. coerulea, we detected a large rearrangement between Chr1 and Chr4, which might have caused the Chr4 of A. oxysepala var. kansuensis to partly deviate from the "decaying" path that was taken before the split of Aquilegia and Semiaquilegia. This high-quality reference genome is fundamental to further investigations on the development and evolution of petal spurs and provides a strong foundation for the breeding of new horticultural Aquilegia cultivars.

Evolutionary strategies drive a balance of the interacting gene products for the CBL and CIPK gene families

Genes encoding interacting proteins tend to be co-retained after whole-genome duplication (WGD). The preferential retention after WGD has been explained by the gene balance hypothesis (GBH). However, small-scale duplications could independently occur in the connected gene families. Certain evolutionary strategies might keep the dosage balanced. Here, we examined the gene duplication, interaction and expression patterns of calcineurin B-like (CBL) and CBL-interacting protein kinase (CIPK) gene families to understand the underlying principles. The ratio of the CBL and CIPK gene numbers evolved from 5 : 7 in Physcomitrella to 10 : 26 in Arabidopsis, and retrotransposition, tandem duplication, and WGDs contributed to the expansion. Two pairs of CBLs and six pairs of CIPKs were retained after the α WGD in Arabidopsis, in which specific interaction patterns were identified. In some cases, two retained CBLs (CIPKs) might compete to interact with a sole CIPK (CBL). Results of gene expression analyses indicated that the relatively over-retained duplicates tend to show asymmetric expression, thus avoiding competition. In conclusion, our results suggested that the highly specific interaction, together with the differential gene expression pattern, jointly maintained the balanced dosage for the interacting CBL and CIPK proteins.

Flossing Is Associated with Improved Oral Health in Older Adults

The effect of preventive oral habits is largely unexplored in older individuals. The purpose of this study was to evaluate the associations between home use of flossing and prevalence of periodontal disease and caries in older adults. Five-year incident tooth loss was also evaluated. Data on 686 individuals ≥65 y-old from the Piedmont 65+ Dental Study were examined including: 1) interproximal clinical attachment level (iCAL), 2) interproximal probing depth (iPD), 3) numbers of caries, and 4) missing teeth. Flossing behavior was evaluated according to the Periodontal Profile Class (PPC) system. Five-year follow-up data (n = 375) was evaluated for incident tooth loss. Dichotomous and categorical variables were analyzed using Pearson chi-square tests as well as covariate-adjusted Cochran-Mantel-Haenszel tests. Multiple linear regression compared clinical parameters based on flossing behavior. Elderly flossers had lower (mean, SE) %iCAL≥3 mm (38.2, 2.38 vs. 48.8, 1.56) and %iPD≥4 mm (8.70, 1.41 vs. 14.4, 0.93) compared to nonflossers (P ≤ 0.005). Flossers showed less coronal caries compared to nonflossers (P = 0.02). Baseline number of missing teeth (mean, SE) was 11.5 (0.35) in nonflossers compared to 8.6 (0.53) in flossers (P < 0.0001). Regular dental visitors had lower oral disease levels compared to episodic dental users. The majority of flossers classified into PPC-Stage I (health) whereas nonflossers classified as PPC-Stages V, VI, and VII (disease). At the 5-y follow-up visit, the average tooth loss for flossers was ~1 tooth compared to ~4 teeth lost for nonflossers (P < 0.0001). Among all teeth, molars showed the highest benefit (>40%) for flossing behavior (P = 0.0005). In conclusion, the extent of oral disease for older individuals was significantly less in flossers than in nonflossers. Flossers showed less periodontal disease, fewer dental caries, and loss of fewer teeth over a 5-y period. These findings further support flossing as an important oral hygiene behavior to prevent oral disease progression in older adults.

[Strategy of nursing care on the face skin injuries caused by wearing medical-grade protective equipment]

For effective resistance to virus attack and infection, reducing virus transmission chance, it is extremely important for the medical staff and related workers to have their own safe protection. This paper summarizes the development causes, common locations, and prevention ways about the device related pressure injuries on the face resulted from wearing medical-grade protective equipment for a long working time. The paper proposes the nursing strategy for device related pressure injuries and other nursing strategy is proposed to take care efficiently the device related pressure injuries. Meantime, a corresponding nursing strategy is also suggested to deal with the correlative skin diseases during the application of medical-grade protective equipment. These paper aims to provide reference for the prevention of device related pressure injuries and the care of skin-related diseases for clinical working staff, especially to the respectable personnel in front line of fighting against Corona virus disease 2019.

A robust model for estimating thermal conductivity of liquid alkyl halides

Thermal conductivity is an essential thermodynamic property in chemical engineering application. As a result, estimating the thermal conductivity of organic compounds is of significance in industry production. Alkyl halides are important organic intermediates and raw materials, but little investigations have been performed to estimate their thermal conductivity. In this study, the structures of compounds were optimized in Gaussian 09W and molecular descriptors were extracted by Dragon software. Finally, we developed a 6-descriptor linear quantitative structure-property relationship (QSPR) model to estimate the thermal conductivity of alkyl halides using the genetic function approximation (GFA) method. Validation proved that the developed model had goodness-of-fit, robustness and predictive ability. The r²_pred and root-mean-square error (RMSE_P) of prediction set for the model were equal to 0.9745 and 0.0035, respectively. Meanwhile, the applicability domain was visualized by means of the Williams plot. This study provides a new model for estimating the thermal conductivity of this important class of chemicals.

Genetic Contribution of Paleopolyploidy to Adaptive Evolution in Angiosperms

Ancient whole-genome duplications (WGDs or polyploidy) are prevalent in plants, and some WGDs occurred during the timing of severe global environmental changes. It has been suggested that WGDs may have contributed to plant adaptation. However, this still lacks empirical evidence at the genetic level to support the hypothesis. Here, we investigated the survivors of gene duplicates from multiple ancient WGD events on the major branches of angiosperm phylogeny, and aimed to explore genetic evidence supporting the significance of polyploidy. Duplicated genes co-retained from three waves of independent WGDs (∼120 million years ago [Ma], ∼66, and <20 Ma) were investigated in 25 selected species. Gene families functioning in low temperature and darkness were commonly retained gene duplicates after the eight independently occurring WGDs in many lineages around the Cretaceous-Paleocene boundary, when the global cooling and darkness were the two main stresses. Moreover, the commonly retained duplicates could be key factors which may have contributed to the robustness of the critical stress-related pathways. In addition, genome-wide transcription factors (TFs) functioning in stresses tend to retain duplicates after waves of WGDs, and the coselected gene duplicates in many lineages may play critical roles during severe environmental stresses. Collectively, these results shed new light on the significant contribution of paleopolyploidy to plant adaptation during global environmental changes in the evolutionary history of angiosperms.

The water lily genome and the early evolution of flowering plants

Water lilies belong to the angiosperm order Nymphaeales. Amborellales, Nymphaeales and Austrobaileyales together form the so-called ANA-grade of angiosperms, which are extant representatives of lineages that diverged the earliest from the lineage leading to the extant mesangiosperms1-3. Here we report the 409-megabase genome sequence of the blue-petal water lily (Nymphaea colorata). Our phylogenomic analyses support Amborellales and Nymphaeales as successive sister lineages to all other extant angiosperms. The N. colorata genome and 19 other water lily transcriptomes reveal a Nymphaealean whole-genome duplication event, which is shared by Nymphaeaceae and possibly Cabombaceae. Among the genes retained from this whole-genome duplication are homologues of genes that regulate flowering transition and flower development. The broad expression of homologues of floral ABCE genes in N. colorata might support a similarly broadly active ancestral ABCE model of floral organ determination in early angiosperms. Water lilies have evolved attractive floral scents and colours, which are features shared with mesangiosperms, and we identified their putative biosynthetic genes in N. colorata. The chemical compounds and biosynthetic genes behind floral scents suggest that they have evolved in parallel to those in mesangiosperms. Because of its unique phylogenetic position, the N. colorata genome sheds light on the early evolution of angiosperms.