High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar.

Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio high-fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the 2 parents of the well-studied F1 hybrid "84K" (Populus alba × Populus tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from 2 small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the 2 subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive-expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77% accuracy on the training set and 74% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids.

Structural basis for the recognition of methylated histone H3 by the Arabidopsis LHP1 chromodomain.

Arabidopsis LHP1 (LIKE HETEROCHROMATIN PROTEIN 1), a unique homolog of HP1 in Drosophila, plays important roles in plant development, growth, and architecture. In contrast to specific binding of the HP1 chromodomain to methylated H3K9 histone tails, the chromodomain of LHP1 has been shown to bind to both methylated H3K9 and H3K27 histone tails, and LHP1 carries out its function mainly via its interaction with these two epigenetic marks. However, the molecular mechanism for the recognition of methylated histone H3K9/27 by the LHP1 chromodomain is still unknown. In this study, we characterized the binding ability of LHP1 to histone H3K9 and H3K27 peptides and found that the chromodomain of LHP1 binds to histone H3K9me2/3 and H3K27me2/3 peptides with comparable affinities, although it exhibited no binding or weak binding to unmodified or monomethylated H3K9/K27 peptides. Our crystal structures of the LHP1 chromodomain in peptide-free and peptide-bound forms coupled with mutagenesis studies reveal that the chromodomain of LHP1 bears a slightly different chromodomain architecture and recognizes methylated H3K9 and H3K27 peptides via a hydrophobic clasp, similar to the chromodomains of human Polycomb proteins, which could not be explained only based on primary structure analysis. Our binding and structural studies of the LHP1 chromodomain illuminate a conserved ligand interaction mode between chromodomains of both animals and plants, and shed light on further functional study of the LHP1 protein.

Chromosome-scale genome assembly and insights into the metabolome and gene regulation of leaf color transition in an important oak species, Quercus dentata.

Quercus dentata Thunb., a dominant forest tree species in northern China, has significant ecological and ornamental value due to its adaptability and beautiful autumn coloration, with color changes from green to yellow into red resulting from the autumnal shifts in leaf pigmentation. However, the key genes and molecular regulatory mechanisms for leaf color transition remain to be investigated. First, we presented a high-quality chromosome-scale assembly for Q. dentata. This 893.54 Mb sized genome (contig N50 = 4.21 Mb, scaffold N50 = 75.55 Mb; 2n = 24) harbors 31 584 protein-coding genes. Second, our metabolome analyses uncovered pelargonidin-3-O-glucoside, cyanidin-3-O-arabinoside, and cyanidin-3-O-glucoside as the main pigments involved in leaf color transition. Third, gene co-expression further identified the MYB-bHLH-WD40 (MBW) transcription activation complex as central to anthocyanin biosynthesis regulation. Notably, transcription factor (TF) QdNAC (QD08G038820) was highly co-expressed with this MBW complex and may regulate anthocyanin accumulation and chlorophyll degradation during leaf senescence through direct interaction with another TF, QdMYB (QD01G020890), as revealed by our further protein-protein and DNA-protein interaction assays. Our high-quality genome assembly, metabolome, and transcriptome resources further enrich Quercus genomics and will facilitate upcoming exploration of ornamental values and environmental adaptability in this important genus.

The risk of congenital heart defects associated with corticosteroids use during the first trimester of pregnancy: a systematic review and meta-analysis.

BACKGROUND: Prior studies have suggested that maternal corticosteroids exposure during the first trimester may be associated with an increased risk of congenital heart defects (CHDs) in offspring. However, the findings are discrepant. Moreover, a complete overview of the existing data in the literature is lacking. Our objective was to identify whether such an association exists. METHODS AND RESULTS: Relevant studies were identified via searching PubMed, Web of Science, Embase, Chinese databases, and the Cochrane Library databases (search date July 15, 2021) and through checking the reference lists of retrieved articles. The overall pooled risk estimate was calculated using random-effect models. We used the GRADE approach to assess the overall strength of the evidence and the Newcastle-Ottawa Scale to assess study quality. Subgroup analyses were performed to evaluate the association within studies or samples with different characteristics. Sensitivity analyses were performed to assess the robustness of the results. Nine studies involving 1,901,599 participants were included in the final analysis. All studies were evaluated as high quality. In the meta-analysis, no statistically significant association was found between maternal corticosteroids exposure during the first trimester and increased risk of CHDs in offspring (OR = 1.06, 95% CI: 1.00-1.13, P = 0.06, low certainty of evidence). Additionally, we also did not find significant differences in subgroup analyses of corticosteroids exposure patterns, including oral corticosteroids exposure (OR = 1.23, 95% CI: 1.00-1.52), ointment corticosteroids exposure (OR = 1.03, 95% CI: 0.90-1.19), inhalation corticosteroids exposure (OR = 1.06, 95% CI: 0.96-1.17), topical corticosteroids or systemic corticosteroids exposure (OR = 0.95, 95% CI: 0.79-1.15), and nasal corticosteroids exposure (OR = 1.12, 95% CI: 0.80-1.57). CONCLUSIONS: Our study does not find an association between maternal corticosteroids exposure during the first trimester and offspring CHDs. However, the existing evidence is of low quality; thus, long-term prospective cohort studies are warranted to verify the safety of corticosteroids in this population, with adequate adjustments for confounding variables.

Correlation between burst suppression and postoperative delirium in elderly patients: a prospective study.

OBJECTIVE: To explore the correlation between intraoperative burst suppression (BS) and postoperative delirium (POD) in elderly patients, and provide more ideas for reducing POD in clinical. METHODS: Ninety patients, aged over 60 years, who underwent lumbar internal fixation surgery in our hospital were selected. General information of patients was obtained and informed consent was signed during preoperative visits. Patients were divided into burst suppression (BS) group and non-burst suppression (NBS) group by intraoperative electroencephalogram monitoring. Intraoperative systolic blood pressure (SBP), diastolic blood pressure (DBP), mean arterial pressure (MAP), and heart rate (HR) were recorded, and the variation and minimum value were obtained by calculating. Hemoglobin (HGB), C-reactive protein (CRP), system immune inflammatory index (SII) at 24 and 72 h after surgery, the incidence of postoperative adverse reactions, postoperative hospital stay, and total cost were recorded after operation. POD assessment was performed using CAM within 7 days after surgery or until discharge. SPSS25.0 was used for statistical analysis. RESULTS: Compared with the NBS group, the number of elderly patients with high frailty level in BS group was more (P = 0.048). There is correlation between BS and POD (OR: 4.954, 95%CI 1.034-23.736, P = 0.045), and most of the POD patients in BS group behave as hyperactive type. CONCLUSION: The occurrence of intraoperative BS is associated with POD, and elderly patients with frailty are more likely to have intraoperative BS. BS can be used as a predictor of POD.

Global diversity of policy, coverage, and demand of COVID-19 vaccines: a descriptive study.

BACKGROUND: Hundreds of millions of doses of coronavirus disease 2019 (COVID-19) vaccines have been administered globally, but progress on vaccination varies considerably between countries. We aimed to provide an overall picture of COVID-19 vaccination campaigns, including policy, coverage, and demand of COVID-19 vaccines. METHODS: We conducted a descriptive study of vaccination policy and doses administered data obtained from multiple public sources as of 8 February 2022. We used these data to develop coverage indicators and explore associations of vaccine coverage with socioeconomic and healthcare-related factors. We estimated vaccine demand as numbers of doses required to complete vaccination of countries' target populations according to their national immunization program policies. RESULTS: Messenger RNA and adenovirus vectored vaccines were the most commonly used COVID-19 vaccines in high-income countries, while adenovirus vectored vaccines were the most widely used vaccines worldwide (180 countries). One hundred ninety-two countries have authorized vaccines for the general public, with 40.1% (77/192) targeting individuals over 12 years and 32.3% (62/192) targeting those ≥ 5 years. Forty-eight and 151 countries have started additional-dose and booster-dose vaccination programs, respectively. Globally, there have been 162.1 doses administered per 100 individuals in target populations, with marked inter-region and inter-country heterogeneity. Completed vaccination series coverage ranged from 0.1% to more than 95.0% of country target populations, and numbers of doses administered per 100 individuals in target populations ranged from 0.2 to 308.6. Doses administered per 100 individuals in whole populations correlated with healthcare access and quality index (R2 = 0.59), socio-demographic index (R2 = 0.52), and gross domestic product per capita (R2 = 0.61). At least 6.4 billion doses will be required to complete interim vaccination programs-3.3 billion for primary immunization and 3.1 billion for additional/booster programs. Globally, 0.53 and 0.74 doses per individual in target populations are needed for primary immunization and additional/booster dose programs, respectively. CONCLUSIONS: There is wide country-level disparity and inequity in COVID-19 vaccines rollout, suggesting large gaps in immunity, especially in low-income countries.

Drug users' awareness of and willingness to use HIV non-occupational post-exposure prophylaxis (nPEP) services in China: a mixed methods study.

BACKGROUND: Drug users are regarded as a high-risk population for HIV infection. Non-occupational post-exposure prophylaxis (nPEP) is internationally regarded as an effective biomedical prevention against HIV but still a small-scale pilot project in China at present. The aim of this study was to understand drug users' awareness of and willingness to use nPEP service in China. METHODS: This mixed methods study consisting of a qualitative study and a cross-sectional survey was conducted in two cities of China from 2018 to 2019. The in-depth interviews were audio-taped, transcribed verbatim and analyzed using thematic framework analysis. Univariate and multivariate logistic regressions were used to examine factors associated with drug users' awareness of and willingness to use nPEP. RESULTS: There were 401 and 19 participants included in quantitative and qualitative study respectively. Among participants in quantitative study, 30.2% had heard of nPEP and 56.7% reported willingness to use nPEP in future HIV exposure. In multivariate analyses, nPEP awareness was associated with age, sex, education level, AIDS knowledge score and HIV risk perception. nPEP willingness was associated with AIDS knowledge score, HIV risk perception, alcohol use, monthly income and awareness of nPEP. The qualitative results showed the barriers to nPEP willingness included the fatigue after taking drugs, high cost and side effects of nPEP medication, long nPEP course, and fear of privacy disclosure. CONCLUSION: Drug users had low nPEP awareness and only about half participants reported willingness to use nPEP. It is essential to promote nPEP education campaigns among drug users, especially for elders, women and those with lower education level. Simultaneously, price regulation, side effect management, psychological support and privacy protection need to be managed well when nPEP is routinized.

Histone and DNA binding ability studies of the NSD subfamily of PWWP domains.

The NSD proteins, namely NSD1, NSD2 and NSD3, are lysine methyltransferases, which catalyze mono- and di-methylation of histone H3K36. They are multi-domain proteins, including two PWWP domains (PWWP1 and PWWP2) separated by some other domains. These proteins act as potent oncoproteins and are implicated in various cancers. However the biological functions of these PWWP domains are still largely unknown. To better understand the functions of these proteins' PWWP domains, we cloned, expressed and purified all the PWWP domains of these NSD proteins to characterize their interactions with methylated histone peptides and dsDNA by quantitative binding assays and crystallographic analysis. Our studies indicate that all these PWWP domains except NSD1_PWWP1 bind to trimethylated H3K36, H3K79 peptides and dsDNA weakly. Our crystal structures uncover that the NDS3_PWWP2 and NSD2_PWWP1 domains, which hold an extremely long α-helix and α-helix bundle, respectively, need a conformation adjustment to interact with nucleosome.

Who should be prioritized for COVID-19 vaccination in China? A descriptive study.

BACKGROUND: All countries are facing decisions about which population groups to prioritize for access to COVID-19 vaccination after the first vaccine products have been licensed, at which time supply shortages are inevitable. Our objective is to define the key target populations, their size, and priority for a COVID-19 vaccination program in the context of China. METHODS: On the basis of utilitarian and egalitarian principles, we define and estimate the size of tiered target population groups for a phased introduction of COVID-19 vaccination, considering evolving goals as vaccine supplies increase, detailed information on the risk of illness and transmission, and past experience with vaccination during the 2009 influenza pandemic. Using publicly available data, we estimated the size of target population groups, and the number of days needed to vaccinate 70% of the target population. Sensitivity analyses considered higher vaccine coverages and scaled up vaccine delivery relative to the 2009 pandemic. RESULTS: Essential workers, including staff in the healthcare, law enforcement, security, nursing homes, social welfare institutes, community services, energy, food and transportation sectors, and overseas workers/students (49.7 million) could be prioritized for vaccination to maintain essential services in the early phase of a vaccination program. Subsequently, older adults, individuals with underlying health conditions and pregnant women (563.6 million) could be targeted for vaccination to reduce the number of individuals with severe COVID-19 outcomes, including hospitalizations, critical care admissions, and deaths. In later stages, the vaccination program could be further extended to target adults without underlying health conditions and children (784.8 million), in order to reduce symptomatic infections and/or to stop virus transmission. Given 10 million doses administered per day, and a two-dose vaccination schedule, it would take 1 week to vaccinate essential workers but likely up to 7 months to vaccinate 70% of the overall population. CONCLUSIONS: The proposed framework is general but could assist Chinese policy-makers in the design of a vaccination program. Additionally, this exercise could be generalized to inform other national and regional strategies for use of COVID-19 vaccines, especially in low- and middle-income countries.

Study of cervical precancerous lesions detection by spectroscopy and support vector machine.

BACKGROUND AND OBJECTIVE: Diffuse reflectance spectroscopy (DRS) offers a fast, non-invasive, and low-cost alternative for cervical cancer diagnosis. We aim to develop a method for screening precancerous lesions based on DRS. MATERIAL AND METHODS: Characteristic parameters of cervical tissue were extracted from spectra, including optical characteristic parameters such as absorption and scattering coefficients, and some slope and area parameters of the spectrum. Data were randomly divided into training (60%) and test (40%) sets. Of the 210 included patients, 166 were healthy, 22 had erosion of the cervix, and 31 had cervical intraepithelial neoplasia (CIN). The support vector machine (SVM) algorithm was used to classify normal and abnormal cervical tissue based on 11 characteristic parameters. RESULTS: The SVM with linear kernel function, applied on the training data, could distinguish tissue with lesions from healthy tissue with an accuracy of 1.00. When the classifiers were applied to the test set, erosion of cervix and CIN could be discriminated from healthy tissue with an accuracy of 0.95 (±0.03). CONCLUSIONS: This research shows that the diagnostic algorithm can be valuable for non-invasive diagnosis of cervical cancer. This is a significant step toward the development of a tool for tissue assessment of cervical cancer.

Prevalence and the influencing factors for critical situation of 6 579 pregnant women with hypertensive disorders complicating pregnancy. / 6 579ä¾‹å¦Šå¨ æœŸé«˜è¡€åŽ‹ç–¾ç— å­•äº§å¦‡çš„æ‚£ç— æƒ å†µåŠå‘ç”Ÿå±é‡æƒ å†µçš„å½±å“å› ç´ .

OBJECTIVES: Hypertensive disorders complicating pregnancy is a kind of disease that seriously endangers the health of pregnant women and fetuses with high incidence. This study aims to analyze the prevalence of pregnant women with hypertensive disorders complicating pregnancy and the influential factors for critical pregnant women, and to provide basis for intervention measures. METHODS: In an institution-based cross-sectional study, 100 683 pregnant women, who gave birth in all maternal and child health hospitals of Hunan Province from January 1, 2012 to December 31, 2019, were collected, and 6 579 pregnant women with hypertensive disorders complicating pregnancy were monitored. All data were analyzed through SAS9.4 software. The basic situation, clinical data, outcome, and complications of pregnant women were analyzed, and the risk factors for critical pregnant women with hypertensive disorders complicating pregnancy were analyzed. RESULTS: The prevalence rate of hypertensive disorder complicating pregnancy was increased from 4.3% in 2012 to 7.1% in 2019, and the proportion of hypertensive disorder complicating pregnant women with complications in the hypertensive disorder complicating pregnant women was increased from 28.1% in 2012 to 83.7% in 2019. Elderly pregnant women accounted for 22.2%, married women accounted for 99.9%, women with university degree accounted for 49.5%, one pregnancy accounted for 38%, and zero delivery accounted for 63.5%. In the past, 18.4% of pregnant women had more than one cesarean section, accounting for 18.4%. About 99.0% of pregnant women had 5-10 antenatal check-ups, 72.6% had complications, and 93.8% were terminated when they were discharged. The first 3 complications were anemia in 2 355 cases (29.3%), gestational diabetes in 1 886 cases (23.4%), and subclinical hypothyroidism in 947 cases (11.8%). Logistic regression analysis showed that uterine rupture, placental abruption, placenta previa, anemia, and heart disease were independent risk factors for critical pregnant women. CONCLUSIONS: The prevalence of hypertensive disorders complicating pregnancy is on the rise. Pregnancy examination should be enhanced to identify the complications such as hypothyroidism, gestational diabetes, and anemia. Prevention and treatment measures should be actively taken for uterine rupture, placental abruption, placenta previa, anemia, and heart disease.

QTL for spike-layer uniformity and their influence on yield-related traits in wheat.

BACKGROUND: Common wheat (Triticum aestivum L.) is one of the most important food crops worldwide. Wheat spike-layer uniformity related traits (SLURTs) were complex traits that directly affect yield potential and appearance. In this study, quantitative trait locus (QTL) for five SLURTs among inter-tillers were first documented using a recombinant inbred line (RIL) mapping population derived from a cross between Kenong9204 and Jing411 (represented by KJ-RILs). Genetic relationships between SLURTs and yield were characterized in detail. RESULTS: The trait phenotypic performances for the 188 KJ-RILs and their parents were evaluated in eight different environments. The genetic data included in a high-density genetic map derived from the Affymetrix 660 K SNP Array and the corresponding genotypes in each lines. Of 99 putative additive QTL 11 were stable across environments and 57 showed significant additive-by-environment interaction effects. These QTL individually explained 1.05-39.62% of the phenotypic variance, with log of odds (LOD) values ranging from 2.00 to 34.01. Genetic relationships between SLURTs and yield indicated that plants with slight uneven spike spatial distribution should be an ideotype for super high-yield in wheat. CONCLUSIONS: The present study will provide assistance in understanding the genetic relationships between SLURTs and yield potential. The 11 stable QTL for SLURTs identified herein may facilitate breeding new wheat varieties with scientifically reasonable spike-layer distribution by marker assisted selection.

Effect of Epoxy Resin on the Actuating Performance of Piezoelectric Fiber Composites.

Piezoelectric fiber composites (PFC) have shown excellent performance in the areas of vibration control and deformation control. The viscosity and rigidity of the epoxy resin before and after curing, respectively, were very important factors that affected the performance of PFC. In this paper, Aradite 2020, DP 460, and DP 490 epoxy resins, with the viscosities of 0.15, 25.0, and 250.0 Pa·s, respectively, were employed to encapsulate the piezoelectric fiber composite. The PFC that was packaged with Araldite 2020 had the best free strain of 1420 ppm and tip displacement of 17.8 mm. DP 490 caused the lowest performance of PFC, due to the highest viscosity. When the environmental temperature increased from -40 to +80 °C, the free strain of PFC with Aradite 2020 increased at first and then decreased, reaching a maximum value of 1440 ppm at 30 °C, which was mainly related to the mismatch of the resin/ceramic thermal expansion coefficient.

Chemical profiling approach to evaluate the influence of traditional and simplified decoction methods on the holistic quality of Da-Huang-Xiao-Shi decoction using high-performance liquid chromatography coupled with diode-array detection and time-of-flight mass spectrometry.

Da-Huang-Xiao-Shi decoction, consisting of Rheum officinale Baill, Mirabilitum, Phellodendron amurense Rupr. and Gardenia jasminoides Ellis, is a traditional Chinese medicine used for the treatment of jaundice. As described in "Jin Kui Yao Lue", a traditional multistep decoction of Da-Huang-Xiao-Shi decoction was required while simplified one-step decoction was used in recent repsorts. To investigate the chemical difference between the decoctions obtained by the traditional and simplified preparations, a sensitive and reliable approach of high-performance liquid chromatography coupled with diode-array detection and electrospray ionization time-of-flight mass spectrometry was established. As a result, a total of 105 compounds were detected and identified. Analysis of the chromatogram profiles of the two decoctions showed that many compounds in the decoction of simplified preparation had changed obviously compared with those in traditional preparation. The changes of constituents would be bound to cause the differences in the therapeutic effects of the two decoctions. The present study demonstrated that certain preparation methods significantly affect the holistic quality of traditional Chinese medicines and the use of a suitable preparation method is crucial for these medicines to produce special clinical curative effect. This research results elucidated the scientific basis of traditional preparation methods in Chinese medicines.

[Simultaneous determination of four anthraquinones in rat plasma by HPLC-FLD method and its pharmacokinetic study].

This paper aims to develop a method for the determination of aloe-emodin, rhein, chrysophanol and physcion and study the pharmacokinetic properties of four anthraquinones in rat plasma after oral administration of gardenia and rhubarb decoction. The plasma concentrations at different time points of four anthraquinones were determined by HPLC-FLD method. Plasma samples were extracted with liquid-liquid extraction procedure. Plasma samples were separated on a C18 column (4.6 mm x 150 mm, 5 µm), using 0.2% acetic acid and methanol as mobile phase at a flow rate of 1.0 mL min(-1) with gradient elution. The excitation and emission wavelengths were set at 430, 525 nm, respectively. DAS 2.0 software was applied to calculate the pharmacokinetic parameters. The results showed four anthraquinones can be absorbed. The main parameters of aloe-emodin, rhein, chrysophanol and physcion were as follows: C(max) for aloe-emodin was (0.085 ± 0.058), (3.772 ± 1.152), (0.464 ± 0.267), (0.028 ± 0.008) mg x L(-1) respectively; t(max) for rhein was (1.042 ± 0.510), (0.805 ± 0.307), (1.167 ± 0.283), (0.616 ± 0.162) h respectively; t½ for chrysophanol was (3.557 ± 1.250), (6.879 ± 1.126), (5.196 ± 2.032), (4.337 ± 1.816) h; AUC(0-t) for physcion was (0.504 ± 0.130), (9.558 ± 1.106), (2.545 ± 1.554), (0.052 ± 0.018) mg x h x L(-1). This paper developed a selective, accurate and sensitive HPLC-FLD method for the simultaneous determination of four anthraquiones in rat plasma.

A enzyme-free fluorescence quenching sensor for amplified detection of kanamycin in milk based on competitive triggering strategies.

In this work, we constructed a FAM fluorescence quenching biosensor based on an aptamer competition recognition and enzyme-free amplification strategy. We design a competing unit consisting of an aptamer chain and a complementary chain, and a catalytic hairpin self-assembly (CHA) unit consisting of two hairpins in which the complementary chain can trigger the catalytic hairpin self-assembly. In the initial state, the aptamer chain is combined with the complementary chain, the catalytic hairpin self-assembly unit is inhibited, the FAM fluorescence group was far away from the BHQ1 quenching group, and the fluorescence is turn-on. In the presence of kanamycin, the aptamer chain recognizes kanamycin and doesn't form double chains, resulting in the free complementary chain triggering hairpin 1 (H1), and then H1 triggering hairpin 2 (H2), FAM fluorophore is close to the BHQ1 quenching group, and the fluorescence is off-on. When H1 and H2 form a cyclic reaction, enzyme-free amplification is achieved and there is significant output of the fluorescence signal. Therefore, the biosensor has good performance in detecting kanamycin, the detection line is 54 nM, the linear range is 54 nM-0.9 µM, and it can achieve highly selective detection of kanamycin. Kanamycin residue may cause serious harm to human health. The high sensitivity detection of kanamycin is urgent, so this project has a great application potential for food detection.

Plant-LncPipe: a computational pipeline providing significant improvement in plant lncRNA identification.

Long non-coding RNAs (lncRNAs) play essential roles in various biological processes, such as chromatin remodeling, post-transcriptional regulation, and epigenetic modifications. Despite their critical functions in regulating plant growth, root development, and seed dormancy, the identification of plant lncRNAs remains a challenge due to the scarcity of specific and extensively tested identification methods. Most mainstream machine learning-based methods used for plant lncRNA identification were initially developed using human or other animal datasets, and their accuracy and effectiveness in predicting plant lncRNAs have not been fully evaluated or exploited. To overcome this limitation, we retrained several models, including CPAT, PLEK, and LncFinder, using plant datasets and compared their performance with mainstream lncRNA prediction tools such as CPC2, CNCI, RNAplonc, and LncADeep. Retraining these models significantly improved their performance, and two of the retrained models, LncFinder-plant and CPAT-plant, alongside their ensemble, emerged as the most suitable tools for plant lncRNA identification. This underscores the importance of model retraining in tackling the challenges associated with plant lncRNA identification. Finally, we developed a pipeline (Plant-LncPipe) that incorporates an ensemble of the two best-performing models and covers the entire data analysis process, including reads mapping, transcript assembly, lncRNA identification, classification, and origin, for the efficient identification of lncRNAs in plants. The pipeline, Plant-LncPipe, is available at: https://github.com/xuechantian/Plant-LncRNA-pipline.

PNPLA3 148M/M Is More Susceptible to Palmitic Acid-Induced Endoplasmic Reticulum Stress-Associated Apoptosis in HepG2 Cells.

Background: Patatin-like phospholipase domain-containing 3 (PNPLA3) is a major susceptibility gene for nonalcoholic fatty liver disease (NAFLD), and its rs738409 (I148M) polymorphism is associated with the occurrence and progression of NAFLD. Endoplasmic reticulum (ER) stress-related hepatocyte lipoapoptosis contributes to the progress of NAFLD. PNPLA3 is also known as a member of the calcium-independent phospholipase A2ε family, which can hydrolyze fatty acids to generate lysophosphatidylcholine (LPC) that induces ER stress-related hepatocyte lipoapoptosis. Whether the PNPLA3 risk genotype 148M/M is involved in more severe ER stress-associated lipoapoptosis is unclear. Methods: A PNPLA3148I knock-in HepG2 cell model was constructed based on HepG2 expressing PNPLA3 148M/M using the Cas9/sgRNA system. PNPLA3 148M/M, I/M, and I/I cells were treated with 0.3 mM palmitic acid (PA) for 24 h to induce lipid deposition. Cellular lipid deposition was detected by oil red staining. Apoptosis was observed by TUNEL. LPC was determined by ELISA, and the expression of PNPLA3, the ER stress marker Bip, molecules involved in the ER stress PERK/elF-2a pathway, and its downstream C/EBP homologous protein (CHOP)-mediated apoptotic pathway were detected by western blot. Results: The results showed no difference in PNPLA3 basal expression and basal hepatocyte lipid content between the three genotypes of cells. Lipid deposition and apoptosis were more severe in PNPLA3 148M/M and 148I/M cells than in I/I cells after PA treatment. PA-induced upregulation of protein expression of Bip, ER stress-responsive PERK pathway molecules p-PERK, p-eIF2α, CHOP, and CHOP-associated apoptotic molecules PUMA and Bax were more pronounced in PNPLA3 148M/M cells than in PNPLA3 148I/I cells. The basal LPC levels and the PA-treated increase of LPC levels in the cell culture supernatants did not differ between the three genotypic cells. Conclusion: PNPLA3 148M/M cells were more susceptible to PA-induced lipid deposition and ER stress-related apoptosis than 148I/I cells, and the proapoptotic susceptibility of PNPLA3 148M/M is independent of LPC.

Transmission Dynamics and Epidemiological Characteristics of the SARS-CoV-2 Delta Variant - Hunan Province, China, 2021.

What is already known about this topic?: Little is known about the epidemiology, natural history, and transmission patterns of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant. Monitoring the evolution of viral fitness of SARS-CoV-2 in the host population is key for preparedness and response planning. What is added by this report?: We analyzed a successfully contained local outbreak of Delta that took place in Hunan, China, and provided estimates of time-to-key event periods, infectiousness over time, and risk factors for SARS-CoV-2 infection and transmission for a still poorly understood variant. What are the implications for public health practice?: Our findings simultaneously shed light on both the characteristics of the Delta variant, by identifying key age groups, risk factors, and transmission pathways, and planning a future response effort against SARS-CoV-2.