Additional file 1. Genomic sequences and their corresponding annotations of 25 flowering plants.

Additional file 6. The collected transcriptome analysis data.

Additional file 4 Significant enrichment functions (n = 39) of conserved lncRNA set (n = 196).

Mosquito-transmitted flaviviruses cause widespread disease across the world. To provide better molecular tools for drug screens and pathogenesis studies, we report a new approach to produce stable NanoLuc-tagged flaviviruses, including dengue virus serotypes 1-4, Japanese encephalitis virus, yellow fever virus, West Nile virus, and Zika virus. Since the reporter gene is often engineered at the capsid gene region, the capsid sequence must be duplicated to flank the reporter gene; such capsid duplication is essential for...

Although members of the Mycobacterium tuberculosis complex (MTBC) exhibit high similarity, they are characterized by differences with respect to virulence, immune response, and transmissibility. To understand the virulence of these bacteria and identify potential novel therapeutic targets, we systemically investigated the total cell protein contents of virulent H37Rv, attenuated H37Ra, and avirulent M. bovis BCG vaccine strains at the log and stationary phases, based on tandem mass tag (TMT) quantitative proteomics. Data analysis revealed that...

The emerging COVID-19 caused by SARS-CoV-2 infection poses severe challenges to global public health. Serum antibody testing is becoming one of the critical methods for the diagnosis of COVID-19 patients. We investigated IgM and IgG responses against SARS-CoV-2 nucleocapsid (N) and spike (S) protein after symptom onset in the intensive care unit (ICU) and non-ICU patients. 130 blood samples from 38 COVID-19 patients were collected. The levels of IgM and IgG specific to N and...

Accurate identification of species from timber is an essential step to help control illegal logging and forest loss. However, current approaches to timber identification based on morphological and anatomical characteristics have limited species resolution. DNA barcoding is a proven tool for plant species identification, but there is a need to build reliable reference data across broad taxonomic and spatial scales. Here, we construct a species barcoding library consisting of 1,550 taxonomically diverse timber species from...

Aberrant DNA methylation is an epigenetic hallmark of malignant tumours. The DNA methylation level is regulated by not only DNA methyltransferases (DNMTs) but also Ten-Eleven Translocation (TET) family proteins. However, the exact role of TET genes in breast cancer remains controversial. Here, we uncover that the ERα-positive breast cancer patients with high TET2 mRNA expression had better overall survival rates. Consistently, knockout of TET2 promotes the tumorigenesis of ERα-positive MCF7 breast cancer cells. Mechanistically, TET2...

Although members of the Mycobacterium tuberculosis complex (MTBC) exhibit high similarity, they are characterized by differences with respect to virulence, immune response, and transmissibility. To understand the virulence of these bacteria and identify potential novel therapeutic targets, we systemically investigated the total cell protein contents of virulent H37Rv, attenuated H37Ra, and avirulent M. bovis BCG vaccine strains at the log and stationary phases, based on tandem mass tag (TMT) quantitative proteomics. Data analysis revealed that...

Heat stress is an environmental challenge that reduces plant productivity and growth. Plants have developed corresponding mechanisms to survive this adverse environmental stress. To demonstrate the mechanisms of how plants adapt to the environmental challenge, the heat response experiments involving Arabidopsis thaliana were retrieved from the GEO database. After quantile normalization of the GEO raw data, the differentially expressed genes (DEGs) in response to heat stress were identified by robust rank aggregation (RRA) algorithm, including...

In the present study, a total of 7793 samples from 5 different types of hosts were collected and tested, with a seroprevalence of 2.4% (184/7793). Although the seroprevalence of human and animal brucellosis is relatively low, numbers of human brucellosis cases reported have increased continuously from 2004 to 2018. A total of 118 Brucella strains containing 4 biotypes were obtained, including Brucella melitensis bv.1 (n = 8) and bv.3 (n = 106), Brucella abortus bv.3...

As the largest family of natural products, terpenoids play valuable roles in medicine, agriculture, cosmetics and food. However, the traditional methods that rely on direct extraction from the original plants not only produce low yields, but also result in waste of resources, and are not applicable at all to endangered species. Modern heterologous biosynthesis is considered a promising, efficient, and sustainable production method, but it relies on the premise of a complete analysis of the...

The high-molecular-weight glutenin subunits (HMW-GS) at Glu-D1 have a larger contribution to the processing property of wheat flours than those at the Glu-A1 and Glu-B1 loci and are always expressed in nature. Wheat lines missing one subunit at Glu-D1, either x or y, attract great interest for their potential quality value. Major quality parameters including SDS-sedimentation value, gluten-related indices, and other dough strength parameters such as development time, stability time, degree of softening, and farinograph...

Phosphorus (P) is a nutrient element triggering eutrophication. Therefore, the removal of excess phosphorus has become an emergent demand. In this study, lanthanum-loaded biochar (La-BC) was prepared via a simple one-step pyrolysis method. Its surface properties and structural characteristics were analyzed by SEM, XRD, FTIR and pHpzc. The phosphate removal by the La-BC was systematically investigated in batch mode. Results showed that the phosphorus adsorption obeyed the pseudo-second-order model and Langmuir isotherm. The calculated maximum...

To assess the feasibility of fetoscopy-guided bipolar umbilical cord coagulation for selective fetal reduction in complicated monochorionic diamniotic (MCDA) twin pregnancies. MCDA twins undergoing fetoscopy-guided bipolar cord coagulation (BCC) were enrolled prospectively between December 2015 to March 2020 in a fetal medicine center. Twenty-three cases undergoing fetoscopy-guided BCC were finally analyzed, including 11 cases for type 2 selective intrauterine growth restriction, 4 cases for twin–twin transfusion syndrome, and 8 cases for a severe discordant anomaly....

To compare cesarean delivery (CD) rates in referral and non-referral hospitals in Maternal Safety Collaboration in Jiangsu province, China. Sixteen participants (4 referral hospitals, 12 non-referral hospitals) from Drum Tower Hospital Collaboration for Maternal Safety reported CD rates in 2019 using ten-group classification system and maternal/neonatal morbidity and mortality. A total of 22,676 CDs were performed among 52,499 deliveries and the average CD rate was 43.2% (range 34.8–69.6%). CD rate in non-referral hospitals (44.7%) was...

The NLRP3 (NLR family pyrin domain containing 3) inflammasome is involved in diverse inflammatory diseases, thus strict control of its activation is necessary to prevent excessive inflammation. Protein ubiquitination has been reported to regulate the assembly, protein expression and activation of the NLRP3 inflammasome. Until now, several deubiquitinases (DUBs) have been reported to affect the degradation of NLRP3 through the proteasome pathway. However, there is no research on DUBs regulating NLRP3 degradation through macroautophagy/autophagy. Here,...

The purpose of this study was to explore the contribution of each factor of the phosphorus metabolism network following phosphorus diet intervention via Granger causality analysis. In this study, a total of six healthy male volunteers were enrolled. All participants sequentially received regular, low-, and high-phosphorus diets. Consumption of each diet lasted for five days, with a 5-day washout period between different diets. Blood and urinary samples were collected on the fifth day of consumption...

To establish the Z-score equation of right pulmonary artery (RPA) segments for some valuable pulse-wave Doppler parameters (PWD) and estimate their reference ranges in normal fetuses. Two hundred and seventy-three normal singleton fetuses at 18–38 weeks were enrolled in this fetal echocardiography of a prospective cross-sectional study. The proximal, middle, and distal segments of RPA of pulsed-wave Doppler parameters, such as peak systolic velocity (PSV) and pulsation index (PI) were obtained by using fetal Doppler...

Leukocyte cell proportion changes affect the detection of cancer-associated aberrant DNA methylation alterations in peripheral blood samples. We aimed to detect cellular DNA methylation changes in ovarian cancer (OVC) blood samples avoiding the above-mentioned cell-composition effects. Based on the within-sample relative methylation orderings (RMOs) of CpG loci in leukocyte subtypes, we developed the Ref-RMO method to detect aberrant methylation alterations from OVC blood samples. Stable CpG pairs with consistent RMOs in different leukocyte subtypes were...

In recent years, genes associated with N6-methyladenosine (m6A) modification were found to participate in modulation of multiple tumor biological processes. Concomitantly, the significantly complicated dual effects of tumor microenvironment have been observed on cancer progression. The present study aims to investigate m6A-related immune genes (m6AIGs) for their signatures and prognostic values in bladder cancer (BC). Out of 2856 differentially expressed genes (DEGs) of BC, a total of 85 genes were obtained following intersection of DEGs,...

Invasion is a critical pathway leading to tumor metastasis. This study constructed an invasion-related polygenic signature to predict osteosarcoma prognosis. We initially determined two molecular subtypes of osteosarcoma, Cluster1 (C1) and Cluster2 (C2).. A 3 invasive-gene signature was established by univariate Cox analysis and least absolute shrinkage and selection operator (LASSO) Cox regression analysis of the differentially expressed genes (DEGs) between the two subtypes, and was validated in internal and two external data sets (GSE21257...

Pediatric sepsis is a great threat to death worldwide. However, the pathogenesis has not been clearly understood until now in sepsis. This study identified differentially expressed mRNAs and lncRNAs based on Gene Expression Omnibus (GEO) database. And the weighted gene co-expression network analysis (WGCNA) was performed to explore co-expression modules associated with pediatric sepsis. Then, Gene Ontology (GO), KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway, mRNA‑lncRNA and mRNA‑lncRNA-pathway co-expression network analysis was conducted in...

Bladder cancer is one of the most severe genitourinary cancers, causing high morbidity worldwide. However, the underlying molecular mechanism is not clear, and it is urgent to find target genes for treatment. G-protein-coupled receptors are currently a target of high interest for drug design. Thus, we aimed to identify a target gene-related to G-protein-coupled receptors for therapy. We used The Cancer Genome Atlas (TCGA) and DepMap databases to obtain the expression and clinical data of...

Long non-coding RNAs (lncRNAs) are related to a variety of human diseases. However, little is known about the role of lncRNA in intervertebral disc degeneration (IDD). LncRNA expression profile of human IDD were downloaded from Gene Expression Omnibus (GEO) database. Potential biomarkers and therapeutic drugs for IDD were analyzed by weighted gene co-expression network analysis (WGCNA), R software package Limma, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). We identified 1455 differentially...