Molecular mechanisms underlying the signal perception and transduction during seed germination.

QuerySeed germination is a vital step in the life cycle of a plant, playing a significant role in seedling establishment and crop yield potential. It is also an important factor in the conservation of plant germplasm resources. This complex process is influenced by a myriad of factors, including environmental conditions, the genetic makeup of the seed, and endogenous hormones. The perception of these environmental signals triggers a cascade of intricate signal transduction events that determine whether a seed germinates or remains dormant. Despite considerable progress in uncovering the molecular mechanisms governing these processes, many questions remain unanswered. In this review, we summarize the current progress in the molecular mechanisms underlying the perception of environmental signals and consequent signal transduction during seed germination, and discuss questions that need to be addressed to better understand the process of seed germination and develop novel strategies for germplasm improvement.

Turning on Singlet Oxygen Generation by Outer-Sphere Microenvironment Modulation in Porphyrinic Covalent Organic Frameworks for Photocatalytic Oxidation.

Singlet oxygen (1 O2 ) is ubiquitously involved in various photocatalytic oxidation reactions; however, efficient and selective production of 1 O2 is still challenging. Herein, we reported the synthesis of nickel porphyrin-based covalent organic frameworks (COFs) incorporating functional groups with different electron-donating/-withdrawing features on their pore walls. These functional groups established a dedicated outer-sphere microenvironment surrounding the Ni catalytic center that tunes the activity of the COFs for 1 O2 -mediated thioether oxidation. With the increase of the electron-donating ability of functional groups, the modulated outer-sphere microenvironment turns on the catalytic activity from a yield of nearly zero by the cyano group functionalized COF to an excellent yield of 98 % by the methoxy group functionalized one. Electronic property investigation and density-functional theory (DFT) calculations suggested that the distinct excitonic behaviors attributed to the diverse band energy levels and orbital compositions are responsible for the different activities. This study represents the first regulation of generating reactive oxygen species (ROS) based on the strategy of outer-sphere microenvironment modulation in COFs.

Clinical experience using peripheral blood parameters to analyse the mutation type of thalassemia carriers in pregnant women.

Thalassaemia is a typically monogenic disease caused by mutations or deletions in the globin gene and has a high prevalence in southern China. Prenatal screening for thalassaemia can be effective in reducing the incidence of thalassaemia. Haematologic parameters of pregnant thalassaemia carriers are diverse and potentially valuable for identifying different types of genotypes. By comparing and evaluating haematological parameters, formulas in the literature, we tried to reveal differences between pregnant women carrying different types of thalassaemia genes. The Mentzer formula (MCV/RBC) showed a strong ability to differentiate thalassaemia genotypes in pregnant women. In addition, combined with haemoglobin electrophoresis HbA2 can further distinguish the -α/αα, αTα/αα, -/αα, ß+/N and ß0/N groups. HbA2 divides them into two groups. Based on the Mentzer formula, we can further decide which type of thalassaemia to screen (α/ß and the subgroups) for genotyping. Therefore, this simpler and more cost-effective workflow has great potential for application in screening pregnant women for thalassaemia carriers.Impact StatementWhat is already known on this subject? Currently, it is known that thalassaemia gene carriers have abnormal blood indicators. Many findings describe their important values in distinguishing thalassaemia and other blood diseases. They combined different metrics as an algorithm to distinguish thalassaemia and iron deficiency anaemia. Prenatal screening is an effective method to reduce the incidence of thalassaemia. The current main method is PCR. Due to technical and financial constraints, many backward places cannot use this technology. The necessity for prenatal screening for thalassaemia has been overlooked.What the results of this study add? Among these algorithms, Mentzer formula revealed differences in haematological parameters during pregnancy between normal individuals and thalassaemia carriers. Combining the HbA2, thalassaemia carriers can be distinguished from normal individuals, including -α/αα, αTα/αα, -/αα, ß0/N and ß+/N.What are the implications of these findings for clinical practice and/or further research? We provide another tool for these hospitals that donot have Hb electrophoresis test and PCR. Then the clinical doctor can get some evidence and suggest women go to another big hospital for essential tests. It is an excellent suggestion. In the future, we will collect more specific gene types and further investigate their potential relationship using these formulas.

Genome-wide analysis of AP2/ERF superfamily in lotus (Nelumbo nucifera) and the association between NnADAP and rhizome morphology.

BACKGROUND: The AP2/ERF family is widely present in plants and plays a crucial regulatory role in plant growth and development. As an essential aquatic horticultural model plant, lotus has an increasingly prominent economic and research value. RESULTS: We have identified and analysed the AP2/ERF gene family in the lotus. Initially, 121 AP2/ERF family genes were identified. By analysing their gene distribution and protein structure, and their expression patterns during the development of lotus rhizome, combined with previous studies, we obtained an SNP (megascaffold_20:3578539) associated with lotus rhizome phenotype. This SNP was in the NnADAP gene of the AP2 subfamily, and the changes in SNP (C/T) caused amino acid conversion (proline/leucine). We constructed a population of 95 lotus varieties for SNP verification. Through population typing experiments, we found that the group with SNP CC had significantly larger lotus rhizome and higher soluble sugar content among the population. CONCLUSIONS: In conclusion, we speculate that the alteration of the SNP in the NnADAP can affect the size and sugar content of the lotus rhizome.

A CONSTANS-LIKE gene of Nelumbo nucifera could promote potato tuberization.

MAIN CONCLUSION: CONSTANS-LIKE 5 of Nelumbo nucifera is capable of promoting potato tuberization through CONSTANS-FLOWERING LOCUS T and gibberellin signaling pathways with a probable association with lotus rhizome enlargement. Lotus (Nelumbo nucifera) is an aquatic plant that is affiliated to the Nelumbonaceace family. It is widely used as an ornamental, vegetable, and medicinal herb with its rhizome being a popular vegetable. To explore the molecular mechanism underlying its rhizome enlargement, we conducted a systematic analysis on the CONSTANS-LIKE (COL) gene family, with the results, indicating that this gene plays a role in regulating potato tuber expansion. These analyses included phylogenetic relationships, gene structure, and expressional patterns of lotus COL family genes. Based on these analyses, NnCOL5 was selected for further study on its potential function in lotus rhizome formation. NnCOL5 was shown to be located in the nucleus, and its expression was positively associated with the enlargement of lotus rhizome. Besides, the overexpression of NnCOL5 in potato led to increased tuber weight and starch content under short-day conditions without changing the number of tubers. Further analysis suggested that the observed tuber changes might be mediated by affecting the expression of genes in CO-FT and GA signaling pathways. These results provide valuable insight in understanding the functions of COL gene as well as the enlargement of lotus rhizome.

Identification of potential biomarkers for abdominal pain in IBS patients by bioinformatics approach.

BACKGROUND: Irritable bowel syndrome (IBS) is the most common functional gastrointestinal disease characterized by chronic abdominal discomfort and pain. The mechanisms of abdominal pain, as a relevant symptom, in IBS are still unclear. We aimed to explore the key genes and neurobiological changes specially involved in abdominal pain in IBS. METHODS: Gene expression data (GSE36701) was downloaded from Gene Expression Omnibus database. Fifty-three rectal mucosa samples from 27 irritable bowel syndrome with diarrhea (IBS-D) patients and 40 samples from 21 healthy volunteers as controls were included. Differentially expressed genes (DEGs) between two groups were identified using the GEO2R online tool. Functional enrichment analysis of DEGs was performed on the DAVID database. Then a protein-protein interaction network was constructed and visualized using STRING database and Cytoscape. RESULTS: The microarray analysis demonstrated a subset of genes (CCKBR, CCL13, ACPP, BDKRB2, GRPR, SLC1A2, NPFF, P2RX4, TRPA1, CCKBR, TLX2, MRGPRX3, PAX2, CXCR1) specially involved in pain transmission. Among these genes, we identified GRPR, NPFF and TRPA1 genes as potential biomarkers for irritating abdominal pain of IBS patients. CONCLUSIONS: Overexpression of certain pain-related genes (GRPR, NPFF and TRPA1) may contribute to chronic visceral hypersensitivity, therefore be partly responsible for recurrent abdominal pain or discomfort in IBS patients. Several synapses modification and biological process of psychological distress may be risk factors of IBS.

Genome-wide identification of MADS-box gene family in sacred lotus (Nelumbo nucifera) identifies a SEPALLATA homolog gene involved in floral development.

BACKGROUND: Sacred lotus (Nelumbo nucifera) is a vital perennial aquatic ornamental plant. Its flower shape determines the horticultural and ornamental values. However, the mechanisms underlying lotus flower development are still elusive. MADS-box transcription factors are crucial in various features of plant development, especially in floral organogenesis and specification. It is still unknown how the MADS-box transcription factors regulate the floral organogenesis in lotus. RESULTS: To obtain a comprehensive insight into the functions of MADS-box genes in sacred lotus flower development, we systematically characterized members of this gene family based on the available genome information. A total of 44 MADS-box genes were identified, of which 16 type I and 28 type II genes were categorized based on the phylogenetic analysis. Furthermore, the structure of MADS-box genes and their expressional patterns were also systematically analyzed. Additionally, subcellular localization analysis showed that they are mainly localized in the nucleus, of which a SEPALLATA3 (SEP3) homolog NnMADS14 was proven to be involved in the floral organogenesis. CONCLUSION: These results provide some fundamental information about the MADS-box gene family and their functions, which might be helpful in not only understanding the mechanisms of floral organogenesis but also breeding of high ornamental value cultivars in lotus.

The Latest Studies on Lotus (Nelumbo nucifera)-an Emerging Horticultural Model Plant.

Lotus (Nelumbo nucifera) is a perennial aquatic basal eudicot belonging to a small family Nelumbonaceace, which contains only one genus with two species. It is an important horticultural plant, with its uses ranging from ornamental, nutritional to medicinal values, and has been widely used, especially in Southeast Asia. Recently, the lotus obtained a lot of attention from the scientific community. An increasing number of research papers focusing on it have been published, which have shed light on the mysteries of this species. Here, we comprehensively reviewed the latest advancement of studies on the lotus, including phylogeny, genomics and the molecular mechanisms underlying its unique properties, its economic important traits, and so on. Meanwhile, current limitations in the research of the lotus were addressed, and the potential prospective were proposed as well. We believe that the lotus will be an important model plant in horticulture with the generation of germplasm suitable for laboratory operation and the establishment of a regeneration and transformation system.

The Rice Alpha-Amylase, Conserved Regulator of Seed Maturation and Germination.

Alpha-amylase, the major form of amylase with secondary carbohydrate binding sites, is a crucial enzyme throughout the growth period and life cycle of angiosperm. In rice, alpha-amylase isozymes are critical for the formation of the storage starch granule during seed maturation and motivate the stored starch to nourish the developing seedling during seed germination which will directly affect the plant growth and field yield. Alpha-amylase has not yet been studied intensely to understand its classification, structure, expression trait, and expression regulation in rice and other crops. Among the 10-rice alpha-amylases, most were exclusively expressed in the developing seed embryo and induced in the seed germination process. During rice seed germination, the expression of alpha-amylase genes is known to be regulated negatively by sugar in embryos, however positively by gibberellin (GA) in endosperm through competitively binding to the specific promoter domain; besides, it is also controlled by a series of other abiotic or biotic factors, such as salinity. In this review, we overviewed the research progress of alpha-amylase with focus on seed germination and reflected on how in-depth work might elucidate its regulation and facilitate crop breeding as an efficient biomarker.

Transcriptomic analysis identifies the key genes involved in stamen petaloid in lotus (Nelumbo nucifera).

BACKGROUND: Flower morphology, a phenomenon regulated by a complex network, is one of the vital ornamental features in Nelumbo nucifera. Stamen petaloid is very prevalent in lotus flowers. However, the mechanism underlying this phenomenon is still obscure. RESULTS: Here, the comparative transcriptomic analysis was performed among petal, stamen petaloid and stamen through RNA-seq. Using pairwise comparison analysis, a large number of genes involved in hormonal signal transduction pathways and transcription factors, especially the MADS-box genes, were identified as candidate genes for stamen petaloid in lotus. CONCLUSIONS: Taken together, these results provide an insight into the molecular networks underlying lotus floral organ development and stamen petaloid.

Retrospective analysis of 15 cases of Penicillium marneffei infection in HIV-positive and HIV-negative patients.

Penicillium marneffei (P. marneffei) causes systemic opportunistic infections in immunocompromised individuals, particularly in those infected with human immunodeficiency virus (HIV), and more rarely in HIV-negative patients. We retrospectively analyzed the cases of 15 patients infected with P. marneffei. The patients were divided into two groups: HIV-negative (n = 4) and HIV-positive (n = 11). Of the cases studied, three (75%) of the HIV-negative and six (55%) of the HIV-positive group had an accompanying lung infection. The ratio of CD4+/CD8+ was 1.2 (SD = 0.99) in the HIV-negative group and 0.10 (SD = 0.095) in the HIV-positive patients. A series of laboratory examinations were performed and bone marrow smears were observed after staining. P. marneffei is a disseminated fungal infection associated with severe disease symptoms and high mortality rates. Our findings indicate that timely diagnosis and treatment by clinicians is crucial for preventing the spread of localized infections into systemic infections, thereby improving the prognosis of patients.

Identification and characterization of NF-Y transcription factor families in Canola (Brassica napus L.).

NF-Y (NUCLEAR FACTOR-Y), a heterotrimeric transcription factor, is composed of NF-YA, NF-YB, and NF-YC proteins in yeast, animal, and plant systems. In plants, each of the NF-YA/B/C subunit forms a multi-member family. NF-Ys are key regulators with important roles in many physiological processes, such as drought tolerance, flowering time, and seed development. In this study, we identified, annotated, and further characterized 14 NF-YA, 14 NF-YB, and 5 NF-YC proteins in Brassica napus (canola). Phylogenetic analysis revealed that the NF-YA/B/C subunits were more closely clustered with the Arabidopsis thaliana (Arabidopsis) homologs than with rice OsHAP2/3/5 subunits. Analyses of the conserved domain indicated that the BnNF-YA/B/C subfamilies, respectively, shared the same conserved domains with those in other organisms, including Homo sapiens, Saccharomyces cerevisiae, Arabidopsis, and Oryza sativa (rice). An examination of exon/intron structures revealed that most gene structures of BnNF-Y were similar to their homologs in Arabidopsis, a model dicot plant, but different from those in the model monocot plant rice, suggesting that plant NF-Ys diverged before monocot and dicot plants differentiated. Spatial-tempo expression patterns, as determined by qRT-PCR, showed that most BnNF-Ys were widely expressed in different tissues throughout the canola life cycle and that several closely related BnNF-Y subunits had similar expression profiles. Based on these findings, we predict that BnNF-Y proteins have functions that are conserved in the homologous proteins in other plants. This study provides the first extensive evaluation of the BnNF-Y family, and provides a useful foundation for dissecting the functions of BnNF-Y.

Promoted hydrogenation of CO2 to methanol over single-atom Cu sites with Na+-decorated microenvironment.

Although single-atom Cu sites exhibit high efficiency in CO2 hydrogenation to methanol, they are prone to forming Cu nanoparticles due to reduction and aggregation under reaction conditions, especially at high temperatures. Herein, single-atom Cu sites stabilized by adjacent Na+ ions have been successfully constructed within a metal-organic framework (MOF)-based catalyst, namely MOF-808-NaCu. It is found that the electrostatic interaction between the Na+ and Hδ- species plays a pivotal role in upholding the atomic dispersion of Cu in MOF-808-NaCu during CO2 hydrogenation, even at temperatures of up to 275°C. This exceptional stabilization effect endows the catalyst with excellent activity (306 g·kgcat-1·h-1), high selectivity to methanol (93%) and long-term stability at elevated reaction temperatures, far surpassing the counterpart in the absence of Na+ (denoted as MOF-808-Cu). This work develops an effective strategy for the fabrication of stable single-atom sites for advanced catalysis by creating an alkali-decorated microenvironment in close proximity.

The Ratio of Monocyte to Apolipoprotein A1 is an Independent Predictor of Breast Cancer: A Retrospective Study.

Objective: To explore the predictive value of the ratio of monocyte to apolipoprotein A1 (MAR) (a new index related to inflammation and lipid in breast cancer (BC)) and its relationship with clinicopathological staging. Methods: The hematological test results of 394 patients with breast diseases, including 276 cases of BC, 118 cases of benign breast disease (BBD), and 219 healthy volunteers (HV), were retrospectively collected. The clinical value of MAR was analyzed with binary logistic regression. Results: Using statistical software analysis, the results showed that MAR level (P<0.001) was the largest in the BC group, followed by BBD, and the lowest in the HV group, and it was found to be an indicator to distinguish BC from BBD, also an independent risk factor for BC. The increase in MAR level showed that the risk of BC was 3.733 times higher than that of HV (P<0.001). In addition, there was a notable difference in MAR between early, middle and late stages of BC patients (P=0.047), with the highest MAR level in late stage (0.510±0.078) and the lowest MAR level in early stage (0.392±0.011); the MAR level of those with tumor invasion depth of Phase 4 was the highest (0.484±0.072), and that of Phase 1/2 was the lowest (0.379±0.010), with a statistically significant difference (P<0.001). MAR was positively correlated with tumor invasion depth (P<0.001, r=0.210), that's, the size of MAR increased when there was more deeper tumor invasion. Conclusion: MAR is a new indicator for the auxiliary differential diagnosis of benign and malignant breast diseases, and is also an independent risk factor for BC. High-level MAR is closely related to late staging and tumor invasion depth of BC. It can be seen that MAR is a potentially valuable predictor of BC, and this is the first study to explore the clinical value of MAR in BC.

Genome-Wide Identification and Characterization of the HAK Gene Family in Quinoa (Chenopodium quinoa Willd.) and Their Expression Profiles under Saline and Alkaline Conditions.

The high-affinity K+ transporter (HAK) family, the most prominent potassium transporter family in plants, which involves K+ transport, plays crucial roles in plant responses to abiotic stresses. However, the HAK gene family remains to be characterized in quinoa (Chenopodium quinoa Willd.). We explored HAKs in quinoa, identifying 30 members (CqHAK1-CqHAK30) in four clusters phylogenetically. Uneven distribution was observed across 18 chromosomes. Furthermore, we investigated the proteins' evolutionary relationships, physicochemical properties, conserved domains and motifs, gene structure, and cis-regulatory elements of the CqHAKs family members. Transcription data analysis showed that CqHAKs have diverse expression patterns among different tissues and in response to abiotic stresses, including drought, heat, low phosphorus, and salt. The expressional changes of CqHAKs in roots were more sensitive in response to abiotic stress than that in shoot apices. Quantitative RT-PCR analysis revealed that under high saline condition, CqHAK1, CqHAK13, CqHAK19, and CqHAK20 were dramatically induced in leaves; under alkaline condition, CqHAK1, CqHAK13, CqHAK19, and CqHAK20 were dramatically induced in leaves, and CqHAK6, CqHAK9, CqHAK13, CqHAK23, and CqHAK29 were significantly induced in roots. Our results establish a foundation for further investigation of the functions of HAKs in quinoa. It is the first study to identify the HAK gene family in quinoa, which provides potential targets for further functional study and contributes to improving the salt and alkali tolerance in quinoa.

Blood biomarkers in the application of diagnosis and prediction of overall survival for 1089 patients with nasopharyngeal carcinoma.

Previous studies have indicated that some blood metrics play a crucial role in the diagnostic and prognostic values of various solid tumours. However, their comprehensive and unbiased comparison for nasopharyngeal carcinoma (NPC) has not been performed. Twenty blood metrics evaluated in tumours or noncancerous diseases were selected. We selected 1089 patients with NPC and analyzed the relationship between these metrics, clinical characteristics, and overall survival (OS). The albumin and prognostic nutritional index (PNI) exhibited a high area under the curve (AUC) value (> 0.7) together with high "sensitivity (Sen) + specificity (Spe) (> 1.5)" or Youden index (> 0.5) when compared to healthy populations. In comparing NPC and nasal polyps, 9 of 20 blood metrics showed a high AUC value (> 0.7). However, only the PNI and international normalised ratio show a sufficiently high Sen + Spe or Youden Index. None of them could distinguish the status of the TNM classification well. Only the lymphocyte-to-monocyte ratio (LMR) could predict the OS of patients with NPC (cut-off, 4.91; p = 0.0069). Blood metrics as non-invasive biomarkers are valuable tools for clinical management. Among these indicators, PNI is the most ideal indicator to distinguish NPC from healthy and nasal polyps. The LMR has good prognostic value.

Linker Engineering of Sandwich-Structured Metal-Organic Framework Composites for Optimized Photocatalytic H2 Production.

While the microenvironment around catalytic sites is recognized to be crucial in thermocatalysis, its roles in photocatalysis remain subtle. In this work, a series of sandwich-structured metal-organic framework (MOF) composites, UiO-66-NH2 @Pt@UiO-66-X (X means functional groups), is rationally constructed for visible-light photocatalytic H2 production. By varying the ─X groups of the UiO-66-X shell, the microenvironment of the Pt sites and photosensitive UiO-66-NH2 core can be simultaneously modulated. Significantly, the MOF composites with identical light absorption and Pt loading present distinctly different photocatalytic H2 production rates, following the ─X group sequence of ─H > â”€Br > â”€NA (naphthalene) > â”€OCH3  > â”€Cl > â”€NO2 . UiO-66-NH2 @Pt@UiO-66-H demonstrates H2 production rate up to 2708.2 µmol g-1  h-1 , ≈222 times that of UiO-66-NH2 @Pt@UiO-66-NO2 . Mechanism investigations suggest that the variation of the ─X group can balance the charge separation of the UiO-66-NH2 core and the proton reduction ability of Pt, leading to an optimal activity of UiO-66-NH2 @Pt@UiO-66-H at the equilibrium point.

De novo transcriptome analysis reveals the molecular regulatory mechanism underlying the response to excess nitrogen in Azolla spp.

Phytoremediation potential of Azolla in removal of nitrogen from wastewater has been promising. However, little is known about the response of Azolla to high concentrations of nitrogen. In this study, the responses of four Azolla species to different concentrations of total nitrogen ranging from 0 to 180 mg L-1 were examined. The responses varied among different species, and the high nitrogen-tolerant species A. caroliniana and A. microphylla could remove nitrogen from aqueous solutions with higher efficiencies. We further performed transcriptome analysis to explore the molecular mechanism underlying the response to high nitrogen stress in Azolla. RNA-seq analysis revealed a synergistic regulatory network of differentially expressed genes (DEGs) involved in nitrogen transport and metabolism in A. microphylla, mainly in the roots. Under high nitrogen treatment, the DEGs encoding nitrate transporters or nitrate transporter 1/peptide transporters (NRTs/NPFs), ammonium transporters (AMTs), nitrate reductase (NIA), nitrite reductase (NIR) and glutamine synthetases/glutamate synthases (GSs/GOGATs) were down-regulated, and the DEGs encoding glutamate dehydrogenases (GDHs) were up-regulated, suggesting that A. microphylla possessed high tolerance against excess nitrogen through down-regulation of nitrate and ammonium uptake and fine regulation of nitrogen assimilation in the roots. Our results provided a theoretical foundation for better utilization of Azolla for wastewater treatment.

Motivating borate doped FeNi layered double hydroxides by molten salt method toward efficient oxygen evolution.

The incorporation of borate is a beneficial strategy to improve the catalytic activity of transition metal-based electrocatalyts for oxygen evolution reaction (OER). However, how to efficiently introduce borate has always been a challenge. Here, a facile and scalable molten salt method is developed to successfully dope borate into FeNi layered double hydroxides (FeBi@FeNi LDH) for efficient OER. The molten salt method can not only promote the formation of evenly dispersed nano-pompous FeBi precursor, thus providing the possibility to realize the direct doping of borate and the increase of mass, charge transfer and oxygen evolution active sites in FeNi LDH, but also promote the in-situ growth of FeBi@FeNi LDH on the conductive iron foam, improvingconductivity and stability of the material. The results indicate that the synthesized FeBi@FeNi LDH shows enhanced OER activity by delivering current densities of 10 and 100 mA cm-2 at low overpotentials of 246 and 295 mV and showing a small Tafel slope of 56.48 mV dec-1, benefiting from the optimization of geometric structure of active sites as well as the adjustment of electron density by borate doping especially in the case of molten salt. In addition, the sample can maintain durability at an industrial current density of 100 mA cm-1 for 90 h. This work provides a new way for the construction of efficient catalysts using boron doping assisted by molten salt.