An optimized protocol for stepwise optimization of real-time RT-PCR analysis

A split ribozyme system for in vivo plant RNA imaging and genetic engineering

RNA plays a central role in plants, governing various cellular and physiological processes. Monitoring its dynamic abundance provides a discerning understanding of molecular mechanisms underlying plant responses to internal (developmental) and external (environmental) stimuli, paving the way for advances in plant biotechnology to engineer crops with improved resilience, quality and productivity. In general, traditional methods for analysis of RNA abundance in plants require destructive, labour-intensive and time-consuming assays. To overcome these limitations, we developed a transformative innovation for in vivo RNA imaging in plants. Specifically, we established a synthetic split ribozyme system that converts various RNA signals to orthogonal protein outputs, enabling in vivo visualisation of various RNA signals in plants. We demonstrated the utility of this system in transient expression experiments (i.e., leaf infiltration in Nicotiana benthamiana) to detect RNAs derived from transgenes and tobacco rattle virus, respectively. Also, we successfully engineered a split ribozyme-based biosensor in Arabidopsis thaliana for in vivo visualisation of endogenous gene expression at the cellular level, demonstrating the feasibility of multi-scale (e.g., cellular and tissue level) RNA imaging in plants. Furthermore, we developed a platform for easy incorporation of different protein outputs, allowing for flexible choice of reporters to optimise the detection of target RNAs.

Analysis of long noncoding gene expression and its interactions with protein-coding genes in vascular endothelial cells in keloids

OBJECTIVES

The purpose of this study was to determine the relationship between protein-coding RNA (messenger RNA, mRNA) and long noncoding RNA (lncRNA) expressed in vascular endothelial cells (VECs) in keloids by reanalyzing Gene Expression Omnibus (GEO) microarray chip data.

MATERIALS AND METHODS

The GSE121618 database and clinical information of these samples were downloaded and reanalyzed by the R language package. Expression differences in mRNA and lncRNA between keloids and normal skin were calculated. GO/KEGG enrichment analysis was conducted to determine the function of these genes, and an interaction network of lncRNAs-mRNAs was constructed. Magnetic Sorting of VECs and qRT-PCR were used to verify these bioinformatic results.

RESULTS

The expression of three hundred and five mRNAs in the keloid group was significantly different from that in the normal group, and 98 lncRNAs were different, 21 of which were upregulated and 118 of which were downregulated. The hub relationship between the upregulated lncRNA‒mRNA interaction was lncRNA LINC01546-RASAL3/COL13A1, while the downregulated hub was lncRNA LOC101929787-PRKAA2/KRT71/SSTR1. qPCR verification result showed no obvious statistical differences.

CONCLUSIONS

Through the in-depth mining of keloid microarray data using bioinformatic methods, we speculated that VECs can affect the development and progression of keloids by epigenomic regulation via lncRNA‒mRNA interactions.

Effect of triple-frequency sono-germination and soaking treatments on techno-functional characteristics of barley

This research aimed to evaluate the effect of triple-frequency ultrasound treatment (TFUT), germination (GE), and traditional soaking (TS) methods on the nutritional and techno-functional properties of two different barley varieties, including ZQ2000 and XMLY22. Both ZQ2000 and XMLY22 varieties exhibited the highest total phenolic content (TPC) with 840.73 ± 23.59 μg of GAE/g DW and 720.33 ± 30.56 μg of GAE/g DW, and total flavonoid content (TFC) with 520.79 ± 23.45 μg of QUE/g DW and 420.84 ± 19.80 μg of QUE/g DW, respectively. Enzyme activities, such as peroxidase (POD) and polyphenol oxidase (PPO), were notably elevated, indicating enhanced defense mechanisms. The study also found increased γ-Aminobutyric Acid (GABA) levels and antidiabetic potential through inhibition of α-amylase and α-glucosidase enzymes. Further, gene expression analysis revealed differential regulation of phenylpropanoid pathway genes, contributing to the bioactive compound enhancement. Strong intermolecular interactions were observed in both ZQ2000 and XMLY22 samples subjected to TFUT, GE, TFUT + GE, and TS, as validated by FTIR and molecular docking analyses. The structural configuration of two barley types, ZQ2000 and XMLY22, was determined using Fourier transform infrared (FTIR) spectroscopy, which indicated an increase in α-helix and β-sheet conformation and a decrease in random coil conformation in samples treated with TFUT + GE. Moreover, SEM observation provides convincing evidence that TFUT + GE improves and speeds up the breakdown of ZQ2000's internal structures. Conclusively, this study suggests that the combination of ultrasound and germination treatments significantly enhances the functional properties of barley, making it a promising method for creating health-enhancing barley-based products offering potential applications in functional food development.

Allelic variation in the promoter of WRKY22 enhances humid adaptation of Arabidopsis thaliana

Submergence stress tolerance is a complex trait governed by multiple loci. Because of its wide distribution across arid and humid regions, Arabidopsis thaliana offers an opportunity to explore the genetic components and their action mechanisms underlying plant adaptation to submergence stress. In this study, using map-based cloning we identified WRKY22 that activates RAP2.12, a locus previously identified to contribute to the submergence stress response, to regulate plant humid adaptation possibly through ethylene signal transduction in Arabidopsis. WRKY22 expression is inhibited by ARABIDOPSIS RESPONSE REGULATORs (ARRs) but activated by the WRKY70 transcription factor. In accessions from humid environments, a two-nucleotide deletion in the WRKY22 promoter region prevents binding of phosphorylated ARRs, thereby maintaining its high expression. Loss of the ARR-binding element in the WRKY22 promoter underwent strong positive selection during colonization of A. thaliana in the humid Yangtze River basin. However, the WRKY70-binding motif in the WRKY22 promoter shows no variation between accessions from humid and arid regions. These findings together establish a novel signaling axis wherein WRKY22 plays a key role in regulating the adaptive response that enables A. thaliana to colonize contrasting habitats. Notably, we further showed functional conservation of this locus in Brassica napus, suggesting that modulating this axis might be useful in the breeding of flood-tolerant crop varieties.

BcWRKY25-BcWRKY33A-BcLRP1/BcCOW1 module promotes root development for improved salt tolerance in Bok choy

Root development is a complex process involving phytohormones and transcription factors. Our previous research has demonstrated that BcWRKY33A is significantly expressed in Bok choy roots under salt stress, and heterologous expression of BcWRKY33A increases salt tolerance and promotes root development in transgenic Arabidopsis. However, the precise molecular mechanisms by which BcWRKY33A governs root development remain elusive. Here, we investigated the role of BcWRKY33A in both root elongation and root hair formation in transgenic Bok choy roots. Our data indicated that overexpression of BcWRKY33A stimulated root growth and stabilized root hair morphology, while silencing BcWRKY33A prevented primary root elongation and resulted in abnormal root hairs morphology. Meanwhile, our research uncovered that BcWRKY33A directly binds to the promoters of BcLRP1 and BcCOW1, leading to an upregulation of their expression. In transgenic Bok choy roots, increased BcLRP1 and BcCOW1 transcript levels improved primary root elongation and root hair formation, respectively. Additionally, we pinpointed BcWRKY25 as a NaCl-responsive gene that directly stimulates the expression of BcWRKY33A in response to salt stress. All results shed light on the regulatory mechanisms governing root development by BcWRKY25-BcWRKY33A-BcLRP1/BcCOW1 module and propose potential strategies for improving salt tolerance in Bok choy.

Therapeutic effects of resveratrol and β-carotene on L-arginine-induced acute pancreatitis through oxidative stress and inflammatory pathways in rats

Acute pancreatitis (AP) is a severe inflammatory condition affecting the pancreas, often leading to systemic inflammation and organ dysfunction. This study evaluated the effects of resveratrol (RES) and β-carotene (βC) on L-arginine-induced AP in rats. Forty-eight male Sprague Dawley rats were divided into six groups: Control (C), RES (20 mg/kg), βC (50 mg/kg), AP, AP + RES, and AP + βC. The AP model was induced with 250 mg/100 g L-arginine intraperitoneally twice daily with a 1-h interval. The AP group showed significantly elevated oxidative stress (MDA) and reduced GSH levels (p < 0.001). Immunohistochemical (IHC) staining with anti-insulin antibody revealed reduced β + langerhans islet size in the AP group. qPCR analysis indicated significant upregulation of inflammatory genes NF-κB, TNF-α, and IL-1β (p < 0.001), and apoptotic genes Bax and Caspase-3, with downregulation of Bcl-2 (p < 0.001). RES and βC treatments significantly reduced MDA levels and increased GSH levels (p < 0.01 for both) compared to the AP group. The AP + RES and AP + βC groups exhibited preserved β + Langerhans islet size (p < 0.01), suppressed NF-κB, TNF-α, and IL-1β expression, reduced Bax and Caspase-3 levels, and increased Bcl-2 levels (p < 0.01). Histopathological findings supported these results. RES and βC confer significant effects against L-arginine-induced acute pancreatitis by reducing oxidative stress, preserving pancreatic islet integrity, suppressing inflammatory responses, and modulating apoptotic pathways. RES demonstrated a slightly superior efficacy in reducing inflammation and oxidative stress markers, suggesting it may be more effective in treating acute pancreatitis.

Gegen Qinlian Decoction Attenuates Colitis-Associated Colorectal Cancer via Suppressing TLR4 Signaling Pathway Based on Network Pharmacology and In Vivo/In Vitro Experimental Validation

Background: Gegen Qinlian Decoction (GQD), is used for intestinal disorders like ulcerative colitis, irritable bowel syndrome, and colorectal cancer. But the precise mechanisms underlying its anti-inflammatory and anti-tumor effects are not fully elucidated. Methods: Use network pharmacology to identify targets and pathways of GQD. In vivo (azoxymethane/dextran sodium sulfate (AOM/DSS)-induced colitis-associated colorectal cancer (CAC) mouse model) and in vitro (lipopolysaccharide (LPS)-stimulated RAW264.7 macrophages) experiments were conducted to explore GQD's anti-inflammatory and anti-tumor effects. We monitored mouse body weight and disease activity index (DAI), and evaluated colon cancer tissues using hematoxylin and eosin staining. Expression of Ki67 and F4/80 was determined by immunohistochemistry analysis. The protein levels of TLR4 signaling pathway were assessed by western blotting analysis. Enzyme-linked immunosorbent assay measured IL-1β, IL-6, and TNF-α levels. Immunofluorescence (IF) staining visualized NF-κB and IRF3 translocation. Results: There were 18, 9, 24 and 77 active ingredients in the four herbs of GQD, respectively, targeting 435, 156, 485 and 691 genes. Through data platform analysis, it was concluded that there were 1104 target genes of GQD and 2022 target genes of CAC. Moreover, there were 99 intersecting genes between GQD and CAC. The core targets of GQD contained NFKB1, IL1B, IL6, TLR4, and TNF, and GQD reduced inflammation by inhibiting the TLR4 signaling pathway. In vivo experiment, GQD increased mouse body weight, lowered DAI scores, while also alleviating histopathological changes in the colon and decreasing the expressions of Ki67 and F4/80 in the AOM/DSS-induced mice. GQD reduced IL-1β, IL-6, and TNF-α levels in the serum and downregulated TLR4, MyD88, and phosphorylation of IκBα, P65, and IRF3 in the colon tissue from AOM/DSS-induced mice. In vitro, GQD suppressed pro-inflammatory cytokines and TLR4 signaling pathway in the LPS-induced RAW264.7 cells, and combined with TAK242, it further reduced the phosphorylation of IκBα, P65. Conclusions: GQD mitigated CAC by inhibiting the TLR4 signaling pathway, offering a potential therapeutic approach for CAC management.

Development of a TaqMan qPCR for the Simultaneous Detection of the TuMV and BBWV2 Viruses Responsible for the Viral Disease in Pseudostellaria heterophylla

Pseudostellaria heterophylla (Miq.) Pax, a highly valued Chinese medicinal plant, is experiencing a notable decline in yield and quality due to viral diseases, particularly caused those by TuMV and BBWV2. Currently, the absence of a quantitative detection method for these viruses in P. heterophylla impedes the accurate diagnosis. The development of an accurate quantitative detection method is thus essential for effectively managing viral diseases in this plant. In this study, singleplex and duplex TaqMan qPCR were developed for the detection of the two viruses, based on two viral cloning vectors. Concurrently, the levels of both viruses were examined in the main produced regions of P. heterophylla. Furthermore, the levels of BBWV2 were examined during its infection of P. heterophylla. The optimal singleplex qPCR employed 0.1 μM of hydrolysis probe and 0.1 μM of primer for TuMV, while 0.2 μM of hydrolysis probe and 0.1 μM of primer were utilised for BBWV2. In contrast, the duplex qPCR employed the use of 0.1 μM of the upstream/downstream primer from each primer pair, with 0.2 μM of the respective hydrolysis probes. The 95% limit of detection (LOD) for singleplex qPCR was 734 copies for TuMV and 20 copies for BBWV2, while the 95% LOD for duplex qPCR was 945 copies for TuMV and 47 copies for BBWV2. Furthermore, the intra- and inter-assay coefficients of variation were found to be less than 1.2% for both singleplex and duplex qPCR. Of the P. heterophylla sampled 60 sites, 96% were found to be infected by one of two viruses. The levels of BBWV2 in N. benthamiana and P. heterophylla demonstrated an initial increase, followed by a subsequent decrease. The TaqMan qPCR methods provide a technical foundation for the monitoring of virus infections in P. heterophylla.

The Effect of Dietary Zinc Oxide Nanoparticles on Growth Performance, Zinc in Tissues, and Immune Response in the Rare Minnow (Gobiocypris rarus)

In recent years, zinc oxide nanoparticles (ZnO NPs) have gained attention as feed additives due to their high bioavailability. However, research on their impact on fish growth and health is limited. To investigate the influences of dietary addition of ZnO NPs on growth performance and immune function of rare minnow, rare minnows were fed diets with different ZnO NPs content. Growth analysis showed that ZnO NPs had a negative effect on the weight of rare minnow, decreasing and then increasing condition factors (CFs) and specific growth rate. Additionally, the accumulated zinc (Zn) level was significantly higher (p  < 0.05), and the liver injury index was significantly higher (p  < 0.05) in the dietary ZnO NPs group compared to the control group. The number of erythrocytes and leukocytes in blood samples increased and then decreased after treatment with ZnO NPs. It was further found that ZnO NPs as a dietary supplement significantly increased the Zn content and markedly repressed the expression of growth-related genes after 60 days of accumulation in muscle tissues, and accumulation in liver tissues for 60 days significantly enhanced the expression of immune modulation-related genes expression (p < 0.05). The findings suggested that short-term supplementation of ZnO NPs could positively affect fish growth and immune function. However, prolonged supplementation of dietary ZnO NPs resulted in reduced body weight and compromised immune function owing to the buildup of Zn in different tissues.

Integrated Metabolomics and Transcriptomics Analyses Reveal the Regulatory Mechanisms of Anthocyanin and Carotenoid Accumulation in the Peel of Coffea arabica

The color of coffee fruits is influenced by several factors, including cultivar, ripening stage, and metabolite composition. However, the metabolic accumulation of pigments and the molecular mechanisms underlying peel coloration during the ripening process of Coffea arabica L. remain relatively understudied. In this study, UPLC-MS/MS-based metabolomics and RNA sequencing (RNA-seq)-based transcriptomics were integrated to investigate the accumulation of anthocyanins and carotenoids in the peel of Coffea arabica at different ripening stages: green peel (GP), green-yellow peel (GYRP), red peel (RP), and red-purple peel (RPP). This integration aimed at elucidating the molecular mechanisms associated with these changes. A total of ten anthocyanins, six carotenoids, and thirty-five xanthophylls were identified throughout the ripening process. The results demonstrated a gradual decrease in the total carotenoid content in the peel with fruit maturation, while anthocyanin content increased significantly. Notably, the accumulation of specific anthocyanins was closely associated with the transition of peel colors from green to red. Integrated metabolomics and transcriptomics analyses identified the GYRP stage as critical for this color transition. A weighted gene co-expression network analysis (WGCNA) revealed that enzyme-coding genes such as 3AT, BZ1, and lcyE, along with transcription factors including MYB, NAC, and bHLH, which interact with PHD and SET TR, may regulate the biosynthesis of anthocyanins and carotenoids, thereby influencing peel pigmentation. These findings provide valuable insights into the molecular mechanisms underlying the accumulation of anthocyanins and carotenoids in Coffea arabica peel during fruit maturation.

Methionine deficiency inhibited pyroptosis in primary hepatocytes of grass carp (Ctenopharyngodon idella): possibly via activating the ROS-AMPK-autophagy axis

BACKGROUND

Methionine (Met) is the only sulfur-containing amino acid among animal essential amino acids, and methionine deficiency (MD) causes tissue damage and cell death in animals. The common modes of cell death include apoptosis, autophagy, pyroptosis, necroptosis. However, the studies about the major modes of cell death caused by MD have not been reported, which worth further study.

METHODS

Primary hepatocytes from grass carp were isolated and treated with different doses of Met (0, 0.5, 1, 1.5, 2, 2.5 mmol/L) to examine the expression of apoptosis, pyroptosis, autophagy and necroptosis-related proteins. Based on this, we subsequently modeled pyroptosis using lipopolysaccharides and nigericin sodium salt, then autophagy inhibitors chloroquine (CQ), AMP-activated protein kinase (AMPK) inhibitors compound C (CC) and reactive oxygen species (ROS) scavengers N-acetyl-L-cysteine (NAC) were further used to examine the expression of proteins related to pyroptosis, autophagy and AMPK pathway in MD-treated cells respectively.

RESULTS

MD up-regulated B-cell lymphoma protein 2 (Bax), microtubule-associated protein 1 light chain 3 II (LC3 II), and down-regulated the protein expression levels of B-cell lymphoma-2 (Bcl-2), sequestosome 1 (p62), cleaved-caspase-1, cleaved-interleukin (IL)-1β, and receptor-interacting protein kinase (RIP) 1 in hepatocytes, while it did not significantly affect RIP3. In addition, MD significantly increased the protein expression of liver kinase B1 (LKB1), p-AMPK, and Unc-51-like kinase 1 (ULK1) without significant effect on p-target of rapamycin. Subsequently, the use of CQ increased the protein expression of NOD-like receptor thermal protein domain associated protein 3 (NLRP3), cleaved-caspase-1, and cleaved-IL-1β inhibited by MD; the use of CC significantly decreased the protein expression of MD-induced LC3 II and increased the protein expression of MD-suppressed p62; then the use of NAC decreased the MD-induced p-AMPK protein expression.

CONCLUSION

MD promoted autophagy and apoptosis, but inhibited pyroptosis and necroptosis. MD inhibited pyroptosis may be related regarding the promotion of autophagy. MD activated AMPK by inducing ROS production which in turn promoted autophagy. These results could provide partial theoretical basis for the possible mechanisms of Met in ensuring the normal structure and function of animal organs. Furthermore, ferroptosis is closely related to redox states, it is worth investigating whether MD affects ferroptosis in hepatocytes.

PLGA-Loaded Nedaplatin (PLGA-NDP) Inhibits 7,12-Dimethylbenz[a]anthracene (DMBA) Induced Oral Carcinogenesis via Modulating Notch Signaling Pathway and Induces Apoptosis in Experimental Hamster Model

The present study is designed to evaluate the nanotherapeutic efficacy of prepared PLGA-loaded Nedaplatin (PLGA-NDP) against 7,12-dimethyl benz(a)anthracene (DMBA)-induced experimental oral carcinogenesis in hamster buccal pouch (HBP) model. The buccal pouch of golden Syrian hamsters was painted with 0.5% DMBA in liquid paraffin three times a week for 14 weeks, ultimately leading to the development of oral squamous cell carcinoma (OSCC). Oral administration of PLGA-NDP (preinitiation) and Cisplatin delivery (5 mg/kg b.wt) started 1 week before the carcinogen exposure and continued on alternative days. Post-administration of PLGA-NDP (5 mg/kg b.wt) started 2 days after carcinogen (DMBA) induction until the end of the experiment. After the 14th week, we observed that DMBA-painted hamsters exhibited tumor formation, morphological alterations, and well-differentiated OSSC in addition to the responsive molecular proteins during oral carcinogenesis. Furthermore, immunoblotting analysis demonstrated that PLGA-NDP inhibits Notch signaling, as evidenced by downregulation of Bcl-Xl, Bcl-2, p21, PGE2, HGF, and CXCL12 proteins, and upregulation of p53 and Bax. This apoptotic response is crucial for PLGA-NDP to induce apoptosis. In addition, RT-PCR results showed that PLGA-NDP nanoparticles play a downregulatory role in the therapeutic action of the notch signaling gene (Notch1, Notch 2, Hes1, Hey1, and Jagged1) at the mRNA transcription level in HBP carcinoma. Taken together, these data indicate that PLGA-NDP is a potent inhibitor of oral carcinogenesis and the expansion of cells that specifically target the Notch signaling pathway indicates that obstructing Notch signaling could potentially serve as a new and innovative therapeutic approach for oral squamous cell carcinoma (OSCC).

Genome-wide identification and expression analysis of histone deacetylase and histone acetyltransferase genes in response to drought in poplars

BACKGROUND

Histone deacetylases (HDACs) and histone acetyltransferases (HATs) are involved in plant growth and development as well as in response to environmental changes, by dynamically regulating gene acetylation levels. Although there have been numerous reports on the identification and function of HDAC and HAT in herbaceous plants, there are fewer report related genes in woody plants under drought stress.

RESULTS

In this study, we performed a genome-wide analysis of the HDAC and HAT families in Populus trichocarpa, including phylogenetic analysis, gene structure, conserved domains, and expression analysis. A total of 16 PtrHDACs and 12 PtrHATs were identified in P. trichocarpa genome. Analysis of cis-elements in the promoters of PtrHDACs and PtrHATs revealed that both gene families could respond to a variety of environmental signals, including hormones and drought. Furthermore, real time quantitative PCR indicated that PtrHDA906 and PtrHAG3 were significantly responsive to drought. PtrHDA906, PtrHAC1, PtrHAC3, PtrHAG2, PtrHAG6 and PtrHAF1 consistently responded to abscisic acid, methyl jasmonate and salicylic acid under drought conditions.

CONCLUSIONS

Our study demonstrates that PtrHDACs and PtrHATs may respond to drought through hormone signaling pathways, which helps to reveal the hub of acetylation modification in hormone regulation of abiotic stress.

Integrated ribosome and proteome analyses reveal insights into sevoflurane-induced long-term social behavior and cognitive dysfunctions through ADNP inhibition in neonatal mice

A growing number of studies have demonstrated that repeated exposure to sevoflurane during development results in persistent social abnormalities and cognitive impairment. Davunetide, an active fragment of the activity-dependent neuroprotective protein (ADNP), has been implicated in social and cognitive protection. However, the potential of davunetide to attenuate social deficits following sevoflurane exposure and the underlying developmental mechanisms remain poorly understood. In this study, ribosome and proteome profiles were analyzed to investigate the molecular basis of sevoflurane-induced social deficits in neonatal mice. The neuropathological basis was also explored using Golgi staining, morphological analysis, western blotting, electrophysiological analysis, and behavioral analysis. Results indicated that ADNP was significantly down-regulated following developmental exposure to sevoflurane. In adulthood, anterior cingulate cortex (ACC) neurons exposed to sevoflurane exhibited a decrease in dendrite number, total dendrite length, and spine density. Furthermore, the expression levels of Homer, PSD95, synaptophysin, and vglut2 were significantly reduced in the sevoflurane group. Patch-clamp recordings indicated reductions in both the frequency and amplitude of miniature excitatory postsynaptic currents (mEPSCs). Notably, davunetide significantly ameliorated the synaptic defects, social behavior deficits, and cognitive impairments induced by sevoflurane. Mechanistic analysis revealed that loss of ADNP led to dysregulation of Ca 2+ activity via the Wnt/β-catenin signaling, resulting in decreased expression of synaptic proteins. Suppression of Wnt signaling was restored in the davunetide-treated group. Thus, ADNP was identified as a promising therapeutic target for the prevention and treatment of neurodevelopmental toxicity caused by general anesthetics. This study provides important insights into the mechanisms underlying social and cognitive disturbances caused by sevoflurane exposure in neonatal mice and elucidates the regulatory pathways involved.

Patterns of alteration in boar semen quality from 9 to 37 months old and improvement by protocatechuic acid

BACKGROUND

Comprehending the patterns of alteration in boar semen quality and identifying effective nutritional interventions are crucial for enhancing the productivity of commercial pig systems. This study aimed to examine the alteration in semen quality in boars, and assess the impact of protocatechuic acid (PCA) on semen quality during the phase of declining semen quality.

METHODS

In Exp. 1, a total of 38 Pig Improvement Company (PIC) boars were selected and their semen quality data were recorded from the age of 9 to 37 months. In Exp. 2, 18 PIC boars (28 months old) were randomly assigned into three groups (n = 6) and fed a basal diet, a basal diet containing 500 or 1,000 mg/kg PCA, respectively. The experiment lasted for 12 weeks.

RESULTS

The semen volume, concentration, and total number of spermatozoa in boars exhibited an increase from 9 to 19 months old and showed a significant linear decreased trend in 28, 24, and 22 months old. Sperm motility displayed an upward trajectory, reaching its peak at 20 months of age, and showed a significant linear decreased trend at 20 months old. Dietary supplementation of PCA demonstrated an effect to mitigate the decrease in semen volume, concentration of spermatozoa, total number of spermatozoa (P > 0.05), and significantly increased the sperm motility (P < 0.05). Moreover, supplementation of 1,000 mg/kg PCA significantly increased the sperm viability (P < 0.05). Analysis on cellular signaling pathways revealed that PCA restored serum testosterone levels and alleviated oxidative damage by upregulating the expression of HO-1, SOD2, and NQO1 in testicular stromal cells. Notably, PCA can enhance phosphorylation by selectively binding to AMP-activated protein kinase (AMPK) protein, thereby improving sperm mitochondrial function and augmenting sperm motility via PGC-1/Nrf1.

CONCLUSIONS

These data elucidated the pattern of semen quality variation in boars within the age range of 9 to 37 months old, and PCA has the potential to be a natural antioxidant to enhance sperm quality through modulation of the AMPK/PGC-1/Nrf1 signaling pathway.

Dehydration-responsive cytoskeleton proteome of rice reveals reprograming of key molecular pathways to mediate metabolic adaptation and cell survival

The plant cytoskeletal proteins play a key role that control cytoskeleton dynamics, contributing to crucial biological processes such as cell wall morphogenesis, stomatal conductance and abscisic acid accumulation in repercussion to water-deficit stress or dehydration. Yet, it is still completely unknown which specific biochemical processes and regulatory mechanisms the cytoskeleton uses to drive dehydration tolerance. To better understand the role of cytoskeleton, we developed the dehydration-responsive cytoskeletal proteome map of a resilient rice cultivar. Initially, four-week-old rice plants were exposed to progressive dehydration, and the magnitude of dehydration-induced compensatory physiological responses was monitored in terms of physicochemical indices. The organelle fractionation in conjunction with label-free quantitative proteome analysis led to the identification of 955 dehydration-responsive cytoskeletal proteins (DRCPs). To our knowledge, this is the first report of a stress-responsive plant cytoskeletal proteome, representing the largest inventory of cytoskeleton and cytoskeleton-associated proteins. The DRCPs were apparently involved in a wide array of intra-cellular molecules transportation, organelles positioning, cytoskeleton organization followed by different metabolic processes including amino acid metabolism. These findings presented open a unique view on global regulation of plant cytoskeletal proteome is intimately linked to cellular metabolic rewiring of adaptive responses, and potentially confer dehydration tolerance, especially in rice, and other crop species, in general.

ZrgA contributes to zinc acquisition in Vibrio parahaemolyticus

Metals are nutrients essential for almost all lifeforms. Bacteria have evolved several mechanisms to overcome the metal restrictions imposed by the host. Vibrio parahaemolyticus causes severe threats to public health and significant economic losses in shrimp aquaculture. Herein, we report that ZrgA contributes to zinc acquisition in this pathogen. The operon VP_RS01455 to VP_RS01475 of V. parahaemolyticus encodes the putative Zn transporter ZrgABCDE, whose homologs are widely distributed in Vibrionaceae. RNA sequencing analysis revealed that V. parahaemolyticus modulates the transcriptome in response to Zn limitation. Genes in the Zinc uptake regulator (Zur) regulon are upregulated during Zn limitation, including three genes annotated to encode Zn-binding proteins. Significant upregulation of these three genes during Zn limitation was also confirmed by quantitative real-time PCR (qRT-PCR) analysis. However, only the mutants containing a VP_RS01470 (zrgA) deletion exhibited impaired growth under Zn-deficient conditions, indicating that VP_RS01470 plays the predominant role in V. parahaemolyticus Zn acquisition. The VP_RS01470 deletion mutant displayed a false appearance of decreased swimming motility under Zn-deficient conditions, as revealed by the fact that the polar flagellar-related genes were not downregulated in the mutant. Moreover, VP_RS01470 deletion produced no noticeable impact on the swarming motility and virulence in mice. qRT-PCR analysis and β-galactosidase activity assays indicated that Zur negatively regulates VP_RS01470 expression in V. parahaemolyticus. Collectively, our findings suggest that ZrgA is required for Zn acquisition in V. parahaemolyticus and highlight the importance of detecting the expression of flagellar genes during analysis of motility of a mutant deficient in growth.

Emergence of colistin-heteroresistant and carbapenem-resistant hypervirulent Klebsiella pneumoniae

OBJECTIVES

To investigate the clinical emergence of colistin-heteroresistant, hypervirulent, and multidrug-resistant Klebsiella pneumoniae, and characterize the underlying molecular mechanisms.

METHODS

The population analysis profiles (PAPs) method was used to detect colistin heteroresistance. The time-killing assay was used to examine the effect of colistin on carbapenem-resistant Klebsiella pneumoniae (CRKP) in vitro. Galleria mellonella larvae infection model was used to test the potential virulence. qRT-PCR assay was conducted to compare the expression levels of efflux pump genes. Next and third-generation sequencing were conducted to analyse the genomic features.

RESULTS

Two colistin-heteroresistant isolates were detected from a multi-center carbapenem-resistant Enterobacterales (CRE) surveillance study in China, which exhibited similar survival rates as the K2 hypervirulent reference strain ATCC 43816 in a G. mellonella larvae model. The two isolates belonged to ST11, harbouring the iucABCD, iutA, iroBCD, and rpmA2 hypervirulent genes and pLVPK-like virulence plasmids. Colistin showed a weak effect on the heteroresistant strains in vitro. The efflux pump genes acrA, acrB, tolC, oqxA, and oqxB were upregulated in this subpopulation compared to the parental strains.

CONCLUSIONS

This study showed the clinical emergence of colistin-heteroresistant, hypervirulent, and multidrug-resistant Klebsiella pneumoniae. AcrAB-TolC and OqxAB efflux overexpression were involved in mediating colistin heteroresistance.

A complex locus regulates highly lobed-leaf formation in Brassica juncea

KEY MESSAGE

Lineage-specific evolution of RCO was described in Brassicaceae. BjRCO.1 and BjRCO.2 within the complex locus regulated highly lobed-leaf formation in Brassica juncea. RCO regulates the formation of lobed leaves in Brassicaceae species. RCO originated from the duplication of LMI1-type sequences and evolved through gene duplication and loss within the Brassicaceae. However, the evolutionary process and diversification of RCO in different lineages of Brassicaceae remain unclear. Although the RCO locus in B. juncea has been associated with lobed-leaf formation, its complexity has remained largely unknown. This study involved the identification of 55 LMI1-like genes in 16 species of Brassicaceae through syntenic analysis. We classified these LMI1-like genes into two types, namely LMI1-type and RCO-type, based on their phylogenetic relationship. Additionally, we proposed two independent lineage-specific evolution routes for RCO following the divergence of Aethionema. Our findings revealed that the LMI1-like loci responsible for lobed-leaf formation in Brassica species are located on the LF subgenomes. For B. juncea (T84-66V2), we discovered that the complex locus underwent duplication through segments of nucleic acid sequence containing Exostosin-LMI1-RCO (E-R-L), resulting in the tandem presence of two RCO-type and two LMI1-type genes on chromosome A10. As additional evidence, we successfully mapped the complex locus responsible for highly lobed-leaf formation to chromosome A10 using a B. juncea F2 population, which corroborated the results of our evolutionary analysis. Furthermore, through transcriptome analysis, we clarified that BjRCO.1 and BjRCO.2 within the complex locus are functional genes involved in the regulation of highly lobed-leaf formation. The findings of this study offer valuable insights into the regulation of leaf morphology for the breeding of Brassica crops.

Combined analysis of microRNA and mRNA profiles provides insights into the pathogenic resistant mechanisms of the lotus rhizome rot

Lotus rhizome rot caused by Fusarium oxysporum is a common vascular fungal disease in plants that significantly impacts the yield. However, only a few studies have studied the mechanism of Nelumbo nucifera responding to lotus rhizome rot. Here, we investigated the pathogenic genes and miRNAs in lotus rhizome rot to uncover the pathogenic resistant mechanisms by transcriptome and small RNA sequencing of lotus roots after inoculation with Fusarium oxysporum. GO and KEGG functional enrichment analysis showed that differential miRNAs were mostly enriched in starch and sucrose metabolism, biosynthesis of secondary metabolites, glutathione metabolism, brassinosteroid biosynthesis and flavonoid biosynthesis pathways. Twenty-seven upregulated miRNAs, 19 downregulated miRNAs and their target genes were identified. Correlation analysis found that miRNAs negatively regulate target genes, which were also enriched in starch and sucrose metabolism and glutathione metabolism pathways. Their expression was measured by reverse transcription quantitative PCR (qRT-PCR), and the results were consistent with the transcriptome analysis, thus verifying the reliability of transcriptome data. We selected three miRNAs (miRNA858-y, miRNA171-z and a novel miRNA novel-m0005-5p) to test the relationship between miRNAs and their target genes. The activity of the GUS testing assay indicated that miRNA could decrease the GUS activity by inhibiting the expression of their target genes. Collectively, this study provides a comprehensive analysis of transcriptome and small RNA sequencing of lotus root after inoculation with Fusarium oxysporum, and we identified candidate miRNAs and their target genes for breeding strategies of Nelumbo nucifera.

Integration of transcriptomic and metabolomic analysis unveils the response mechanism of sugar metabolism in Cyclocarya paliurus seedlings subjected to PEG-induced drought stress

Cyclocarya paliurus (Batal.) Iljinskaja is a multiple function tree species used for functional food and valued timber production. Carbohydrates, especially water-soluble carbohydrates, play an important role in osmotic protection, signal transduction and carbon storage. Under the circumstance of global climate change the abiotic stress would restrict the development of C. paliurus plantation, whereas there is few knowledge on the regulatory mechanisms of sugar metabolism under drought stress in C. paliurus. To investigate the drought response of C. paliurus at molecular level, we conducted an integrated analysis of transcriptomic and metabolomic of C. paliurus at three PEG-induced drought stress levels (0%: control; 15%: moderate drought; 25%: severe drought) in short term. Both moderate and severe drought treatments activated the chemical defense with lowering relative water content, and enhancing the contents of soluble protein, proline and malondialdehyde in the leaves. Meanwhile, alterations in the expression of differentially expressed genes and carbohydrate metabolism profiles were observed among the treatments. Weighted gene co-expression network analysis (WGCNA) showed 3 key modules, 8 structural genes (such as genes encoding beta-fructofuranosidase (INV), sucrose synthase (SUS), raffinose synthase (RS)) and 14 regulatory transcription factors were closely linked to sugar metabolism. Our results provided the foundation to understand the response mechanism of sugar metabolism in C. paliurus under drought stress, and would drive progress in breeding of drought-tolerant varieties and plantation development of the species.

WISP2 downregulation inhibits the osteogenic differentiation of BMSCs in congenital scoliosis by regulating Wnt/β-catenin pathway

OBJECTIVES

Bone marrow mesenchymal stem cells (BMSCs) are instrumental in bone development, metabolism, and marrow microenvironment homeostasis. Despite this, the relevant effects and mechanisms of BMSCs on congenital scoliosis (CS) remain undefined. Herein, it becomes our focus to reveal the corresponding effects and mechanisms implicated.

METHODS

BMSCs from CS patients (hereafter referred as CS-BMSCs) and healthy donors (NC-BMSCs) were observed and identified. Differentially expressed genes in BMSCs were analyzed utilizing scRNA-seq and RNA-seq profiles. The multi-differentiation potential of BMSCs following the transfection or infection was evaluated. The expression levels of factors related to osteogenic differentiation and Wnt/β-catenin pathway were further determined as appropriate.

RESULTS

A decreased osteogenic differentiation ability was shown in CS-BMSCs. Both the proportion of LEPR⁺ BMSCs and the expression level of WNT1-inducible-signaling pathway protein 2 (WISP2) were decreased in CS-BMSCs. WISP2 knockdown suppressed the osteogenic differentiation of NC-BMSCs, while WISP2 overexpression facilitated the osteogenesis of CS-BMSCs via acting on the Wnt/β-catenin pathway.

CONCLUSIONS

Our study collectively indicates WISP2 knockdown blocks the osteogenic differentiation of BMSCs in CS by regulating Wnt/β-catenin signaling, thus providing new insights into the aetiology of CS.

LkARF7 and LkARF19 overexpression promote adventitious root formation in a heterologous poplar model by positively regulating LkBBM1

Cuttage propagation involves adventitious root formation induced by auxin. In our previous study, Larix kaempferi BABY BOOM 1 (LkBBM1), which is known to regulate adventitious root formation, was affected by auxin. However, the relationship between LkBBM1 and auxin remains unclear. Auxin response factors (ARFs) are a class of important transcription factors in the auxin signaling pathway and modulate the expression of early auxin-responsive genes by binding to auxin response elements. In the present study, we identified 14 L. kaempferi ARFs (LkARFs), and found LkARF7 and LkARF19 bound to LkBBM1 promoter and enhanced its transcription using yeast one-hybrid, ChIP-qPCR, and dual-luciferase assays. In addition, the treatment with naphthalene acetic acid promoted the expression of LkARF7 and LkARF19. We also found that overexpression of these two genes in poplar promoted adventitious root formation. Furthermore, LkARF19 interacted with the DEAD-box ATP-dependent RNA helicase 53-like protein to form a heterodimer to regulate adventitious root formation. Altogether, our results reveal an additional regulatory mechanism underlying the control of adventitious root formation by auxin.

Dexmedetomidine attenuates hepatic ischemia-reperfusion injury-induced apoptosis via reducing oxidative stress and endoplasmic reticulum stress

Dexmedetomidine (DEX) affords a hepatoprotective effect during ischemia-reperfusion (IR) injury (IRI); however, the underlying mechanism remains elusive. In this work, using a rat liver IR model and a BRL-3A cell hypoxia-reoxygenation (HR) model, we explored whether DEX protects the liver against IRI by decreasing oxidative stress (OS), endoplasmic reticulum stress (ERS), and apoptotic pathways. We found that DEX significantly increased SOD and GSH activity while decreasing ROS and MDA levels in BRL-3A cells, successfully preventing HR-induced OS damage. DEX administration reduced JNK, ERK, and P38 phosphorylation and blocked HR-induced MAPK signaling pathway activation. Additionally, DEX administration reduced the expression of GRP78, IRE1α, XBP1, TRAF2, and CHOP, which reduced HR-induced ERS. NAC prevented the MAPK pathway from being activated and inhibited the ERS pathway. Further research showed that DEX significantly reduced HR-induced apoptosis by suppressing the expression of Bax/Bcl-2 and cleaved caspase-3. Similarly, animal studies demonstrated DEX exerted a protective effect of the liver by alleviating histopathological injury and enhancing liver function, mechanically DEX reduced cell apoptosis in liver tissue by reducing oxidative stress and ERS. In conclusion, DEX mitigates OS and ERS during IR, thereby suppressing cell apoptosis, thus providing protection to the liver.

Transcriptome analysis reveals new insights in the starch biosynthesis of non-waxy and waxy broomcorn millet (Panicum miliaceum L.)

Broomcorn millet is a popular cereal with health benefits, and its grains are rich in starch. However, the differences in the pathway and key genes involved in starch biosynthesis of waxy and non-waxy broomcorn millet grain remain unclear. Therefore, the grain and starch physicochemical index and transcriptomic analyses of two genotypes of broomcorn millet were conducted at 3, 6, 9, 12, 15, 18, and 21 days after pollination. The phenotypic and physiological results indicated that the starch synthetic process of non-waxy and waxy broomcorn millet was significantly different. The amylose, amylopectin, and total starch contents of non-waxy broomcorn millet were 1.99, 4.74, and 6.73 mg/grain, while those of waxy broomcorn millet were 0.34, 5.94, and 6.28 mg/grain, respectively. The transcriptomic analysis revealed that 106 differentially expressed genes were identified, which were mainly enriched in the "amino sugar and nucleotide sugar metabolism", "pyruvate metabolism", "galactose metabolism", and "starch and sucrose metabolism" pathways. The WGCNA suggested that a total of 31 hub genes were correlated with starch biosynthesis. These findings provide a new approach to studying the starch synthesis in broomcorn millet.

Engineered Cleistogamy in Camelina sativa for bioconfinement

Camelina sativa is a self-pollinating and facultative outcrossing oilseed crop. Genetic engineering has been used to improve camelina yield potential for altered fatty acid composition, modified protein profiles, improved seed and oil yield, and enhanced drought resistance. The deployment of transgenic camelina in the field posits high risks related to the introgression of transgenes into non-transgenic camelina and wild relatives. Thus, effective bioconfinement strategies need to be developed to prevent pollen-mediated gene flow (PMGF) from transgenic camelina. In the present study, we overexpressed the cleistogamy (i.e. floral petal non-openness)-inducing PpJAZ1 gene from peach in transgenic camelina. Transgenic camelina overexpressing PpJAZ1 showed three levels of cleistogamy, affected pollen germination rates after anthesis but not during anthesis, and caused a minor silicle abortion only on the main branches. We also conducted field trials to examine the effects of the overexpressed PpJAZ1 on PMGF in the field, and found that the overexpressed PpJAZ1 dramatically inhibited PMGF from transgenic camelina to non-transgenic camelina under the field conditions. Thus, the engineered cleistogamy using the overexpressed PpJAZ1 is a highly effective bioconfinement strategy to limit PMGF from transgenic camelina, and could be used for bioconfinement in other dicot species.

Long-term cadmium exposure impairs cognitive function by activating lnc-Gm10532/m6A/FIS1 axis-mediated mitochondrial fission and dysfunction

Cadmium (Cd), a ubiquitous environmental contaminant, is deemed a possible aetiological cause of cognitive disorders in humans. Nevertheless, the exact mechanism by which chronic exposure to Cd causes neurotoxicity is not fully understood. In this study, mouse neuroblastoma cells (Neuro-2a cells) and primary hippocampal neurons were exposed to low-dose (1, 2, and 4 μM for Neuro-2a cells or 0.5, 1, and 1.5 μM for hippocampal neurons) cadmium chloride (CdCl₂) for 72 h (h), and male mice (C57BL/6J, 8 weeks) were orally administered CdCl₂ (0.6 mg/L, approximately equal to 2.58 μg/kg·bw/d) for 6 months to investigate the effects and mechanism of chronic Cd-induced neurotoxicity. Here, chronic exposure to Cd impaired mitochondrial function by promoting excess reactive oxygen species (ROS) production, altering mitochondrial membrane potential (Δψm) and reducing adenosine triphosphate (ATP) content, contributing to neuronal cell death. Specifically, microarray analysis revealed that the long noncoding RNA Gm10532 (lnc-Gm10532) was most highly expressed in Neuro-2a cells exposed to 4 μM CdCl₂ for 72 h compared with controls, and inhibition of lnc-Gm10532 significantly antagonized CdCl₂-induced mitochondrial dysfunction and neurotoxicity. Mechanistically, lnc-Gm10532 increased Fission 1 (FIS1) expression and mitochondrial fission by recruiting the m6A writer methyltransferase-like 14 (METTL14) and enhancing m6A modification of Fis1 mRNA. Moreover, lnc-Gm10532 was also required for chronic Cd-induced mitochondrial dysfunction and memory deficits in a rodent model. Therefore, data of this study reveal a new epigenetic mechanism of chronic Cd neurotoxicity.

Stepwise Optimization of Real-Time RT-PCR Analysis

Quantitative real-time reverse transcription PCR (qRT-PCR) analysis has been used routinely to quantify gene expression levels. Primer design and the optimization of qRT-PCR parameters are critical for the accuracy and reproducibility of qRT-PCR analysis. Computational tool-assisted primer design often overlooks the presence of homologous sequences of the gene of interest and the sequence similarities between homologous genes in a plant genome. This sometimes results in skipping the optimization of qRT-PCR parameters due to the false confidence in the quality of the designed primers. Here we present a stepwise optimization protocol for single nucleotide polymorphisms (SNPs)-based sequence-specific primer design and sequential optimization of primer sequences, annealing temperatures, primer concentrations, and cDNA concentration range for each reference and target gene. The goal of this optimization protocol is to achieve a standard cDNA concentration curve with an R² ≥ 0.9999 and efficiency (E) = 100 ± 5% for the best primer pair of each gene, which serves as the prerequisite for using the 2^-ΔΔCT method for data analysis.

Genome-Wide Identification of WRKY Family Genes and the Expression Profiles in Response to Nitrogen Deficiency in Poplar

The fast-growing arbor poplar is widely distributed across the world and is susceptible to nitrogen availability. The WRKY transcription factor is an important regulatory node of stress tolerance as well as nutrient utilization. However, the potential response mechanism of WRKY genes toward nitrogen is poorly understood. Therefore, the identification of WRKY genes on the Populus trichocarpa genome was performed, and 98 PtWRKYs (i.e., PtWRKY1 to PtWRKY98) were identified. Phylogenetic analysis and the promoter cis-acting element detection revealed that PtWRKYs have multiple functions, including phosphorus and nitrogen homeostasis. By constructing multilayer-hierarchical gene regulatory networks (ML-hGRNs), it was predicted that many WRKY transcription factors were involved in the nitrogen response, such as PtWRKY33 and PtWRKY95. They mainly regulated the expression of primary nitrogen-responsive genes (NRGs), such as PtNRT2.5A, PtNR2 and PtGLT2. The integrative analysis of transcriptome and RT-qPCR results show that the expression levels of 6 and 15 PtWRKYs were regulated by nitrogen availability in roots and leaves, respectively, and those were also found in ML-hGRN. Our study demonstrates that PtWRKYs respond to nitrogen by regulating NRGs, which enriches the nitrate-responsive transcription factor network and helps to uncover the hub of nitrate and its related signaling regulation.

Global transcriptome and coexpression network analyses reveal cultivar-specific molecular signatures associated with different rooting depth responses to drought stress in potato

Potato is one of the most important vegetable crops worldwide. Its growth, development and ultimately yield is hindered by drought stress condition. Breeding and selection of deep-rooted and drought-tolerant potato varieties has become a prime approach for improving the yield and quality of potato (Solanum tuberosum L.) in arid and semiarid areas. A comprehensive understanding of root development-related genes has enabled scientists to formulate strategies to incorporate them into breeding to improve complex agronomic traits and provide opportunities for the development of stress tolerant germplasm. Root response to drought stress is an intricate process regulated through complex transcriptional regulatory network. To understand the rooting depth and molecular mechanism, regulating root response to drought stress in potato, transcriptome dynamics of roots at different stages of drought stress were analyzed in deep (C119) and shallow-rooted (C16) cultivars. Stage-specific expression was observed for a significant proportion of genes in each cultivar and it was inferred that as compared to C16 (shallow-rooted), approximately half of the genes were differentially expressed in deep-rooted cultivar (C119). In C16 and C119, 11 and 14 coexpressed gene modules, respectively, were significantly associated with physiological traits under drought stress. In a comparative analysis, some modules were different between the two cultivars and were associated with differential response to specific drought stress stage. Transcriptional regulatory networks were constructed, and key components determining rooting depth were identified. Through the results, we found that rooting depth (shallow vs deep) was largely determined by plant-type, cell wall organization or biogenesis, hemicellulose metabolic process, and polysaccharide metabolic process. In addition, candidate genes responding to drought stress were identified in deep (C119) and shallow (C16) rooted potato varieties. The results of this study will be a valuable source for further investigations on the role of candidate gene(s) that affect rooting depth and drought tolerance mechanisms in potato.

Overexpression of fibroblast growth factor 13 ameliorates amyloid-β-induced neuronal damage

Previous studies have shown that fibroblast growth factor 13 is downregulated in the brain of both Alzheimer's disease mouse models and patients, and that it plays a vital role in the learning and memory. However, the underlying mechanisms of fibroblast growth factor 13 in Alzheimer's disease remain unclear. In this study, we established rat models of Alzheimer's disease by stereotaxic injection of amyloid-β (Aβ_1-42)-induced into bilateral hippocampus. We also injected lentivirus containing fibroblast growth factor 13 into bilateral hippocampus to overexpress fibroblast growth factor 13. The expression of fibroblast growth factor 13 was downregulated in the brain of the Alzheimer's disease model rats. After overexpression of fibroblast growth factor 13, learning and memory abilities of the Alzheimer's disease model rats were remarkably improved. Fibroblast growth factor 13 overexpression increased brain expression levels of oxidative stress-related markers glutathione, superoxide dismutase, phosphatidylinositol-3-kinase, AKT and glycogen synthase kinase 3β, and anti-apoptotic factor BCL. Furthermore, fibroblast growth factor 13 overexpression decreased the number of apoptotic cells, expression of pro-apoptotic factor BAX, cleaved-caspase 3 and amyloid-β expression, and levels of tau phosphorylation, malondialdehyde, reactive oxygen species and acetylcholinesterase in the brain of Alzheimer's disease model rats. The changes were reversed by the phosphatidylinositol-3-kinase inhibitor LY294002. These findings suggest that overexpression of fibroblast growth factor 13 improved neuronal damage in a rat model of Alzheimer's disease through activation of the phosphatidylinositol-3-kinase/AKT/glycogen synthase kinase 3β signaling pathway.

Sulfation and Its Effect on the Bioactivity of Magnolol, the Main Active Ingredient of Magnolia Officinalis

Magnolol, the main active ingredient of Magnolia officinalis, has been reported to display anti-inflammatory activity. Sulfation plays an important role in the metabolism of magnolol. The magnolol sulfated metabolite was identified by the ultra-performance liquid chromatography to quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) and a proton nuclear magnetic resonance (1H-NMR). The magnolol sulfation activity of seven major recombinant sulfotransferases (SULTs) isoforms (SULT1A1*1, SULT1A1*2, SULT1A2, SULT1A3, SULT1B1, SULT1E1, and SULT2A1) was analyzed. The metabolic profile of magnolol was investigated in liver S9 fractions from human (HLS9), rat (RLS9), and mouse (MLS9). The anti-inflammatory effects of magnolol and its sulfated metabolite were evaluated in RAW264.7 cells stimulated by lipopolysaccharide (LPS). Magnolol was metabolized into a mono-sulfated metabolite by SULTs. Of the seven recombinant SULT isoforms examined, SULT1B1 exhibited the highest magnolol sulfation activity. In liver S9 fractions from different species, the CLint value of magnolol sulfation in HLS9 (0.96 µL/min/mg) was similar to that in RLS9 (0.99 µL/min/mg) but significantly higher than that in MLS9 (0.30 µL/min/mg). Magnolol and its sulfated metabolite both significantly downregulated the production of inflammatory mediators (IL-1β, IL-6 and TNF-α) stimulated by LPS (p < 0.001). These results indicated that SULT1B1 was the major enzyme responsible for the sulfation of magnolol and that the magnolol sulfated metabolite exhibited potential anti-inflammatory effects.

Lilium pumilum stress-responsive NAC transcription factor LpNAC17 enhances salt stress tolerance in tobacco

Lilium pumilum is a perennial herb with ornamental edible and medicinal value. It is an excellent wild germplasm resource with wide distribution and strong resistance. The NAC family of transcription factors is unique to higher plants. The NAC family plays a regulatory role in plant growth and development and participates in plant responses to biotic and abiotic stresses. The LpNAC17 gene of L. pumilum was cloned and transformed into tobacco to investigate the response of transgenic tobacco to salt stress. The results showed that the net photosynthetic rate and contents of chlorophyll in LpNAC17 over-expressed tobacco were higher than those in the control plants, while the stomatal conductance, transpiration rate and intercellular CO₂ concentration were lower than those in the controls. The activity of superoxide dismutase, peroxidase, catalase, and the content of proline in LpNAC17 over-expressed tobacco were higher than those in the controls, while the content of malondialdehyde, superoxide anion, and hydrogen peroxide were lower than that in the control. Nitro-blue tetrazolium staining and 3,3'-diaminobenzidine tissue localization showed that the contents of O 2 - and H₂O₂ in transgenic tobacco was lower than in the controls. The expression levels of NtSOD, NtPOD, NtCAT, NtHAK1, NtPMA4, and NtSOS1 in the transgenic tobacco were higher than those in the controls. Therefore, this study provides a gene source for molecular breeding of salt-tolerant plants through genetic engineering, and lays a foundation for further research on salt-tolerant Lily.

Effects of Lactiplantibacillus plantarum 19-2 on immunomodulatory function and gut microbiota in mice

This study aims to evaluate the effects of Lactiplantibacillus plantarum 19-2 (L. plantarum 19-2) on mice treated with the alkylating agent cyclophosphamide (CTX). Our findings show that L. plantarum 19-2 restored the spleen and thymus index and the number of white blood cells and lymphocytes% in CTX treated mice. Serum immunoglobulin levels in CTX-treated mice were increased by L. plantarum 19-2. In addition, as compared to the model group, L. plantarum 19-2 upregulated the content of SIgA, while L. plantarum 19-2 regulates the mRNA and protein expression levels of GATA-3, T-bet, IFN-γ, and IL-4 in small intestinal tissues, which adjusted mucosal barriers, structural status, and the balance of Helper T-cell 1 and Helper T-cell 2. Lactiplantibacillus plantarum 19-2 regulated the distribution of intestinal flora in mice, promoting the growth of Bacteroides and Proteobacteria. In addition, L. plantarum 19-2 inhibited the growth of several harmful bacteria, including Actinobacteria and Firmicutes.

Integrated mRNA and Small RNA Sequencing Reveals a microRNA Regulatory Network Associated with Starch Biosynthesis in Lotus (Nelumbo nucifera Gaertn.) Rhizomes

Internode starch biosynthesis is one of the most important traits in lotus rhizome because of its relation to crop productivity. Understanding the microRNA (miRNA) and mRNA expression profiles related to lotus internode starch biosynthesis would help develop molecular improvement strategies, but they are not yet well-investigated. To identify genes and miRNAs involved in internode starch biosynthesis, the cDNA and small RNA libraries of Z6-1, Z6-2, and Z6-3 were sequenced, and their expression were further studied. Through combined analyses of transcriptome data and small RNA sequencing data, a complex co-expression regulatory network was constructed, in which 20 miRNAs could modulate starch biosynthesis in different internodes by tuning the expression of 10 target genes. QRT-PCR analysis, transient co-expression experiment and dual luciferase assay comprehensively confirmed that NnumiR396a down-regulated the expression of NnSS2 and ultimately prevents the synthesis of amylopectin, and NnumiR396b down-regulated the expression of NnPGM2 and ultimately prevents the synthesis of total starch. Our results suggest that miRNAs play a critical role in starch biosynthesis in lotus rhizome, and that miRNA-mediated networks could modulate starch biosynthesis in this tissue. These results have provided important insights into the molecular mechanism of starch biosynthesis in developing lotus rhizome.

BrABF3 promotes flowering through the direct activation of CONSTANS transcription in pak choi

Drought stress triggers the accumulation of the phytohormone abscisic acid (ABA), which in turn activates the expression of the floral integrator gene CONSTANS (CO), accelerating flowering. However, the molecular mechanism of ABA-induced CO activation remains elusive. Here, we conducted a yeast one-hybrid assay using the CO promoter from Brassica campestris (syn. Brassica rapa) ssp. chinensis (pak choi) to screen the ABA-induced pak choi library and identified the transcription activator ABF3 (BrABF3). BrABF3, the expression of which was induced by ABA in pak choi, directly bound to the CO promoter from both pak choi and Arabidopsis. The BrABF3 promoter is specifically active in the Arabidopsis leaf vascular tissue, where CO is mainly expressed. Impaired BrABF3 expression in pak choi decreased BrCO expression levels and delayed flowering, whereas ectopic expression of BrABF3 in Arabidopsis increased CO expression and induced earlier flowering under the long-day conditions. Electrophoretic mobility shift assay analysis showed that BrABF3 was enriched at the canonical ABA-responsive element-ABRE binding factor (ABRE-ABF) binding motifs of the BrCO promoter. The direct binding of BrABF3 to the ABRE elements of CO was further confirmed by chromatin immunoprecipitation quantitative PCR. In addition, the induction of BrCO transcription by BrABF3 could be repressed by BrCDF1 in the morning. Thus, our results suggest that ABA could accelerate the floral transition by directly activating BrCO transcription through BrABF3 in pak choi.

Coordinated transcriptional regulation of the carotenoid biosynthesis contributes to fruit lycopene content in high-lycopene tomato genotypes

Lycopene content in tomato fruit is largely under genetic control and varies greatly among genotypes. Continued improvement of lycopene content in elite varieties with conventional breeding has become challenging, in part because little is known about the underlying molecular mechanisms in high-lycopene tomatoes (HLYs). We collected 42 HLYs with different genetic backgrounds worldwide. High-performance liquid chromatography (HPLC) analysis revealed lycopene contents differed among the positive control wild tomato Solanum pimpinellifolium, HLYs, the normal lycopene cultivar "Moneymaker", and the non-lycopene cultivar NC 1Y at the pink and red ripe stages. Real-time RT-PCR analysis of expression of the 25 carotenoid biosynthesis pathway genes of each genotype showed a significantly higher expression in nine upstream genes (GGPPS1, GGPPS2, GGPPS3, TPT1, SSU II, PSY2, ZDS, CrtISO and CrtISO-L1 but not the well-studied PSY1, PDS and Z-ISO) at the breaker and/or red ripe stages in HLYs compared to Moneymaker, indicating a higher metabolic flux flow into carotenoid biosynthesis pathway in HLYs. Further conversion of lycopene to carotenes may be prevented via the two downstream genes (β-LCY2 and ε-LCY), which had low-abundance transcripts at either or both stages. Additionally, the significantly higher expression of four downstream genes (BCH1, ZEP, VDE, and CYP97C11) at either or both ripeness stages leads to significantly lower fruit lycopene content in HLYs than in the wild tomato. This is the first systematic investigation of the role of the complete pathway genes in regulating fruit lycopene biosynthesis across many HLYs, and enables tomato breeding and gene editing for increased fruit lycopene content.

Identification of Novel Genomic Regions for Bacterial Leaf Pustule (BLP) Resistance in Soybean (Glycine max L.) via Integrating Linkage Mapping and Association Analysis

Bacterial leaf pustule (BLP), caused by Xanthornonas axonopodis pv. glycines (Xag), is a worldwide disease of soybean, particularly in warm and humid regions. To date, little is known about the underlying molecular mechanisms of BLP resistance. The only single recessive resistance gene rxp has not been functionally identified yet, even though the genotypes carrying the gene have been widely used for BLP resistance breeding. Using a linkage mapping in a recombinant inbred line (RIL) population against the Xag strain Chinese C5, we identified that quantitative trait locus (QTL) qrxp-17-2 accounted for 74.33% of the total phenotypic variations. We also identified two minor QTLs, qrxp-05-1 and qrxp-17-1, that accounted for 7.26% and 22.26% of the total phenotypic variations, respectively, for the first time. Using a genome-wide association study (GWAS) in 476 cultivars of a soybean breeding germplasm population, we identified a total of 38 quantitative trait nucleotides (QTNs) on chromosomes (Chr) 5, 7, 8, 9,15, 17, 19, and 20 under artificial infection with C5, and 34 QTNs on Chr 4, 5, 6, 9, 13, 16, 17, 18, and 20 under natural morbidity condition. Taken together, three QTLs and 11 stable QTNs were detected in both linkage mapping and GWAS analysis, and located in three genomic regions with the major genomic region containing qrxp_17_2. Real-time RT-PCR analysis of the relative expression levels of five potential candidate genes in the resistant soybean cultivar W82 following Xag treatment showed that of Glyma.17G086300, which is located in qrxp-17-2, significantly increased in W82 at 24 and 72 h post-inoculation (hpi) when compared to that in the susceptible cultivar Jack. These results indicate that Glyma.17G086300 is a potential candidate gene for rxp and the QTLs and QTNs identified in this study will be useful for marker development for the breeding of Xag-resistant soybean cultivars.

RT-qPCR Detection of SARS-CoV-2: No Need for a Dedicated Reverse Transcription Step

Reverse transcription of RNA coupled to amplification of the resulting cDNA by the polymerase chain reaction (RT-PCR) is one of the principal molecular technologies in use today, with applications across all areas of science and medicine. In its real-time, fluorescence-based usage (RT-qPCR), it has long been a core technology driving the accurate, rapid and sensitive laboratory diagnosis of infectious diseases. However, RT-qPCR protocols have changed little over the past 30 years, with the RT step constituting a significant percentage of the time taken to complete a typical RT-qPCR assay. When applied to research investigations, reverse transcription has been evaluated by criteria such as maximum yield, length of transcription, fidelity, and faithful representation of an RNA pool. Crucially, however, these are of less relevance in a diagnostic RT-PCR test, where speed and sensitivity are the prime RT imperatives, with specificity contributed by the PCR component. We propose a paradigm shift that omits the requirement for a separate high-temperature RT step at the beginning of an RT-qPCR assay. This is achieved by means of an innovative protocol that incorporates suitable reagents with a revised primer and amplicon design and we demonstrate a proof of principle that incorporates the RT step as part of the PCR assay setup at room temperature. Use of this modification as part of a diagnostic assay will of course require additional characterisation, validation and optimisation of the PCR step. Combining this revision with our previous development of fast qPCR protocols allows completion of a 40 cycle RT-qPCR run on a suitable commercial instrument in approximately 15 min. Even faster times, in combination with extreme PCR procedures, can be achieved.