Exploring the regulatory role of non-coding RNAs in fiber development and direct regulation of GhKCR2 in the fatty acid metabolic pathway in upland cotton.

Cotton fiber holds immense importance as the primary raw material for the textile industry. Consequently, comprehending the regulatory mechanisms governing fiber development is pivotal for enhancing fiber quality. Our study aimed to construct a regulatory network of competing endogenous RNAs (ceRNAs) and assess the impact of non-coding RNAs on gene expression throughout fiber development. Through whole transcriptome data analysis, we identified differentially expressed genes (DEGs) regulated by non-coding RNA (ncRNA) that were predominantly enriched in phenylpropanoid biosynthesis and the fatty acid elongation pathway. This analysis involved two contrasting phenotypic materials (J02-508 and ZRI015) at five stages of fiber development. Additionally, we conducted a detailed analysis of genes involved in fatty acid elongation, including KCS, KCR, HACD, ECR, and ACOT, to unveil the factors contributing to the variation in fatty acid elongation between J02-508 and ZRI015. Through the integration of histochemical GUS staining, dual luciferase assay experiments, and correlation analysis of expression levels during fiber development stages for lncRNA MSTRG.44818.23 (MST23) and GhKCR2, we elucidated that MST23 positively regulates GhKCR2 expression in the fatty acid elongation pathway. This identification provides valuable insights into the molecular mechanisms underlying fiber development, emphasizing the intricate interplay between non-coding RNAs and protein-coding genes.

[Determination of 222 pesticide residues in olive oil by fully automatic QuEChERS pre-treatment instrument coupled with gas chromatography-quadrupole-time-of-flight mass spectrometry].

Pesticide residues may be present in olive oil because pesticides are applied to olive trees during their cultivation and growth for pest prevention and some of these pesticides are not easily degraded. Studies on pesticide residues in olive oil have mainly focused on the detection of single types of pesticide residues, and reports on the simultaneous detection of multiple pesticide residues are limited. At present, hundreds of pesticides with different polarities and chemical properties are used in practice. In this study, an analytical method based on fully automatic QuEChERS pretreatment instrument coupled with gas chromatography-quadrupole time-of-flight mass spectrometry (GC-QTOF-MS) was established for the rapid determination of 222 pesticide residues in olive oil. The effects of acetonitrile acidification concentration, n-hexane volume, oscillation time, centrifugation temperature, and purification agent on the determination of the 222 pesticide residues were investigated. First, ions with good responses and no obvious interference were selected for quantification and characterization. The purification process was then developed by setting the parameters of the fully automatic QuEChERS pretreatment instrument to optimal values. The sample was extracted with acetonitrile containing 2% formic acid, and the supernatant was purified by centrifugation in a centrifuge tube containing 400 mg N-propylethylenediamine (PSA), 400 mg octadecylsilane-bonded silica gel (C18), and 1200 mg anhydrous magnesium sulfate. The purified solution was blown dry with nitrogen and then fixed with ethyl acetate for instrumental analysis. Finally, a matrix standard solution was used for quantification. The method was validated in terms of matrix effects, linear ranges, limits of detection (LODs) and quantification (LOQs), accuracies, and precisions. The results showed that 86.04% of the 222 pesticides had linear ranges of 0.02-2.00 µg/mL, 10.81% had linear ranges of 0.10-2.00 µg/mL, and 3.15% had linear ranges of 0.20-2.00 µg/mL. The pesticide residues showed good relationships within their respective linear ranges, and the correlation coefficients (R2) were greater than 0.99. The LODs of all tested pesticides ranged from 0.002 to 0.050 mg/kg, and their LOQs ranged from 0.007 to 0.167 mg/kg. Among the 222 pesticides determined, 170 pesticides had LOQs of 0.007 mg/kg while 21 pesticides had LOQs of 0.017 mg/kg. At the three spiked levels of 0.2, 0.5, and 0.8 mg/kg, 79.58% of all tested pesticides had average recoveries of 70%-120% while 65.92% had average recoveries of 80%-110%. In addition, 93.54% of all tested pesticides had relative standard deviations (RSDs, n=6)<10% while 98.35% had RSDs (n=6)<20%. The method was applied to 14 commercially available olive oil samples, and seven pesticides were detected in the range of 0.0044-0.0490 mg/kg. The residues of fenbuconazole, chlorpyrifos, and methoprene did not exceed the maximum limits stated in GB 2763-2021. The maximum residual limits of molinate, monolinuron, benalaxyl, and thiobencarb have not been established. The method utilizes the high mass resolution capability of TOF-MS, which can improve the detection throughput while ensuring good sensitivity. In addition, high-resolution and accurate mass measurements render the screening results more reliable, which is necessary for the high-throughput detection of pesticide residues. The use of a fully automatic QuEChERS instrument in the pretreatment step reduces personnel errors and labor costs, especially when a large number of samples must be processed, thereby offering significant advantages over other approaches. Moreover, the method is simple, rapid, sensitive, highly automatable, accurate, and precise. Thus, it meets requirements for the high-throughput detection of pesticide residues in olive oil and provides a reference for the development of detection methods for pesticide residues in other types of oils as well as the automatic pretreatment of complex matrices.

CD11b + CD43 hi Ly6C lo splenocyte-derived macrophages exacerbate liver fibrosis via spleen-liver axis.

BACKGROUND AND AIMS: Monocyte-derived macrophages (MoMFs), a dominant population of hepatic macrophages under inflammation, play a crucial role in liver fibrosis progression. The spleen serves as an extra monocyte reservoir in inflammatory conditions; however, the precise mechanisms of involvement of the spleen in the pathogenesis of liver fibrosis remain unclear. APPROACH AND RESULTS: By splenectomy and splenocyte transfusion, it was observed that splenic CD11b + cells accumulated intrahepatically as Ly6C lo MoMFs to exacerbate CCl 4 -induced liver fibrosis. The splenocyte migration into the fibrotic liver was further directly visualized by spleen-specific photoconversion with KikGR mice and confirmed by CD45.1 + /CD45.2 + spleen transplantation. Spleen-derived CD11b + cells purified from fibrotic livers were then annotated by single-cell RNA sequencing, and a subtype of CD11b + CD43 hi Ly6C lo splenic monocytes (sM-1s) was identified, which was markedly expanded in both spleens and livers of mice with liver fibrosis. sM-1s exhibited mature feature with high expressions of F4/80, produced much ROS, and manifested preferential migration into livers. Once recruited, sM-1s underwent sequential transformation to sM-2s (highly expressed Mif , Msr1 , Clec4d , and Cstb ) and then to spleen-derived macrophages (sMφs) with macrophage features of higher expressions of CX 3 CR1, F4/80, MHC class II, and CD64 in the fibrotic hepatic milieu. Furthermore, sM-2s and sMφs were demonstrated capable of activating hepatic stellate cells and thus exacerbating liver fibrosis. CONCLUSIONS: CD11b + CD43 hi Ly6C lo splenic monocytes migrate into the liver and shift to macrophages, which account for the exacerbation of liver fibrosis. These findings reveal precise mechanisms of spleen-liver axis in hepatic pathogenesis and shed light on the potential of sM-1 as candidate target for controlling liver diseases.

miR-3,178 contributes to the therapeutic action of baicalein against hepatocellular carcinoma cells via modulating HDAC10.

Hepatocellular carcinoma (HCC) is the most common type of hepatic malignancies with high mortality and poor prognosis. Baicalein, one of the major and bioactive flavonoids isolated from Scutellaria baicalensis Georgi, which is reported to have anti-proliferation effect in varying cancers, including HCC, whose underlying molecular mechanism is still largely unknown. In this study, we found that baicalein significantly inhibited proliferation and colony formation, blocked cell cycle, and promoted apoptosis in HCC cells MHCC-97H and SMMC-7721 in vitro and reduced tumor volume and weight in vivo. Increased microRNA (miR)-3,178 levels and decreased histone deacetylase 10 (HDAC10) expression were found in cells treated with baicalein and in patients' HCC tissues. HDAC10 was identified as a target gene of miR-3,178 by luciferase activity and western blot. Both baicalein treatment and overexpression of miR-3,178 could downregulate HDAC10 protein expression and inactivated AKT, MDM2/p53/Bcl2/Bax and FoxO3α/p27/CDK2/Cyclin E1 signal pathways. Not only that, knockdown of miR-3,178 could partly abolish the effects of baicalein and the restoration of HDAC10 could abated miR-3,178-mediated role in HCC cells. Collectively, baicalein inhibits cell viability, blocks cell cycle, and induces apoptosis in HCC cells by regulating the miR-3,178/HDAC10 pathway. This finding indicated that baicalein might be promising for treatment of HCC.

Extracellular vesicle-derived miR-1249-5p regulates influenza A virus-induced acute lung injury in RAW246.7 cells through targeting SLC4A1.

Acute lung injury (ALI) is characterized by tissue damage that leads to pulmonary epithelial membrane dysfunction and macrophage activation. Currently however, the exact mechanism by which the initial mediators of mouse lung epithelial (MLE-12) cells induce inflammation remines unclear. We constructed co-culture systems of MLE-12 cells with mouse macrophage cells RAW246.7 which were realized by the supernatant and Transwell chamber. In previous study, we successfully constructed an influenza A virus-induced MLE-12 cells model. Extracellular Vesicles (EVs) from cells supernatant were isolated by differential ultracentrifugation and confirmed by transmission electron microscopy. High-throughput sequencing results showed that MLE-12 cells stimulated by influenza A virus had higher level of miR-1249-5p. The results were validated by RT-qPCR analysis. The research aimed to investigate the roles and mechanisms of miR-1249-5p in ALI. RAW246.7 cells were transfected with miR-1249-5p mimic/inhibitor. The concentrations of TNF-α, IL-6 were determined by ELISA and the uptake of EVs was monitored by confocal laser scanning microscope. Western blotting detected changes in the SLC4A1 and NF-κB signaling pathway. The results indicated that miR-1249-5p played an important role in ALI, and further investigation of its target gene SLC4A1 and NF-κB signaling pathway provides ideas for new therapeutic targets and strategies for ALI.

Human chorionic gonadotropin improves endometrial receptivity by increasing the expression of homeobox A10.

Homeobox A10 (HOXA10) is a characterized marker of endometrial receptivity. The mechanism by which hCG intrauterine infusion promotes embryo implantation is still unclear. This study seeks to investigate whether hCG improves endometrial receptivity by increasing expression of HOXA10. HOXA10 expression with human chorionic gonadotropin stimulation was analyzed in vitro and in vivo. Our results demonstrate that HOXA10 was decreased in the endometria of recurrent implantation failure patients compared to that in the healthy control fertile group, also we observed that hCG intrauterine infusion increased endometrial HOXA10 expression. HOXA10, blastocyst-like spheroid expansion area was increased, whereas DNA (cytosine-5-)-methyltransferase 1 was decreased when human endometrial stromal cells (hESCs) were treated with 0.2 IU/ml of hCG for 48 h. HOXA10 promoter methylation was also reduced after hCG treatment. Collagen XV (ColXV) can repress the expression of DNA (cytosine-5-)-methyltransferase 1, and hCG treatment increased the expression of ColXV. However, when the hESCs were treated with LH/hCG receptor small interfering RNA to knock down LH/hCG receptor, hCG treatment failed to repress DNA (cytosine-5-)-methyltransferase 1 expression or to increase ColXV expression. Our findings suggest that hCG may promote embryo implantation by increasing the expression of HOXA10.

Silencing of long noncoding RNA HOXD-AS1 inhibits proliferation, cell cycle progression, migration and invasion of hepatocellular carcinoma cells through MEK/ERK pathway.

Accumulating findings reveal that long noncoding RNAs (lncRNAs) as crucial regulatory molecules serve vital functions in the progression of hepatocellular carcinoma (HCC). This study aims to investigate the biological roles and mechanisms of lncRNA HOXD cluster antisense RNA 1 (HOXD-AS1) in HCC cells based on transcriptome analysis. The Cancer Genome Atlas data analysis and experimental validation showed that HOXD-AS1 was increased in HCC tissues/cell lines and positively relevant to histologic grade. The subcellular localization results indicated HOXD-AS1 was dispersed both in the nucleus as well as the cytoplasm of HCC cells. In vitro loss-of-function experiments revealed that silencing of HOXD-AS1 could dramatically suppress the proliferation, migration, and invasion, and induce S or/and G2/M phase cell cycle arrest as well as apoptosis of Bel-7402 and MHCC97H cells accompanying the changes in expression levels of cyclin B1, cyclin D1, BCL-2, BAX, and MMP2. In vivo assay also showed that HOXD-AS1 silencing could markedly reduce xenograft tumor volume and weight of HCC cells. Transcriptome and bioinformatic analysis indicated that a total of 1103 genes were significantly altered by HOXD-AS1 silencing, of which 132 genes exhibited a significant correlation with HOXD-AS1 expression in HCC tissues. Gene Ontology (GO) enrichment analysis revealed differentially expressed genes were remarkably enriched in several cancer-related biological processes (cell proliferation, cell cycle, apoptosis, migration, angiogenesis, and hypoxic response). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated that HOXD-AS1 has the potential to affect p53, tumor necrosis factor (TNF), mitogen-activated protein kinase (MAPK) pathway, and Western blot results further validated that HOXD-AS1 silencing could inhibit the MEK/ERK pathway in Bel-7402 cells. Collectively, HOXD-AS1, as an oncogenic lncRNA, might exert crucial functions in HCC progression and serve as a potential diagnostic biomarker and therapeutic target for HCC.

Influence of surgical evacuation on pregnancy outcomes of subsequent embryo transfer cycle following miscarriage in an initial IVF cycle: a retrospective cohort study.

BACKGROUND: It is still uncertain whether surgical evacuation adversely affects subsequent embryo transfer. The present study aims to assess the influence of surgical evacuation on the pregnancy outcomes of subsequent embryo transfer cycle following first trimester miscarriage in an initial in vitro fertilization and embryo transfer (IVF-ET) cycle. METHODS: A total of 645 patients who underwent their first trimester miscarriage in an initial IVF cycle between January 2013 and May 2016 in Nanjing Drum Tower Hospital were enrolled. Surgical evacuation was performed when the products of conception were retained more than 8 h after medical evacuation. Characteristics and pregnancy outcomes were compared between surgical evacuation patients and no surgical evacuation patients. The pregnancy outcomes following surgical evacuation were further compared between patients with ≥ 8 mm or < 8 mm endometrial thickness (EMT), and with the different EMT changes. RESULTS: The EMT in the subsequent embryo transfer cycle of surgical evacuation group was much thinner when compared with that in the no surgical evacuation group (9.0 ± 1.6 mm vs. 9.4 ± 1.9 mm, P = 0.01). There was no significant difference in implantation rate, clinical pregnancy rate, live birth rate or miscarriage rate between surgical evacuation group and no surgical evacuation group (P > 0.05). The live birth rate was higher in EMT ≥ 8 mm group when compared to < 8 mm group in surgical evacuation patients (43.0% vs. 17.4%, P < 0.05). CONCLUSIONS: There was no significant difference in the pregnancy outcomes of subsequent embryo transfer cycle between surgical evacuation patients and no surgical evacuation patients. Surgical evacuation led to the decrease of EMT, especially when the EMT < 8 mm was association with a lower live birth rate.

A predictive formula for selecting individual FSH starting dose based on ovarian reserve markers in IVF/ICSI cycles.

BACKGROUND: Although exogenous follicle-stimulating hormone (FSH) has been used for decades and millions of cycles have been performed worldwide until now, criteria for selecting the proper FSH starting dose have not been clearly identified. The aim of this study was to elaborate a formula based on markers of ovarian reserve for the calculation of the appropriate starting dose of FSH. METHODS: A total of 931 patients underwent in vitro fertilization (IVF) treatment using long GnRH agonist protocol was retrospectively identified and reviewed. 673 cases of them with a normal ovarian response (4-14 retrieved oocytes) were used to analysis the predictive formula. All follicles 4-7 mm in diameter were counted in the same day of blood sample in both ovaries using transvaginal ultrasound scan. The modified protocol of each patient was recorded and analyzed in the same center. In another center were the numbers of retrieved oocytes of 750 validated patients recorded and analyzed. RESULTS: A formula model based on age, AMH, and antral follicle count (AFC) was able to accurately predict the ovarian sensitivity and accounted for 57.2% of the variability of ovarian response to FSH. When tested in the same total population used to elaborate the model it predicts a high 46.88% rate of step-down protocol in higher-starting FSH dose group and about 57.92% of patients had their dose step-up modified in lower-starting FSH dose group during their treatment, respectively. And when tested in different population from another center used to elaborate the model it predicts a high 64.40% rate of ≥ 15 retrieved oocytes in higher-starting FSH dose group and about 22.50% of patients had ≤ 7 retrieved oocytes in lower-starting FSH dose group during their treatment, respectively. CONCLUSIONS: In the present study we demonstrated that the individualized FSH starting dose may be calculated on the basis of a woman's age, AMH and AFC. The formula model might be a useful, immediate, and easily applicable tool for clinicians to predict the tailored starting dose of FSH during their daily clinical practice.

High granulocytic myeloid-derived suppressor cell levels in the peripheral blood predict a better IVF treatment outcome.

Objective: Myeloid-derived suppressor cells (MDSCs) have been described as important immunosuppressive cells for maternal immune tolerance. The aim of this study was to detect whether there was any association between the peripheral blood MDSCs level and in vitro fertilization (IVF) treatment outcomes. Methods: This prospective observational study randomly recruited 85 women who underwent IVF treatment from May 2016 to June 2016. The levels of peripheral blood granulocytic MDSC (G-MDSC), monocytic MDSC (M-MDSC) and their relations to IVF treatment outcomes were analyzed. Results: The circulating G-MDSC level was significantly increased in the clinical pregnant group when compared to that in the nonclinical pregnant group (p = .014), while M-MDSC had no significant difference. The G-MDSC level was an independent predictive factor for clinical pregnancy with odds ratios 12.7 (95% CI: 1.53-105.4, p = .018) when using multiple logistic regression analysis. A receiver operating characteristic analysis (area under curve = 0.634) found the clinical pregnancy rate in women with G-MDSC >2.38% was higher than that in women below this level (96 versus 66.7%, p = .004). The high G-MDSC level in the peripheral blood was associated with clinical pregnancy, with a sensitivity of 37.5%, specificity of 95.2%. Conclusion: High circulating G-MDSC level was associated with elevated clinical pregnancy rate. G-MDSC might be a new therapeutic target for better IVF treatment outcome.

Modeling Inhibitory Interneurons in Efficient Sensory Coding Models.

There is still much unknown regarding the computational role of inhibitory cells in the sensory cortex. While modeling studies could potentially shed light on the critical role played by inhibition in cortical computation, there is a gap between the simplicity of many models of sensory coding and the biological complexity of the inhibitory subpopulation. In particular, many models do not respect that inhibition must be implemented in a separate subpopulation, with those inhibitory interneurons having a diversity of tuning properties and characteristic E/I cell ratios. In this study we demonstrate a computational framework for implementing inhibition in dynamical systems models that better respects these biophysical observations about inhibitory interneurons. The main approach leverages recent work related to decomposing matrices into low-rank and sparse components via convex optimization, and explicitly exploits the fact that models and input statistics often have low-dimensional structure that can be exploited for efficient implementations. While this approach is applicable to a wide range of sensory coding models (including a family of models based on Bayesian inference in a linear generative model), for concreteness we demonstrate the approach on a network implementing sparse coding. We show that the resulting implementation stays faithful to the original coding goals while using inhibitory interneurons that are much more biophysically plausible.

Optimal sparse approximation with integrate and fire neurons.

Sparse approximation is a hypothesized coding strategy where a population of sensory neurons (e.g. V1) encodes a stimulus using as few active neurons as possible. We present the Spiking LCA (locally competitive algorithm), a rate encoded Spiking Neural Network (SNN) of integrate and fire neurons that calculate sparse approximations. The Spiking LCA is designed to be equivalent to the nonspiking LCA, an analog dynamical system that converges on a ℓ(1)-norm sparse approximations exponentially. We show that the firing rate of the Spiking LCA converges on the same solution as the analog LCA, with an error inversely proportional to the sampling time. We simulate in NEURON a network of 128 neuron pairs that encode 8 × 8 pixel image patches, demonstrating that the network converges to nearly optimal encodings within 20 ms of biological time. We also show that when using more biophysically realistic parameters in the neurons, the gain function encourages additional ℓ(0)-norm sparsity in the encoding, relative both to ideal neurons and digital solvers.

Visual nonclassical receptive field effects emerge from sparse coding in a dynamical system.

Extensive electrophysiology studies have shown that many V1 simple cells have nonlinear response properties to stimuli within their classical receptive field (CRF) and receive contextual influence from stimuli outside the CRF modulating the cell's response. Models seeking to explain these non-classical receptive field (nCRF) effects in terms of circuit mechanisms, input-output descriptions, or individual visual tasks provide limited insight into the functional significance of these response properties, because they do not connect the full range of nCRF effects to optimal sensory coding strategies. The (population) sparse coding hypothesis conjectures an optimal sensory coding approach where a neural population uses as few active units as possible to represent a stimulus. We demonstrate that a wide variety of nCRF effects are emergent properties of a single sparse coding model implemented in a neurally plausible network structure (requiring no parameter tuning to produce different effects). Specifically, we replicate a wide variety of nCRF electrophysiology experiments (e.g., end-stopping, surround suppression, contrast invariance of orientation tuning, cross-orientation suppression, etc.) on a dynamical system implementing sparse coding, showing that this model produces individual units that reproduce the canonical nCRF effects. Furthermore, when the population diversity of an nCRF effect has also been reported in the literature, we show that this model produces many of the same population characteristics. These results show that the sparse coding hypothesis, when coupled with a biophysically plausible implementation, can provide a unified high-level functional interpretation to many response properties that have generally been viewed through distinct mechanistic or phenomenological models.

Real-time image-based B-mode ultrasound image simulation of needles using tensor-product interpolation.

In this paper, we propose an interpolation-based method for simulating rigid needles in B-mode ultrasound images in real time. We parameterize the needle B-mode image as a function of needle position and orientation. We collect needle images under various spatial configurations in a water-tank using a needle guidance robot. Then we use multidimensional tensor-product interpolation to simulate images of needles with arbitrary poses and positions using collected images. After further processing, the interpolated needle and seed images are superimposed on top of phantom or tissue image backgrounds. The similarity between the simulated and the real images is measured using a correlation metric. A comparison is also performed with in vivo images obtained during prostate brachytherapy. Our results, carried out for both the convex (transverse plane) and linear (sagittal/para-sagittal plane) arrays of a trans-rectal transducer indicate that our interpolation method produces good results while requiring modest computing resources. The needle simulation method we present can be extended to the simulation of ultrasound images of other wire-like objects. In particular, we have shown that the proposed approach can be used to simulate brachytherapy seeds.

Real time ultrasound needle image simulation using multi-dimensional interpolation.

In this paper, we propose an interpolation-based method for simulating needle images in B-mode ultrasound. We parametrize the needle image as a function of needle position and orientation. We collect needle images under various spatial configurations in a water-tank using a guidance robot. Then we use multi-dimensional tensor-product interpolation to simulate images of needles with arbitrary poses and positions using the collected images. Interpolated needle images are superimposed on top of phantom image backgrounds. The similarity between the simulated and the real images is measured using a correlation metric. A comparison with in-vivo images is also performed. The simulation procedure is demonstrated using transverse needle images and extended to sagittal needle images and brachytherapy seed images. The proposed method could be used in clinical procedure training simulators.