ASTER: accurately estimating the number of cell types in single-cell chromatin accessibility data.

SUMMARY: Recent innovations in single-cell chromatin accessibility sequencing (scCAS) have revolutionized the characterization of epigenomic heterogeneity. Estimation of the number of cell types is a crucial step for downstream analyses and biological implications. However, efforts to perform estimation specifically for scCAS data are limited. Here, we propose ASTER, an ensemble learning-based tool for accurately estimating the number of cell types in scCAS data. ASTER outperformed baseline methods in systematic evaluation on 27 datasets of various protocols, sizes, numbers of cell types, degrees of cell-type imbalance, cell states and qualities, providing valuable guidance for scCAS data analysis. AVAILABILITY AND IMPLEMENTATION: ASTER along with detailed documentation is freely accessible at https://aster.readthedocs.io/ under the MIT License. It can be seamlessly integrated into existing scCAS analysis workflows. The source code is available at https://github.com/biox-nku/aster. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

External bending of cryodevice during vitrification leads to cryoprotectant cracks and damage to embryo blastomeres.

RESEARCH QUESTION: Embryo blastomeres and the zona pellucida are occasionally damaged during vitrification; is this a result of crack-induced mechanical damage in the glass state, caused by external bending of the device? DESIGN: A stereomicroscope was used to observe external bending-induced cracks in a cryoprotectant. Thereafter, 309 human cleavage-stage embryos derived from abnormally fertilized eggs were used to assess embryo damage under two external bending conditions: forward bending and backward bending, with three bending degrees applied. Three distinct embryo positions were used to examine the correlation between bending and embryo damage. Damage was assessed by looking at blastomere lysis rates, and overall rates of damaged and surviving embryos. RESULTS: A series of parallel cracks were identified in the cryoprotectant used for external bending, which led to damage to the embryo blastomeres. Compared with forward bending and control, the embryos were found to be more easily damaged by backward bending, indicated by significantly higher blastomere lysis and embryo damage rates, and lower embryo survival rate of backward bending than forward bending (P < 0.001). The degree of embryo damage also increased as the degree of external forces increased. Embryo position correlated with degree of embryo damage. CONCLUSIONS: Cryoprotectant crack-induced damage was identified as the cause of embryo damage. Mechanical damage to the glass state occurs because of improper external bending of the cryodevice strip in liquid nitrogen during vitrification. To prevent damage, bending of the strip should be avoided and the embryos should be placed near the tip of the strip.

WEE1 promotes endometriosis via the Wnt/ß-catenin signaling pathway.

BACKGROUND: Endometriosis, the presence of active endometrial tissue outside the lining membrane of the uterine cavity, is a common disease in women of childbearing age. The ectopic endometrium has some characteristics of tumor tissue, including invasive and migratory abilities. In addition, endometriosis is associated with inflammation and reduced cellular apoptosis. METHODS: Western blot analysis, qPCR, immunohistochemistry, immunofluorescence microscopy, Transwell assay, wound healing assay, and TUNEL staining. RESULTS: Interleukin-1ß (IL-1ß) induced WEE1 expression in endometrial stromal cells (ESCs), suggesting that WEE1 may be upregulated during the endometriosis-induced inflammatory response. Overexpression of WEE1 in cultured ESCs promoted ESC migration while inhibiting apoptosis, whereas WEE1 knockdown reduced ESC migration while promoting apoptosis. Inhibition of WEE1 attenuates fibrosis in ESCs and female C57BL/6 J mice. This pro-fibrotic effect of WEE1 was significantly decreased by treatment with the Wnt/ß-catenin inhibitor XAV939, suggesting that WEE1 acts via the Wnt/ß-catenin signaling pathway. CONCLUSION: Our study demonstrates that WEE1 promotes ESC migration and fibrosis via the Wnt/ß-catenin signaling pathway. Thus, WEE1 may serve as a potential therapeutic target for the treatment of endometriosis.

A novel homozygous variant in NLRP5 is associate with human early embryonic arrest in a consanguineous Chinese family.

Early embryonic arrest is one of the major causes of recurrent assisted reproduction failure. It is characterized by delayed embryonic development and failure to form viable eight-cell stage embryos on day 3 of an assisted reproduction cycle. A recent study reported that biallelic mutations in NLRP5 can cause early embryonic arrest. NLRP5 is a member of subcortical maternal complex, which plays a significant role in embryogenesis. In this study, we described a female in a consanguineous Chinese family who displayed clinical features of early embryonic arrest and identified a novel homozygous variant c.1061C>T (p.Pro354Leu) in NLRP5. This is the second report of the biallelic NLRP5 variant that associates with early embryonic arrest in humans, further confirming the role of NLRP5 variants in early embryonic arrest and expanding the spectrum of known pathogenic variants in NLRP5.

Roles of estrogen and its receptors in polycystic ovary syndrome.

Polycystic ovary syndrome (PCOS) is an endocrine disorder characterized by abnormal steroid hormone levels in peripheral blood and poor-quality oocytes. In the ovary, androgen is produced by theca cells, and estrogen is produced by granulosa cells. Androgen is converted to estrogen in granulosa cells, with cytochrome P450 aromatase as the limiting enzyme during this process. Estrogen receptors (ER) include ER alpha, ER beta, and membrane receptor GPR30. Studies have demonstrated that the abnormal functions of estrogen and its receptors and estradiol synthesis-related enzymes are closely related to PCOS. In recent years, some estrogen-related drugs have made significant progress in clinical application for subfertility with PCOS, such as letrozole and clomiphene. This article will elaborate on the recent advances in PCOS caused by abnormal expression of estrogen and its receptors and the application of related targeted small molecule drugs in clinical research and treatment.

Seasonal urban surface thermal environment analysis based on local climate zones: A case study of Chongqing.

The rapid urbanization has exacerbated the heat island effect, impacting city development and residents' health. This study, using Local Climate Zones (LCZ) as a framework, connects spatial structure, resource allocation, and thermal environment research. It investigates the spatiotemporal heterogeneity of the surface thermal environment and its driving forces, crucial for mitigating heat issues. Utilizing various data sources like remote sensing images, road network data, land use data, high-resolution street view data, and building data, the research employs the random forest algorithm to map LCZs in Chongqing's central urban area. Through mathematical statistics, equi-sector analysis, ring-layer analysis, and Pearson correlation analysis, the study examines seasonal variations in spatiotemporal heterogeneity and driving mechanisms of the surface thermal environment. Key findings include: (1) The central urban area of Chongqing is dominated by open-building and vegetation-type LCZs, with building-type LCZs showing a "clustered" distribution, while natural-type LCZs are mainly found in the suburbs with ribbon and block distribution in the urban area. (2) The surface thermal environment in the study area correlates strongly with surface cover and exhibits significant high temperature effects in summer. (3) The surface thermal conditions vary significantly among different LCZs and exhibit seasonal patterns, natural-type LCZs generally have lower temperatures compared to building-type LCZs.(4) The surface thermal characteristics within the same category of LCZs in different locations display distinct differences and seasonal variations. (5) The internal temperatures of LCZs are significantly linked to four surface attributes, each displaying seasonal fluctuations. Greenness, height, and wetness are inversely related to the surface thermal conditions, while brightness shows a positive correlation. Both seasonal variations and LCZ types differences have a noticeable influence on their respective driving mechanisms to some degree.

scCASE: accurate and interpretable enhancement for single-cell chromatin accessibility sequencing data.

Single-cell chromatin accessibility sequencing (scCAS) has emerged as a valuable tool for interrogating and elucidating epigenomic heterogeneity and gene regulation. However, scCAS data inherently suffers from limitations such as high sparsity and dimensionality, which pose significant challenges for downstream analyses. Although several methods are proposed to enhance scCAS data, there are still challenges and limitations that hinder the effectiveness of these methods. Here, we propose scCASE, a scCAS data enhancement method based on non-negative matrix factorization which incorporates an iteratively updating cell-to-cell similarity matrix. Through comprehensive experiments on multiple datasets, we demonstrate the advantages of scCASE over existing methods for scCAS data enhancement. The interpretable cell type-specific peaks identified by scCASE can provide valuable biological insights into cell subpopulations. Moreover, to leverage the large compendia of available omics data as a reference, we further expand scCASE to scCASER, which enables the incorporation of external reference data to improve enhancement performance.

An innovative design for trophectoderm biopsy without laser pulses: a step-by-step demonstration.

OBJECTIVE: To present a novel trophectoderm biopsy method, independent of laser pulses, using innovatively designed micropipettes on blastocysts at different stages and show variable characteristics. DESIGN: A step-by-step demonstration of this method with narrated video. SETTING: In vitro laboratory fertilization. PATIENTS: Individuals whose embryos underwent preimplantation genetic testing. INTERVENTIONS: Trophectoderm biopsy is accomplished using micropipettes that contain a set of innovative designs. Both biopsy and holding pipettes are characterized by sharp, flat opening ends. The holding pipette is designed with an inclined plane on the outer wall surface of its opening end. It is used to help the biopsy pipette make contact with the holding pipette with increased stability, preventing slipping during the detachment of the trophectoderm cells. There is a narrow structure inside the biopsy pipette, which is designed to trap released fragments and prevent sample loss. A trophectoderm biopsy for fully expanded blastocysts starts from artificial shrinkage, followed by zona pellucida drilling. Then, 5-10 trophectoderm cells are aspirated into a biopsy pipette. The blastocyst is released from the holding pipette, the edge of the opening end of the biopsy pipette is tightly pressed onto the inclined plane of the holding pipette, and the biopsy pipette is flicked directly without laser pulses or pulling off the trophectoderm cells. The aspirated trophectoderm cells are subsequently detached by mechanical friction between the edges of the biopsy and holding pipettes. Apart from drilling the zona pellucida for fully expanded blastocysts, the remaining steps do not require lasers. For hatching (including peanut-shaped and 8-shaped) and hatched blastocysts, a trophectoderm biopsy is accomplished by aspirating the cells without securing the blastocyst with a holding pipette, followed by detachment using the direct flicking method. MAIN OUTCOME MEASURES: The biopsy time, sample loss rate, successful DNA amplification rate, and survival rate. RESULTS: The innovatively designed micropipettes facilitate the successful detachment of trophectoderm cells through a single direct flicking procedure. This eliminates thermal damage caused by laser pulses, notably simplifying operational steps and shortening the biopsy time. Significant differences were noted between the direct flicking and conventional methods, wherein laser pulses and pulling of trophectoderm cells are prerequisites for cell detachment. When comparing the average biopsy time of fully expanded blastocyst (61 ± 8s vs. 104 ± 9s, P<.05), peanut-shaped hatching blastocyst (35 ± 6s vs. 113 ± 13s, P<.05), 8-shaped hatching blastocyst (32 ± 4s vs. 59 ± 6s, P<.05), and hatched blastocyst (34 ± 4s vs. 67 ± 8s, P<.05), the direct flicking method shows a significantly decreased biopsy time. The narrow structure inside the biopsy pipette effectively prevents sample loss, showing a significantly reduced sample loss rate (0%) compared with the conventional biopsy method (18%) for trainees. Moreover, a satisfactory survival rate (100%) and successful DNA amplification rate (99.5%) were achieved using the direct flicking method. CONCLUSIONS: This innovative trophectoderm biopsy method, independent of laser pulses, has wide applicability and a satisfactory, stable performance. Moreover, the simplicity of the method makes it easy to master.

Melatonin Improves Quality of Repeated-Poor and Frozen-Thawed Embryos in Human, a Prospective Clinical Trial.

Objective: In this study, two experiments were performed to assess the effect and the role of melatonin on human in vitro embryo quality. Methods: Experiment I: A total of 42 repeated-poor-quality-embryo patients were enrolled, with a total of 181 oocytes retrieval cycles. After IVF, for the same patient, the MT cycles group (10-7 M melatonin added to the culture medium; n=48) were compared with the previous non-MT cycles group (n=133), following by in vitro culture to blastocyst stage and embryo transfer. 31 patients were transplanted with 65 embryo transfer, including 24 MT embryo transfer, 41 non-MT embryo transfer. Cycle outcomes were compared between the two groups. Experiment II:A total of 143 supernumerary human cleavage-stage embryos (from non-repeated-poor-quality-embryo patients) vitrified on Day 3 after IVF were warmed and randomized into two groups: melatonin group (10-7 M melatonin added to the culture medium; n=71) and control group (n=72), and then cultured for 72 h. Rate of blastocyst and high-quality blastocyst, reactive oxygen species (ROS) levels of culture media as well as embryonic GPX1, CAT, Mn-SOD, Cu/Zn-SOD, BCL-2, BAX gene expression levels were analyzed. Results: Experiment I: Results showed that the rate of Day 3 high-quality embryos (29.6% vs.19.5%) in the MT cycles group was significantly higher than that in the non-MT cycles group (P<0.05). The rate of available blastocysts (17.1% vs.12.7%) and clinical pregnancy rate (25.0% vs.17.1%) were in tendency higher in the group treated with melatonin (P>0.05). Experiment II:Results showed that the blastocyst rates in the melatonin administered group were significantly higher than in control group (42.25% vs.26.38%, P<0.05). There were no significant differences in high-quality blastocyst rates. In addition, quantitative PCR showed that the expression of CAT was significantly upregulated by melatonin treatment (P<0.05), while there were no significant differences in the expression of GPX1, Mn-SOD, Cu/Zn-SOD, BAX and BCL-2 gene as well as the levels of ROS. Conclusion: These data showed that melatonin supplement in the culture medium will improve Day 3 high-quality embryos rate of repeated-poor-quality-embryo patients and improve blastocyst rate of vitrified-warmed cleavage-stage embryos, suggesting that melatonin intervention may provide a potential rescue strategy for IVF failures. Clinical Trial Registration: identifier [ChiCTR2200059773].

The E3 Ubiquitin Ligase SYVN1 Plays an Antiapoptotic Role in Polycystic Ovary Syndrome by Regulating Mitochondrial Fission.

Polycystic ovary syndrome (PCOS) is one of the most common hormonal disorders among premenopausal women. PCOS is accompanied by many other reproductive, endocrinal, and metabolic disorders thus amassing the difficulties encountered by the women affected. However, there is limited information on its molecular etiology. Synoviolin (SYVN1) is an E3 ubiquitin ligase that is thought to participate in the pathology of PCOS. However, the expression and function of SYVN1 in PCOS are unknown. In this study, we found that downregulation of SYVN1 expression was followed by increased apoptosis in the granulosa cells (GCs) of patients with PCOS. Subsequent in vitro experiments indicated that the overexpression of SYVN1 inhibited apoptosis and mitochondrial fission. Furthermore, using immunoprecipitation and western blotting, we identified that SYVN1 promoted the degradation of Drp1 via the proteasome-dependent pathway. Additionally, we generated a PCOS model in female Sprague Dawley rats and treated them with an SYVN1 inhibitor, LS-102. We observed that the inhibition of SYVN1 increased Drp1 levels and exacerbated the degeneration of GCs in the PCOS rat model. Finally, in vitro and in vivo experiments showed that SYVN1 inhibits apoptosis and mitochondrial fission by promoting Drp1 degradation in GCs. These results highlight the function of SYVN1 in PCOS and provide a potential target for the clinical treatment of PCOS.

Tie1 contributes to the development of ovarian hyperstimulation syndrome under the regulation of EGR1 in granulosa cells.

The expression of tyrosine kinase with immunoglobulin-like and epidermal growth factor-like domains 1 (Tie1), a transmembrane protein expressed almost exclusively by endothelial cells, has been reported in granulosa cells. However, its significance in ovarian hyperstimulation syndrome (OHSS), which can occur after the injection of gonadotropins in infertile women undergoing controlled ovarian stimulation, is unknown. Here, we report significantly increased Tie1 and vascular endothelial growth factor (VEGF) expression in cultured granulosa cells from OHSS patients, as well as ovaries from rats with experimentally established OHSS, compared to controls, with the levels of both proteins also increasing in granulosa and SVOG cells (a nontumorigenic human granulosa-lutein cell line) treated with an acute dose of human chorionic gonadotropin (hCG). Tie1 silencing abolished the hCG-induced VEGF level in SVOG cells and attenuated the progression of OHSS in rats, as determined by histological analysis. Further studies in SVOG cells revealed that the hCG-induced upregulation of Tie1 expression involved the phosphoinositide 3-kinase/protein kinase B signaling pathway. We also report that early growth response protein 1 (EGR1), whose expression was also upregulated by hCG, bound directly to the Tie1 promoter and activated its transcription. Taken together, our results indicate that Tie1 may be a therapeutic target in cases of moderate-to-severe OHSS. Further studies are needed to address its clinical relevance.

Novel Homozygous PADI6 Variants in Infertile Females with Early Embryonic Arrest.

Early embryonic arrest denotes premature termination of development in preimplantation embryos, which is one of the major phenotypes of recurrent assisted reproduction failure. Padi6 is proven to be a member of the subcortical maternal complex (SCMC) in mice, which is essential in oocyte maturation and embryogenesis. We and other groups previously found that biallelic mutations in PADI6 caused female infertility manifesting as early embryonic arrest. In this study, we identified two novel homozygous variants (p.Cys163Arg, and p. Trp475*) of PADI6 in two infertile patients from a cohort of 75 females with the phenotype of early embryonic arrest. An in vitro expression study indicated severe decrease of PADI6, which might destruct the stability of SCMC. Our study expands the mutational spectrum of PADI6 and further supports the causality between PADI6 mutations and female infertility.

Circadian Clock Genes REV-ERBs Inhibits Granulosa Cells Apoptosis by Regulating Mitochondrial Biogenesis and Autophagy in Polycystic Ovary Syndrome.

Polycystic ovary syndrome (PCOS) is an endocrinopathy with complex pathophysiology that is a common cause of anovulatory infertility in women. Although the disruption of circadian rhythms is indicated in PCOS, the role of the clock in the etiology of these pathologies has yet to be appreciated. The nuclear receptors REV-ERBα and REV-ERBß are core modulators of the circadian clock and participate in the regulation of a diverse set of biological functions. However, in PCOS, the expression of REV-ERBs and their effects remain unclear. Here, we demonstrate that the levels of REV-ERBα and REV-ERBß expression were lower in the granulosa cells of PCOS patients than in control subjects. In vitro, we found that the overexpression of REV-ERBα and REV-ERBß, and their agonist SR9009, promoted the expression of mitochondrial biosynthesis genes PGC-1α, NRF1, and TFAM and inhibited autophagy in KGN cells. Our results also indicate that REV-ERBα and REV-ERBß can inhibit apoptosis in granulosa cells and promote proliferation. Importantly, the REV-ERB agonist SR9009 ameliorates abnormal follicular development by promoting mitochondrial biosynthesis and inhibiting autophagy in a mouse PCOS model. This allows us to speculate that SR9009 has potential as a therapeutic agent for the treatment of PCOS.

[Determination of paprazine in Polygonum orientale of different commodities by HPLC].

OBJECTIVE: To establish a method for the content determination of paprazine in Polygonum orientale, and provide a new evaluation index for the quality control for P. orientale. METHOD: HPLC was carried out on Agilent C18 (4.6 mm x 150 mm, 5 microm) with methanol-water (40:60) as mobile phase. The flow rate was 1.0 mL x min(-1) and the wavelength of UV detector was set at 290 nm. RESULT: The calibration curve was linear in the range of 0. 038-0.190 microg (r = 0.9999). The average recovery was 98.7% with the RSD of 2.36%. CONCLUSION: The method appears to be simple, accurate and reproducible, it can be used to determine the content of paprazine in P. orientale.

[Determination of eight kinds of ginsenosides in Shizhu ginseng].

OBJECTIVE: To establish the method for determining simultaneously eight kinds of ginsenoside Rg1, Re, Rf, Rg2, Rb1, Rc, Rb3 and Rd and their contents in Shizhu ginseng. METHOD: HPLC was carried out on Agilent TC-C18 (4.6 mm x 150 mm, 5 microm) with acetonitrile -0.05% phosphoric acid, gradient elution, the volume of flow 1 mL x min(-1), column temperature 30 degrees C and detection wavelength 203 nm. RESULT: The contents of eight kinds of ginsenosides in Shizhu ginseng were 1.32, 2.08, 0.72, 0. 24, 2.12, 1.06, 0.35, 0.55 mg x g(-1), respectively. CONCLUSION: The contents of ginsenoside ingredients in Shizhu ginseng were determined in the first time. The established method can be used in determining the contents of multiple gensenosides in herb ginseng simultaneously.

HPLC determination of eight polyphenols in the leaves of Crataegus pinnatifida Bge. var. major.

A simple high-performance liquid chromatographic (HPLC) assay using the internal standard method is developed for the simultaneous determination of eight polyphenols. The analyzed compounds isolated from the leaves of Crataegus pinnatifida Bge. var. major include chlorogenic acid, vitexin-4"-O-glucoside, vitexin-2"-O-rhamnoside, vitexin, rutin, hyperoside, isoquercitrin, and quercetin. HPLC analysis is performed on a Diamonsil C18 analytical column (150 x 4.6 mm, i.d., 5-microm) using solvent (A) acetonitrile-tetrahydrofuran (95:5, v/v) and (B) 1% aqueous phosphoric acid as the mobile phase with UV absorption at 270 nm. The calibration curves of the eight polyphenols are linear (r(2) > 0.9992) over the concentration range of 0.0894-120.0 microg/mL. The mean recoveries are 95.4% to 98.1%. The results indicate that the HPLC method developed can easily be applied to the determination of eight polyphenols in the leaves of Crataegus pinnatifida Bge. var. major.

Melatonin Reduces Androgen Production and Upregulates Heme Oxygenase-1 Expression in Granulosa Cells from PCOS Patients with Hypoestrogenia and Hyperandrogenia.

BACKGROUND/AIMS: Polycystic ovary syndrome (PCOS) is an endocrine disorder characterized by abnormal hormone levels in peripheral blood and poor-quality oocytes. PCOS is a pathophysiological syndrome caused by chronic inflammation and oxidative stress. The aim of this study was to investigate the mechanism of melatonin regulation on androgen production and antioxidative damage in granulosa cells from PCOS patients with hypoestrogenia and hyperandrogenia. METHODS: Cumulus-oocyte complexes were collected from PCOS patients who had low levels of estrogen in follicular fluids. RESULTS: Melatonin triggered upregulation of cytochrome P450 family 19 subfamily A member 1 (CYP19A1) expression via the extracellular signal-regulated kinase pathway in luteinized granulosa cells. As a result, conversion of androgen to 17ß-estradiol was accelerated. We also found that melatonin significantly reduced the levels of inducible nitric oxide (NO) synthetase and NO in luteinized granulosa cells. Levels of transcripts encoding NF-E2-related factor-2 and its downstream target heme oxygenase-1 were also increased, leading to anti-inflammatory and antioxidant effects. We also found that melatonin could improve oocyte development potential. CONCLUSION: Our preliminary results showed that melatonin had a positive impact on oocyte quality in PCOS patients with hypoestrogenia and hyperandrogenia.

[Microscopic quantitative study on Saiga tatarica in "lingyang qing fei pill"].

OBJECTIVE: To determine Saiga tatarica content in "Lingyang Qing Fei Pill". METHODS: Volumetric analysis combined with quantitative microscopy was used to determine Saiga tatarica content by sample itself as standard substance. RESULT AND CONCLUSION: The method of determining the content of Saiga tatarica is simple and creditable.

De Novo characterization of a Cephalotaxus hainanensis transcriptome and genes related to paclitaxel biosynthesis.

Cephalotaxus hainanensis, an endangered plant, is known to contain several metabolites with anti-cancer activity. Despite its clinical impact, the alkaloid metabolism of this species has remained largely uncharacterized. The potential of Cephalotaxus for metabolic engineering of medically interesting compounds has, so far, not been exploited, due to the almost complete lack of molecular information. We have therefore performed a high throughput RNA-seq analysis and assembled the transcriptome de novo. Raw reads comprising 4.3 Gbp were assembled de novo into 39,416 unique sequences (unigenes) with a mean length of 1,089.8 bp and a total assembly size of 45.8 Mbp, which equals to more than 50 times the number of Cephalotaxaceae sequences currently deposited in the GenBank (as of August 2013). As proof of principle for medically interesting pathways, gene fragments related to paclitaxel biosynthesis were searched and detected. To verify their functionality, the metabolic product paclitaxel, and its precursor baccatin III, were identified in the leaves of C. hainanensis by HPLC, and shown to be induced by MeJA. This finding demonstrates exemplarily the potential of the annotated transcriptome as information resource for the biotechnological exploitation of plant secondary metabolism.