Retinal ganglion cells encode differently in the myopic mouse retina?

The etiology of myopia remains unclear. This study investigated whether retinal ganglion cells (RGCs) in the myopic retina encode visual information differently from the normal retina and to determine the role of Connexin (Cx) 36 in this process. Generalized linear models (GLMs), which can capture stimulus-dependent changes in real neurons with spike timing precision and reliability, were used to predict RGCs responses to focused and defocused images in the retinas of wild-type (normal) and Lens-Induced Myopia (LIM) mice. As the predominant subunit of gap junctions in the mouse retina and a plausible modulator in myopia development, Cx36 knockout (KO) mice were used as a control for an intact retinal circuit. The kinetics of excitatory postsynaptic currents (EPSCs) of a single αRGC could reflect projection of both focused and defocused images in the retinas of normal and LIM, but not in the Cx36 knockout mice. Poisson GLMs revealed that RGC encoding of visual stimuli in the LIM retina was similar to that of the normal retina. In the LIM retinas, the linear-Gaussian GLM model with offset was a better fit for predicting the spike count under a focused image than the defocused image. Akaike information criterion (AIC) indicated that nonparametric GLM (np-GLM) model predicted focused/defocused images better in both LIM and normal retinas. However, the spike counts in 33% of αRGCs in LIM retinas were better fitted by exponential GLM (exp-GLM) under defocus, compared to only 13% αRGCs in normal retinas. The differences in encoding performance between LIM and normal retinas indicated the possible amendment and plasticity of the retinal circuit in myopic retinas. The absence of a similar response between Cx36 KO mice and normal/LIM mice might suggest that Cx36, which is associated with myopia development, plays a role in encoding focused and defocused images.

Transplantation of insulin-producing cells derived from human MSCs to treat diabetes in a non-human primate model.

BACKGROUND: Islet cell transplantation is an emerging therapy in the treatment of diabetes mellitus. Differentiation of islet cells from mesenchymal stem cells (MSCs) is a potential solution to the challenge of insufficient donor sources. This study investigated whether human umbilical cord-derived MSCs could effectively differentiate into insulin-producing cells (IPCs) and evaluated the therapeutic efficacy of IPCs in treating diabetes. METHODS: IPCs were induced from MSCs by a two-step protocol. IPC expression products were evaluated by western blot and real-time PCR. IPC insulin secretion was evaluated by ELISA. The viability of IPCs was measured by FDA/PI and dithizone staining. The non-human primate tree shrew was used as a diabetes model. After a single STZ induction into a diabetes model, a single intraportal transplantation of IPCs, MSCs, or normal saline was performed (n = 6 per group). Blood glucose was monitored for 3 weeks, then the animals were euthanized and the distribution of IPCs in the liver was examined pathologically. RESULTS: After about 3 weeks of in vitro induction, IPCs formed microspheres of 100-200 µm, with >95% viable cells that were dithizone stain positive. IPCs expressed islet-related genes and proteins and secreted high levels of insulin whether stimulated by low or high levels of glucose. After transplantation of IPCs into diabetic tree shrews, blood glucose levels decreased rapidly to near normal and were significantly lower than the MSC or saline groups for 3 weeks thereafter. CONCLUSION: We present the novel discovery that IPCs derived from human umbilical cord MSCs exert a therapeutic effect in a non-human primate model of diabetes. This study provides a preliminary experimental basis for the use of autologous MSC-derived IPCs in the treatment of human diabetes.

Prenatal Diagnosis of Structural Anomaly Among Singletons and Twins: Eight-Year Experience in a Chinese Tertiary Center.

OBJECTIVES: This study was designed to reveal structural abnormalities in singleton and twin pregnancies in the Chinese population. METHODS: This retrospective study spanned 8 years and included 1228 singleton pregnancies (112,919 examinees) and 49 twin pregnancies (1865 examinees) with structural anomalies diagnosed by ultrasound. Detailed descriptions of anomalies, gestational weeks at diagnosis, and maternal age were recorded. The odds ratio was evaluated in twin pregnancies with detectable structural anomalies. RESULTS: The annual average "ultrasound prevalence of fetal anomalies" among singleton and twin pregnancies were 1.09 and 3.06%, respectively. Mothers with twin anomalies were older (P < .001), and twin pregnancies were diagnosed with anomalies in earlier gestational weeks than singleton (P = .011). No differences were found in the types of anomalies between singleton and twin pregnancies. Central nervous system anomaly was the most common type in singleton and twin pregnancies. Twin pregnancies had higher rates of major anomalies than singleton (total OR 2.45), especially cardiovascular, central nervous, and gastrointestinal systems and ear/eye/face/neck disorders. CONCLUSIONS: Compared with singleton, twin pregnancies had higher odds of detectable structural anomalies. Twin pregnancies with structural anomalies were diagnosed at earlier gestational age and associated with older maternal age. Central nervous system anomaly was the most common type in singleton and twin pregnancies.

DEGENERATED LEMMA (DEL) regulates lemma development and affects rice grain yield.

In grass, the lemma is a unique floral organ structure that directly determines grain size and yield. Despite a great deal of research on grain enlargement caused by changes in glume cells, the importance of normal development of the glume for normal grain development has been poorly studied. In this study, we investigated a rice spikelet mutant, degenerated lemma (del), which developed florets with a slightly degenerated or rod-like lemma. More importantly, del also showed a significant reduction in grain length and width, seed setting rate, and 1000-grain weight, which led to a reduction in yield. The results indicate that the mutation of the DEL gene further affects rice grain yield. Map-based cloning shows a single-nucleotide substitution from T to A within Os01g0527600/DEL/OsRDR6, causing an amino acid mutation of Leu-34 to His-34 in the del mutant. Compared with the wild type, the expression of DEL in del was significantly reduced, which might be caused by single base substitution. In addition, the expression level of tasiR-ARF in del was lower than that of the wild type. RT-qPCR results show that the expression of some floral organ identity genes was changed, which indicates that the DEL gene regulates lemma development by modulating the expression of these genes. The present results suggest that the normal expression of DEL is necessary for the formation of lemma and the normal development of grain morphology and therefore has an important effect on the yield. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-023-01297-6.

Preliminary evaluation of the efficacy and safety of brimonidine for general anesthesia.

BACKGROUND: To determine the hypnotic and analgesic effects of brimonidine, and evaluate its efficacy and safety for general anesthesia. Potentiation of pentobarbital sleeping time following brimonidine administration was observed in mice, as was the analgesic activity of brimonidine. METHODS: The median effective dose (ED50) and lethal dose (LD50) of intraperitoneally injected brimonidine were determined in hypnotized mice. In addition, the LD50 of intravenously injected brimonidine, and ED50 of intravenously, intramuscularly, and intrarectally injected brimonidine in hypnotized rabbits were determined. Finally, the synergistic anesthetic effect of brimonidine and chloral hydrate was evaluated in rabbits. RESULTS: Intraperitoneal injection of 10 mg/kg brimonidine enhanced the hypnotic effect of a threshold dose of pentobarbital. Intraperitoneally injected brimonidine produced dose-related analgesic effects in mice. The ED50 of intraperitoneally administered brimonidine in hypnotized mice was 75.7 mg/kg and the LD50 was 379 mg/kg. ED50 values of intravenous, intramuscular, and intrarectal brimonidine for hypnosis in rabbits were 5.2 mg/kg, 8.8 mg/kg, and 8.7 mg/kg, respectively; the LD50 of intravenous brimonidine was 146 mg/kg. Combined intravenous administration of 0.6 mg/kg brimonidine and 0.03 g/kg chloral hydrate had a synergistic anesthetic effect. CONCLUSIONS: Brimonidine elicited hypnotic and analgesic effects after systemic administration and exhibited safety. Moreover, brimonidine enhanced the effects of other types of narcotics when combined.

[Preparation and quality evaluation of orodispersible film containing ginkgolide B novel nanosuspension lyophilized powder].

To prepare a new dosage form that can improve the drug loading of the film--ginkgolide B nanosuspension lyophilized powder orodispersible film(GB-NS-LP-ODF) and to evaluate its quality. Firstly, ginkgolide B nanosuspension(GB-NS) was prepared by media milling method, and then ginkgolide B nanosuspension lyophilized powder(GB-NS-LP) was prepared with freeze-drying method. The mannitol was used as lyoprotectant and its dosage was also investigated. GB-NS-LP-ODF was prepared by solvent casting method and its formulation was screened by single factor test method and optimized by orthogonal test. The appearance, mechanical properties, content uniformity and in vitro dissolution of the optimized GB-NS-LP-ODF were investigated. The particle size of prepared GB-NS was about 201 nm, and the optimal dosage of mannitol was 8%. According to the optimal formula, the GB-NS-LP-ODF was prepared with GB-NS-LP 35.6%, PVA 0588 49.4%, PEG 400 10.7% and CMS-Na 4.3%, and completely disintegrated in about 30 s, and the particle size of reconstituted GB nanoparticles from ODF was about 210 nm. The film with smooth appearance and good mechanical properties was stable within 30 days and the content uniformity(A+2.2 S<15) conformed to the regulations. Scanning electron microscope(SEM) showed that GB-NS-LP-ODFs were evenly distributed and the particle size was about 200 nm. X-rays diffraction(XRD) showed that its crystallinity was significantly lower than that of GB raw drug and GB-ODF. The results of in vitro release test showed that the drug film was completely dissoluted within 10 minutes. These results indicated that nanosuspension lyophilized powder was prepared by freeze drying of nanosuspensions, and then loaded into the orodispersible film to effectively increase the drug loading of the ODF and have broad application prospects.

[Identification of metabolites of Zhali Nusi Prescription in rat plasma, bile, urine and feces after oral administration].

This study was designed to determine the metabolites of Zhali Nusi Prescription(ZLNSP) in rats. The ultra-high performance liquid chromatography-LTQ Orbitrap mass spectrometric(UHPLC-LTQ-Orbitrap-MS) and mass defect filter techniques were applied to analyze the metabolites of ZLNSP in rat plasma, bile, urine and feces. The biological samples were analyzed by ACQUITY UPLC BEH T_3 column(2.1 mm×100 mm,1.7 µm), with 0.1% formic acid water(A)-acetonitrile(B) as mobile phase, and the biological samples were analyzed in negative ion mode by electrospray ionization mass spectrometry(ESI-MS). An analytical method for biological samples of rats was established, and 8 prototype components and 36 metabolites were identified. The results showed that the metabolic pathways of the main components of ZLNSP in rats included methylation, glucuronidation, sulfation and so on. It provi-ded information for the therapeutic effect of ZLNSP in vivo.

[Chemical constituents and their biosynthesis mechanisms of Polygonum cuspidatum].

This article reviews the research progress of the chemical constituents and biosynthesis mechanisms of Polygonum cuspidatum. The chemistry components isolated from P. cuspidatum are mainly anthraquinones, naphthoquinones, stilbenes, flavonoids, and other compounds. The synthase genes involved in the biosynthesis process were summarized. The biosynthesis mechanism of stilbenes and anthraquinones was discussed. This article hopefully to provide a reference for further research, development and utilization of P. cuspidatum.

Hydrotalcite Can Prevent the Damaging Effects of Helicobacter Pylori on Gastric Epithelial Cells.

BACKGROUND: Helicobacter pylori is a major cause of gastric diseases including gastric cancer. This study was aimed to explore whether hydrotalcite can inhibit H. pylori infection of gastric epithelial cells. METHODS: the gastric epithelial cell line GES-1 and the gastric cancer cell line BGC823 were infected with H. pylori at multiplicities of infections (MOIs) of 50:1 and 100:1. Hydrotalcite was added to cell cultures. Cell apoptosis and cell cycle analysis were performed to measure the situation of cell growth. The main changes of cell ultrastructure were observed by transmission electron microscopy. H. pylori cell adhesion was observed by scanning electron microscopy. RESULTS: hydrotalcite could significantly inhibit cell apoptosis of GES-1 and cell proliferation of BGC823 induced by H. pylori infection at an MOI of 50:1. Hydrotalcite treatment protected gastric cells from H. pylori infection, and H. pylori adhesion to gastric cells was reduced. However, hydrotalcite could not reverse damage induced by H. pylori infection at an MOI of 100:1. CONCLUSION: hydrotalcite can protect gastric cells from H. pylori infection when cell damage is not serious. It can weaken the damage of cells induced by H. pylori and decrease H. pylori adhesion to gastric cells.

Effects of home-based long-term care services on caregiver health according to age.

BACKGROUND: Caregiver health is a crucial public health concern due to the increasing number of elderly people with disabilities. Elderly caregivers are more likely to have poorer health and be a care recipient than younger caregivers. The Taiwan government offers home-based long-term care (LTC) services to provide formal care and decrease the burden of caregivers. This study examined the effects of home-based LTC services on caregiver health according to caregiver age. METHODS: This cross-sectional study included a simple random sample of care recipients and their caregivers. The care recipients had used LTC services under the Ten-Year Long-Term Care Project (TLTCP) in Taiwan. Data were collected through self-administered questionnaires from September 2012 to January 2013. The following variables were assessed for caregivers: health, sex, marital status, education level, relationship with care recipient, quality of relationship with care recipient, job, household monthly income, family income spent on caring for the care recipient (%) and caregiving period. Furthermore, the following factors were assessed for care recipients: age, sex, marital status, education level, living alone, number of family members living with the care recipient, quality of relationship with family and dependency level. The health of the caregivers and care recipients was measured using a self-rated question (self-rated health [SRH] was rated as very poor, poor, fair, good and very good). RESULTS: The study revealed that home nursing care was significantly associated with the health of caregivers aged 65 years or older; however, caregivers aged less than 65 who had used home nursing care, rehabilitation or respite care had poorer health than those who had not used these services. In addition, the following variables significantly improved the health of caregivers aged 65 years or older: caregiver employment, 20% or less of family income spent on caregiving than 81%-100% and higher care recipient health. The involvement of daughters-in-law, rather than spouses, and care recipient health were positively related to the health of caregivers aged less than 65 years. CONCLUSIONS: The findings suggest that home-based LTC service use benefits the health of elderly caregivers. By contrast, home-based LTC service use may be negatively correlated with the health of the caregivers aged less than 65 years.

SENP1 regulates cell migration and invasion in neuroblastoma.

Neuroblastoma (NB) is an embryonic solid tumor derived from precursor cells of the sympathetic nervous system, and accounts for 11% of childhood cancers and around 15% of cancer deaths in children. SUMOylation and deSUMOylation are dynamic mechanisms regulating a spectrum of protein activities. The SUMO proteases (SENP) remove SUMO conjugate from proteins, and their expression is deregulated in diverse cancers. However, nothing is known about the role of SENPs in NBL. In the present study, we found that SENP1 expression was significantly high in metastatic NB tissues compared with primary NB tissues. Overexpression of SENP1 promoted NB cells migration and invasion. Inhibition of SENP1 could significantly suppress NB cell migration and invasion. Moreover, we found that SENP1 could regulate the expression of CDH1, MMP9, and MMP2. In summary, the data presented here indicate a significant role of SENP1 in the regulation of cell migration and invasion in NB and suppress SENP1 expression as promising candidates for novel treatment strategies of NB.

Coverage, quality of and barriers to postnatal care in rural Hebei, China: a mixed method study.

BACKGROUND: Postnatal care is an important link in the continuum of care for maternal and child health. However, coverage and quality of postnatal care are poor in low- and middle-income countries. In 2009, the Chinese government set a policy providing free postnatal care services to all mothers and their newborns in China. Our study aimed at exploring coverage, quality of care, reasons for not receiving and barriers to providing postnatal care after introduction of this new policy. METHODS: We carried out a mixed method study in Zhao County, Hebei Province, China from July to August 2011. To quantify the coverage, quality of care and reasons for not using postnatal care, we conducted a household survey with 1601 caregivers of children younger than two years of age. We also conducted semi-structured interviews with 24 township maternal and child healthcare workers to evaluate their views on workload, in-service training and barriers to postnatal home visits. RESULTS: Of 1442 (90% of surveyed caregivers) women who completed the postnatal care survey module, 8% received a timely postnatal home visit (within one week after delivery) and 24% of women received postnatal care within 42 days after delivery. Among women who received postnatal care, 37% received counseling or guidance on infant feeding and 32% on cord care. 24% of women reported that the service provider checked jaundice of their newborns and 18% were consulted on danger signs and thermal care of their newborns. Of 991 mothers who did not seek postnatal care within 42 days after birth, 65% of them said that they did not knew about postnatal care and 24% of them thought it was unnecessary. Qualitative findings revealed that staff shortages and inconvenient transportation limited maternal and child healthcare workers in reaching out to women at home. In addition, maternal and child healthcare workers said that in-service training was inadequate and more training on postnatal care, hands-on practice, and supervision were needed. CONCLUSIONS: Coverage and quality of postnatal care were low in rural Hebei Province and far below the targets set by Chinese government. We identified barriers both from the supply and demand side.

An Updated Comprehensive Pharmacovigilance Study of Drug-Induced Thrombocytopenia Based on FDA Adverse Event Reporting System Data.

Drug-induced thrombocytopenia (DIT) deserves both clinical and research attention for the serious clinical consequences and high prevalence of the condition. The current study aimed to perform a comprehensive pharmacovigilance analysis of DIT reported in the US Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS) database, with a particular focus on drugs associated with thrombocytopenia events. A disproportionality analysis of DIT was conducted using reports submitted to FARES from January 2004 to December 2022. Both the information component (IC) and reporting odds ratio (ROR) algorithms were applied to identify an association between target drugs and DIT events. A total of 15,940,383 cases were gathered in FAERS, 168,657 of which were related to DIT events. The top 50 drugs ranked by number of cases and ranked by signal strength were documented. The top 5 drugs ranked by number of cases were lenalidomide (10,601 cases), niraparib (3726 cases), ruxolitinib (3624 cases), eltrombopag (3483 cases), and heparin (3478 cases). The top 5 drugs ranked by signal strength were danaparoid (ROR 37.61, 95%CI 30.46-46.45), eptifibatide (ROR 34.75, 95%CI 30.65-39.4), inotersen (ROR 34.00, 95%CI 29.47-39.23), niraparib (ROR 30.53, 95%CI 29.42-31.69), and heparin (ROR 28.84, 95%CI 27.76-29.97). The top 3 involved drug groups were protein kinase inhibitors, antimetabolites, and monoclonal antibodies and antibody-drug conjugates. The current comprehensive pharmacovigilance study identified more drugs associated with thrombocytopenia. Although the mechanisms of DIT have been elucidated for some drugs, others still require further investigation.

Exosomal-microRNAs Improve Islet Cell Survival and Function In Islet Transplantation.

Exosomal-microRNAs (Exo-miRNAs) are key regulators of islet cell function, including insulin expression, processing, and secretion. Exo-miRNAs have a significant impact on the outcomes of islet transplantation as biomarkers for evaluating islet cell function and survival. Furthermore, they have been linked to vascular remodeling and immune regulation following islet transplantation. Mesenchymal stem cell-derived exosomes have been shown in preliminary studies to improve islet cell viability and function when injected or transplanted into mice. Overall, Exo-miRNAs have emerged as novel agents for improving islet transplantation success rates. The role of islet-derived Exo-miRNAs and mesenchymal stem cells-derived Exo-miRNAs as biomarkers and immunomodulators in islet regeneration, as well as their role in improving islet cell viability and function in islet transplantation, are discussed in this review.

Evaluating the link between immune characteristics and attention deficit hyperactivity disorder through a bi-directional Mendelian randomization study.

Context: Despite the recognition of attention deficit hyperactivity disorder (ADHD) as a multifaceted neurodevelopmental disorder, its core causes are still ambiguous. The objective of this study was to explore if the traits of circulating immune cells contribute causally to susceptibility to ADHD. Methods: By employing a unified GWAS summary data covering 731 immune traits from the GWAS Catalog (accession numbers from GCST0001391 to GCST0002121), our analysis focused on the flow cytometry of lymphocyte clusters, encompassing 3,757 Sardinians, to identify genetically expected immune cells. Furthermore, we obtained summarized GWAS statistics from the Psychiatric Genomics Consortium to evaluate the genetic forecasting of ADHD. The studies employed ADHD2019 (20,183 cases and 35,191 controls from the 2019 GWAS ADHD dataset) and ADHD2022 (38,691 cases and 275,986 controls from the 2022 GWAS ADHD dataset). Through the examination of genome-wide association signals, we identified shared genetic variances between circulating immune cells and ADHD, employing the comprehensive ADHD2022 dataset. We primarily utilized inverse variance weighted (IVW) and weighted median methods in our Mendelian randomization research and sensitivity assessments to evaluate diversity and pleiotropy. Results: After adjusting for false discovery rate (FDR), three distinct immunophenotypes were identified as associated with the risk of ADHD: CD33 in Im MDSC (OR=1.03, CI: 1.01~1.04, P=3.04×10-5, PFDR =0.015), CD8br NKT %T cell (OR=1.08, 95%CI: 1.04~1.12, P=9.33×10-5, PFDR =0.023), and CD8br NKT %lymphocyte (OR=1.08, 95%CI: 1.03~1.12, P=3.59×10-4, PFDR =0.066). Furthermore, ADHD showed no statistical effects on immunophenotypes. It's worth noting that 20 phenotypes exist where ADHD's appearance could diminish 85% of immune cells, including FSC-A in myeloid DC (ß= -0.278, 95% CI: 0.616~0.931, P=0.008), CD3 in CD45RA- CD4+ (ß= -0.233, 95% CI: 0.654~0.960, P=0.017), CD62L- monocyte AC (ß=0.227, 95% CI: 0.038~1.518, P=0.019), CD33 in CD33br HLA DR+ CD14dim (ß= -0.331, 95% CI: 0.543~0.950, P=0.020), and CD25 in CD39+ resting Treg (ß=0.226, 95% CI: 1.522, P=0.022), and FSC-A in monocytes (ß= -0.255, 95% CI: 0.621~0.967, P=0.234), among others. Conclusion: Studies indicate that the immune system's response influences the emergence of ADHD. The findings greatly improve our understanding of the interplay between immune responses and ADHD risk, aiding in the development of treatment strategies from an immunological perspective.

Digital identification and adulteration analysis of Pulsatilla Radix and Pulsatilla Cernua based on "digital identity" and UHPLC-QTOF-MSE.

Under the background of digitalization of traditional Chinese medicine (TCM), to realize the quick identification and adulteration analysis of Pulsatilla Radix (PR), adhering to digital conviction, this study conducted UHPLC-QTOF-MSE analysis on PR and its adulterant-Pulsatilla Cernua (PC) from different batches and based on digital conversion, the shared ions were extracted from different batches of PR and PC as their "ions representation", respectively. Further, the data set of unique ions of PR relative to PC and PC relative to PR were screened out as the "digital identities" of PR and PC respectively. Further, above the "digital identities" of PR and PC were used as the benchmarks for matching and identifying to feedback give a matching credibility (MC). The results showed that based on the "digital identities" of PR and PC, the digital identification of two herbal samples can be realized efficiently and accurately at the individual level with the MC≥70.00 %, even if 5 % of PC in the mixed samples can still be identified efficiently and accurately. The study is of great practical significance for improving the identification efficiency of PR and PC, cracking down on adulterated and counterfeit drugs, and strengthening the quality control of PR. In addition, it has important reference significance for developing non-targeted digital identification of herbal medicines at the individual level based on UHPLC-QTOF-MSE and the "digital identity", which was beneficial to the construction of digital Chinese medicine and digital quality control.

Pharmacogenetic angiogenesis profiling for first-line chemotherapy in patients with advanced gastric cancer.

We retrospectively investigated germline polymorphisms in angiogenesis pathway genes (14 SNPs) and their correlation to clinical outcome (progression free survival and overall survival) in 128 patients with unresectable-advanced gastric carcinoma (AGC) treated with first-line chemotherapy. Our analysis revealed that Endostatin +4349 G>A polymorphism exhibited a worse progression free survival (PFS) and overall survival (OS) compared with the GG genotype. Significant OS difference was also observed in the endothelial nitric oxide synthase (eNOS)-786 T>C polymorphism. Hence, common germline variants in Endostatin and eNOS genes have predictive significance for clinical outcome and survivality in AGC patients treated with first-line chemotherapy.

[Genome-scale sequence data processing and epigenetic analysis of DNA methylation].

A new approach recently developed for detecting cytosine DNA methylation (mC) and analyzing the genome-scale DNA methylation profiling, is called BS-Seq which is based on bisulfite conversion of genomic DNA combined with next-generation sequencing. The method can not only provide an insight into the difference of genome-scale DNA methylation among different organisms, but also reveal the conservation of DNA methylation in all contexts and nucleotide preference for different genomic regions, including genes, exons, and repetitive DNA sequences. It will be helpful to under-stand the epigenetic impacts of cytosine DNA methylation on the regulation of gene expression and maintaining silence of repetitive sequences, such as transposable elements. In this paper, we introduce the preprocessing steps of DNA methylation data, by which cytosine (C) and guanine (G) in the reference sequence are transferred to thymine (T) and adenine (A), and cytosine in reads is transferred to thymine, respectively. We also comprehensively review the main content of the DNA methylation analysis on the genomic scale: (1) the cytosine methylation under the context of different sequences; (2) the distribution of genomic methylcytosine; (3) DNA methylation context and the preference for the nucleotides; (4) DNA- protein interaction sites of DNA methylation; (5) degree of methylation of cytosine in the different structural elements of genes. DNA methylation analysis technique provides a powerful tool for the epigenome study in human and other species, and genes and environment interaction, and founds the theoretical basis for further development of disease diagnostics and therapeutics in human.

Population Diversity Analysis Provide Insights into Provenance Identification of Dendrobium catenatum.

Dendrobium catenatum (Dendrobium officinale) is a valuable genuine herb. The source of this species is difficult to be identified by traditional methods including morphology, spectroscopy, and chromatography. We used the restriction site-associated DNA sequencing (RAD-seq) approach to perform the high-throughput sequencing of 24 D. catenatum provenances. In this study, 371.18 Gb clean data were obtained, and 655,057 high-quality SNPs were selected after their filtration. We used phylogenetic tree, genetic structure, and principal component analyses to examine the genetic diversities and genetic relationships of the 109 accessions. We found that D. catenatum could be divided into two groups, and each group was closely related to the distribution of the sampling sites. At the population level, the average nucleotide diversity (π) of the D. catenatum population mutation parameters was 0.1584 and the expected heterozygosity (HE) was 0.1575. The GXLPTP07 accessions showed the highest genetic diversity in terms of the private allele number, observed heterozygosity, and nucleotide diversity. The Mantel test showed a significant positive correlation between the genetic and geographic distances among the overall distribution. A genetic information database of D. catenatum was established, which confirmed that RAD-seq technology has the potential to be applied in the identification of medicinal Dendrobium of different origins.

Untying the Gordian knot of plastid phylogenomic conflict: A case from ferns.

Phylogenomic studies based on plastid genome have resolved recalcitrant relationships among various plants, yet the phylogeny of Dennstaedtiaceae at the level of family and genera remains unresolved due to conflicting plastid genes, limited molecular data and incomplete taxon sampling of previous studies. The present study generated 30 new plastid genomes of Dennstaedtiaceae (9 genera, 29 species), which were combined with 42 publicly available plastid genomes (including 24 families, 27 genera, 42 species) to explore the evolution of Dennstaedtiaceae. In order to minimize the impact of systematic errors on the resolution of phylogenetic inference, we applied six strategies to generate 30 datasets based on CDS, intergenic spacers, and whole plastome, and two tree inference methods (maximum-likelihood, ML; and multispecies coalescent, MSC) to comprehensively analyze the plastome-scale data. Besides, the phylogenetic signal among all loci was quantified for controversial nodes using ML framework, and different topologies hypotheses among all datasets were tested. The species trees based on different datasets and methods revealed obvious conflicts at the base of the polypody ferns. The topology of the "CDS-codon-align-rm3" (CDS with the removal of the third codon) matrix was selected as the primary reference or summary tree. The final phylogenetic tree supported Dennstaedtiaceae as the sister group to eupolypods, and Dennstaedtioideae was divided into four clades with full support. This robust reconstructed phylogenetic backbone establishes a framework for future studies on Dennstaedtiaceae classification, evolution and diversification. The present study suggests considering plastid phylogenomic conflict when using plastid genomes. From our results, reducing saturated genes or sites can effectively mitigate tree conflicts for distantly related taxa. Moreover, phylogenetic trees based on amino acid sequences can be used as a comparison to verify the confidence of nucleotide-based trees.