Comparative transcriptome and methylome of polar bears, giant and red pandas reveal diet-driven adaptive evolution.

Epigenetic regulation plays an important role in the evolution of species adaptations, yet little information is available on the epigenetic mechanisms underlying the adaptive evolution of bamboo-eating in both giant pandas (Ailuropoda melanoleuca) and red pandas (Ailurus fulgens). To investigate the potential contribution of epigenetic to the adaptive evolution of bamboo-eating in giant and red pandas, we performed hepatic comparative transcriptome and methylome analyses between bamboo-eating pandas and carnivorous polar bears (Ursus maritimus). We found that genes involved in carbohydrate, lipid, amino acid, and protein metabolism showed significant differences in methylation and expression levels between the two panda species and polar bears. Clustering analysis of gene expression revealed that giant pandas did not form a sister group with the more closely related polar bears, suggesting that the expression pattern of genes in livers of giant pandas and red pandas have evolved convergently driven by their similar diets. Compared to polar bears, some key genes involved in carbohydrate metabolism and biological oxidation and cholesterol synthesis showed hypomethylation and higher expression in giant and red pandas, while genes involved in fat digestion and absorption, fatty acid metabolism, lysine degradation, resistance to lipid peroxidation and detoxification showed hypermethylation and low expression. Our study elucidates the special nutrient utilization mechanism of giant pandas and red pandas and provides some insights into the molecular mechanism of their adaptive evolution of bamboo feeding. This has important implications for the breeding and conservation of giant pandas and red pandas.

Enhancing antimicrobial resistance detection with MetaGeneMiner: Targeted gene extraction from metagenomes.

BACKGROUND: Accurately and efficiently extracting microbial genomic sequences from complex metagenomic data is crucial for advancing our understanding in fields such as clinical diagnostics, environmental microbiology, and biodiversity. As sequencing technologies evolve, this task becomes increasingly challenging due to the intricate nature of microbial communities and the vast amount of data generated. Especially in intensive care units (ICUs), infections caused by antibiotic-resistant bacteria are increasingly prevalent among critically ill patients, significantly impacting the effectiveness of treatments and patient prognoses. Therefore, obtaining timely and accurate information about infectious pathogens is of paramount importance for the treatment of patients with severe infections, which enables precisely targeted anti-infection therapies, and a tool that can extract microbial genomic sequences from metagenomic dataset would be of help. METHODS: We developed MetaGeneMiner to help with retrieving specific microbial genomic sequences from metagenomes using a k-mer-based approach. It facilitates the rapid and accurate identification and analysis of pathogens. The tool is designed to be user-friendly and efficient on standard personal computers, allowing its use across a wide variety of settings. We validated MetaGeneMiner using eight metagenomic samples from ICU patients, which demonstrated its efficiency and accuracy. RESULTS: The software extensively retrieved coding sequences of pathogens Acinetobacter baumannii and herpes simplex virus type 1 and detected a variety of resistance genes. All documentation and source codes for MetaGeneMiner are freely available at https://gitee.com/sculab/MetaGeneMiner. CONCLUSIONS: It is foreseeable that MetaGeneMiner possesses the potential for applications across multiple domains, including clinical diagnostics, environmental microbiology, gut microbiome research, as well as biodiversity and conservation biology. Particularly in ICU settings, MetaGeneMiner introduces a novel, rapid, and precise method for diagnosing and treating infections in critically ill patients. This tool is capable of efficiently identifying infectious pathogens, guiding personalized and precise treatment strategies, and monitoring the development of antibiotic resistance, significantly impacting the diagnosis and treatment of severe infections.

Study on the ideal sagittal position of the lower third of the face in high-angle patients with different forehead forms / 口腔疾病防治

Objective@#To explore the ideal sagittal position of the lower third of the face in high-angle patients with different forehead forms and to provide a reference for clinical treatment. @*Methods@#Informed consent and portrait authorization were obtained from all patients, and the study passed the ethical review of the unit. We categorized forehead forms into four types: straight, rounded, type I angular (angled at the middle third of the forehead) and type II angular (angled at the upper third of the forehead). Profiles of high-angle patients with different forehead forms were collected. The initial position was when the facial axis point (FA point) was positioned at the goal anterior-limit line (GALL). After being silhouetted, the lower third of the face was moved forward and backward by 1 mm, 2 mm, 3 mm, and 4 mm each, plus the initial silhouetted picture, to obtain 9 images for each patient. A survey was created with these lateral profile silhouettes, and the silhouette images were ranked by 30 orthodontists and 30 laypersons. @*Results@# There were significant differences in profile scores at different movement distances of the lower third of the face among high-angle patients with different forehead shapes (P<0.05). Overall, high-angle patients with straight or type II angular foreheads had higher scores when the lower third of the face did not move. For high-angle patients with a rounded forehead, orthodontists and laypersons gave the highest scores when the lower third of the face was moved backward by 2 mm and 4 mm, respectively. For high-angle patients with a type I angular forehead, orthodontists thought the scores of backward movement of 4 mm were the highest, and laypersons thought the scores of backward movement of 3 mm were the highest. No significant difference was found in scores between orthodontists and laypersons (P>0.05). @*Conclusion @#The forehead forms and the sagittal position of the lower third of the face will affect the face’s profile aesthetics. Patients with straight and type Ⅱ angular foreheads has the best profile when the FA point is located on the GALL line. For patients with rounded and type Ⅰ angular foreheads, a posterior location of the lower third of the face is more desirable than the initial position.

Genome of Lindera glauca provides insights into the evolution of biosynthesis genes for aromatic compounds.

Lindera glauca is a crucial source of diverse industrial oil and medicines. The spicy aroma of tender leaves is caused by the presence of abundant aromatic compounds. Here, we present its chromosome-level genome assembly comprising 12 pseudochromosomes (2,092.2 Mb; scaffold N50: 186.5 Mb), which was predicted to have 65,145 protein-coding genes. Comparative genomic analyses indicated two whole-genome duplication (WGD) events in the Lauraceae family, contributing to the production of numerous terpene synthase (TPS) genes. We identified 138 TPS genes in L. glauca. Comparative transcriptomic analyses revealed high expression of genes Lg03G2346 and Lg08G140 in TPS-a and Lg07G2961 and Lg12G971 in TPS-b subfamilies, which regulated the biosynthesis of the monoterpenoid ß-ocimene and sesquiterpenoid D-germacrene in L. glauca. The results suggested a molecular basis for species-specific terpenoid biosynthesis and provided a foundation for molecular breeding to produce desired characteristics and a valuable reference genome.

Dahuang Mudan decoction repairs intestinal barrier in chronic colitic mice by regulating the function of ILC3.

ETHNOPHARMACOLOGICAL RELEVANCE: Dahuang Mudan decoction (DMD) is a classic prescription for treating intestinal carbuncle from Zhang Zhongjing's "Essentials of the Golden Chamber" in the Han Dynasty. Recent studies also prove that DMD has a therapeutic effect on ulcerative colitis (UC), but its mechanism is still unclear. AIM OF STUDY: In this study, we aim to assess the therapeutic effect of DMD on DSS-induced chronic colitis in mice and deeply expound its underlying regulative mechanism. MATERIALS AND METHODS: The efficacy of DMD on mice with 2% DSS-induced chronic colitis was examined by changes in mouse body weight, DAI score, colon length changes, peripheral blood white blood cells (WBC) and red blood cells (RBC) counts, and hemoglobin (HGB) content, using mesalazine as a positive control. A small animal imaging system observed the FITC-Dextran fluorescence distribution in mice, and the contents of IL-22 and IL-17A in colon tissue homogenate supernatant and LPS in peripheral blood were detected by ELISA. Fluorescence in situ molecular hybridization and bacterial culture were used to investigate bacterial infiltration in intestinal mucosa and bacterial translocation in mesenteric lymph nodes and spleen. Mice immune function was further evaluated by analyzing the changes in spleen index, thymus index, and the ratio of peripheral blood granulocytes, monocytes, and lymphocytes. Meanwhile, the proportion of NCR+ group 3 innate lymphoid cells (ILC3), NCR-ILC3, and IL-22+ILC3 in colonic lamina propria lymphocytes of mice was detected by flow cytometry. The contents of effectors IL-22, IL-17A, and GM-CSF were detected by RT-PCR. We use cell scratching to determine the effect of DMD conditioned medium on the migration of Caco-2 cells by establishing an in vitro model of MNK-3 conditioned medium (CM) intervening Caco-2 cells. RT-PCR and WB detect the expression of tight junction ZO-1, Occludin, and Claudin-1. RESULTS: DMD restored the body weight, colon length, peripheral blood RBC numbers, and HGB content of chronic colitis mice and reduced peripheral blood WBC and colon inflammatory cell infiltration. Moreover, DMD decreased LPS content in serum, bacterial infiltration of colonic mucosa, and bacterial translocation in spleen and mesenteric lymph nodes. Simultaneously, DMD intensified the expression of ZO-1, Occludin, and Claudin-1, the ratio of NCR+ILC3 and IL-22+ILC3, and decreased the proportion of NCR-ILC3. In vitro studies also confirmed that the conditioned medium of DMD promoted the migration of Caco-2 cells and the expression of tight junction proteins. CONCLUSION: Our results confirm that DMD improves inflammation and restores intestinal epithelial function in mice with chronic colitis, and the mechanism may be related to regulating ILC3 function.

Comparison of 2D Optical Imaging and 3D Microtomography Shape Measurements of a Coastal Bioclastic Calcareous Sand.

This article compares measurements of particle shape parameters from three-dimensional (3D) X-ray micro-computed tomography (µCT) and two-dimensional (2D) dynamic image analysis (DIA) from the optical microscopy of a coastal bioclastic calcareous sand from Western Australia. This biogenic sand from a high energy environment consists largely of the shells and tests of marine organisms and their clasts. A significant difference was observed between the two imaging techniques for measurements of aspect ratio, convexity, and sphericity. Measured values of aspect ratio, sphericity, and convexity are larger in 2D than in 3D. Correlation analysis indicates that sphericity is correlated with convexity in both 2D and 3D. These results are attributed to inherent limitations of DIA when applied to platy sand grains and to the shape being, in part, dependent on the biology of the grain rather than a purely random clastic process, like typical siliceous sands. The statistical data has also been fitted to Johnson Bounded Distribution for the ease of future use. Overall, this research demonstrates the need for high-quality 3D microscopy when conducting a micromechanical analysis of biogenic calcareous sands.

Visualization of Interstitial Pore Fluid Flow.

Pore scale analysis of flow through porous media is of interest because it is essential for understanding internal erosion and piping, among other applications. Past studies have mainly focused on exploring macroscopic flow to infer microscopic phenomena. An innovative method is introduced in this study which permits visualization of interstitial fluid flow through the pores of a saturated synthetic transparent granular medium at the microscale. Several representative images of Ottawa sand were obtained using dynamic image analysis (DIA), for comparison with flow through perfect cylinders. Magnified transparent soil particles made of hydrogel were cast in 3D printed molds. Custom 3D printed jigs were employed for accurate positioning of the particles to ensure that particles have the same flow area within the soil. The pore fluid was embedded with silver-coated hollow microspheres that allowed for their florescence and tracking their movement within the model when illuminated by a laser light source. Images of the flow were captured from the model using a high-speed camera. This, along with particle image velocimetry (PIV) provided for the velocity and direction analysis of fluid flow movements within the pore space of a planar 2D model. Comparison of interstitial flow through homogeneous porosity-controlled Ottawa-shaped and cylindrical particles demonstrates that the magnitude of turbulence is related to particle roundness.

Roasting intervention for the volatile composition of three varieties of nuts originating from Torreya yunnanensis.

For the first time, the volatiles of three varieties of fresh and roasted Torreya yunnanensis nuts were investigated by solid-phase microextraction-gas chromatography-mass spectrometry. The results indicated that roasting had the greatest effect on the volatiles of millet capsules. Fresh nuts had many terpenes, esters, and aldehydes, while roasting led to the formation of pyrazines and furans. In subsequent work, short-term low temperature and small sample area exposed to high temperature had a large effect on the increase in some volatiles and was characterized by a green flavor, such as α-pinene, while ultrahigh-temperature (200 and 230°C) resulted in a decrease in the total volatiles with the generation of unpleasant flavors. Finally, the combination of 170°C for 40 min and slight crushing was found to be the best roasting conditions for samples by means of GC-MS and two-dimensional gas chromatography and time-of-flight mass spectrometry (GC × GC/TOF-MS). PRACTICAL APPLICATIONS: Torreya yunnanensis and its nuts have broad development prospects because of their wide use and rich nutrition. However, inappropriate processing and lack of attention to natural materials such as nuts and wood leads to their poor usage. In addition, volatile compounds make a major contribution to the nut aroma, which is an important indicator of their sensory quality. However, no one has applied roasting technology to Torreya yunnanensis nuts or studied the volatile compounds of the roasted nuts. This study revealed the changes in the composition and content of volatile compounds in Torreya yunnanensis nuts before and after roasting, and the influence of different process points, suggesting that they are key contributors to the development of the related products.

Multigene Phylogeny, Diversity and Antimicrobial Potential of Endophytic Sordariomycetes From Rosa roxburghii.

Rosa roxburghii Tratt. is widely applied in food, cosmetics, and traditional medicine, and has been demonstrated to possess diverse bioactivities. Plant endophytic fungi are important microbial resources with great potential for application in many fields. They not only establish mutualistic symbiosis with host plants but also produce a variety of bioactive compounds. Therefore, in the present study, endophytic fungi were isolated from R. roxburghii, the diversity and antimicrobial activities were evaluated. As a result, 242 strains of endophytic Sordariomycetes were successfully isolated. Multigene phylogenetic analyses showed that these isolates included eight orders, 19 families, 33 genera. The dominant genera were Diaporthe (31.4%), Fusarium (14.4%), Chaetomium (7.9%), Dactylonectria (7.0%), Graphium (4.5%), Colletotrichum (4.1%), and Clonostachys (4.1%). For different tissues of R. roxburghii, alpha diversity analysis revealed that the diversity of fungal communities decreased in the order of root, fruit, stem, flower, leaf, and seed, and Clonostachys and Dactylonectria exhibited obvious tissue specificity. Meanwhile, functional annotation of 33 genera indicated that some fungi have multitrophic lifestyles combining endophytic, pathogenic, and saprophytic behavior. Additionally, antimicrobial activities of endophytic Sordariomycetes against Lasiodiplodia theobromae, Botryosphaeria dothidea, Colletotrichum capsici, Pyricularia oryzae, Rhizoctonia solani, Fusarium oxysporum, Pseudomonas syringae, Pantoea agglomerans, Staphylococcus aureus, Bacillus subtilis, Escherichia coli, and Pseudomonas aeruginosa were screened. Dual culture test assays showed that there were 40 different endophytic species with strong inhibition of at least one or moderate inhibition of two or more against the 12 tested strains. The results from the filter paper diffusion method suggested that extracellular metabolites may be more advantageous than intracellular metabolites in the development of antimicrobial agents. Eleven isolates with good activities were screened. In particular, Hypomontagnella monticulosa HGUP194009 and Nigrospora sphaerica HGUP191020 have shown promise in both broad-spectrum and intensity. Finally, some fungi that commonly cause disease have been observed to have beneficial biological activities as endophytic fungi. In conclusion, this study showed the species composition, alpha diversity, and lifestyle diversity of endophytic Sordariomycetes from R. roxburghii and demonstrated these isolates are potential sources for exploring antimicrobial agents.

Prognostic factors of regression and relapse of complex atypical hyperplasia and well-differentiated endometrioid carcinoma with conservative treatment.

OBJECTIVE: To evaluate possible prognostic factors regarding regression and relapse of complex atypical hyperplasia (CAH) and well-differentiated endometrioid adenocarcinoma (WDC) treated with conservative treatment. METHODS: The retrospective study reviewed clinicopathologic, treatment, regression and relapse data from patients diagnosed with CAH or WDC who were treated with conservative treatment at 4 institutions. Potential factor evaluation was performed. SPSS 16 was used for statistical analyses. RESULTS: Eighty-eight patients were included (51 had WDC, and 37 had CAH). Regression was evaluated in 88 patients, with a median follow-up of 61 (range 15-95) months. Seventy-seven (87.5%) patients regressed, and 11 (12.5%) had persistent or progressive disease. Univariate and multivariate analyses showed no factors associated with regression. Relapse was evaluated in 71 patients, with median follow-up of 54 (range 8-86) months. Twenty-five/71 (35.2%) patients experienced relapse. On univariate analysis, body mass index (BMI) 30 or higher (p=0.001), WCD at initial biopsy (p=0.017) and positive expression of post-treatment ki67 (p=0.033) were associated to a higher relapse probability. However, only BMI 30 or higher was significant on multivariate analysis (p=0.012). The Kaplan-Meier analysis revealed a higher relapse probability in the patients with BMI 30 or higher (p=0.001). CONCLUSION: Obesity seems to be a risk factor for relapse of CAH or WDC with conservative treatment.