ABSTRACT
Sepsis is a complex syndrome characterized by multi-organ dysfunction, due to the presence of harmful microorganisms in blood which could cause mortality. Complications associated with sepsis involve multiple organ dysfunction. The pathogenesis of sepsis remains intricate, with limited treatment options and high mortality rates. Traditional Chinese medicine (TCM) has consistently demonstrated to have a potential on various disease management. Its complements include reduction of oxidative stress, inhibiting inflammatory pathways, regulating immune responses, and improving microcirculation. Traditional Chinese medicine can mitigate or even treat sepsis in a human system. This review examines progress on the use of TCM extracts for treating sepsis through different pharmacological action and its mechanisms. The potential targets of TCM extracts and active ingredients for the treatment of sepsis and its complications have been elucidated through molecular biology research, network pharmacology prediction, molecular docking analysis, and visualization analysis. Our aim is to provide a theoretical basis and empirical support for utilizing TCM in the treatment of sepsis and its complications while also serving as a reference for future research and development of sepsis drugs.
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Phthalate acid esters (PAEs) and their metabolites, such as di-n-butyl phthalate (DBP) and mono-n-butyl phthalate (MBP), are known to cause male reproductive damage. Lactiplantibacillus plantarum RS20D has demonstrated the ability to remove both DBP and MBP in vitro, suggesting its potential as a detoxifying agent against these compounds. This study aimed to investigate the protective effects of RS20D on DBP or MBP-induced male reproductive toxicity in adolescent rats. Oral administration of RS20D significantly mitigated the histological damage to the testes caused by MBP or DBP, restored sperm concentration, morphological abnormalities, and the proliferation index in MBP-exposed rats, and partially reversed spermatogenic damage in DBP-exposed rats. Furthermore, RS20D restored serum levels of estradiol (E2) and testosterone, and superoxide dismutase (SOD) activity in DBP-exposed rats, significantly increased testosterone levels in MBP-exposed rats, and restored copper (Cu) concentrations in the testes after exposure to DBP or MBP. Additionally, RS20D effectively modulated the intestinal microbiota in DBP-exposed rats and partially ameliorated dysbiosis induced by MBP, which may be associated with the alleviation of reproductive toxic effects induced by DBP or MBP. In conclusion, this study demonstrates that RS20D administration can alleviate male reproductive toxicity and gut dysbacteriosis induced by DBP or MBP exposure, providing a dietary strategy for the bioremediation of PAEs and their metabolites.
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Objective: To investigate the correlation between GAL-3, Klotho, calcium and phosphorus indexes and cardiovascular complications in patients with chronic kidney disease (CKD). Methods: This is a retrospective study. Forty patients with CKD and cardiovascular complications admitted to the Affiliated Hospital of Hebei University from February 20, 2022 to February 20, 2023 were selected as the experimental group, and another 40 patients with CKD without cardiovascular complications were selected as the control group. The differences in serum Ca+2, PO- 4, GAL-3 and Klotho levels between the two groups were analyzed, and the correlations between the above indicators levels and creatinine levels were analyzed. The correlation between the above indicators levels and cardiac function classification was analyzed, and analyzed the risk factors of CKD complicated with cardiovascular complications. Results: The levels of Ca+2, PO- 4 and GAL-3 in the experimental group were significantly higher than those in the control group, while the level of Klotho was significantly lower than that in the control group. The levels of Ca+2 and PO- 4 were positively correlated with the level of Creatinine (Cr), while the level of Klotho was negatively correlated with the Cr. The levels of Ca+2 and PO- 4 were positively correlated with cardiac function classification, while the level of Klotho was negatively correlated with cardiac function classification. Logistic regression analysis showed that hypertension, BMI, Cr, Ca+2, PO- 4 and VLDL were risk factors for cardiovascular complications, and Klotho level was a protective factor. Conclusion: A positive correlation can be seen between the levels of Ca+2, PO- 4 and cardiac function classification in patients with CKD. Klotho is a protective factor for cardiovascular diseases.
ABSTRACT
Oomycetes, particularly those from the genus Phytophthora, are significant threats to global food security and natural ecosystems. Oxathiapiprolin (OXA) is an effective oomycete fungicide that targets an oxysterol binding protein (OSBP), while the binding mechanism of OXA is still unclear, which limits the pesticide design, induced by the low sequence identity of Phytophthora and template models. Herein, we generated the OSBP model of the well-reported Phytophthora capsici using AlphaFold 2 and studied the binding mechanism of OXA. Based on it, a series of OXA analogues were designed. Then, compound 2l, the most potent candidate, was successfully designed and synthesized, showing a control efficiency comparable to that of OXA. Moreover, field trial experiments showed that 2l exhibited nearly the same activity (72.4%) as OXA against cucumber downy mildew at 25 g/ha. The present work indicated that 2l could be used as a leading compound for the discovery of new OSBP fungicides.
Subject(s)
Fungicides, Industrial , Phytophthora , Ecosystem , Plant Diseases , Fungicides, Industrial/pharmacologyABSTRACT
Background: The Basal ganglia (BG) played a crucial role in the brain-level mechanisms of chronic pain disorders. However, the functional changes of BG in chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) are still poorly understood. This study investigated the BG subregions' resting-state functional connectivity (rs-FC) in CP/CPPS patients compared with healthy controls. Methods: Twenty eight patients with CP/CPPS and 28 age- and education-matched healthy males underwent clinical measurements and 3T brain MR imaging, including T1-weighted structural images and resting-state functional imaging. The data were analyzed by the seeded-based rs-FC analysis. Then, a machine learning method was applied to assess the feasibility of detecting CP/CPPS patients through the changed rs-FC. Results: Compared with healthy males, patients presented decreased rs-FC between the BG subregions and right middle cingulate cortex, and correlated with pain (r = 0.51, p-uncorrected = 0.005) and urinary symptoms (r = -0.4, p-uncorrected = 0.034). The left superior temporal gyrus and right supramarginal gyrus showed decreased rs-FC with the BG subregions as well. The area under the receiver operating characteristic curve of 0.943 (accuracy = 80%, F1-score = 80.6%) was achieved for the classification of CP/CPPS patients and healthy males with support vector machine (SVM) based on the changed rs-FC. Conclusion: These findings provide evidence of altered BG subregions' rs-FC in CP/CPPS, which may contribute to our understanding of the BG's role in CP/CPPS.
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A new chromone glycoside, 8-O-ß-D-Glucopyranosyl-2-methylchromone (1), together with eight known compounds (2-9) were isolated from the Tibetan medicine plant of Swertia punicea. All compounds of this plant were reported for the first time. The structures of these metabolites were elucidated by analysis of their HR-ESI-MS, 1D and 2D NMR spectroscopic data and comparison with data reported in the literature. In vitro test, all compounds were evaluated for their anti-inflammatory activity through the determination of nitric oxide production. Compounds 1-2 were evaluated for cytotoxic activities against three human cancer cell lines (HeLa, MDA-MB-231 and A375) by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) method. Furthermore, the chemotaxonomic significance of these compounds has also been described.
Subject(s)
Swertia , Chromones , Glycosides/pharmacology , Humans , Medicine, Tibetan Traditional , Molecular StructureABSTRACT
The photodegradation of dissolved organic sulfur (DOS) is a potential source of aqueous sulfate and its chemical precursors in surface water. However, the photochemical fate of DOS and factors that control its fate still remain unclear. Herein, we employed a DOS model featuring a photosensitizer (humic acids, HA) to investigate the photochemical degradation pathways of DOS in various natural water sources, from which we observed the substantial photosensitized formation of sulfate, methanesulfonic acid (MSA), carbonyl sulfide (COS), and carbon disulfide (CS2). However, the photochemical production of sulfate and MSA tends to be more efficient than COS and CS2. The formation of sulfur-containing photodegradation products was also strongly affected by the identity of the organic sulfur precursor, the oxygen concentration, and the pH, while the salinity did not significantly influence the production ratios. Our results revealed that the photosensitization of DOS contributed significantly to the overall production of sulfate and MSA production, especially in acidic and oxygen-enriched environments, which was attributed to the photochemical production of reactive intermediates, such as excited CDOM (3CDOM*) and reactive oxygen species (ROS). Considering the coexistence of DOS and photosensitizers in aquatic environments, photochemistry may play an essential role in the fate of aquatic DOS.
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The spatial distributions, fluxes, and environmental effects of non-methane hydrocarbons (NMHCs) were investigated in the Yellow Sea (YS) and the East China Sea (ECS) in spring. The average concentrations of ethane, propane, i-/n-butane, ethylene, propylene and isoprene in the seawater were 18.1 ± 6.4, 15.4 ± 4.7, 6.8 ± 2.9, 6.4 ± 3.2, 67.1 ± 26.7, 20.5 ± 8.7 and 17.1 ± 11.1 pmol L-1, respectively. The alkenes in the surface seawater were more abundant than their saturated homologs and NMHCs concentrations (with the exception of isoprene) decreased with carbon number. The spatial variations of isoprene were consistent with the distributions of chlorophyll a (Chl-a) and Chaetoceros, Skeletonema, Nitzschia mainly contributed to the production of isoprene, while the others' distributions might be related to their photochemical production. Observations in atmospheric NMHCs indicated alkanes in the marine atmosphere decreased from inshore to offshore due to influence of the continental emissions, while alkenes were largely derived from the oceanic source. In addition, no apparent diurnal discrepancy of atmospheric NMHCs (except for isoprene) were found between daytime and night. As the main sink of NMHCs in seawater, the average sea-to-air fluxes of ethane, propane, i-/n-butane, ethylene and propylene were 31.70, 29.75, 18.49, 15.89, 239.6, 67.94 and 52.41 nmol m-2 d-1, respectively. The average annual emissions of isoprene accounted for 0.1-1.3% of the global ocean emissions, which indicated that the coastal and shelf areas might be significant sources of isoprene. Furthermore, this study represents the first effort to estimate the environmental effects caused by NMHCs over the YS and the ECS and the results demonstrated contributions of alkanes to ozone and secondary organic aerosol (SOA) formation were lower than those of the alkenes and the largest contributor was isoprene.
Subject(s)
Air Pollutants , Methane , Air Pollutants/analysis , China , Chlorophyll A , Environmental Monitoring , Hydrocarbons/analysis , Oceans and Seas , SeasonsABSTRACT
Marine-derived reactive gases constitute a substantial fraction of volatile organic compounds and directly impact atmospheric chemistry and the global climate. Light alkene emissions from marginal seas are limited, and their contribution to atmospheric concentrations is likely underestimated. We surveyed oceanic emissions of ethylene, propylene, and isoprene, as well as their potential controlling factors in the marginal seas of China during the cruises in 2014-2015. Significant temporal-spatial variations in ethylene, propylene, and isoprene concentrations were observed, with the highest occurring in summer near the coastal regions. Isoprene concentrations were primarily controlled by phytoplankton biomass (i.e., Chl-a) in coastal regions, while the elevated concentrations of ethylene and propylene were attributed to photochemical reactions with the high levels of dissolved organic matter (DOM). Additionally, the vertical distributions of ethylene and propylene mirrored light penetration, with exponential decrease in concentrations with depth. However, there were high values of ethylene and propylene observed at deep chlorophyll maximum, suggesting the existence of non-photochemical production pathways, most likely biological origin. Emissions of ethylene, propylene, and isoprene from the marginal seas of China were estimated to be 0.022, 0.024, and 0.011 Tg C yr-1, respectively, indicating they are important contributors to global non-methane hydrocarbons. Due to the scarcity of alkene emission data for marginal seas, current global emissions have been underestimated to some extent. It is essential to incorporate the contributions from marginal seas to accurately estimate alkene budgets on global scales.
ABSTRACT
Oxathiapiprolin, the first successful oxysterol binding protein (OSBP) inhibitor for oomycete control, is regarded as an important milestone in the history of fungicide discovery. However, its interaction with OSBP remain unclear. Moreover, some plant pathogenic oomycetes have developed medium to high resistance to oxathiapiprolin. In this paper, the three-dimensional (3D) structure of OSBP from Phytophthora capsici (pcOSBP) was built, and its interaction with oxathiapiprolin was systematically investigated by integrating molecular docking, molecular dynamics simulations, and molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) calculations. The computational results showed that oxathiapiprolin bound to pcOSBP forms H-bonds with Leu73, Lys74, Ser69, and water molecules. Then, based on its interaction with pcOSBP, oxathiapiprolin was structurally modified to discover new analogs with high fungicidal activity and a low risk of resistance. Fortunately, compound 1e was successfully designed and synthesized as the most potent candidate, and it showed a much lower resistance risk (RF < 1) against LP3-M and LP3-H in P. capsici. The present work indicated that the piperidinyl-thiazole-isoxazoline moiety is useful for further optimization. Furthermore, compound 1e could be used as a lead compound for the discovery of new OSBP inhibitors.
Subject(s)
Fungicides, Industrial , Hydrocarbons, Fluorinated , Molecular Docking Simulation , Plant Diseases , Protein Binding , Pyrazoles , Receptors, SteroidABSTRACT
OBJECTIVE: To analyze the pathological characteristics and explore the optimal surgical margins (SM) of nephron-sparing surgery (NSS) for stage T 1b renal carcinoma (4-7 cm) on preoperative imaging. METHODS: The clinical and pathological data of 245 cases of stage T 1b kidney cancer from September 2013 to December 2017 were collected and reviewed retrospectively. The radical nephrectomy (RN) was performed on 174 cases and other 71 cases accepted NSS. There were 158 males and 87 females, with a mean age of 59.6 years and mean tumor size of 5.3 cm. RESULTS: Through postoperative pathological examination, 209 (85.3%) cases were confirmed renal clear cell carcinoma and 219 (89.4%) cases were surrounded with visible peritumoralpseudocapsule (PC). 26 (10.6%) cases of cancerous cells invaded beyond peritumoral PC and into renal parenchyma. The infiltrative depth into renal parenchyma beyond PC was all limited in 3 mm and the cases of ≤1, 1-2 and 2-3 mm were 7 (26.9%), 16 (61.5%) and 3 (11.5%), respectively. Multifocal tumors were discovered in 24 (9.8%) cases. The average resection margin for partial nephrectomy was 5 mm (3-7 mm). CONCLUSION: For stage T 1b renal tumors, NSS is acceptable and a 3 mm of surgical margin is safe and suitable to avoid positive SM.
Subject(s)
Carcinoma, Renal Cell , Kidney Neoplasms , Margins of Excision , Nephrectomy , Carcinoma, Renal Cell/surgery , Female , Humans , Kidney Neoplasms/surgery , Male , Middle Aged , Nephrectomy/methods , Nephrons/surgery , Retrospective StudiesABSTRACT
The Empoasca onukii (Hemiptera: Cicadellidae) female lays its eggs inside the epidermis of the tea plant shoots. This has led to speculation that shoot harvesting could represent a method of egg removal. To verify the validity of this hypothesis, we sought to determine which part of the shoot was used for the oviposition and how the value of the harvested shoot affects the cost of the egg removal. In this study, four tea cultivars were chosen to examine the preferences for the site of oviposition. In addition, a mathematical model was used to describe the correlation between the economic value of the selected shoot and eggs laid within the shoot. Our study revealed that the pest preferred the 3rd and 4th leaf order intervals of the shoot as the oviposition sites, and the oviposition preferences was dependent on the leaf order interval class across all tea cultivars. In addition, a significant negative exponential relationship was found between the economic value of the selected shoot and the percentage of the eggs laid within the shoot, indicating that egg removal through shoot harvesting was limited. The findings of this study could be used to better understand the role of shoot harvesting in egg removal and would provide new insights into the understanding of the incidence of this pest.
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Two new norlignans together with two known phenylpropanoids were isolated from the whole herb of Anemone vitifolia. All compounds were reported from this plant for the first time. The structures of these compounds were identified by comprehensive HR-ESI-MS, 1D and 2D NMR spectroscopic data analysis and comparison with literature data. Additionally, bioactivity study results showed that two new compounds have potential anti-inflammatory activity. The plausible biosynthetic pathway for these compounds were also speculated in this article.
Subject(s)
Anemone/chemistry , Anti-Inflammatory Agents, Non-Steroidal/pharmacology , Drugs, Chinese Herbal/pharmacology , Lignans/pharmacology , Nitric Oxide/antagonists & inhibitors , Animals , Anti-Inflammatory Agents, Non-Steroidal/chemistry , Anti-Inflammatory Agents, Non-Steroidal/isolation & purification , Cell Survival/drug effects , Dose-Response Relationship, Drug , Drugs, Chinese Herbal/chemistry , Drugs, Chinese Herbal/isolation & purification , Lignans/chemistry , Lignans/isolation & purification , Lipopolysaccharides/antagonists & inhibitors , Lipopolysaccharides/pharmacology , Mice , Molecular Structure , Nitric Oxide/biosynthesis , Propanols/chemistry , Propanols/isolation & purification , Propanols/pharmacology , RAW 264.7 Cells , Structure-Activity RelationshipABSTRACT
Drought disaster space agglomeration assessment is one of the important components of meteorological disaster prevention and mitigation. Agriculture affected by drought disaster is not only a serious threat to world food security, but also an obstacle to sustainable development. Additionally, China is an important agricultural import and export country in the world. Therefore, we used the global Moran's I and the local indicators of spatial autocorrelation (LISA) to reveal the spatial agglomeration of agricultural drought disaster in China from1978 to 2016, respectively. The results showed that China's agricultural drought disaster presents local spatial autocorrelation of geographical agglomeration at national level during the study period. The spatial agglomeration regions of China's agricultural drought disaster were in Inner Mongolia, Jilin province, Heilongjiang province, Liaoning province, Shanxi province, Hebei province, Shandong province, Shaanxi province and Henan province, indicating that agricultural drought disaster mainly distributed in North and Northwest China, especially occurred in the Yellow River Basin and its north areas. We also found that the overall movement direction of agricultural drought disaster agglomeration regions was northwest, and the maximum moving distance was 722.16 km. Our results might provide insight in early warning and prevention for drought disaster.
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We estimated grassland NPP using CASA model in the Loess Plateau during 2000-2015 and further analyzed the spatiotemporal dynamics, stability and persistence of grassland NPP. The driving factors of grassland NPP were analyzed from four aspects, i.e., vegetation types, topographic factors, climate change, and human activities. The results showed that the average NPP was 202.93 g C·m-2·a-1. The grassland NPP showed an increasing trend with an average increase rate of 2.43 g C·m-2·a-1. The distribution of NPP in grassland had obvious spatial heterogeneity, which was generally high in the south and low in the north. 91.2% of the total grassland area showed an increasing trend, mainly distributed in most areas of Shaanxi Province, Longdong and Longzhong areas of Gansu Province, and most parts of Qinghai Province. The regions with a stable growth condition of grassland NPP mainly located in the south of Ordos, northern Shaanxi, and Gansu. The future change trend of grassland NPP would be consistent with that of the past in most areas. The grassland NPP would continue to increase in most areas of Shaanxi Province, Longzhong and Longdong areas in Gansu Province. The average NPP of slope grassland was 703.37 g C·m-2·a-1, while that of alpine and subalpine grassland was 57.28 g C·m-2·a-1. The grassland NPP was higher in high altitude area and relative low in plain and hilly area. The increased precipitation promoted the increase of grassland NPP during the study period. Human activities such as improvement of overgrazing and returning cropland to grassland also played an important role in the increase of grassland NPP in the Loess Plateau.
Subject(s)
Grassland , Models, Theoretical , China , Climate Change , Human ActivitiesABSTRACT
During an oceanographic campaign in the western Pacific Ocean from 12 August to 3 October 2014, the concentrations of five non-methane hydrocarbons (NMHCs) were measured in marine atmosphere and seawater. The average mixing ratios of ethane, ethylene, propane, propylene, and isoprene were 1.109⯱â¯0.359, 0.658⯱â¯0.137, 0.711⯱â¯0.377, 0.429⯱â¯0.139, and 0.255⯱â¯0.201â¯ppbv, respectively. In general, atmospheric concentrations of ethane and propane showed significant decrease from the inshore area to the open ocean, while ethylene and propylene exhibited decreasing trends from low latitudes to high latitudes. The results suggested that atmospheric ethane and propane with long lifetimes were more likely influenced by the air mass transported from continent, while ethylene, propylene and isoprene with short lifetimes were mainly derived from the surface seawater. The average concentrations of ethane, ethylene, propane, propylene, and isoprene in the surface seawater were 6.6⯱â¯5.8, 51.9⯱â¯23.5, 15.4⯱â¯4.3, 17.2⯱â¯3.8, and 23.5⯱â¯8.6â¯pmolâ¯L-1, respectively. A significant positive correlation was observed between ethane and propane (R2â¯=â¯0.45, nâ¯=â¯39, pâ¯<â¯0.001), implying that their production and removal pathways in the surface seawater were similar. High concentrations of isoprene were observed in the waters with high Chl-a values, suggesting that the biological process was a controlling factor. The estimated sea-to-air fluxes of ethane, propane, ethylene, propylene, and isoprene were in the range of 0.1-24.9, 4.2-235, 1.0-43.8, 1.5-90.2, and 2.1-149â¯nmolâ¯m-2â¯d-1, respectively. This study is of great importance to the contribution to the atmospheric NMHCs from the western Pacific Ocean and provides data supporting for global NMHCs emission estimates.
Subject(s)
Aqueous Humor/virology , Immunocompetence/immunology , Inflammation/virology , Adult , Aged , Female , Humans , Male , Middle Aged , Retrospective Studies , Young AdultABSTRACT
BACKGROUND: Skewed X chromosome inactivation (XCI), which is a non-random process, is frequently observed in both healthy and affected females. Furthermore, skewed XCI has been reported to be related to many X-linked diseases. However, no statistical method is available in the literature to measure the degree of the skewness of XCI for case-control design. Therefore, it is necessary to develop methods for such a task. RESULTS: In this article, we first proposed a statistical measure for the degree of XCI skewing by using a case-control design, which is a ratio of two logistic regression coefficients after a simple reparameterization. Based on the point estimate of the ratio, we further developed three types of confidence intervals (the likelihood ratio, Fieller's and delta methods) to evaluate its variation. Simulation results demonstrated that the likelihood ratio method and the Fieller's method have more accurate coverage probability and more balanced tail errors than the delta method. We also applied these proposed methods to analyze the Graves' disease data for their practical use and found that rs3827440 probably undergoes a skewed XCI pattern with 68.7% of cells in heterozygous females having the risk allele T active, while the other 31.3% of cells keeping the normal allele C active. CONCLUSIONS: For practical application, we suggest using the Fieller's method in large samples due to the non-iterative computation procedure and using the LR method otherwise for its robustness despite its slightly heavy computational burden.
Subject(s)
Chromosomes, Human, X/genetics , Genes, X-Linked , Heterozygote , Models, Statistical , X Chromosome Inactivation , Alleles , Case-Control Studies , Female , HumansABSTRACT
A Gram-stain-negative bacterium, designated LY-1T, was isolated from the soil sample collected from a chemical factory in Fuyang city, Anhui province, China. Cells of strain LY-1T were strictly aerobic, non-motile and rod-shaped. Strain LY-1T grew optimally at pH 7.0 and at 30-35 °C. The taxonomic position was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain LY-1T was a member of the genus Chitinophaga and showed the highest sequence similarity to Chitinophaga costaii A37T2T (97.5â%) and lower (<97.0â%) sequence similarity to other known Chitinophaga species. Chemotaxonomic analysis revealed that strain LY-1T possessed menaquinone-7 as the major isoprenoid quinone; and iso-C15â:â0 (46.4â%), C16â:â1ω5c (27.8â%) and iso-C17â:â0 3-OH (9.0â%) were the predominant fatty acids. The polar lipids of strain LY-1T consisted of phosphatidylethanolamine, three unidentified phosphoaminolipids, one unidentified phospholipid, four unidentified lipids, two unidentified aminolipids and two unidentified glycolipids. The genomic DNA G+C content of strain LY-1T was 52.4 mol% based on total genome calculations. The average nucleotide identity and the digital DNA-DNA hybridization value of the draft genomes between strain LY-1T and strain A37T2T were 76.8 and 19.8â%, respectively. Based on the phylogenetic and phenotypic characteristics, chemotaxonomic data, and DNA-DNA hybridization, strain LY-1T is considered a novel species of the genus Chitinophaga, for which the name Chitinophagaparva sp. nov. (type strain LY-1T=CCTCC AB 2018018T=KCTC 62444T) is proposed.
Subject(s)
Bacteroidetes/classification , Chemical Industry , Phylogeny , Soil Microbiology , Bacterial Typing Techniques , Bacteroidetes/genetics , Bacteroidetes/isolation & purification , Base Composition , China , DNA, Bacterial/genetics , Fatty Acids/chemistry , Nucleic Acid Hybridization , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistryABSTRACT
BACKGROUND: Genomic imprinting is one of the well-known epigenetic factors causing the association between traits and genes, and has generally been examined by detecting parent-of-origin effects of alleles. A lot of methods have been proposed to test for parent-of-origin effects on autosomes based on nuclear families and general pedigrees. Although these parent-of-origin effects tests on autosomes have been available for more than 15 years, there has been no statistical test developed to test for parent-of-origin effects on X chromosome, until the parental-asymmetry test on X chromosome (XPAT) and its extensions were recently proposed. However, these methods on X chromosome are only applicable to nuclear families and thus are not suitable for general pedigrees. RESULTS: In this article, we propose the pedigree parental-asymmetry test on X chromosome (XPPAT) statistic to test for parent-of-origin effects in the presence of association, which can accommodate general pedigrees. When there are missing genotypes in some pedigrees, we further develop the Monte Carlo pedigree parental-asymmetry test on X chromosome (XMCPPAT) to test for parent-of-origin effects, by inferring the missing genotypes given the observed genotypes based on a Monte Carlo estimation. An extensive simulation study has been carried out to investigate the type I error rates and the powers of the proposed tests. Our simulation results show that the proposed methods control the size well under the null hypothesis of no parent-of-origin effects. Moreover, XMCPPAT substantially outperforms the existing tests and has a much higher power than XPPAT which only uses complete nuclear families (with both parents) from pedigrees. We also apply the proposed methods to analyze rheumatoid arthritis data for their practical use. CONCLUSIONS: The proposed XPPAT and XMCPPAT test statistics are valid and powerful in detecting parent-of-origin effects on X chromosome for qualitative traits based on general pedigrees and thus are recommended.