Separation of Nucleotides in Swine Tissues Using Capillary Zone Electrophoresis

Capillary zone electrophoresis has been applied to the analysis of nucleotides. The effects of buffer concentration. pH and other operating conditions on the separation were investigated and optimized. By using the method, separation and identification of nuclotides in swine tissues were completed.

Nucleotide excision repair gene polymorphisms and hepatoblastoma susceptibility in Eastern Chinese children:A five-center case-control study

Objective:Nucleotide excision repair(NER)plays a vital role in maintaining genome stability,and the effect of NER gene polymorphisms on hepatoblastoma susceptibility is still under investigation.This study aimed to evaluate the relationship between NER gene polymorphisms and the risk of hepatoblastoma in Eastern Chinese Han children.Methods:In this five-center case-control study,we enrolled 966 subjects from East China(193 hepatoblastoma patients and 773 healthy controls).The TaqMan method was used to genotype 19 single nucleotide polymorphisms(SNPs)in NER pathway genes,including ERCC1,XPA,XPC,XPD,XPF,and XPG.Then,multivariate logistic regression analysis was performed,and odds ratios(ORs)and 95%confidence intervals(95%CIs)were utilized to assess the strength of associations.Results:Three SNPs were related to hepatoblastoma risk.XPC rs2229090 and XPD rs3810366 significantly contributed to hepatoblastoma risk according to the dominant model(adjusted OR=1.49,95%CI=1.07−2.08,P=0.019;adjusted OR=1.66,95%CI=1.12−2.45,P=0.012,respectively).However,XPD rs238406 conferred a significantly decreased risk of hepatoblastoma under the dominant model(adjusted OR=0.68,95%CI=0.49−0.95;P=0.024).Stratified analysis demonstrated that these significant associations were more prominent in certain subgroups.Moreover,there was evidence of functional implications of these significant SNPs suggested by online expression quantitative trait loci(eQTLs)and splicing quantitative trait loci(sQTLs)analysis.Conclusions:In summary,NER pathway gene polymorphisms(XPC rs2229090,XPD rs3810366,and XPD rs238406)are significantly associated with hepatoblastoma risk,and further research is required to verify these findings.

Exploring Capillary Fringe Flow:Quasilinear Modeling with Kirchhoff Transforms and Gardner Model

Recent studies have underscored the significance of the capillary fringe in hydrological and biochemical processes.Moreover,its role in shallow waters is expected to be considerable.Traditionally,the study of groundwater flow has centered on unsaturated-saturated zones,often overlooking the impact of the capillary fringe.In this study,we introduce a steady-state two-dimensional model that integrates the capillary fringe into a 2-D numerical solution.Our novel approach employs the potential form of the Richards equation,facilitating the determination of boundaries,pressures,and velocities across different ground surface zones.We utilized a two-dimensional Freefem++finite element model to compute the stationary solution.The validation of the model was conducted using experimental data.We employed the OFAT(One_Factor-At-Time)method to identify the most sensitive soil parameters and understand how changes in these parameters may affect the behavior and water dynamics of the capillary fringe.The results emphasize the role of hydraulic conductivity as a key parameter influencing capillary fringe shape and dynamics.Velocity values within the capillary fringe suggest the prevalence of horizontal flow.By variation of the water table level and the incoming flow q0,we have shown the correlation between water table elevation and the upper limit of the capillary fringe.

A new interacting capillary bundle model on the multiphase flow in micropores of tight rocks

Surfactants are widely used in the fracturing fluid to enhance the imbibition and thus the oil recovery rate. However, current numerical models cannot capture the physics behind capillary imbibition during the wettability alteration by surfactants. Although the interacting capillary bundle(ICB) model shows potential in characterizing imbibition rates in different pores during wettability alteration, the existing ICB models neglect the influence of wettability and viscosity ratio on the imbibition behavior, making it difficult to accurately describe the oil-water imbibition behavior within the porous media. In this work,a new ICB mathematical model is established by introducing pressure balance without assuming the position of the leading front to comprehensively describe the imbibition behavior in a porous medium under different conditions, including gas-liquid spontaneous imbibition and oil-water imbibition.When the pore size distribution of a tight rock is known, this new model can predict the changes of water saturation during the displacement process in the tight rock, and also determine the imbibition rate in pores of different sizes. The water saturation profiles obtained from the new model are validated against the waterflooding simulation results from the CMG, while the imbibition rates calculated by the model are validated against the experimental observations of gas-liquid spontaneous imbibition. The good match above indicates the newly proposed model can show the water saturation profile at a macroscopic scale while capture the underlying physics of the multiphase flow in a porous medium at a microscopic scale. Simulation results obtained from this model indicate that both wettability and viscosity ratio can affect the sequence of fluid imbibition into pores of different sizes during the multiphase flow, where less-viscous wetting fluid is preferentially imbibed into larger pores while more-viscous wetting fluid tends to be imbibed into smaller pores. Furthermore, this model provides an avenue to calculate the imbibition rate in pores of different sizes during wettability alteration and capture the non-Darcy effect in micro-and nano-scale pores.

Nucleotide Contribution to the Functioning of SERT, Na /K ATPase and GPCR Proteins

Purine nucleotides are crucial for the effective operation of cell membrane proteins maintaining the neurotransmitter responses of 5-HT. Major protein targets in the treatment of depression include SERT, N/K ATPase and GPCR. Each protein target is responsive to a specific complement of drugs: antidepressants (SERT), lithium and cardiogenic steroids (N/K ATPase), 5-HT receptor ligands (GPCR). Computational software is useful for comparing molecular similarity within ligand-ligand and ligand-nucleotide structures. Previous studies demonstrate that GPCR ligands of different pharmacologic classes display relative molecular similarity to nucleotide structures. The current study applies this methodology to compound structures modulating SERT and N/K ATPase receptors. Minimum energy conformers of SERT antagonists demonstrate relative molecular similarity to the structural template of GTP nucleotide. GTP template fits of 5-HT and psilocin are similar, whereas a SERT-like fit is one of several for the ketamine structure. Endogenous and pharmaceutical modulators of Na/K ATPase relate to adenine nucleotide. The fits of cardiogenic steroids to a cGMP template demonstrate similarities and differences between compounds. Relative molecular similarity within the structures of hormones, drugs and nucleotides has implications for neurotransmitter transport and cell signal transduction processes.

Capillary Property of Entangled Porous Metallic Wire materials and Its Application in Fluid Buffers:Theoretical Analysis and Experimental Study

Strong impact does serious harm to the military industries so it is necessary to choose reasonable cushioning material and design effective buffers to prevent the impact of equipment.Based on the capillary property entangled porous metallic wire materials(EPMWM),this paper designed a composite buffer which uses EPMWM and viscous fluid as cushioning materials under the low-speed impact of the recoil force device of weapon equipment(such as artillery,mortar,etc.).Combined with the capillary model,porosity,hydraulic diameter,maximum pore diameter and pore distribution were used to characterize the pore structure characteristics of EPMWM.The calculation model of the damping force of the composite buffer was established.The low-speed impact test of the composite buffer was conducted.The parameters of the buffer under low-speed impact were identified according to the model,and the nonlinear model of damping force was obtained.The test results show that the composite buffer with EPMWM and viscous fluid can absorb the impact energy from the recoil movement effectively,and provide a new method for the buffer design of weapon equipment(such as artillery,mortar,etc.).

Reservoir quality evaluation of the Narimba Formation in Bass Basin,Australia:Implications from petrophysical analysis,sedimentological features,capillary pressure and wetting fluid saturation

The evaluation of reservoir quality was accomplished on the Late Paleocene to Early Eocene Narimba Formation in Bass Basin,Australia.This study involved combination methods such as petrophysical analysis,petrography and sedimentological studies,reservoir quality and fluid flow units from derivative parameters,and capillary pressure and wetting fluid saturation relationship.Textural and diagenetic features are affecting the reservoir quality.Cementation,compaction,and presence of clay minerals such as kaolinite are found to reduce the quality while dissolution and secondary porosity are noticed to improve it.It is believed that the Narimba Formation is a potential reservoir with a wide range of porosity and permeability.Porosity ranges from 3.1%to 25.4%with a mean of 15.84%,while permeability ranges between 0.01 mD and 510 mD,with a mean of 31.05 mD.Based on the heterogenous lithology,the formation has been categorized into five groups based on permeability variations.Group I showed an excellent to good quality reservoir with coarse grains.The impacts of both textural and diagenetic features improve the reservoir and producing higher reservoir quality index(RQI)and flow zone indicators(FZI)as well as mostly mega pores.The non-wetting fluid migration has the higher possibility to flow in the formation while displacement pressure recorded as zero.Group II showed a fair quality reservoir with lower petrophysical properties in macro pores.The irreducible water saturation is increasing while the textural and digenetic properties are still enhancing the reservoir quality.Group III reflects lower quality reservoir with mostly macro pores and higher displacement pressure.It may indicate smaller grain size and increasing amount of cement and clay minerals.Group IV,and V are interpreted as a poor-quality reservoir that has lower RQI and FZI.The textural and digenetic features are negatively affecting the reservoir and are leading to smaller pore size and pore throat radii(r35)values to be within the range of macro,meso-,micro-,and nano pores.The capillary displacement pressure curves of the three groups show increases reaching the maximum value of 400 psia in group V.Agreement with the classification of permeability,r35 values,and pore type can be used in identifying the quality of reservoir.

Comparative Quantitative Analysis of Retinal Superficial Capillary Plexus in Patients with Retinal Vein Occlusion and Unaffected Fellow Eyes

Purpose: To evaluate optical coherence tomography angiography (OCT-A) data obtained from the superficial retinal capillary plexus of patients with retinal vein occlusion and comparative analysis with data registered from unaffected fellow eyes. Methods: The examined patients were classified into 2 groups: group 1—eyes with established retinal vein occlusion (n = 29) and group 2—unaffected fellow eyes of patients with retinal vein occlusion (n = 24). The scanning protocol “Angiography 3 × 3 mm” of Zeiss Cirrus HD-OCT 6000, AngioPlex Metrix was used to evaluate the retinal superficial capillary plexus. The analyzed parameters were vascular density and perfusion density, as well as the area, perimeter, and circularity of the foveolar avascular zone (FAZ). Results: The comparative analysis of FAZ parameters at the superficial capillary plexus (SCP) between group 1 (eyes with retinal vein occlusion) and group 2 (unaffected fellow eyes) showed significant results for the three parameters, respectively area (p = 0.003), perimeter (p ≤ 0.001), and circularity (p = 0.011) of FAZ. The comparative analysis of the vascular network at SCP in patients with diagnosed retinal vein occlusion and unaffected fellow eyes showed significant results for vascular density (VD) in the central (p = 0.038) and inner (p ≤ 0.001) zones as well as total VD (p ≤ 0.001) were statistically significant. Moreover, the results obtained in the study of vascular perfusion (VP) indicated significant results in the inner zone (p ≤ 0.001) and total VP (p = 0.001). Vascular perfusion in the central zone (p = 0.116) was the only parameter not to meet significant results. Conclusion: The current study observed a significant enlargement of the FAZ and loss of its circularity, along with a reduction in vascular network parameters at the superficial retinal capillary plexus level.

Microvascular structural changes in esophageal squamous cell carcinoma pathology according to intrapapillary capillary loop types under magnifying endoscopy

BACKGROUND The intrapapillary capillary loop(IPCL)characteristics,visualized using magnifying endoscopy,are commonly assessed for preoperative evaluation of the infiltration depth of esophageal squamous cell carcinoma(ESCC).Japan Esophageal Society(JES)classification is the most widely used classification.Microvascular structural changes are evaluated by magnifying endoscopy for the presence or absence of each morphological factor:tortuosity,dilatation,irregular caliber,and different shapes.However,the pathological characteristics of IPCLs have not been thoroughly investigated,especially the microvascular structures corresponding to the deepest parts of the lesions'infiltration.AIM To investigate differences in pathological microvascular structures of ESCC,which correspond to the deepest parts of the lesions'infiltration.METHODS Patients with ESCC and precancerous lesions diagnosed at Peking University Third Hospital were enrolled between January 2019 and April 2023.Patients first underwent magnified endoscopic examination,followed by endoscopic submucosal dissection or surgical treatment.Pathological images were scanned using a threedimensional slice scanner,and the pathological structural differences in different types,according to the JES classification,were analyzed using nonparametric tests and t-tests.RESULTS The 35 lesions were divided into four groups according to the JES classification:A,B1,B2,and B3.Statistical analyses revealed significant differences(aP<0.05)in the short and long calibers,area,location,and density between types A and B.Notably,there were no significant differences in these parameters between types B1 and B2 and between types B2 and B3(P>0.05).However,significant differences in the short calibers,long calibers,and area of IPCL were observed between types B1 and B3(aP<0.05);no significant differences were found in the density or location(P>0.05).CONCLUSION Pathological structures of IPCLs in the deepest infiltrating regions differ among various IPCL types classified by the JES classification under magnifying endoscopy,especially between the types A and B.

Capillary Zone Electrophoretic Separation of Proteins in Polymer Coated Capillaries

Fused-silica capillaries used in capillary zone electrophoresis were statically coated with γ- glycidoxypropyltrimethoxysilane and epoxy polymer in order to suppress wall adsorption in the separation of proteins. It has been shown that a significant decrease in adsorption was obtained and eletroosmotic flow was the diminished in the pH range 3-5. However with higher pH values, appreciable peak deformation and decreases in the resolving power were observed. Under pH 5, the epoxy polymer coating was shown to be quite stable and exhibited reproducible separations from run-to-run and day-to-day over a period of time.

Synthesis of Isonucleoside-Incorporated Oligonucleotides and Their Binding Abilities with Complementary Sequences

Aim To synthesize isonucleoside-incorporated oligonucleotides and investigatetheir binding abilities with complementary sequences. Methods The synthesis was performed on DNAsynthesizer, and the binding behavior was investigated by thermal denaturation studies. Results Fourkinds of single isonucleoside containing oligonucleotides were synthesized. The results of thermaldenaturation showed that the existence of isonucleoside decreased the stability of duplex, and theeffect was more obvious when the isonucleoside was in the middle of the sequence. No obviousdifference was observed when 6'-OH of isonucleoside was free or was protected by allyl group.Conclusions The existence of isonucleoside in oli-gonucleotide makes chain twist and decreased thestability of duplex.

Response to an Escherichia coli K88 oral challenge and productivity of weanling pigs receiving a dietary nucleotides supplement

Background： Dietary nucleotides, considered as antibiotics alternative, were shown to have positive effects on intestinal hyperaemia, systemic immunity, small-intestinal growth, and hepatic composition in pigs. However, there is no previous research on nucleotide supplementation in weanling pigs under an oral challenged E. coil K88. Therefore, 2 experiments were conducted to investigate the effects of dietary nucleotides on weanling pig growth performance, nutrient digestibility, fecal score, and blood profile after being orally challenged with E. coli K88. Methods： In Exp. 1, a total of 140 weanling pigs [8.33 ± 0.33 kg of body weight （BW）, 28-d old] were used in this 42-d feeding trial. Pigs were distributed into 1 of 4 treatments, 5 pigs/pen （3 barrows and 2 gilts） and 7 pens/treatment. Treatments were a control basal diet （CON） or the CON supplemented with 150 （R150）, 220 （R220）, or 275 （R275） mg/kg to give the three treatment diets. In Exp. 2, 28 weanling pigs （BW = 8.40 ± 0.22 kg, 28-d old） were distributed into 1 of 4 treatments to give 1 pig/pen and 7 pens/treatment in a 42-d feeding and challenge trial. Dietary treatments were the same as in Exp. 1. 0n d 14, all those pigs （BW= 13.3±0.15 kg, 42-d old） were orally dosed with 1.5 mL suspension containing 10 cfu/mL of E. coli K88. Twenty four hours after challenge, blood and excreta samples were collected from each pigs for analysis. Fecal scores were measured on d 7, 14, 21, and 28 of the study. Results： In Exp. 1, overall BW, average daily gain （ADG）, gain/feed （G/F） ratio, and nutrient digestibilities were lower （P 〈 0.05） in CON group compared with the nucleotides fed pigs. In Exp. 2, after challenge, IgA, IgM, and IGF-I were higher （P〈 0.05） in the nucleotide groups compared with CON. However, the nucleotide groups had lower （P 〈 0.05） cortisol and TNF-o compared with CON. Fecal E. coil counts and fecal score for the nucleotide groups were lower （P 〈 0.05） than for CON. Conclusions： In conclusion, dietary nucleotides supplementation could improve growth performance, nutrient digestibility, immune status, microbial balance, reduce diarrhea, and provide protection against enterotoxigenic E. coli K88 infection in weanling pigs.

Individual and Combined Effects of Nucleotides and Human Milk Oligosaccharides on Proliferation, Apoptosis and Necrosis in a Human Fetal Intestinal Cell Line

Nucleotides (NT) and human milk oligosaccharides (HMO) individually affect epithelial cell growth, but their combined effects had not been studied. Herein, the impact of NT and HMO on cell proliferation, apoptosis, necrosis and cell cycle in the fetal epithelial cell line (FHs-74 Int) was determined. Cells were incubated with media containing 2.5% FBS and no epidermal growth factor (Control);fucosyllactose (FL) mix [85% 2’FL/15% 3’FL], sialyllactose (SL) mix [40% 6’SL/10% 3’SL/50% sialic acid (SA)] or LNnT at 125, 250, 500 or 1000 μg/mL with and without 250 μg/mL NT (43% CMP, 18.5% UMP, 16.4% AMP, and 22.0% GMP) for 24 or 72 h. NT alone significantly increased proliferation, but did not affect cell cycle or apoptosis/necrosis. All HMO treatments at 1000 μg/mL significantly decreased proliferation and some were also inhibitory at 250 or 500 μg/mL. When NT and HMO were simultaneously added, NT ameliorated the anti-proliferative effect of HMO. FL significantly increased cells in S phase and SL and LNnT treatments significantly increased cells in G2/M and S phases, which concomitantly decreased cells in G0/G1. HMO with NT significantly decreased the percent of cells in the G2/M phase compared to HMO alone. Higher HMO doses significantly increased the percentage of apoptotic and necrotic cells compared to control. In conclusion, HMO reduced cell proliferation and this effect is partially ameliorated by NT. It appears that HMO initially induced apoptosis/necrosis, which was later evidenced by G2/M cell cycle arrest and decreased proliferation.

Purine nucleotides and their metabolites in patients with type 1 and 2 diabetes mellitus

We measured the erythrocyte levels of principal nucleotides (ATP, ADP, AMP, GTP, GDP, GMP, IMP), nucleosides (Ado, Guo, Ino) and Hyp with HPLC. Purine concentrations were determined in the erythrocytes of 36 type 1 and 40 type 2 diabetic patients. The increased dephosphorylation of adenine and guanine nucleotides, indicated by increased Ado, Ino, Guo and Hyp concentrations as the products of purine nucleotide degradation, suggests serious energy metabolism disruptions in diabetes. An increase in AMP, GMP, IMP concentrations, as well as a decrease in AEC and GEC values, points to significant alterations in erythrocyte purine nucleotide concentration.

Frequency and Correlation of Nearest Neighboring Nucleotides in Human Genome

Zipf＇s approach in linguistics is utilized to analyze the statistical features of frequency and correlation of 16 nearest neighboring nucleotides （AA, AC, AG, …, TT） in 12 human chro- mosomes （Y, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, and 12）. It is found that these statistical features of nearest neighboring nucleotides in human genome： （i） the frequency distribution is a linear function, and （ii） the correlation distribution is an inverse function. The coefficients of the linear function and inverse function depend on the GC content. It proposes the correlation distribution of nearest neighboring nucleotides for the first time and extends the descriptor about nearest neighboring nueleotides.

Cleavage of Nucleotides by Lanthanide Metal Complexes

The present work revealed that the praseodymium()complex of 2carboxyethylgermanium sesquioxide(Ge132)promotes the hydrolysis of the phosphodiester linkages of 3,5cyclic adenosine monophosphate(cAMP),3,5cyclic deoxyadenosine monophosphate(dcAMP),5adenosine monophosphate(5AMP)and 5deoxyadenosine monophosphate(5dAMP)under mild conditions.Both cAMP and dcAMP were hydrolyzed sitespecifically,yielding predominantly 3monophosphates,the main products of the cleavage of 5AMP and 5dAMP included adenosine(Ado),deoxyadenosine(dAdo)and free phosphates respectively.A hydrolytic mechanism was proposed for cAMP,dcAMP,5AMP and 5dAMP.

Recent applications and chiral separation development based on stationary phases in open tubular capillary electrochromatography(2019–2022)

Capillary electrochromatography(CEC)plays a significant role in chiral separation via the double separation principle,partition coefficient difference between the two phases,and electroosmotic flow-driven separation.Given the distinct properties of the inner wall stationary phase(SP),the separation ability of each SP differs from one another.Particularly,it provides large room for promising applications of open tubular capillary electrochromatography(OT-CEC).We divided the OT-CEC SPs developed over the past four years into six types:ionic liquids,nanoparticle materials,microporous materials,biomaterials,non-nanopolymers,and others,to mainly introduce their characteristics in chiral drug separation.There also added a few classic SPs that occurred within ten years as supplements to enrich the features of each SP.Additionally,we discuss their applications in metabolomics,food,cosmetics,environment,and biology as analytes in addition to chiral drugs.OT-CEC plays an increasingly significant role in chiral separation and may promote the development of capillary electrophoresis(CE)combined with other instruments in recent years,such as CE with mass spectrometry(CE/MS)and CE with ultraviolet light detector(CE/UV).

Correction of distorted X-ray absorption spectra collected with capillary sample cell

In certain exceptional cases,capillary samples must be used to measure X-ray absorption spectra(XAS).However,the inho-mogeneous thickness of capillary samples causes XAS distortion.This study discusses the distortion and correction of the XAS curve caused by the inhomogeneous thickness of capillary samples.The relationship between the distorted XAS curveμ′d_(eq)(measured values)and the real absorption coefficientμ_(s)d_(eq)(true values)of the sample was established.The distortion was slight and negligible when the vertical size(2h)of the X-ray beam spot was smaller than 60%of the capillary tube’s inner diameter(2R_(in)).When h/R_(in)>1,X-ray leakage is inevitable and should be avoided during measurement.Partial X-ray leakage caused by an X-ray beam spot size larger than the inner diameter of the capillary tube leads to serious compressed distortion of the XAS curve.When h/R_(in)<1,the distorted XAS data were well corrected.Possible errors and their influence on the corrected XAS are also discussed.Simulations and corrections for distortions verify the feasibility and effectiveness of the corrected method.

Quick and Simple Spectrophotometric Method of Identification of the Thermal State of Meat on the Basis of Composition and Content of Free Nucleotides

At present, there is no method for identifying meat frozen in a thermal state acceptable for production control. The role of free nucleotides in the processes of refrigeration and storage of meat, affecting the structural and mechanical properties of muscle tissue, the formation of taste and its biological value is known. In this article we compared methods for identifying the thermal state of meat based on the determination of the composition and content of free nucleotides by high-performance liquid chromatography (HPLC) and spectrophotometry [SF]. High-purity reference substances were used: free nucleotides—ATP, ADP, AMP, IMP and nucleosides-inosine and hypoxanthine. It has been experimentally established that the characteristic peaks of the absorption spectra for extracts of free nucleotides of meat frozen depended from thermal state of meat. The content of ATP is 21.8 times higher in meat frozen in a fresh state, and the amount of IMF is 12.3 times lower than in meat frozen after cooling. The results of studies of meat frozen using the HPLC method and the developed SF method show the adequacy of the data obtained by both methods. SF-method based on the determination of the optical density of the extracts of free nucleotides is recommended to justify the choice of technological process meat defrost modes.

DNA sequence representation by trianders and determinative degree of nucleotides

A new version of DNA walks, where nucleotides are regarded unequal in their contribution to a walk is introduced, which allows us to study thoroughly the “fine structure” of nucleotide sequences. The approach is based on the assumption that nucleotides have an inner abstract characteristic, the determinative degree, which reflects genetic code phenomenological prop-erties and is adjusted to nucleotides physical properties. We consider each codon position independently, which gives three separate walks characterized by different angles and lengths, and that such an object is called triander which reflects the “strength” of branch. A general method for identifying DNA sequence “by triander” which can be treated as a unique “genogram” (or “gene passport”) is proposed. The two- and three-dimensional trianders are considered. The difference of sequences fine structure in genes and the intergenic space is shown. A clear triplet signal in coding sequences was found which is absent in the intergenic space and is independent from the sequence length. This paper presents the topological classification of trianders which can allow us to provide a detailed working out signatures of functionally different genomic regions.