Population structure and selection signal analysis of indigenous sheep from the southern edge of the Taklamakan Desert.

Analyzing the genetic diversity and selection characteristics of sheep (Ovis aries) holds significant value in understanding their environmental adaptability, enhancing breeding efficiency, and achieving effective conservation and rational utilization of genetic resources. In this study, we utilized Illumina Ovine SNP 50 K BeadChip data from four indigenous sheep breeds from the southern margin of the Taklamakan Desert (Duolang sheep: n = 36, Hetian sheep: n = 74, Kunlun sheep: n = 27, Qira black sheep: n = 178) and three foreign meat sheep breeds (Poll Dorset sheep: n = 105, Suffolk sheep: n = 153, Texel sheep: n = 150) to investigate the population structure, genetic diversity, and genomic signals of positive selection within the indigenous sheep. According to the Principal component analysis (PCA), the Neighbor-Joining tree (NJ tree), and Admixture, we revealed distinct clustering patterns of these seven sheep breeds based on their geographical distribution. Then used Cross Population Extended Haplotype Homozygosity (XP-EHH), Fixation Index (FST), and Integrated Haplotype Score (iHS), we identified a collective set of 32 overlapping genes under positive selection across four indigenous sheep breeds. These genes are associated with wool follicle development and wool traits, desert environmental adaptability, disease resistance, reproduction, and high-altitude adaptability. This study reveals the population structure and genomic selection characteristics in the extreme desert environments of native sheep breeds from the southern edge of the Taklimakan Desert, providing new insights into the conservation and sustainable use of indigenous sheep genetic resources in extreme environments. Additionally, these findings offer valuable genetic resources for sheep and other mammals to adapt to global climate change.

Analysis of full and empty ratio of EV71 virus by using capillary zone electrophoresis.

Hand, foot, and mouth disease is a serious public health problem, and the main pathogen is enterovirus 71 (EV71). Its capsid assembly mechanism including capsid protein processing has been widely studied. Full and empty capsids have different immunological efficacy. Therefore, tracking full/empty capsid ratio throughout the EV71 production process is important to ensure consistent product quality and proper dosing response. The analysis of full/empty capsid ratio of intact virus has been widely reported as well. A variety of techniques have been employed to evaluate the full/empty capsid ratios. However, there has not been a rapid, reproducible, and robust assay to determine the full/empty capsid ratios of final and in-process products. In this study, a novel assay based on capillary zone electrophoresis was established. The separation of full and empty species could be achieved within 10 min and the ratio of peak areas was used to calculate the full/empty capsid ratio directly. The results showed good reproducibility and linearity for the determination of full/empty capsid ratios.

Highly Efficient and Selective Dissolution Separation of Fission Products by an Ionic Liquid [Hbet][Tf2N]: A New Approach to Spent Nuclear Fuel Recycling.

Here, we propose the use of carboxyl-functionalized ionic liquid, [Hbet][Tf2N], to separate the fission products from spent nuclear fuels. This innovative method allows the selective dissolution of neutron poisons, lanthanides oxide, as well as some fission products with high yield, leaving most of the UO2 matrix and minor actinides behind in the spent nuclear fuel and accomplishing the actinides recovery as a group. Water-saturated [Hbet][Tf2N] can dissolve lanthanides oxide from simulated spent nuclear fuel with a dissolution ratio of 100% at 40 °C. However, the dissolution of uranium is almost negligible (<1%) under the same conditions. This big difference in dissolution provides a novel separation approach to spent nuclear fuel recycling and may open new perspectives for spent nuclear fuel reprocessing. The recovery of Nd and U from metal-loaded ionic liquids and the recyclability of the ionic liquid [Hbet][Tf2N] have also been investigated. Furthermore, a U/ x value related to the lattice energy U of metal compound M xO y is used to elaborate the solubility. This work represents the first case for efficient fission products removal by selective dissolution, avoiding the complete dissolution of spent nuclear fuel, the producing of the large high-level radioactive waste, and reducing environmental hazards.

Effects of melatonin on sperm quality, enzyme activity, antioxidant gene expression and fertility of cryopreserved bovine semen.

Melatonin (MLT) has strong antioxidant capacity and can reduce the damage caused by oxidative stress in sperm, but there is still little content in the field we have studied. In this study, we are committed to scientific research on adding melatonin to Belgian blue bull semen diluent for cryopreservation. Different concentrations (0, 0.1, 0.3, 0.5 or 0.7 mg/mL) of MLT were added diluent. Sperm kinetic parameters, enzyme activity, antioxidant gene expression and fertility were analyzed after thawing. The results showed that MLT concentration of 0.3 mg/mL exerted positive effects on post-thaw kinetic parameters. Compared with other groups, 0.3 mg/mL MLT treated sperm acrosome and plasma membrane integrity, catalase (CAT), superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) levels significantly increased. Meanwhile, the mRNA expression of antioxidant genes SOD2, CAT and GPx increased in the 0.3 mg/mL MLT treatment group, and the mRNA expression of apoptosis genes Caspase-3 and Bax were significantly reduced. In addition, in vitro fertilization (IVF) embryo cleavage, blastocyst rate and artificial insemination (AI) pregnancy rate were higher in 0.3 mg/mL MLT. Therefore, MLT showed cryoprotective capacity to the freezing diluent used for Belgian blue bull sperm during the process of freezing-thawing, and the optimal concentration of MLT for the frozen diluent was 0.3 mg/mL.

Pangenome obtained by long-read sequencing of 11 genomes reveal hidden functional structural variants in pigs.

Long-read sequencing (LRS) facilitates both the genome assembly and the discovery of structural variants (SVs). Here, we built a graph-based pig pangenome by incorporating 11 LRS genomes with an average of 94.01% BUSCO completeness score, revealing 206-Mb novel sequences. We discovered 183,352 nonredundant SVs (63% novel), representing 12.12% of the reference genome. By genotyping SVs in an additional 196 short-read sequencing samples, we identified thousands of population stratified SVs. Particularly, we detected 7,568 Tibetan specific SVs, some of which demonstrate significant population differentiation between Tibetan and low-altitude pigs, which might be associated with the high-altitude hypoxia adaptation in Tibetan pigs. Further integrating functional genomic data, the most promising candidate genes within the SVs that might contribute to the high-altitude hypoxia adaptation were discovered. Overall, our study generates a benchmark pangenome resource for illustrating the important roles of SVs in adaptive evolution, domestication, and genetic improvement of agronomic traits in pigs.

[Clinical studies of dynamic changes on the renal injury indicators of acute paraquat poisoning].

OBJECTIVE: To investigate the clinical significance of dynamic changes of blood urea nitrogen (BUN), serum creatinine (Cr), serum cystatin (Cys C) and urinary protein on renal injury with paraquat poisoning. METHODS: According to the clinical manifestation and curative effect, the clinical information was analyzed retrospectively in 35 cases of acute paraquat poisoning, survival after eight weeks as the standard. Poisoning patients were taken a fasting blood 5 ml and the middle of urinary on the 1st day, 3rd day, 7th day, 14th day, 21st day and 8 weeks after the poisoning. Then the levels of serum BUN, Cr, Cys C and urinary protein were detected by automatic biochemistry analyzer. 30 cases healthy subjects were randomly selected as normal control group, and discharged kidney disease and other diseases of urinary system history. The same laboratory subjects have been done. RESULTS: The level of serum Bun, Cr, Cys C of survival group increased significantly compared with control group within 21 days (P < 0.05). The level of serum BUN, Cr Cys C decreased on the 14th day. The decreased level of serum Cys C was lower than that of serum BUN and Cr. The renal function of 29 cases among 35 cases survival patients recovered on 21st day. The renal function of 31 cases among 35 cases survival patients recovered 8 weeks late. The positive rate of urinary protein of survival patients was high in the early intoxication (76.9%). CONCLUSION: Serum Cys C is sensitive indicator to reveal the kidney injury on paraquat poisoning patients and have higher value of clinical applications in the diagnosis of the kidney injury of paraquat poisoning, which sensitivity is higher than serum BUN and Cr. The kidney injury caused by paraquat poisoning is reversible.

A butterfly shaped Eu4(OH)2 cluster-based luminescent metal-organic framework with Lewis basic triazole sites demonstrating turn off sensing in the presence of organic amines.

The effective detection of organic amines is particularly important for environmental protection and human health. Herein, according to hard and soft acid base theory, a novel three-dimensional (3D) butterfly shaped Eu4(OH)2 cluster-based metal-organic framework with Lewis basic triazole sites, {[Eu4(taip)4(ox)(OH)2(H2O)4]·3H2O}n (1) (H2taip = 5-(1,2,4-triazol-1-yl) isophthalic acid, H2ox = oxalic acid), was successfully synthesized under solvothermal conditions, and was characterized by single crystal X-ray diffraction, powder X-ray diffraction, elemental analysis, infrared spectroscopy and thermogravimetric analysis. Structural analysis reveals that compound 1 is a 3D net constructed from butterfly shaped Eu4(OH)2 clusters and contains isosceles triangular channels with dimensions of 8.84 × 8.84 × 8.63 Å3, which shows an unprecedented 8-connected topology with a Schläfli symbol {36·418·53·6}. Fluorescence experiments of compound 1 show sensitive luminescence quenching responses to organic amines such as diethylamine (DEA), trimethylamine (TMA), triethylamine (TEA), ethylenediamine (EDA) and aniline, and the quenching constants (KSV) decrease in the following order: EDA > DEA > TMA > TEA > aniline. The fluorescence quenching responses may be attributed to the energy gap between the LUMO energy values of H2taip and organic amines, which hinders the transfer of excited state energy to the emission state of Eu3+ and results in luminescence quenching. The fluorescence lifetimes of compound 1 in ethanol and organic anilines indicate that the fluorescence recognition process of organic amines was static.

Inhibitory effects of aloperine on voltage-gated Na+ channels in rat ventricular myocytes.

Aloperine (ALO), a quinolizidine alkaloid extracted from Sophora alopecuroides L., modulates hypertension, ventricular remodeling, and myocardial ischemia. However, few studies have evaluated the effects of ALO on other cardiovascular parameters. Accordingly, in this study, we used a rat model of aconitine-induced ventricular arrhythmia to assess the effects of ALO. Notably, ALO pretreatment delayed the onset of ventricular premature and ventricular tachycardia and reduced the incidence of fatal ventricular fibrillation. Moreover, whole-cell patch-clamp assays in rats' ventricular myocyte showed that ALO (3, 10, and 30 µM) significantly reduced the peak sodium current density of voltage-gated Na+ channel currents (INa) in a concentration-dependent manner. The gating kinetics characteristics showed that the steady-state activation and recovery curve were shifted in positive direction along the voltage axis, respectively, and the steady-state inactivation curve was shifted in negative direction along the voltage axis, i.e., which was similar to the inhibitory effects of amiodarone. These results indicated that ALO had anti-arrhythmic effects, partly attributed to INa inhibition. ALO may act as a class I sodium channel anti-arrhythmia agent.

A susceptibility locus at chromosome 3p21 linked to familial nasopharyngeal carcinoma.

Nasopharyngeal carcinoma (NPC) poses one of the serious health problems in southern Chinese, with an incidence rate ranging from 15 to 50/100,000. Chromosome translocation t(1;3) and frequent loss of heterogeneity on short arms of chromosome 3 and 9 have been reported to be associated with NPC, and a genome-wide scan identified an NPC susceptibility locus on chromosome 4p15.1-q12 recently. In our study, we collected samples from 18 families at high risk of NPC from the Hunan province in southern China, genotyped with a panel of polymorphic markers on short arms of chromosomes 3, 9, and 4p15.1-q12. A locus on 3p21 was identified to link to NPC with a maximum logarithm of odds for linkage score of 4.18. Fine mapping located the locus to a 13.6-cM region on 3p21.31-21.2, where a tumor suppressor gene cluster resided. Our findings identified a novel locus for NPC and provided a map location for susceptibility genes candidates. In contrast to a recent study, no significant evidence for NPC linkage to chromosomes 4 and 9 was observed.

[Function of a novel brain-specific gene LRRC4].

OBJECTIVE: To study the suppressive effect of LRRC4 gene on human glioma U251 cells and further investigate its biological functions. METHODS: H&E, DNA and AgNORs stainings were performed on LRRC4-transfected U251 cells, mock-transfected U251 cells and non-transfected U251 cells, respectively. Quantitative analysis including cell morphometry, DNA content, DNA ploidy, silver stained argyrophilic nucleolar organizer regions (AgNORs) were investigated by image analysis. Flow cytometry was employed to determine the difference of cell cycle distribution and MTT staining was used to elucidate the activity of the LRRC4-transfected U251 cells. RESULTS: The morphological cell parameters such as area, perimeter and diameter, DNA content, chromosomal aneupoloidy, mean area of AgNORs particles and mean nucleus area of the LRRC4-transfected U251 cells were remarkably decreased compared to those of the mock-transfected and non-transfected U251 cells (P < 0.05, P < 0.01). Meanwhile, significant accumulation of cells in G(0)/G(1) phase but decrease of cells in S and G(2)/M phase, was observed in transfected U251 cells compared to those of the mock-transfected and non-transfected U251 cells (P < 0.05, P < 0.01). MTT staining showed that proliferation activity of both the mock- and non-trasfected U251 cells was significantly higher than that of the U251 cells transfected with LRRC4 gene (P < 0.01). CONCLUSION: LRRC4 gene might be involved in tumor suppression by restraining DNA synthesis and the nucleoli organizer regions-associated proteins, keeping the cell cycles in phase G(0)/G(1) and reducing proliferation activity of the glioma cells. Morphometry combined with other techniques such as flow cytometry and MTT staining can well elucidate the biological function of novel genes.

An R2R3-MYB gene, LeAN2, positively regulated the thermo-tolerance in transgenic tomato.

LeAN2 is an anthocyanin-associated R2R3-MYB transcription factor, but little is known about its function in imparting thermo-tolerance to higher plants. To examine the function of LeAN2 in the regulation of heat stress in tomato, LeAN2 was isolated and transgenic tomato plants were obtained. Overexpression of LeAN2 under the control of the CaMV35S promoter in tomato induced the up-regulation of several structural genes in the anthocyanin biosynthetic pathway as well as anthocyanin accumulation in transgenic tomato plants. Transgenic tomato plants showed enhanced tolerance to heat stress by maintaining higher fresh weight (FW), net photosynthetic rate (Pn) and maximal photochemical efficiency of photosystem II (PSII) (Fv/Fm) compared with wild-type (WT) plants. Furthermore, transgenic plants showed higher non-enzymatic antioxidant activity, lower levels of reactive oxygen species (ROS), and higher contents of D1 protein than that in WT plants under heat stress. These results indicate that LeAN2 had an important function in heat stress resistance.

Expression of tumor related genes NGX6, NAG-7, BRD7 in gastric and colorectal cancer.

AIM: NGX6, NAG-7 and BRD7 genes are tumor related genes, which have been newly cloned by positional candidate cloning strategy. This study was designed to investigate the expression levels of NGX6, NAG-7 and BRD7 genes in human gastric and colorectal cancer tissues, and their corresponding normal tissues, and to investigate whether these genes play a role in the pathogenesis of gastric and colorectal cancers. METHODS: Reverse transcription-polymerase chain reaction (RT-PCR), dot hybridization and Northern blot analysis were used to compare the expression levels of NGX6, NAG-7 and BRD7 genes in 34 gastric cancer tissues and 34 colorectal cancer tissues with their corresponding normal tissues of the same patients, respectively. RESULTS: Among the 34 colorectal cancer specimens and the 34 gastric cancer specimens, the expression of NGX6 in 25 colorectal cancer tissues was absent or very weak (73.5 %) by RT-PCR analysis. The down-regulation rate of NGX6 in colorectal cancer tissues was significantly higher than that in corresponding normal tissues (26.5 %,9/34) (P<0.005). Moreover, the down-regulation of NGX6 was significantly correlated with lymph node and/or distance metastases. Patients with lymph node and/or distance metastasis had much higher down-regulation rate of NGX6 than patients without metastases (93.8 % vs 55.6 %, P<0.05). However no correlation was found between the expression of NGX6 and pathologic type of colorectal cancer in this study, and also the expression of NGX6 did not display any difference between gastric cancer and corresponding normal tissues (58.8 % vs 70.6 %, P>0.25). Dot hybridization and Northern blot analysis confirmed the results of RT-PCR. Furthermore, NAG-7 and BRD7 mRNA was not up- or down-regulated in gastric and colorectal cancers compared with their corresponding normal tissues in our study. CONCLUSION: The down-regulation of NGX6 may be closely associated with tumorigenesis and metastasis of colorectal carcinoma. However, it may not contribute to the development and progression of gastric carcinoma. In addition, the expression levels of NAG-7, and BRD7 did not alter in gastric and colorectal cancers. This seems to suggest that NAG-7 and BRD7 genes may not play a role in gastric and colorectal carcinogenesis.

Expression of tumor related gene NAG6 in gastric cancer and restriction fragment length polymorphism analysis.

AIM: NAG6 gene is a novel tumor related gene identified recently. This study was designed to examine the expression of this gene in gastric cancer and corresponding normal tissues, and to investigate its role in the occurrence and development of gastric cancer, also to study if the genetic structure of NAG6 was altered in gastric cancer. METHODS: Reverse transcription-polymerase chain reaction (RT-PCR), Northern blot analysis and dot hybridization were used to compare the expression level of NAG6 gene in 42 cases of gastric cancer tissues with their corresponding normal tissues of the same patients respectively. In addition, restriction fragment length polymorphism (RFLP) analysis was adopted to study if the genetic structure of NAG6 was altered in gastric carcinomas. RESULTS: The expression of NAG6 in 57.1% gastric cancer tissues (25/42) was absent by RT-PCR analysis. The down-regulation rate of NAG6 in gastric cancer tissues was significantly higher than that in corresponding normal tissues (P<0.01). However no correlation between the down-regulation of NAG6 and lymph-node and/or distance metastasis was found in this study (P>0.05). Dot hybridization confirmed the results of RT-PCR. Furthermore, the results of EcoRI RFLP analysis of NAG6 gene demonstrated that 3 of 7 cases of gastric cancer showed loss of 5 kb fragment in comparison with their corresponding normal tissues. CONCLUSION: NAG6 gene is significantly down regulated in gastric cancer. The loss of genetic materials may be the cause of down-regulation of NAG6 expression. This seems to suggest that NAG6 may represent a candidate of putative tumor suppressor gene at 7q31-32 loci associated with gastric carcinoma. The down-regulation of this gene may play a role in occurrence and development of this disease, however it may not be associated with lymph node and/or distance metastasis.

Preliminary Function Study of NAG7 Using Two-dimensional Electrophoresis and Mass Spectrometry.

In search of mechanisms of function of NAG7 gene, a powerful new tool for the unambiguous characterization of gel-separated proteins is accomplished by the combination of mass spectrometry and sequence database searching. NAG7, a novel putative tumor suppressor gene, located on 3p25.3, was introduced into HNE1 cells by liposome transfection. We used two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) to identify proteins that were overexpressed in NAG7 transfected cells. After staining and image analysis, spots of interest were isolated and subjected to mass spectrometry (MS). We found nine proteins, which up-regulated in NAG7 transfected cells and be identified by MS. These proteins included growth arrest specific protein, DNA binding protein, c-myc promoter-binding protein and caspase 6 etc., which involved in cell cycling, transcription regulation, and apoptosis. NAG7 may exert the function by up-regulating the expression of these proteins.

Cloning and Expression Analysis of a Novel Gene, UBAP1, Possibly Involved in Ubiquitin Pathway.

The 9p21-22 region shows loss of heterozygosity in up to 60% of human nasopharyngeal carcinomas (NPC), indicating the presence of a tumor suppressor gene in this region. We have identified a novel minimal common deletion region at 9p21-22. Twenty-two epithelial-derived expressed sequence tags (ESTs) in this critical region were systematically screened by differential RT-PCR to investigate the expression patterns in NPC cell line HNE1 and primary cultures of normal nasopharyngeal epithelial cells. One of these ESTs was found down-expressed in HNE1, whose differential expression was confirmed by Northern blot. Subsequently the corresponding gene sequence for this EST was established by cDNA cloning and RACE procedures (GenBank Accession No.AF222043). Furthermore, a mouse homologueof this gene was identified (GenBank Accession No.AF275549). This gene is 2.7 kb long and contains two UBA domains. It is a new member of UBA domain protein family, encoding a putative protein of 502 amino acids with a theoretical molecular mass of 55 kD, so we have named this gene UBAP1 for ubiquitin associated protein 1 (HUGO Gene Nomenclature Committee-approved symbol). Northern blot and RT-PCR analysis demonstrated a ubiquitous pattern of gene expression in human and mouse tissues. Direct sequencing analysis of the coding region of hUBAP1 following RT-PCR failed to reveal any mutations in a preliminary screening of NPC cell line HNE1 and primary nasopharyngeal carcinomas samples. However, more detailed analysis is to be performed to reveal if fine mutations of this gene are present in NPC.