Whole-Genome Resequencing Analysis of the Camelus bactrianus (Bactrian Camel) Genome Identifies Mutations and Genes Affecting Milk Production Traits.

Milk production is an important trait that influences the economic value of camels. However, the genetic regulatory mechanisms underlying milk production in camels have not yet been elucidated. We aimed to identify candidate molecular markers that affect camel milk production. We classified Junggar Bactrian camels (9-10-year-old) as low-yield (<1.96 kg/d) or high-yield (>2.75 kg/d) based on milk production performance. Milk fat (5.16 ± 0.51 g/100 g) and milk protein (3.59 ± 0.22 g/100 g) concentrations were significantly lower in high-yielding camels than those in low-yielding camels (6.21 ± 0.59 g/100 g, and 3.93 ± 0.27 g/100 g, respectively) (p < 0.01). There were no apparent differences in gland tissue morphology between the low- and high-production groups. Whole-genome resequencing of 12 low- and 12 high-yield camels was performed. The results of selection mapping methods, performed using two methods (FST and θπ), showed that 264 single nucleotide polymorphism sites (SNPs) overlapped between the two methods, identifying 181 genes. These genes were mainly associated with the regulation of oxytocin, estrogen, ErbB, Wnt, mTOR, PI3K-Akt, growth hormone synthesis/secretion/action, and MAPK signaling pathways. A total of 123 SNPs were selected, based on significantly associated genomic regions and important pathways for SNP genotyping, for verification in 521 additional Bactrian camels. This analysis showed that 13 SNPs were significantly associated with camel milk production yield and 18 SNPs were significantly associated with camel milk composition percentages. Most of these SNPs were located in coding regions of the genome. However, five and two important mutation sites were found in the introns of CSN2 (ß-casein) and CSN3 (κ-casein), respectively. Among the candidate genes, NR4A1, ADCY8, PPARG, CSN2, and CSN3 have previously been well studied in dairy livestock. These observations provide a basis for understanding the molecular mechanisms underlying milk production in camels as well as genetic markers for breeding programs aimed at improving milk production.

Transcriptome analysis of the Bactrian camel (Camelus bactrianus) reveals candidate genes affecting milk production traits.

BACKGROUND: Milk production traits are complex traits with vital economic importance in the camel industry. However, the genetic mechanisms regulating milk production traits in camels remain poorly understood. Therefore, we aimed to identify candidate genes and metabolic pathways that affect milk production traits in Bactrian camels. METHODS: We classified camels (fourth parity) as low- or high-yield, examined pregnant camels using B-mode ultrasonography, observed the microscopic changes in the mammary gland using hematoxylin and eosin (HE) staining, and used RNA sequencing to identify differentially expressed genes (DEGs) and pathways. RESULTS: The average standard milk yield over the 300 days during parity was recorded as 470.18 ± 9.75 and 978.34 ± 3.80 kg in low- and high-performance camels, respectively. Nine female Junggar Bactrian camels were subjected to transcriptome sequencing, and 609 and 393 DEGs were identified in the low-yield vs. high-yield (WDL vs. WGH) and pregnancy versus colostrum period (RSQ vs. CRQ) comparison groups, respectively. The DEGs were compared with genes associated with milk production traits in the Animal Quantitative Trait Loci database and in Alashan Bactrian camels, and 65 and 46 overlapping candidate genes were obtained, respectively. Functional enrichment and protein-protein interaction network analyses of the DEGs and candidate genes were conducted. After comparing our results with those of other livestock studies, we identified 16 signaling pathways and 27 core candidate genes associated with maternal parturition, estrogen regulation, initiation of lactation, and milk production traits. The pathways suggest that emerged milk production involves the regulation of multiple complex metabolic and cellular developmental processes in camels. Finally, the RNA sequencing results were validated using quantitative real-time PCR; the 15 selected genes exhibited consistent expression changes. CONCLUSIONS: This study identified DEGs and metabolic pathways affecting maternal parturition and milk production traits. The results provides a theoretical foundation for further research on the molecular mechanism of genes related to milk production traits in camels. Furthermore, these findings will help improve breeding strategies to achieve the desired milk yield in camels.

The Real-Valued Sparse Direction of Arrival (DOA) Estimation Based on the Khatri-Rao Product.

There is a problem that complex operation which leads to a heavy calculation burden is required when the direction of arrival (DOA) of a sparse signal is estimated by using the array covariance matrix. The solution of the multiple measurement vectors (MMV) model is difficult. In this paper, a real-valued sparse DOA estimation algorithm based on the Khatri-Rao (KR) product called the L1-RVSKR is proposed. The proposed algorithm is based on the sparse representation of the array covariance matrix. The array covariance matrix is transformed to a real-valued matrix via a unitary transformation so that a real-valued sparse model is achieved. The real-valued sparse model is vectorized for transforming to a single measurement vector (SMV) model, and a new virtual overcomplete dictionary is constructed according to the KR product's property. Finally, the sparse DOA estimation is solved by utilizing the idea of a sparse representation of array covariance vectors (SRACV). The simulation results demonstrate the superior performance and the low computational complexity of the proposed algorithm.

A novel signature constructed by cuproptosis-related RNA methylation regulators suggesting downregulation of YTHDC2 may induce cuproptosis resistance in colorectal cancer.

BACKGROUND: A newly identified type of cell death due to intracellular copper accumulation is known as cuproptosis and RNA methylation is a post-transcriptional modification mechanism, both of which perform vital roles in the immune microenvironment of colorectal cancer (CRC), but the link between the two needs more research. METHODS: TCGA database provided RNA-seq data and details clinically of CRC samples. Cuproptosis-related RNA methylation regulators (CRRMRs) were identified by correlation analysis. We screened 6 CRRMRs for prognostic model construction by employing LASSO-Cox regression analysis and calculated risk scores by CRRMRs (CuMS). GSE39582 and GSE38832 cohort were used as external validation sets. This research concentrated on the connection between the prognostic model and somatic mutation, anti-cancer drug sensitivity, immune infiltration, immune checkpoint expression. In addition, we investigated the differential expression of YTHDC2 in epithelial cell subpopulations by single-cell analysis with GSE166555, calculated cuproptosis scores and performed pathway enrichment. In vitro experiments were performed to explore the consequences of knockdown of YTHDC2 on CRC cell proliferation and migration, as well as changes in CRC cell viability in response to elesclomol after knockdown of YTHDC2. In vivo experiments, we constructed the cell line-derived xenograft model to further validate the results of the in vitro experiments. RESULTS: The prognosis of CRC can be predicted by CuMS, which GSE39582 and GSE38832 confirmed. Two CuMS groups showed different tumor mutation burden (TMB) and immune infiltration. CuMS was connected to emerging immune checkpoints CD47 and PVR, therefore, it can be clinically complementary to TMB and microsatellite instability (MSI) status. In single-cell analysis, a subpopulation of epithelial cells with high YTHDC2 expression had a high cuproptosis score. In vitro experiments, knocking down YTHDC2 promoted cell proliferation and migration in CRC, and weaken the inhibitory effect of elesclomol and elesclomol-Cu on cell viability, which in vivo experiments validated. CONCLUSION: We developed a prognostic model constructed by 6 CRRMRs to assess overall survival and immune microenvironment of CRC patients. YTHDC2 might regulate cuproptosis in multiple ways.

Transcriptome analysis to identify candidate genes related to mammary gland development of Bactrian camel (Camelus bactrianus).

Introduction: The demand for camel milk, which has unique therapeutic properties, is increasing. The mammary gland is the organ in mammals responsible for the production and quality of milk. However, few studies have investigated the genes or pathways related to mammary gland growth and development in Bactrian camels. This study aimed to compare the morphological changes in mammary gland tissue and transcriptome expression profiles between young and adult female Bactrian camels and to explore the potential candidate genes and signaling pathways related to mammary gland development. Methods: Three 2 years-old female camels and three 5 years-old adult female camels were maintained in the same environment. The parenchyma of the mammary gland tissue was sampled from the camels using percutaneous needle biopsy. Morphological changes were observed using hematoxylin-eosin staining. High-throughput RNA sequencing was performed using the Illumina HiSeq platform to analyze changes in the transcriptome between young and adult camels. Functional enrichment, pathway enrichment, and protein-protein interaction networks were also analyzed. Gene expression was verified using quantitative real-time polymerase chain reaction (qRT-PCR). Results: Histomorphological analysis showed that the mammary ducts and mammary epithelial cells in adult female camels were greatly developed and differentiated from those in young camels. Transcriptome analysis showed that 2,851 differentially expressed genes were obtained in the adult camel group compared to the young camel group, of which 1,420 were upregulated, 1,431 were downregulated, and 2,419 encoded proteins. Functional enrichment analysis revealed that the upregulated genes were significantly enriched for 24 pathways, including the Hedgehog signaling pathway which is closely related to mammary gland development. The downregulated genes were significantly enriched for seven pathways, among these the Wnt signaling pathway was significantly related to mammary gland development. The protein-protein interaction network sorted the nodes according to the degree of gene interaction and identified nine candidate genes: PRKAB2, PRKAG3, PLCB4, BTRC, GLI1, WIF1, DKK2, FZD3, and WNT4. The expression of fifteen genes randomly detected by qRT-PCR showed results consistent with those of the transcriptome analysis. Discussion: Preliminary findings indicate that the Hedgehog, Wnt, oxytocin, insulin, and steroid biosynthesis signaling pathways have important effects on mammary gland development in dairy camels. Given the importance of these pathways and the interconnections of the involved genes, the genes in these pathways should be considered potential candidate genes. This study provides a theoretical basis for elucidating the molecular mechanisms associated with mammary gland development and milk production in Bactrian camels.

Roasting treatments affect oil extraction rate, fatty acids, oxidative stability, antioxidant activity, and flavor of walnut oil.

Introduction: The quality of pressed walnut oil can be improved by moderate roasting treatment. Methods: This study compared physicochemical characteristics and antioxidant ability of walnut oils pressed from differently roasted pretreated walnuts, analyzed the correlation among these indicators by using Pearson correlation coefficient and correlation coefficient heatmap, and evaluated the volatile organic compounds (VOCs) of walnut oil under optimal pretreatment roasting conditions using headspace-gas chromatography-ion mobility spectrometry (HS-GC-IMS). Results: Hierarchical cluster analysis (HCA) and principal component analysis (PCA) were able to remarkably distinguish walnut oil produced by different roasting processes. In addition, correlation analysis showed that there was a significant impact among indicators. There were 73 VOCs were identified in the optimum roasted treated walnut oil, consisting of 30 aldehydes, 13 alcohols, 11 ketones, 10 esters, 5 acids, 2 oxygen-containing heterocycles, 1 nitrogen-containing heterocycle and 1 other compound. GC-IMS results showed that aldehydes contributed significantly to the volatile flavor profile of walnut oil, especially (E)-2-heptenal, (E)-2-pentenal and hexenal. Discussion: The properties of walnut oil based on varying roasting pretreatment of walnut kernels were significantly differentiated. Roasting at 120°C for 20 min is a suitable pretreatment roasting condition for pressing walnut oil. Roasting at 120°C for 20 min is a suitable pretreatment roasting condition for pressing walnut oil.

Camel whey protein (CWP) ameliorates liver injury in type 2 diabetes mellitus rats and insulin resistance (IR) in HepG2 cells via activation of the PI3K/Akt signaling pathway.

This research investigated the effects of camel whey protein (CWP) treatment on type 2 diabetes mellitus (T2DM) rats and insulin resistance (IR) HepG2 cell models. Body weight and fasting blood glucose were observed in type 2 diabetes mellitus (T2DM) rats every week, and biochemical parameters in serum samples were evaluated after 6 weeks. Antioxidant activity in the liver was estimated, and histological examination of the liver tissues was conducted. After CWP treatment, the glucose uptake and lipid accumulation were examined in insulin-resistant HepG2 cells. Our results indicated that CWP mitigated the body weight loss, reversed dyslipidemia, and inhibited the inflammatory response, in T2DM rats. Meanwhile, it protected the liver from being injured by reducing the level of oxidative stress. In the CWP group, the pathological changes were significantly reduced, while the liver lobule structure, liver cell arrangement, as well as congestion, edema, and vacuolization were improved. Our results from quantitative real-time PCR and western blot analyses showed that CWP could up-regulate the expression levels of insulin receptor substrate-2 (IRS-2), phosphoinositide3-kinase (PI3K), protein kinase B (AKT), and glycogen synthase (GS). An active protein component CWP8 was isolated and identified, which was shown to be able to stimulate glycogen synthesis and ameliorate lipid accumulation in IR HepG2 cells. These data indicate that CWP and CWP8 might act as potential natural products regulating glucose and lipid metabolism in T2DM.

Comparative Analysis of the Endophytic Bacterial Diversity of Populus euphratica Oliv. in Environments of Different Salinity Intensities.

Populus euphratica Oliv. has a high tolerance for drought, salinity, and alkalinity. The main purpose of this study is to explore the effects of environments of different salinity intensities on endophytic community structure and the possible roles of endophytes in the tolerance of host plants. The characterization of endogenous bacteria in diversity has been investigated by using the Illumina high-throughput sequencing technique. The research showed that endophytic bacteria of P. euphratica in an extremely saline environment had low species diversity, especially in sap tissue. The dominant phyla in all groups were Proteobacteria, Actinobacteria, and Bacteroidetes. Notably, Firmicutes (relative abundance >5%) was a different dominant phylum in the samples from the high-saline environment compared with the relatively low-saline-environment group. The linear discriminant analysis effect size (LEfSe) analysis found that there were significant differences in different saline environments of Cytophagaceae (family), Rhodobacteraceae (family), and Rhodobacterales (order). These results indicated that the composition of the endogenous bacterial community was related to the growth environment of host plants. The predictive analysis of KEGG pathways and enzymes showed that the abundance of some enzymes and metabolic pathways of endophytes of P. euphratica increased with the increase of soil salinity, and most of the enzymes were related to energy metabolism and carbohydrate metabolism. These findings suggested that the endogenous bacteria of the host plant had different expression mechanisms under different degrees of stress, and this mechanism was very obvious in the distribution of endophytes, while the function of the endogenous bacteria needs to be further explored. IMPORTANCE Euphrates poplar (Populus euphratica Oliv.), as the only tree species that grows in the desert, has tenacious vitality with the characteristics of cold tolerance, drought tolerance, salt-alkali tolerance, and wind-sand resistance. P. euphratica has a long growth cycle and a high growth rate, which can break wind, fix sand, green the environment, and protect farmland, making it an important afforestation tree species in arid and semiarid areas. The area of P. euphratica in Xinjiang accounts for 91.1% of its area in China. Studying the endophytic bacteria of P. euphratica can give people a systematic understanding of it and the adaptability of the endogenous flora to the host and special environments. In this study, by analyzing the endophytic bacteria of P. euphratica in different saline-alkali regions of Xinjiang, it was found that the bacteria in different tissues of P. euphratica changed with the change of soil salinity. Especially in the sap tissue of P. euphratica under extremely high salinity, the diversity of endogenous bacteria was significantly lower than that in other tissues. These differential bacteria under different salinities were mostly related to the stress resistance of themselves and the host. Not only that, we also selected a strain of Bacillus with high stress resistance from the tissues of P. euphratica, which can survive under the extreme conditions of 10% NaCl and pH 11. We obtained a genome completion map of this strain, named it Bacillus haynesii P19 (GenBank accession no. PRJNA648288), and tried to use it for fermentation but in a different work, so as to develop it into a promising industrial fermentation chassis bacterium. Therefore, this study was of great significance for the understanding of endophytic bacteria in P. euphratica and the acquisition of extremophilic microbial resources.

Erratum: Role of ursolic acid chalcone, a synthetic analogue of ursolic acid, in inhibiting the properties of CD133(+) sphere-forming cells in liver stem cells.

[This corrects the article on p. 1427 in vol. 8, PMID: 25973027.].

Role of ursolic acid chalcone, a synthetic analogue of ursolic acid, in inhibiting the properties of CD133(+) sphere-forming cells in liver stem cells.

The expression of CD133 decreases with differentiation of tumor cell, indicating that CD133 is a specific marker for isolation and identification of CSCs. In the present study the effect of Ursolic acid chalcone (UAC) on CD133(+) hepatocellular carcinoma cell (HCC CSCs) differentiation, their self-renewal, tumorigenic capacity and sensitivity to chemotherapeutic drugs was studied. The results demonstrated that UAC inhibits the expression of CD133(+) in a dose and time-dependent manner in PLC/PRF/5 and Huh7 HCC cells. The inhibition was significant at 50 µM and on day 8. The percentage of CD133(+) cells decreased from an initial 59.3% in PLC/PRF/5 to 37.1% and 78.2% in Huh7 to 59.2% on treatment with UAC. There was inhibition of Oct4, Tert, Bmi1, ß-catenin, ABCG2, and tumor sphere-related gene Ep300. In addition it also decreased number of CK19-positive cells and increased number of CK8/18-positive cells. UAC treatment caused a decrease in self-renewal capability and increase in sensitivity to doxorubicin and vincristine drugs in CD133(+) HCC CSCs. Therefore, UAC can be a potent therapeutic agent to target differentiation of CSC in HCC.

Aminosilanization nanoadhesive layer for nanoelectric circuits with porous ultralow dielectric film.

An ultrathin layer is investigated for its potential application of replacing conventional diffusion barriers and promoting interface adhesion for nanoelectric circuits with porous ultralow dielectrics. The porous ultralow dielectric (k ≈ 2.5) substrate is silanized by 3-aminopropyltrimethoxysilane (APTMS) to form the nanoadhesive layer by performing oxygen plasma modification and tailoring the silanization conditions appropriately. The high primary amine content is obtained in favor of strong interaction between amino groups and copper. And the results of leakage current measurements of metal-oxide-semiconductor capacitor structure demonstrate that the aminosilanization nanoadhesive layer can block copper diffusion effectively and guarantee the performance of devices. Furthermore, the results of four-point bending tests indicate that the nanoadhesive layer with monolayer structure can provide the satisfactory interface toughness up to 6.7 ± 0.5 J/m(2) for Cu/ultralow-k interface. Additionally, an annealing-enhanced interface toughness effect occurs because of the formation of Cu-N bonding and siloxane bridges below 500 °C. However, the interface is weakened on account of the oxidization of amines and copper as well as the breaking of Cu-N bonding above 500 °C. It is also found that APTMS nanoadhesive layer with multilayer structure provides relatively low interface toughness compared with monolayer structure, which is mainly correlated to the breaking of interlayer hydrogen bonding.