Genome-Wide SNP Data Revealed the Extent of Linkage Disequilibrium, Persistence of Phase and Effective Population Size in Purebred and Crossbred Buffalo Populations

Linkage disequilibrium (LD) is a useful parameter for guiding the accuracy and power of both genome-wide association studies (GWAS) and genomic selection (GS) among different livestock species. The present study evaluated the extent of LD, persistence of phase and effective population size (Ne) for the purebred (Mediterranean buffalo; n = 411) and crossbred [Mediterranean × Jianghan × Nili-Ravi buffalo, n = 9; Murrah × Nili-Ravi × local (Xilin or Fuzhong) buffalo, n = 36] buffalo populations using the 90K Buffalo SNP genotyping array. The results showed that the average square of correlation coefficient (r2) between adjacent SNP was 0.13 ± 0.19 across all autosomes for purebred and 0.09 ± 0.13 for crossbred, and the most rapid decline in LD was observed over the first 200 kb. Estimated r2 ≥ 0.2 extended up to ~50 kb in crossbred and 170 kb in purebred populations, while average r2 values ≥0.3 were respectively observed in the ~10 and 60 kb in the crossbred and purebred populations. The largest phase correlation (RP, C = 0.47) was observed at the distance of 100 kb, suggesting that this phase was not actively preserved between the two populations. Estimated Ne for the purebred and crossbred population at the current generation was 387 and 113 individuals, respectively. These findings may provide useful information to guide the GS and GWAS in buffaloes

Integrative Analysis of Transcriptome and GWAS Data to Identify the Hub Genes Associated With Milk Yield Trait in Buffalo

The mammary gland is the production organ in mammals that is of great importance for milk production and quality. However, characterization of the buffalo mammary gland transcriptome and identification of the valuable candidate genes that affect milk production is limited. Here, we performed the differential expressed genes (DEGs) analysis of mammary gland tissue on day 7, 50, 140, and 280 after calving and conducted gene-based genome-wide association studies (GWAS) of milk yield in 935 Mediterranean buffaloes. We then employed weighted gene co-expression network analysis (WGCNA) to identify specific modules and hub genes related to milk yield based on gene expression profiles and GWAS data. The results of the DEGs analysis showed that a total of 1,420 DEGs were detected across different lactation points. In the gene-based analysis, 976 genes were found to have genome-wide association (P ≤ 0.05) that could be defined as the nominally significant GWAS geneset (NSGG), 9 of which were suggestively associated with milk yield (P < 10−4). Using the WGCNA analysis, 544 and 225 genes associated with milk yield in the turquoise module were identified from DEGs and NSGG datasets, respectively. Several genes (including BNIPL, TUBA1C, C2CD4B, DCP1B, MAP3K5, PDCD11, SRGAP1, GDPD5, BARX2, SCARA3, CTU2, and RPL27A) were identified and considered as the hub genes because they were involved in multiple pathways related to milk production. Our findings provide an insight into the dynamic characterization of the buffalo mammary gland transcriptome, and these potential candidate genes may be valuable for future functional characterization of the buffalo mammary gland

Identifying Hub Genes for Heat Tolerance in Water Buffalo (Bubalus bubalis) Using Transcriptome Data

Heat stress has a detrimental effect on the physiological and production performance of buffaloes. Elucidating the underlying mechanisms of heat stress is challenging, therefore identifying candidate genes is urgent and necessary. We evaluated the response of buffaloes (n = 30) to heat stress using the physiological parameters, ELISA indexes, and hematological parameters. We then performed mRNA and microRNA (miRNA) expression profiles analysis between heat tolerant (HT, n = 4) and non-heat tolerant (NHT, n = 4) buffaloes, as well as the specific modules, significant genes, and miRNAs related to the heat tolerance identified using the weighted gene co-expression network analysis (WGCNA). The results indicated that the buffaloes in HT had a significantly lower rectal temperature (RT) and respiratory rate (RR) and displayed a higher plasma heat shock protein (HSP70 and HSP90) and cortisol (COR) levels than those of NHT buffaloes. Differentially expressed analysis revealed a total of 753 differentially expressed genes (DEGs) and 16 differentially expressed miRNAs (DEmiRNAs) were identified between HT and NHT. Using the WGCNA analysis, these DEGs assigned into 5 modules, 4 of which were significantly correlation with the heat stress indexes. Interestingly, 158 DEGs associated with heat tolerance in the turquoise module were identified, 35 of which were found within the protein-protein interaction network. Several hub genes (IL18RAP, IL6R, CCR1, PPBP, IL1B, and IL1R1) were identified that significantly enriched in the Cytokine-cytokine receptor interaction. The findings may help further elucidate the underlying mechanisms of heat tolerance in buffaloes

A preliminary study on the interaction between Asn-Gly-Arg (NGR)-modified multifunctional nanoparticles and vascular epithelial cells

Previously developed Asn-Gly-Arg (NGR) peptide-modified multifunctional poly(ethyleneimine)–poly(ethylene glycol) (PEI–PEG)-based nanoparticles (TPIC) have been considered to be promising carriers for the co-delivery of DNA and doxorubicin (DOX). As a continued effort, the aim of the present study was to further evaluate the interaction between TPIC and human umbilical vein endothelial cells (HUVEC) to better understand the cellular entry mechanism. In the present investigation, experiments relevant to co-localization, endocytosis inhibitors and factors influencing the internalization were performed. Without any treatment, there was no co-localization between aminopeptidase N/CD13 (APN/CD13) and caveolin 1 (CAV1). However, co-localization between CD13 and CAV1 was observed when cells were incubated with an anti-CD13 antibody or TPIC. As compared with antibody treatment, TPIC accelerated the speed and enhanced the degree of co-localization. TPIC entered HUVEC not only together with CD13 but also together with CAV1. However, this internalization was not dependent on the enzyme activity of CD13 but could be inhibited by methyl-β-eyclodextfin (MβCD), further identifying the involvement of caveolae-mediated endocytosis (CvME). This conclusion was also verified by endocytosis inhibitor experiments

Hyaluronic Acid-Chitosan Nanoparticles to Deliver Gd-DTPA for MR Cancer Imaging

Molecular imaging is essential to increase the sensitivity and selectivity of cancer diagnosis especially at the early stage of tumors. Recently, polyionic nanocomplexes (PICs), which are composed of polyanions and opposite polycations, have been demonstrated to be a promising strategy for biomedical applications. In this work, chitosan-hyaluronic acid nanoparticles (GCHN) were developed to deliver Gd-DTPA as MRI contrast agents for tumor diagnosis. The Gd-labeled conjugates (CS-DTPA-Gd) were successfully synthesized by carbodiimide reaction, and then GCHN were prepared by ionic gelation using the obtained CS-DTPA-Gd and hyaluronic acid. The morphology of GCHN was spherical or ellipsoidal, which is observed by transmission electronic microscopy (TEM). The mean particle size and zeta potential of GCHN were 213.8 ± 2.6 nm and 19.92 ± 1.69 mV, respectively. The significant enhancement of signal intensity induced by GCHN was observed both in vitro and in vivo. Also, compared with Magnevist, GCHN was witnessed for a prolonged imaging time in the B16 tumor-bearing mice model. Furthermore, GCHN were verified as below toxic both in vitro and in vivo. These results indicated that GCHN could potentially be an alternative to current MRI contrast agents for tumor diagnosis

The Role of ZNF275/AKT Pathway in Carcinogenesis and Cisplatin Chemosensitivity of Cervical Cancer Using Patient-Derived Xenograft Models

Zinc finger protein 275 (ZNF275) is a C2H2-type transcription factor that is localized on chromosome Xq28. Whether ZNF275 participates in modulating the biological behaviors of cervical cancer has not been determined to our knowledge. The present study employed CCK-8, BrdU, flow cytometry, and a transwell assay to investigate the cell viability, proliferation, apoptosis, migration, and invasion of cervical cancer cells. The application of Western blotting and immunohistochemistry (IHC) aims to assess ZNF275 protein expression and identify the signaling pathway relevant to ZNF275-mediated effects on cervical cancer. The therapeutic impact of the combined therapy of the AKT inhibitor triciribine and cisplatin was evaluated on cervical cancer patient-derived xenograft (PDX) models expressing high ZNF275. The current research illustrated that cervical cancer tissue exhibited a higher expression of ZNF275 in contrast to the surrounding normal cervical tissue. The downregulation of ZNF275 suppressed cell viability, migration, and invasion, and facilitated the apoptosis of SiHa and HeLa cells via weakening AKT/Bcl-2 signaling pathway. Moreover, triciribine synergized with cisplatin to reduce cell proliferation, migration, and invasion, and enhanced the apoptosis of SiHa cells expressing high ZNF275. In addition, the combination treatment of triciribine and cisplatin was more effective in inducing tumor regression than single agents in cervical cancer PDX models expressing high ZNF275. Collectively, the current findings demonstrated that ZNF275 serves as a sufficiently predictive indicator of the therapeutic effectiveness of the combined treatment of triciribine and cisplatin on cervical cancer. Combining triciribine with cisplatin greatly broadens the therapeutic options for cervical cancer expressing high ZNF275, but further research is needed to confirm these results

Data from: Genome-wide SNP data revealed the extent of linkage disequilibrium, persistence of phase and effective population size in purebred and crossbred buffalo populations

Linkage disequilibrium (LD) is a useful parameter for guiding the accuracy and power of both genome-wide association studies (GWAS) and genomic selection (GS) among different livestock species. The present study evaluated the extent of LD, persistence of phase and effective population size (Ne) for the purebred (Mediterranean buffalo; n=411) and crossbred [Mediterranean × Jianghan × Nili-Ravi buffalo, n=9; Murrah × Nili-Ravi × local (Xilin or Fuzhong) buffalo, n=36] buffalo populations using the 90K Buffalo SNP genotyping array. The results showed that the average square of correlation coefficient (r2) between adjacent SNP was 0.13 ± 0.19 across all autosomes for purebred and 0.09 ± 0.13 for crossbred, and the most rapid decline in LD was observed over the first 200 kb. Estimated r2 ≥ 0.2 extended up to approximately 50 kb in crossbred and 170 kb in purebred populations, while average r2 values ≥ 0.3 were respectively observed in the approximately 10 kb and 60 kb in the crossbred and purebred populations. The largest phase correlation (RP,C = 0.47) was observed at the distance of 100 kb, suggesting that this phase was not actively preserved between the two populations. Estimated Ne for the purebred and crossbred population at the current generation was 387 and 113 individuals, respectively. These findings may provide useful information to guide the GS and GWAS in buffaloes

Cervical kyphosis in patients with Lenke type 1 adolescent idiopathic scoliosis: the prediction of thoracic inlet angle

Abstract Background Several studies have explored cervical kyphosis (CK) in adolescent idiopathic scoliosis (AIS) patients. However, few studies have evaluated the cervical alignment in these patients according to their coronal curve type. The aim of this study was to analyze the radiological features of cervical sagittal alignment in Lenke 1 AIS patients before and after surgery. Methods This is a retrospective study enrolled 50 patients. Preoperative and postoperative standing full-length radiographs (at last follow-up after operation) were used to measure the coronal and sagittal parameters. Main sagittal parameters included C2–C7 angle, thoracic inlet angle (TIA), T1 slope, proximal thoracic kyphosis (PTK, T1-5 kyphosis) and thoracic kyphosis (TK, T5-12 kyphosis). Results The TIA of patients with CK was significantly smaller than that of patients with CL (63.0° vs. 76.3°, p < 0.05) and the cutoff value was 71°. The TIA of patients with CK after surgery was significantly smaller than that of patients with CL postoperatively (62.5° vs. 74.6°, p < 0.05) and the cutoff value was 62°. In patients with postoperative CL, there was a significant increase in their PTK and a reduction in their TK, regardless of preoperative CL or CK. In patients whose CL deteriorated to CK after surgery, both their PTK and TK significantly decreased after surgery. Conclusions Patients with TIA less than 71° were more likely to have CK. And patients with TIA less than 62° would lead to the postoperative uncorrected or new onset of CK. The increased PTK after operation could have a beneficial effect on the improvement of CL