Identification of novel microRNAs in primates by using the synteny information and small RNA deep sequencing data.

Current technologies that are used for genome-wide microRNA (miRNA) prediction are mainly based on BLAST tool. They often produce a large number of false positives. Here, we describe an effective approach for identifying orthologous pre-miRNAs in several primates based on syntenic information. Some of them have been validated by small RNA high throughput sequencing data. This approach uses the synteny information and experimentally validated miRNAs of human, and incorporates currently available algorithms and tools to identify the pre-miRNAs in five other primates. First, we identified 929 potential pre-miRNAs in the marmoset in which miRNAs have not yet been reported. Then, we predicted the miRNAs in other primates, and we successfully re-identified most of the published miRNAs and found 721, 979, 650 and 639 new potential pre-miRNAs in chimpanzee, gorilla, orangutan and rhesus macaque, respectively. Furthermore, the miRNA transcriptome in the four primates have been re-analyzed and some novel predicted miRNAs have been supported by the small RNA sequencing data. Finally, we analyzed the potential functions of those validated miRNAs and explored the regulatory elements and transcription factors of some validated miRNA genes of interest. The results show that our approach can effectively identify novel miRNAs and some miRNAs that supported by small RNA sequencing data maybe play roles in the nervous system.

FOS gene associated immune infiltration signature in perivascular adipose tissues of abdominal aortic aneurysm.

Abdominal aortic aneurysms (AAA) are pathological dilations in local aortic wall. The inflammatory infiltrates of the perivascular adipose tissue (PAT) surrounding AAAs were associated with AAAs and have been shown to contribute vascular pathology. However, the mechanism by which PAT inflammation contributes to vascular pathology in AAA remains to be clarified. This study aimed to explore the association between immune cell infiltration and key gene expression profile in PAT of AAA. For that, a gene expression dataset of human dilated perivascular adipose tissue (dPAT), non-dilated perivascular adipose tissue (ndPAT), subcutaneous abdominal fat (SAF) and omental-visceral fat (OVF) samples, as well as another microarray dataset of the abdominal perivascular adipose tissue in peripheral artery disease patients were downloaded from GEO database for analysis in this study. The CIBERSORT algorithm, weighted gene co-expression network analysis (WGCNA) and LASSO algorithm were used for the identification of immune infiltration, immune-related genes and the development of diagnostic signature. Our data discovered a significant higher proportion of activated mast cells and follicular helper T (Tfh) cells in dPAT than ndPAT, OVT and SAF samples. Moreover, AP-1 family members (FOS, FOSB, ATF3, JUN and JUNB) were found to compose the hub genes of purple module in WGCNA. Among them, FOS gene acts as a higher efficient marker to discriminate dPAT from ndPAT, OVT and SAF in AAA. Meanwhile, the expression profiles of the AP-1 family members are all significantly positive correlated with activated mast cell, plasma cell and Tfh cell infiltration in dPAT of AAA. Therefore, in the PAT surrounding AAA, the signature of inflammatory infiltration might be represented by a FOS-dominated cell network consist of activated mast cell, plasma cell and Tfh cell. Given the complicated etiology of AAA, our results are likely to shed new light on the pathophysiologic mechanism of AAA influenced by the local dPAT.

The relationship between MHC-peptide interaction and resistance to virus in chickens.

INTRODUCTION: The MHC-peptide interaction has a subtle influence on host resistance to virus. This paper aims to study the relationship between MHC-peptide interaction and MHC-related virus-resistance. METHODS: By 3D homology modeling, the structure of chicken BF2 molecule BF2*0201 (PDB code: 4d0d) was studied and compared with the known structures of BF2 molecule BF2*0401 (PDB code: 4e0r) to elucidate the characteristics of BF2*0201-binding antigenic peptides. RESULTS: The results show that due to the amino acid difference between the two binding groove of 4e0r and 4d0d, the size of the binding groove of the two are 1130 ų and1380 ų respectively, indicating the amino acid species that 4e0r binding peptide has lower selectivity than 4d0d; and because of large side chain conformation of Arg (especially Arg111) of 4e0r replaced by small side chain Tyr111 of 4d0d, the volume of central part of the binding groove of 4d0d is obviously larger than that of 4e0r, indicating that the restrictive of binding antigenic peptides for 4d0d is narrower than that of 4e0r; and on account of the chargeability of the binding groove of the two are different, namely the binding groove chargeability of 4e0r (strong positive polarity) and 4d0d (weak negative polarity). CONCLUSION: There are generally more peptides presented by the BF2 of B2 haplotype than by that of B4 haplotype, leading to more resistance of B2 than that of B4 to virus.

Study on the contrast of the MHC-peptide interaction of B2/B21 haplotype and MHC-related virus resistance in chickens.

INTRODUCTION: Three-dimensional (3D) structures of MHC class I exert some influence by the MHC-peptide interaction over host resistance to the virus. The thesis aims at studying the connection between MHC-peptide interaction of B2/B21 haplotype and MHC-related resistance to the virus. METHODS: The structure of chicken MHC class I BF2*0201 from B2 haplotype was studied and contrasted with that of BF2*2101 from B21 haplotype by using DNAMAN and PyMol software. RESULTS: The amino acid difference resulted in the difference in size and changeability of the binding groove of the two, resulting in different choices on the binding polypeptide. 3bew's (the crystal structure of BF2*2101 bound to peptide RV10) small side chain His111 replaces the short side chain Tyr111 of 4cvx (the crystal structure of BF2*0201 bound to peptide YL9), and the very small amino acid of Ser69 and Ser97 make the middle of the 3bew's binding groove become apparently broad and bound restrictive of amino acid smaller. Moreover, due to the specific amino acids-Arg9, Asp24, and Asp73 of 4cvx and Arg9, Asp24, and His111 of 3bew, the effect of the polypeptide and the binding groove differ between the two, and 3bew tends to bind polypeptides with negatively charged amino acids, but the large space in the middle can also accommodate other amino acids. Contrasted with the binding groove characteristic of 4cvx, it can be said that the selectivity of 3bew is higher than that of 4cvx in the amino acid type of the binding polypeptide, so the B21 haplotype has more host resistance to the virus than that of the B2 haplotype in chicken. CONCLUSION: There are usually various kinds of peptides presented by the BF2*2101 molecules of B21 haplotypes, resulting in resistance to pathogenic microorganisms, such as Rous sarcoma virus and/or Marek's disease virus. These findings may have an important theoretical foundation for screening of virus antigen, vaccine design, and genetic resistance breeding.

Visualized Analysis of Heavy Ion Radiotherapy: Development, Barriers and Future Directions.

BACKGROUND: Heavy ion radiotherapy (HIRT) has great advantages as tumor radiotherapy. METHODS: Based on 1,558 literatures from core collections of Web of Science from 1980 to 2020, this study visually analyzes the evolution of HIRT research, and sorts out the hotspots and trends of HIRT research using CiteSpace software. RESULTS: Research on HIRT has received more extensive attention over the last 40 years. The development of HIRT is not only closely related to radiation and oncology, but also closely related to the development of human society. In terms of citation frequency, "International Journal of Radiation Oncology*Biology*Physics" was the top journal. In terms of influence, "Radiotherapy and Oncology" was the top journal. "Radiation therapy" and "carbon ion radiotherapy" were the two most frequently used keywords in this field. CONCLUSION: The evolution of the HIRT research has occurred in approximately three stages, including technological exploration, safety and effectiveness research and technological breakthroughs. Finally, some suggestions for future research are put forward.

Perfluorodecanoic acid induces meiotic defects and deterioration of mice oocytes in vitro.

Perfluorodecanoic acid (PFDA) is a member of the perfluoroalkyl substances, which are toxic to organic functions. Recently, it has been found in follicular fluid, seriously interfering with reproduction. Follicular fluid provides the oocyte with necessary resources during the process of oocytes maturation. However, the effects of PFDA on the oocyte need investigation. Our study evaluated the impacts of PFDA on the meiosis and development potential of mouse oocytes by exposing oocytes to PFDA in vitro at 350, 400, and 450 µM concentrations. The results showed that exposure to PFDA resulted in the first meiotic prophase arrest by obstructing the function of the maturation-promoting factor. It also induced the dysfunction of the spindle assembly checkpoint, expedited the progression of the first meiotic process, and increased the risk of aneuploidy. The oocytes treated with PFDA had a broken cytoskeleton which also contributed to meiotic maturation failure. Besides, PFDA exposure caused mitochondria defections, increased the reactive oxygen species level in oocytes, and consequently induced oocyte apoptosis. Moreover, PFDA produced epigenetic modifications in oocytes and increased the frequency of mature oocytes with declined development potential. In summary, our data indicated that PFDA disturbs the meiotic process and induces oocyte quality deterioration.

The Efficacy and Safety of Carbon Ion Radiotherapy for Meningiomas: A Systematic Review and Meta-Analysis.

OBJECTIVE: The purpose of this systematic review and meta-analysis is to evaluate the efficacy and safety of carbon ion radiotherapy (CI-RT) in improving meningioma by comparing photon and protons radiotherapy. METHODS: A comprehensive search for relevant studies published until March 17, 2021, was conducted in PubMed, the Cochrane Library, Chinese Biomedical Literature Database and EMBASE. Statistical analyses were performed with R 4.0.3. RESULTS: We identified 396 studies, of which 18 studies involving 985 participants were included. Except for one low quality study, the quality of the included studies was found to be either moderate or high quality. The analyses conducted according random effects model indicated that the 1-year overall survival rate (OS) of benign and non-benign meningiomas after the CI-RT treatment was 99% (95%CL=.91-1.00, I 2 = 0%). The overall average 5-year OS for meningiomas was 72% (95%CL=0.52-0.86, I 2 = 35%), not as effective as proton radiotherapy (PR-RT) 85% (95%CL=.72-.93, I 2 = 73, Q=4.17, df=2, p=.12). Additionally, 5-year OS of atypical meningiomas (81%) was found to be significantly higher than anaplastic meningiomas (52%). The 10-year OS after CI-RT of patients with mixed grade meningioma was 91% (95%CL=.75-.97, I 2 = 73%). The 15-year OS after CI-RT 87% (95%CL=.11-1.00) or PR-RT 87% (95%CL=.23-.99, I 2 = 79%) were the same (Q=0, df=1, p=.99). After undergoing CI-RT for 3 and 5 years, the LC for benign meningioma was 100% and 88%, respectively, while the 2-year LC of non-benign meningiomas (atypical/anaplastic) was 33%. Headache, sensory impairment, cognitive impairment, and hearing impairment were found to be the most common adverse reactions, with individual incidences of 19.4%, 23.7%, 9.1%, and 9.1%, respectively. CONCLUSION: CI-RT is a rapidly developing technique that has been proven to be an effective treatment against meningioma. The efficacy and safety of CI-RT for meningiomas were similar to those of PR-RT, better than photon radiotherapy (PH-RT). However, there is a need for more prospective trials in the future that can help provide more supportive evidence.

Mitochondrial genome and phylogenetic analysis of Gaojiao chicken (Gallus gallus).

In this study, the complete mitochondrial genome of Gaojiao chicken (Gallus gallus) was sequenced using samples collected from Puding county of Guizhou province, China. The mitogenome of Gaojiao chicken is 16,786 bp in length, and it contained 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, 13 protein-coding genes (PCGs), and a control region (D-loop), the overall base nucleotide compositions encoded are 30.27% A, 32.52% C, 13.49% G, and 23.72% T. The phylogenetic tree was constructed using neighbor-joining (N-J) method, which indicated that the Gaojiao chicken has the close relationship with Nandan chicken, Daweishan chicken, Wuding chicken, and Guangxi three-buff chicken.

Heat stress impacts on broiler performance: a systematic review and meta-analysis.

Heat stress (HS) is a major problem in poultry business which affects chickens' performance and may trigger large economic losses. This study intends to analyze the impact of HS on broiler chickens' performance compared with those under normal condition. A literature search was performed on PubMed, Web of Science, and Cochrane Library for studies published in English up to January 17, 2020. Outcomes of body weight gain (BWG), feed intake (FI), feed conversion ratio (FCR), and mortality were calculated by weighted difference (WMD) or odds ratio (OR) with 95% confidence interval (CI). A total of 12 studies with 470 broiler chickens were included. HS significantly decreased FI (11 trials: WMD = -97.95, 95% CI: -141.70, -54.20) and BWG (7 trials: WMD = -151.40, 95% CI: -198.59, -104.21) and significantly increased FCR (9 trials: WMD = 0.17, 95% CI: 0.04, 0.29) and mortality (8 trials: OR = 3.74, 95% CI: 1.39, 10.12) compared with the control. In conclusion, HS significantly affected broiler chickens' BWG, FI, FCR, and mortality, indicating the importance to control housing temperature to avoid unnecessary costs.

Variability of miRNA expression during the differentiation of human embryonic stem cells into retinal pigment epithelial cells.

Embryonic stem cells (ESCs) and induced pluripotent stem cells can be induced to differentiate into retinal pigment epithelium (RPE). MiRNAs have been characterized and found playing important roles in the differentiation process of ESCs, but their length and sequence heterogeneity (isomiRs), and their non-canonical forms of miRNAs are underestimated or ignored. In this report, we found some non-canonical miRNAs (dominant isomiRs) in all differentiation stages, and 27 statistically significant editing sites were identified in 24 different miRNAs. Moreover, we found marked major-to-minor arm-switching events in 14 pre-miRNAs during the hESC to RPE cell differentiation phases. Our study for the first time reports exploring the variability of miRNA expression during the differentiation of hESCs into RPE cells and the results show that miRNA variability is a ubiquitous phenomenon in the ESC differentiation.