biological function
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2022 ◽  
Vol 74 ◽  
pp. 66-74
Author(s):  
Om Prakash Gupta ◽  
Rupesh Deshmukh ◽  
Awadhesh Kumar ◽  
Sanjay Kumar Singh ◽  
Pradeep Sharma ◽  
...  

Mobile DNA ◽  
2022 ◽  
Vol 13 (1) ◽  
Author(s):  
Kenji Ichiyanagi ◽  
Kuniaki Saito

AbstractThe fifth Japanese meeting on host–transposon interactions, titled “Biological Function and Evolution through Interactions between Hosts and Transposable Elements (TEs),” was held online on August 26–27, 2021. The meeting was supported by National Institute of Genetics and aimed to bring together researchers studying the diverse roles of TEs in genome function and evolution, as well as host defense systems against TE mobility by chromatin and RNA modifications and protein-protein interactions. Here, we present the highlights of the talks.


2022 ◽  
Vol 12 ◽  
Author(s):  
Bharti Mangla ◽  
Shamama Javed ◽  
Muhammad H. Sultan ◽  
Waquar Ahsan ◽  
Geeta Aggarwal ◽  
...  

Drug delivery using oral route is the most popular, convenient, safest and least expensive approach. It includes oral transmucosal delivery of bioactive compounds as the mucosal cavity offers an intriguing approach for systemic drug distribution. Owing to the dense vascular architecture and high blood flow, oral mucosal layers are easily permeable and can be an ideal site for drug administration. Recently, the transmucosal route is being investigated for other therapeutic candidates such as vaccines for their efficient delivery. Vaccines have the potential to trigger immune reactions and can act as both prophylactic and therapeutic conduit to a variety of diseases. Administration of vaccines using transmucosal route offers multiple advantages, the most important one being the needle-free (non-invasive) delivery. Development of needle-free devices are the most recent and pioneering breakthrough in the delivery of drugs and vaccines, enabling patients to avoid needles, reducing anxiety, pain and fear as well as improving compliance. Oral, nasal and aerosol vaccination is a novel immunization approach that utilizes a nanocarrier to administer the vaccine. Nanocarriers improve the bioavailability and serve as adjuvants to elicit a stronger immune response, resulting in increased effectiveness of vaccination. Drugs and vaccines with lower penetration abilities can also be delivered transmucosally while maintaining their biological function. The development of micro/nanocarriers for transmucosal delivery of macromolecules, vaccines and other substances is currently drawing much attention and a number of studies were performed recently. This comprehensive review is aimed to summarize the most recent investigations on needle-free and non-invasive approaches for the delivery of vaccines using oral transmucosal route, their strengths and associated challenges. The oral transmucosal vaccine delivery by nanocarriers is the most upcoming advancement in efficient vaccine delivery and this review would help further research and trials in this field.


2022 ◽  
Author(s):  
Amy Moore ◽  
Jesse Marks ◽  
Bryan C Quach ◽  
Yuelong Guo ◽  
Laura J Bierut ◽  
...  

Where sufficiently large genome-wide association study (GWAS) samples are not currently available or feasible, methods that leverage increasing knowledge of the biological function of variants may illuminate discoveries without increasing sample size. We comprehensively evaluated 18 functional weighting methods for identifying novel associations. We assessed the performance of these methods using published results from multiple GWAS waves across each of five complex traits. Although no method achieved both high sensitivity and positive predictive value (PPV) for any trait, a subset of methods utilizing pleiotropy and expression quantitative trait loci nominated variants with high PPV (>75%) for multiple traits. Application of functionally weighting methods to enhance GWAS power for locus discovery is unlikely to circumvent the need for larger sample sizes in truly underpowered GWAS, but these results suggest that applying functional weighting to GWAS can accurately nominate additional novel loci from available samples for follow-up studies.


2022 ◽  
Vol 2022 ◽  
pp. 1-13
Author(s):  
Rongqi Li ◽  
Rongqiang Liu ◽  
Shiyang Zheng ◽  
Wenbin Liu ◽  
Hui Li ◽  
...  

Background. Hepatocellular carcinoma (HCC) is one of the most common malignant tumors in the world, and its incidence is obviously increasing. The NT5DC family has been shown to be involved in the progression of many tumors. However, the biological function of NT5DC family members in HCC is still not well understood. Methods. Oncomine, Gene Expression Profiling Interactive Analysis (GEPIA), UALCAN, Kaplan–Meier plotter, cBioPortal, GeneMANIA, Metascape, and TIMER were applied to assess the biological function of NT5DC family members in HCC. Results. Most of the NT5DC family members were highly expressed in HCC. High expression of NT5C2, NT5DC2, and NT5DC3 was closely associated with higher tumor stage and poor overall survival (OS). In addition, high NT5DC2 and NT5DC3 expression also predicted poor disease-free survival (DFS). Enrichment analysis revealed that the NT5DC family in HCC mainly involved the IMP metabolic process, purine ribonucleoside monophosphate metabolic process, and purine nucleoside monophosphate metabolic process. The expression of NT5DC family members was closely related to the infiltration of some immune cells, such as B cells, CD8+ T cells, CD4+ T cells, macrophages, neutrophils, and dendritic cells. Conclusion. Our findings provided new insights into the biological function and prognostic value of NT5DC family members in HCC.


2022 ◽  
Vol 12 ◽  
Author(s):  
Zijian Liu ◽  
Jinlan He ◽  
Jiaqi Han ◽  
Jiangping Yang ◽  
Wenjun Liao ◽  
...  

BackgroundThe role of RNA N6-methyladenosine (m6A) modification in tumor progression and metastasis has been demonstrated. Nonetheless, potential biological function of m6A modification patterns in nasopharyngeal carcinoma (NPC) remains unknown.MethodsThe m6A modification patterns were comprehensively evaluated based on 26 m6A regulators in NPC, and m6A subtype and also m6A score were identified and systematically correlated with representative tumor characteristics.ResultsTwo distinct m6A subtypes were determined and were highly consistent with immune activated and immune suppressed phenotypes, respectively. More representative m6A scores of individual tumors could predict tumor microenvironment (TME) infiltration, mRNA based stemness index (mRNAsi), EBV gene expression, genetic variation, and prognosis of NPC patients. Low m6A score, characterized by activation of immunity and suppression of mRNAsi and EBV gene, indicated an activated TME phenotype and better PFS and also lower risk of recurrence and metastasis. High m6A score, characterized by activation of Wnt and NF-κB signaling pathway and lack of effective immune infiltration, indicated an immune suppressed TME phenotype and poorer survival. Low m6A score was also correlated with increased tumor mutation burden (TMB) and better response to immunotherapy, and vice versa. A significant therapeutic advantage in patients with low m6A score was confirmed with an anti-PDL1 immunotherapy cohort.Conclusionsm6A patterns played an important role in the diversity and complexity of TME. m6A score could be used to evaluate the m6A pattern of individual tumor to enhance our understanding of TME infiltration and guide more effective immunotherapy strategies.


2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Xuemin Dong ◽  
Shanshan Dong ◽  
Shengkai Pan ◽  
Xiangjiang Zhan

Abstract Background Understanding the transcriptome has become an essential step towards the full interpretation of the biological function of a cell, a tissue or even an organ. Many tools are available for either processing, analysing transcriptome data, or visualizing analysis results. However, most existing tools are limited to data from a single sequencing platform and only several of them could handle more than one analysis module, which are far from enough to meet the requirements of users, especially those without advanced programming skills. Hence, we still lack an open-source toolkit that enables both bioinformatician and non-bioinformatician users to process and analyze the large transcriptome data from different sequencing platforms and visualize the results. Results We present a Linux-based toolkit, RNA-combine, to automatically perform the quality assessment, downstream analysis of the transcriptome data generated from different sequencing platforms, including bulk RNA-seq (Illumina platform), single cell RNA-seq (10x Genomics) and Iso-Seq (PacBio) and visualization of the results. Besides, this toolkit is implemented with at least 10 analysis modules more than other toolkits examined in this study. Source codes of RNA-combine are available on GitHub: https://github.com/dongxuemin666/RNA-combine. Conclusion Our results suggest that RNA-combine is a reliable tool for transcriptome data processing and result interpretation for both bioinformaticians and non-bioinformaticians.


PLoS Biology ◽  
2022 ◽  
Vol 20 (1) ◽  
pp. e3001481
Author(s):  
Eugene V. Koonin ◽  
Kira S. Makarova

The principal biological function of bacterial and archaeal CRISPR systems is RNA-guided adaptive immunity against viruses and other mobile genetic elements (MGEs). These systems show remarkable evolutionary plasticity and functional versatility at multiple levels, including both the defense mechanisms that lead to direct, specific elimination of the target DNA or RNA and those that cause programmed cell death (PCD) or induction of dormancy. This flexibility is also evident in the recruitment of CRISPR systems for nondefense functions. Defective CRISPR systems or individual CRISPR components have been recruited by transposons for RNA-guided transposition, by plasmids for interplasmid competition, and by viruses for antidefense and interviral conflicts. Additionally, multiple highly derived CRISPR variants of yet unknown functions have been discovered. A major route of innovation in CRISPR evolution is the repurposing of diverged repeat variants encoded outside CRISPR arrays for various structural and regulatory functions. The evolutionary plasticity and functional versatility of CRISPR systems are striking manifestations of the ubiquitous interplay between defense and “normal” cellular functions.


2022 ◽  
Vol 12 ◽  
Author(s):  
Shuang Xu ◽  
Xiuzhen Hu ◽  
Zhenxing Feng ◽  
Jing Pang ◽  
Kai Sun ◽  
...  

The realization of many protein functions is inseparable from the interaction with ligands; in particular, the combination of protein and metal ion ligands performs an important biological function. Currently, it is a challenging work to identify the metal ion ligand-binding residues accurately by computational approaches. In this study, we proposed an improved method to predict the binding residues of 10 metal ion ligands (Zn2+, Cu2+, Fe2+, Fe3+, Co2+, Mn2+, Ca2+, Mg2+, Na+, and K+). Based on the basic feature parameters of amino acids, and physicochemical and predicted structural information, we added another two features of amino acid correlation information and binding residue propensity factors. With the optimized parameters, we used the GBM algorithm to predict metal ion ligand-binding residues. In the obtained results, the Sn and MCC values were over 10.17% and 0.297, respectively. Besides, the Sn and MCC values of transition metals were higher than 34.46% and 0.564, respectively. In order to test the validity of our model, another method (Random Forest) was also used in comparison. The better results of this work indicated that the proposed method would be a valuable tool to predict metal ion ligand-binding residues.


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