scholarly journals Overexpression of lncRNAs with endogenous lengths and functions using a lncRNA delivery system based on transposon

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Yin Zhang ◽  
Yong-Xin Huang ◽  
Xin Jin ◽  
Jie Chen ◽  
Li Peng ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Lentiviral Vector ◽  
Lentiviral Vectors ◽  
Delivery Systems ◽  
Stable Expression ◽  
Delivery Method ◽  
Molecular Action ◽  
Efficient Delivery ◽  
Flanking Sequences ◽  
And Function

Abstract Background Long noncoding RNAs (lncRNAs) play important roles in many physiological and pathological processes, this indicates that lncRNAs can serve as potential targets for gene therapy. Stable expression is a fundamental technology in the study of lncRNAs. The lentivirus is one of the most widely used delivery systems for stable expression. However, it was initially designed for mRNAs, and the applicability of lentiviral vectors for lncRNAs is largely unknown. Results We found that the lentiviral vector produces lncRNAs with improper termination, appending an extra fragment of ~ 2 kb to the 3ʹ-end. Consequently, the secondary structures were changed, the RNA–protein interactions were blocked, and the functions were impaired in certain lncRNAs, which indicated that lentiviral vectors are not ideal delivery systems of lncRNAs. Here, we developed a novel lncRNA delivery method called the Expression of LncRNAs with Endogenous Characteristics using the Transposon System (ELECTS). By inserting a termination signal after the lncRNA sequence, ELECTS produces transcripts without 3ʹ-flanking sequences and retains the native features and function of lncRNAs, which cannot be achieved by lentiviral vectors. Moreover, ELECTS presents no potential risk of infection for the operators and it takes much less time. ELECTS provides a reliable, convenient, safe, and efficient delivery method for stable expression of lncRNAs. Conclusions Our study demonstrated that improper transcriptional termination from lentiviral vectors have fundamental effects on molecular action and cellular function of lncRNAs. The ELECTS system developed in this study will provide a convenient and reliable method for the lncRNA study. Graphic Abstract

scholarly journals Protein interactions and consensus clustering analysis uncover insights into herpesvirus virion structure and function relationships

PLoS Biology ◽  
2019 ◽  
Vol 17 (6) ◽  
pp. e3000316 ◽  
Author(s):  
Anna Hernández Durán ◽  
Todd M. Greco ◽  
Benjamin Vollmer ◽  
Ileana M. Cristea ◽  
Kay Grünewald ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Clustering Analysis ◽  
Structure And Function ◽  
Consensus Clustering ◽  
Virion Structure ◽  
And Function

Recent trends in nano-based drug delivery systems for efficient delivery of phytochemicals in chemotherapy

RSC Advances ◽  
2016 ◽  
Vol 6 (54) ◽  
pp. 48294-48314 ◽  
Author(s):  
A. P. Subramanian ◽  
S. K. Jaganathan ◽  
A. Manikandan ◽  
K. N. Pandiaraj ◽  
Gomathi N ◽  
...  
Keyword(s):  
Drug Delivery ◽  
Cancer Cells ◽  
Drug Delivery Systems ◽  
Delivery Systems ◽  
Free Form ◽  
Remarkable Effect ◽  
Efficient Delivery ◽  
Recent Trends

The phytochemicals were found to become more soluble when delivered by the nanocarriers and exhibited a remarkable effect on the cancer cells compared to its free form.

scholarly journals Transactivation Functions of the N-Terminal Domains of Nuclear Hormone Receptors: Protein Folding and Coactivator Interactions

2003 ◽  
Vol 17 (1) ◽  
pp. 1-10 ◽  
Author(s):  
Raj Kumar ◽  
E. Brad Thompson
Keyword(s):  
Dna Binding ◽  
Protein Interactions ◽  
Hormone Receptors ◽  
Nuclear Hormone Receptor ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Protein Protein Interactions ◽  
Carboxy Terminal ◽  
And Function ◽  
Terminal Domains

Abstract The N-terminal domains (NTDs) of many members of the nuclear hormone receptor (NHR) family contain potent transcription-activating functions (AFs). Knowledge of the mechanisms of action of the NTD AFs has lagged, compared with that concerning other important domains of the NHRs. In part, this is because the NTD AFs appear to be unfolded when expressed as recombinant proteins. Recent studies have begun to shed light on the structure and function of the NTD AFs. Recombinant NTD AFs can be made to fold by application of certain osmolytes or when expressed in conjunction with a DNA-binding domain by binding that DNA-binding domain to a DNA response element. The sequence of the DNA binding site may affect the functional state of the AFs domain. If properly folded, NTD AFs can bind certain cofactors and primary transcription factors. Through these, and/or by direct interactions, the NTD AFs may interact with the AF2 domain in the ligand binding, carboxy-terminal portion of the NHRs. We propose models for the folding of the NTD AFs and their protein-protein interactions.

scholarly journals Dynamics and mechanism of ultrafast water–protein interactions

2016 ◽  
Vol 113 (30) ◽  
pp. 8424-8429 ◽  
Author(s):  
Yangzhong Qin ◽  
Lijuan Wang ◽  
Dongping Zhong
Keyword(s):  
Protein Interactions ◽  
Hydration Shell ◽  
Water Dynamics ◽  
Side Chain ◽  
Water Molecules ◽  
Ultrafast Dynamics ◽  
Hydration Water ◽  
Water Side ◽  
Dynamics And Function ◽  
And Function

Protein hydration is essential to its structure, dynamics, and function, but water–protein interactions have not been directly observed in real time at physiological temperature to our awareness. By using a tryptophan scan with femtosecond spectroscopy, we simultaneously measured the hydration water dynamics and protein side-chain motions with temperature dependence. We observed the heterogeneous hydration dynamics around the global protein surface with two types of coupled motions, collective water/side-chain reorientation in a few picoseconds and cooperative water/side-chain restructuring in tens of picoseconds. The ultrafast dynamics in hundreds of femtoseconds is from the outer-layer, bulk-type mobile water molecules in the hydration shell. We also found that the hydration water dynamics are always faster than protein side-chain relaxations but with the same energy barriers, indicating hydration shell fluctuations driving protein side-chain motions on the picosecond time scales and thus elucidating their ultimate relationship.

Non-primate Lentiviral Vector Administration in the TMJ

2004 ◽  
Vol 83 (1) ◽  
pp. 65-70 ◽  
Author(s):  
S. Kyrkanides ◽  
P. Kambylafkas ◽  
J.H. Miller ◽  
R.H. Tallents
Keyword(s):  
Temporomandibular Joint ◽  
Reporter Gene ◽  
Soft Tissues ◽  
Lentiviral Vector ◽  
Retrograde Transport ◽  
Lentiviral Vectors ◽  
Treatment Method ◽  
Joint Space ◽  
Nerve Fibers ◽  
Temporomandibular Joint Disorders

Gene therapy is emerging as a novel treatment method for the management of temporomandibular joint disorders. The aim of this investigation was to study the effects of lentiviral vectors on the temporomandibular joint. Consequently, we injected into the articular joint space a defective feline immunodeficiency virus capable of infecting dividing as well as terminally differentiated cells with the reporter gene lacZ, the expression of which was studied by means of PCR, X-gal histochemistry, and β-galactosidase immunocytochemistry. Our results showed successful transduction of hard and soft tissues of the temporomandibular joint. Interestingly, a subset of primary sensory neurons of the ipsilateral trigeminal ganglion also stained positive for the reporter gene, presumably following uptake of the lentiviral vector by peripheral nerve fibers and retrograde transport to the nucleus. These findings suggest that lentiviral vectors can potentially serve as a platform for the transfer of anti-nociceptive genes for the management of temporomandibular joint pain.

scholarly journals iProteinDB: an integrative database of Drosophila post-translational modifications

2018 ◽  
Author(s):  
Yanhui Hu ◽  
Richelle Sopko ◽  
Verena Chung ◽  
Romain A. Studer ◽  
Sean D. Landry ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Protein Function ◽  
Large Scale ◽  
Model Organisms ◽  
General Strategy ◽  
Post Translational Modification ◽  
Post Translational Modifications ◽  
Functional Sites ◽  
Evolutionarily Conserved ◽  
And Function

AbstractPost-translational modification (PTM) serves as a regulatory mechanism for protein function, influencing stability, protein interactions, activity and localization, and is critical in many signaling pathways. The best characterized PTM is phosphorylation, whereby a phosphate is added to an acceptor residue, commonly serine, threonine and tyrosine. As proteins are often phosphorylated at multiple sites, identifying those sites that are important for function is a challenging problem. Considering that many phosphorylation sites may be non-functional, prioritizing evolutionarily conserved phosphosites provides a general strategy to identify the putative functional sites with regards to regulation and function. To facilitate the identification of conserved phosphosites, we generated a large-scale phosphoproteomics dataset from Drosophila embryos collected from six closely-related species. We built iProteinDB (https://www.flyrnai.org/tools/iproteindb/), a resource integrating these data with other high-throughput PTM datasets, including vertebrates, and manually curated information for Drosophila. At iProteinDB, scientists can view the PTM landscape for any Drosophila protein and identify predicted functional phosphosites based on a comparative analysis of data from closely-related Drosophila species. Further, iProteinDB enables comparison of PTM data from Drosophila to that of orthologous proteins from other model organisms, including human, mouse, rat, Xenopus laevis, Danio rerio, and Caenorhabditis elegans.

scholarly journals Identification of sulfenylated cysteines in Arabidopsis thaliana proteins using a disulfide-linked peptide reporter

2020 ◽  
Author(s):  
Bo Wei ◽  
Patrick Willems ◽  
Jingjing Huang ◽  
Caiping Tian ◽  
Jing Yang ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Protein Interactions ◽  
Affinity Purification ◽  
Mass Spectrometry Analysis ◽  
Technological Advancement ◽  
Amino Acid Residues ◽  
Cysteine Oxidation ◽  
Spectrometry Analysis ◽  
Mixed Disulfide ◽  
And Function

ABSTRACTIn proteins, hydrogen peroxide (H2O2) reacts with redox-sensitive cysteines to form cysteine sulfenic acid, also known as S-sulfenylation. These cysteine oxidation events can steer diverse cellular processes by altering protein interactions, trafficking, conformation, and function. Previously, we had identified S-sulfenylated proteins by using a tagged proteinaceous probe based on the yeast AP-1–like (Yap1) transcription factor that specifically reacts with sulfenic acids and traps them through a mixed disulfide bond. However, the identity of the S-sulfenylated amino acid residues remained enigmatic. Here, we present a technological advancement to identify in situ sulfenylated cysteines directly by means of the transgenic Yap1 probe. In Arabidopsis thaliana cells, after an initial affinity purification and a tryptic digestion, we further enriched the mixed disulfide-linked peptides with an antibody targeting the YAP1C-derived peptide (C598SEIWDR) that entails the redox-active cysteine. Subsequent mass spectrometry analysis with pLink 2 identified 1,745 YAP1C cross-linked peptides, indicating sulfenylated cysteines in over 1,000 proteins. Approximately 55% of these YAP1C-linked cysteines had previously been reported as redox-sensitive cysteines (S-sulfenylation, S-nitrosylation, and reversibly oxidized cysteines). The presented methodology provides a noninvasive approach to identify sulfenylated cysteines in any species that can be genetically modified.

scholarly journals Therapeutic potential of exosomes and their derivatives

2018 ◽  
pp. 129-131
Author(s):  
И.Ю. Малышев ◽  
Л.В. Кузнецова ◽  
О.П. Буданова
Keyword(s):  
Drug Delivery ◽  
Immune System ◽  
Drug Delivery Systems ◽  
Therapeutic Potential ◽  
Delivery Systems ◽  
Current Data ◽  
Natural Origin ◽  
Advantages And Disadvantages ◽  
Efficient Delivery ◽  
Synthetic Drug

В обзоре представлены современные данные о механизмах диагностики, планирования и оценки успешности терапии различных заболеваний с помощью экзосом, об использовании их как нанопереносчиков (т.е. нановезикул для эффективной доставки молекул). За последние годы разработано большое количество разных, в основном синтетических, систем доставки лекарственных средств, недостатками этих систем является плохая биосовместимость и органическая неспособность к высокоточной доставке загруженных веществ. По сравнению с синтетическими системами доставки лекарственных средств, экзосомы - вследствие своего естественного происхождения - могут обладать большими преимуществами, такими, как лучшая биосовместимость и повышенная устойчивость к разрушительному воздействию иммунной системы. Описана технология производства наноструктур, разработка и производство с помощью бионанотехнологий так называемых «полностью синтетических экзосомоподобных нановезикул», преимущества и недостатки этих методов. This review presents current data on mechanisms for diagnosis, planning, and evaluation of success in the treatment of various diseases using exosomes as nanocarriers (i.e., nanovesicles for efficient delivery of molecules). In recent years, a large number of different, mainly synthetic drug delivery systems has been developed. Disadvantages of these systems are poor biocompatibility and organic inability to deliver high-precision loaded substances. Compared with synthetic drug delivery systems, exosomes due to their natural origin may provide great advantages, such as better biocompatibility and increased resistance to detrimental effects of the immune system. This review describes in detail a technology of nanostructure production, the development and production of so-called fully synthetic exosome-like nanovesicles using bionanotechnology, and advantages and disadvantages of these methods.

Akan Deities as Agents of Conflict Resolution Mechanism in Ghana

2021 ◽  
pp. 1-16
Author(s):  
Seth Tweneboah
Keyword(s):  
Conflict Resolution ◽  
Qualitative Analysis ◽  
Public Domain ◽  
Delivery Systems ◽  
Religious Communities ◽  
Delivery Method ◽  
Regulatory Frameworks ◽  
The Everyday

The chapter takes an integrative look at a largely neglected field of conflict resolution mechanism in Ghana: the extent to which belief in traditional deities both enhance and undercut justice delivery systems in society. It contends that through duabɔ (imprecation) there is an enduring influence of traditional deities as part of legal regulatory frameworks in society. The chapter, thus, uncovers the hidden resources of traditional deities as useful channels of conflict resolution. The chapter draws on proceedings from the Akan customary conflict resolution mechanism to demonstrate both the usefulness and challenges of traditional justice delivery method in contemporary Ghana and encourages the need for its modification to suit the needs of legal modernity. The chapter is the product of a qualitative analysis of empirical ethnographic material gathered from the everyday facts of Ghanaian religious communities and public domain.

Synonymous mutation rs2515641 affects CYP2E1 mRNA and protein expression and susceptibility to drug-induced liver injury

2020 ◽  
Vol 21 (7) ◽  
pp. 459-470
Author(s):  
Keguang Chen ◽  
Ruichen Guo ◽  
Chunmin Wei
Keyword(s):  
Gene Expression ◽  
Drug Disposition ◽  
Lentiviral Vector ◽  
Drug Induced ◽  
Drug Induced Liver Injury ◽  
Cyp2e1 Gene ◽  
Recombinant Cells ◽  
Mrna And Protein Expression ◽  
Cyp2e1 Expression ◽  
And Function

Aim: To evaluate whether the synonymous mutant rs2515641 could affect cytochrome P450 2E1 ( CYP2E1) expression and the response to acetaminophen (APAP) or triptolide (TP) treatment. Materials & methods: HepG2 cells were transfected with lentiviral vector containing either CYP2E1-1263C or CYP2E1-1263T. Some of these recombinant cells were then treated with APAP or TP. CYP2E1 gene expression was detected by PCR and western blot. Results: CYP2E1 gene expression decreased significantly both in mRNA and protein level after rs2515641 mutation, indicating that this polymorphism can affect both transcription and translation. Furthermore, rs2515641 mutation dramatically changes the response of CYP2E1 expression to APAP or TP treatment. Conclusion: Rs2515641 significantly changes CYP2E1 expression and function, which would be expected to affect drug disposition and response.

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