• Title/Summary/Keyword: molecular design

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Circular RNAs in and out of Cells: Therapeutic Usages of Circular RNAs

  • Mingyu Ju;Dayeon Kim;Geurim Son;Jinju Han
    • Molecules and Cells
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    • v.46 no.1
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    • pp.33-40
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    • 2023
  • RNAs are versatile molecules that are primarily involved in gene regulation and can thus be widely used to advance the fields of therapeutics and diagnostics. In particular, circular RNAs which are highly stable, have emerged as strong candidates for use on next-generation therapeutic platforms. Endogenous circular RNAs control gene regulatory networks by interacting with other biomolecules or through translation into polypeptides. Circular RNAs exhibit cell-type specific expression patterns, which can be altered in tissues and body fluids depending on pathophysiological conditions. Circular RNAs that are aberrantly expressed in diseases can function as biomarkers or therapeutic targets. Moreover, exogenous circular RNAs synthesized in vitro can be introduced into cells as therapeutic molecules to modulate gene expression networks in vivo. Depending on the purpose, synthetic circular RNA sequences can either be identical to endogenous circular RNA sequences or artificially designed. In this review, we introduce the life cycle and known functions of intracellular circular RNAs. The current stage of endogenous circular RNAs as biomarkers and therapeutic targets is also described. Finally, approaches and considerations that are important for applying the available knowledge on endogenous circular RNAs to design exogenous circular RNAs for therapeutic purposes are presented.

THE INFLUENCE OF SOY ISOFLAVON TO THE SKIN AGING IN PRE- MENOPAUSAL WOMEN

  • Subchan, P.;Tranggono, R.I.S.;Djajadisastra, J.
    • Proceedings of the SCSK Conference
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    • 2003.09a
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    • pp.73-84
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    • 2003
  • Skin aging process on pre-menopausal women is a problem that needs to be prevented as early as possible. The decrease of oestrogen level which is one of the intrinsic factors of the skin aging process will affect the skin biological process, due to oestrogen receptors on the skin. A number of researches conducted on pre-menopausal women with the allocation of oestrogen hormone resulted in delaying the skin aging process. The administration of soy isoflavon, a phytoestrogen found in daily food, on pre-menopausal women is hoped to be able to prevent skin aging process, even clinically or molecular biologically. This research aims to explain the benefit of administering of soy isoflavon on skin aging process. The design of the research is randomised controlled trial (RCT). As many as 60 pre-menopausal women were collected with simple random sampling method. Soy isoflavon is an independent variable, while skin aging process is a dependent variable assessed from the hydration, sebum level, average roughness, depth of wrinkles, skin clarity, length of the telomere. Analysis was conducted using t and MANDVA tests and.the result showed a significance (F = 10,439; p = 0,001) over the allocation of soy isoflavon to the whole variable dependent, including the telomere length and the skin hydration, meant that allocation of soy isoflavon could delay skin aging process.

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A Pumilio Activity Sensor Reveals Bag-of-Marbles Inhibition of Pum Activity in the Drosophila Ovary

  • Wijeong Jang;Changsoo Kim
    • Development and Reproduction
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    • v.27 no.1
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    • pp.39-46
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    • 2023
  • Pumilio (Pum) is an RNA-binding protein and translational repressor important to diverse biological processes. In the Drosophila ovary, Pum is expressed in female germline stem cells (GSCs), wherein it acts as an intrinsic stem cell maintenance factor via repressing target mRNAs that are as yet mostly unknown. Pum recognizes the Pum binding sequence (PBS) in the mRNA 3'UTR through its C-terminus Puf domain. Translational repression is mediated through its N-terminal domain, but the molecular mechanism remains largely unknown. We previously showed that Bag-of-marbles, a critical differentiation-promoting factor of female GSCs, physically interacts with the N-terminus of Pum. We further showed that this interaction is critical to Bam inhibition of Pum repressive action in cultured cells, but the physiological relevance was not addressed. Here we design an in vivo GFP translational reporter bearing the PBS in its 3'UTR and show that GFP expression is reduced in cells wherein Pum is known to be active. Furthermore, we demonstrate in pum mutant ovary that this GFP repression requires Pum, and also that the sensor faithfully monitors Pum activity. Finally, we show that forced expression of Bam inhibits Pum-mediated repression, validating that Bam inhibits Pum activity in vivo.

Atomistic simulations of defect accumulation and evolution in heavily irradiated titanium for nuclear-powered spacecraft

  • Hai Huang;Xiaoting Yuan;Longjingrui Ma;Jiwei Lin;Guopeng Zhang;Bin Cai
    • Nuclear Engineering and Technology
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    • v.55 no.6
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    • pp.2298-2304
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    • 2023
  • Titanium alloys are expected to become one of the candidate materials for nuclear-powered spacecraft due to their excellent overall performance. Nevertheless, atomistic mechanisms of the defect accumulation and evolution of the materials due to long-term exposure to irradiation remain scarcely understood by far. Here we investigate the heavy irradiation damage in a-titanium with a dose as high as 4.0 canonical displacements per atom (cDPA) using atomistic simulations of Frenkel pair accumulation. Results show that the content of surviving defects increases sharply before 0.04 cDPA and then decreases slowly to stabilize, exhibiting a strong correlation with the system energy. Under the current simulation conditions, the defect clustering fraction may be not directly dependent on the irradiation dose. Compared to vacancies, interstitials are more likely to form clusters, which may further cause the formation of 1/3<1210> interstitial-type dislocation loops extended along the (1010) plane. This study provides an important insight into the understanding of the irradiation damage behaviors for titanium.

A Study on the Change of Mechanical Property According to the Aging of Polymer Electrolyte Membrane (고분자전해질막의 노후화에 따른 기계적 특성 변화에 관한 연구)

  • KIM, SEUNGHWAN;EO, JUNWOO;SEO, YOUNGJIN;HWANG, CHULMIN;JUNG, YOUNGGUAN
    • Journal of Hydrogen and New Energy
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    • v.33 no.2
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    • pp.176-182
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    • 2022
  • Since the various characteristics of the polymer electrolyte membrane are not clearly identified, it is difficult to predict and design applications for various conditions. In this study, as a previous study on the aging of the polymer electrolyte membrane, a study was conducted on the change of mechanical properties according to the aging of the polymer electrolyte membrane. Through the tensile test of Nafion 117, the mechanical properties change due to aging was confirmed. As a result of the tensile test, it was confirmed that the aged Nafion 117 had reduced tensile strength. Through DSC measurement, aged Nafion confirmed that the glass transition temperature and enthalpy change were low, which is thought to be the effect of molecular motion and transition due to the lapse of time. The effect is thought to cause a difference in the amount of change in enthalpy, resulting in a difference in mechanical properties during tension.

Natural Killer Cell and Cancer Immunotherapy (자연살해세포와 항암면역치료)

  • Kim, Hun Sik
    • Hanyang Medical Reviews
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    • v.33 no.1
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    • pp.59-64
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    • 2013
  • Cancer remains the leading cause of death worldwide despite intense efforts in developing innovative treatments. Current approaches in cancer therapy are mainly directed to a selective targeting of cancer cells to avoid potential side effects associated with conventional therapy. In this respect, Natural killer (NK) cells have gained growing attention and are now being considered as promising therapeutic tools for cancer therapy owing to their intrinsic ability to rapidly recognize and kill cancer cells, while sparing normal healthy cells. NK cells play a key role in the first line of defense against transformed and virus-infected cells. NK cells sense their target through a whole array of receptors, both activating and inhibitory. Functional outcome of NK cell against target cells is determined by the balance of signals transmitted from diverse activating and inhibiting receptors. Despite significant progress made in the role of NK cells attack as a pivotal sentinel in tumor surveillance, the molecular has been that regulate NK cell responses remain unclear, which restricts the use of NK cells as a therapeutic measure. Accordingly, current efforts for NK cell-based cancer therapy have largely relied on the strategies that are based on the manipulation of inhibitory receptor function. However, if we better understand the mechanisms governing NK cell activation, including those mediated by diverse activating receptors, this knowledge can be applied to the development of optimal design for cancer immunotherapy by targeting NK cells.

Unraveling Bonding Mechanisms and Electronic Structure of Pyridine Oximes on Fe(110) Surface: A Computational Study (Fe(110) 표면의 피리딘 옥심 결합 메커니즘 및 전자 구조 해명: 전산 연구)

  • Hassane, Lgaz;Lee, Han-Seung
    • Proceedings of the Korean Institute of Building Construction Conference
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    • 2023.05a
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    • pp.255-256
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    • 2023
  • The development of corrosion inhibitors with outstanding performance is a never-ending and complex process engaged in by researchers, engineers and practitioners. Computational assessment of organic corrosion inhibitors performance is a crucial step towards the design of new task-pecific materials. Herein, electronic features, adsorption characteristics and bonding mechanisms of two pyridine oximes, namely 2-pyridylaldoxime (2POH) and 3-pyridylaldoxime (3POH) with the iron surface were investigated using molecular dynamics (MD), and self-consistent-charge density-unctional tight-binding (SCC-DFTB) simulations. SCC-DFTB simulations revealed that 3POH molecule can form covalent bonds with iron atoms in its neutral and protonated states, while 2POH molecule can only bond with iron through its protonated form, resulting in interaction energies of -2.534, -2.007, -1.897, and -0.007 eV for 3POH, 3POH+, 2POH+, and 2POH, respectively. Projected density of states (PDOSs) analysis of pyridines-Fe(110) interactions indicated that pyridine molecules chemically adsorbed on the iron surface.

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M Protein from Dengue virus oligomerizes to pentameric channel protein: in silico analysis study

  • Ayesha Zeba;Kanagaraj Sekar;Anjali Ganjiwale
    • Genomics & Informatics
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    • v.21 no.3
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    • pp.41.1-41.11
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    • 2023
  • The Dengue virus M protein is a 75 amino acid polypeptide with two helical transmembranes (TM). The TM domain oligomerizes to form an ion channel, facilitating viral release from the host cells. The M protein has a critical role in the virus entry and life cycle, making it a potent drug target. The oligomerization of the monomeric protein was studied using ab initio modeling and molecular dynamics simulation in an implicit membrane environment. The representative structures obtained showed pentamer as the most stable oligomeric state, resembling an ion channel. Glutamic acid, threonine, serine, tryptophan, alanine, isoleucine form the pore-lining residues of the pentameric channel, conferring an overall negative charge to the channel with approximate length of 51.9 Å. Residue interaction analysis for M protein shows that Ala94, Leu95, Ser112, Glu124, and Phe155 are the central hub residues representing the physicochemical interactions between domains. The virtual screening with 165 different ion channel inhibitors from the ion channel library shows monovalent ion channel blockers, namely lumacaftor, glipizide, gliquidone, glisoxepide, and azelnidipine to be the inhibitors with high docking scores. Understanding the three-dimensional structure of M protein will help design therapeutics and vaccines for Dengue infection.

Immunoinformatics studies and design of a novel multi-epitope peptide vaccine against Toxoplasma gondii based on calcium-dependent protein kinases antigens through an in-silico analysis

  • Ali Dalir Ghaffari;Fardin Rahimi
    • Clinical and Experimental Vaccine Research
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    • v.13 no.2
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    • pp.146-154
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    • 2024
  • Purpose: Infection by the intracellular apicomplexan parasite Toxoplasma gondii has serious clinical consequences in humans and veterinarians around the world. Although about a third of the world's population is infected with T. gondii, there is still no effective vaccine against this disease. The aim of this study was to develop and evaluate a multimeric vaccine against T. gondii using the proteins calcium-dependent protein kinase (CDPK)1, CDPK2, CDPK3, and CDPK5. Materials and Methods: Top-ranked major histocompatibility complex (MHC)-I and MHC-II binding as well as shared, immunodominant linear B-cell epitopes were predicted and linked using appropriate linkers. Moreover, the 50S ribosomal protein L7/L12 (adjuvant) was mixed with the construct's N-terminal to increase the immunogenicity. Then, the vaccine's physicochemical characteristics, antigenicity, allergenicity, secondary and tertiary structure were predicted. Results: The finally-engineered chimeric vaccine had a length of 680 amino acids with a molecular weight of 74.66 kDa. Analyses of immunogenicity, allergenicity, and multiple physiochemical parameters indicated that the constructed vaccine candidate was soluble, non-allergenic, and immunogenic, making it compatible with humans and hence, a potentially viable and safe vaccine candidate against T. gondii parasite. Conclusion: In silico, the vaccine construct was able to trigger primary immune responses. However, further laboratory studies are needed to confirm its effectiveness and safety.

Manganese and Iron Interaction: a Mechanism of Manganese-Induced Parkinsonism

  • Zheng, Wei
    • Proceedings of the Korea Environmental Mutagen Society Conference
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    • 2003.10a
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    • pp.34-63
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    • 2003
  • Occupational and environmental exposure to manganese continue to represent a realistic public health problem in both developed and developing countries. Increased utility of MMT as a replacement for lead in gasoline creates a new source of environmental exposure to manganese. It is, therefore, imperative that further attention be directed at molecular neurotoxicology of manganese. A Need for a more complete understanding of manganese functions both in health and disease, and for a better defined role of manganese in iron metabolism is well substantiated. The in-depth studies in this area should provide novel information on the potential public health risk associated with manganese exposure. It will also explore novel mechanism(s) of manganese-induced neurotoxicity from the angle of Mn-Fe interaction at both systemic and cellular levels. More importantly, the result of these studies will offer clues to the etiology of IPD and its associated abnormal iron and energy metabolism. To achieve these goals, however, a number of outstanding questions remain to be resolved. First, one must understand what species of manganese in the biological matrices plays critical role in the induction of neurotoxicity, Mn(II) or Mn(III)? In our own studies with aconitase, Cpx-I, and Cpx-II, manganese was added to the buffers as the divalent salt, i.e., $MnCl_2$. While it is quite reasonable to suggest that the effect on aconitase and/or Cpx-I activites was associated with the divalent species of manganese, the experimental design does not preclude the possibility that a manganese species of higher oxidation state, such as Mn(III), is required for the induction of these effects. The ionic radius of Mn(III) is 65 ppm, which is similar to the ionic size to Fe(III) (65 ppm at the high spin state) in aconitase (Nieboer and Fletcher, 1996; Sneed et al., 1953). Thus it is plausible that the higher oxidation state of manganese optimally fits into the geometric space of aconitase, serving as the active species in this enzymatic reaction. In the current literature, most of the studies on manganese toxicity have used Mn(II) as $MnCl_2$ rather than Mn(III). The obvious advantage of Mn(II) is its good water solubility, which allows effortless preparation in either in vivo or in vitro investigation, whereas almost all of the Mn(III) salt products on the comparison between two valent manganese species nearly infeasible. Thus a more intimate collaboration with physiochemists to develop a better way to study Mn(III) species in biological matrices is pressingly needed. Second, In spite of the special affinity of manganese for mitochondria and its similar chemical properties to iron, there is a sound reason to postulate that manganese may act as an iron surrogate in certain iron-requiring enzymes. It is, therefore, imperative to design the physiochemical studies to determine whether manganese can indeed exchange with iron in proteins, and to understand how manganese interacts with tertiary structure of proteins. The studies on binding properties (such as affinity constant, dissociation parameter, etc.) of manganese and iron to key enzymes associated with iron and energy regulation would add additional information to our knowledge of Mn-Fe neurotoxicity. Third, manganese exposure, either in vivo or in vitro, promotes cellular overload of iron. It is still unclear, however, how exactly manganese interacts with cellular iron regulatory processes and what is the mechanism underlying this cellular iron overload. As discussed above, the binding of IRP-I to TfR mRNA leads to the expression of TfR, thereby increasing cellular iron uptake. The sequence encoding TfR mRNA, in particular IRE fragments, has been well-documented in literature. It is therefore possible to use molecular technique to elaborate whether manganese cytotoxicity influences the mRNA expression of iron regulatory proteins and how manganese exposure alters the binding activity of IPRs to TfR mRNA. Finally, the current manganese investigation has largely focused on the issues ranging from disposition/toxicity study to the characterization of clinical symptoms. Much less has been done regarding the risk assessment of environmenta/occupational exposure. One of the unsolved, pressing puzzles is the lack of reliable biomarker(s) for manganese-induced neurologic lesions in long-term, low-level exposure situation. Lack of such a diagnostic means renders it impossible to assess the human health risk and long-term social impact associated with potentially elevated manganese in environment. The biochemical interaction between manganese and iron, particularly the ensuing subtle changes of certain relevant proteins, provides the opportunity to identify and develop such a specific biomarker for manganese-induced neuronal damage. By learning the molecular mechanism of cytotoxicity, one will be able to find a better way for prediction and treatment of manganese-initiated neurodegenerative diseases.

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