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Topic Review
Probe for Single-Molecule Fluorescence Microscopy
Probe choice in single-molecule microscopy requires deeper evaluations than those adopted for less sensitive fluorescence microscopy studies. Fluorophore characteristics can alter or hide subtle phenomena observable at the single-molecule level, wasting the potential of the sophisticated instrumentation and algorithms developed for this kind of advanced applications. The three typical groups of fluorophores are fluorescent proteins, organic dyes and quantum dots; here their advantages, drawbacks and use in single-molecule microscopy are discussed. Some requirements are common to all applications, such as high brightness and photostability, specific and efficient labeling, controlled stoichiometry, no perturbation on the system. Other requirements depend on the specific type of single-molecule technique; some of them are here described with their specific requirements for probe choice.
  • 1.4K
  • 13 Feb 2023
Topic Review
PBK/TOPK
T-lymphokine-activated killer cell-originated protein kinase (TOPK, also known as PDZ-binding kinase or PBK) plays a crucial role in cell cycle regulation and mitotic progression. Abnormal overexpression or activation of TOPK has been observed in many cancers, including colorectal cancer, triple-negative breast cancer, and melanoma, and it is associated with increased development, dissemination, and poor clinical outcomes and prognosis in cancer. Moreover, TOPK phosphorylates p38, JNK, ERK, and AKT, which are involved in many cellular functions, and participates in the activation of multiple signaling pathways related to MAPK, PI3K/PTEN/AKT, and NOTCH1; thus, the direct or indirect interactions of TOPK make it a highly attractive yet elusive target for cancer therapy. Small molecule inhibitors targeting TOPK have shown great therapeutic potential in the treatment of cancer both in vitro and in vivo, even in combination with chemotherapy or radiotherapy. Therefore, targeting TOPK could be an important approach for cancer prevention and therapy.
  • 1.4K
  • 22 Sep 2021
Topic Review
Vincristine-Induced Pediatric Peripheral Neuropathy
Vincristine-induced peripheral neurotoxicity (VIPN) is a very common side effect of vincristine chemotherapy among pediatric patients with cancer. 
  • 1.4K
  • 21 May 2021
Topic Review
PARP in DNA Damage Repair
Poly (ADP-ribose) polymerases (PARP) 1-3 are well-known multi-domain enzymes, catalysing the covalent modification of proteins, DNA, and themselves. They attach mono- or poly-ADP-ribose to targets using NAD+ as a substrate. Poly-ADP-ribosylation (PARylation) is central to the important functions of PARP enzymes in the DNA damage response and nucleosome remodelling. Activation of PARP happens through DNA binding via zinc fingers and/or the WGR domain. Modulation of their activity using PARP inhibitors occupying the NAD+ binding site has proven successful in cancer therapies. For decades, studies set out to elucidate their full-length molecular structure and activation mechanism. 
  • 1.4K
  • 02 Sep 2021
Topic Review
Oral Sulfated Fucose-Rich Polysaccharides
Sulfated fucose-rich polysaccharides from marine organisms are unique molecules with various pharmacological effects. They might have promising therapeutic applications in different diseases.
  • 1.4K
  • 24 Sep 2021
Topic Review
Mitochondrial Calcium
Mitochondria calcium is a double-edged sword. The low levels of calcium are essential to maintain optimal rates of ATP production, extreme levels of calcium overcoming the mitochondrial calcium retention capacity leads to loss of mitochondrial function. In moderate amounts, ATP synthesis rates are inhibited in a calcium-titratable manner.
  • 1.4K
  • 31 Jan 2023
Topic Review
Phycobilisomes and Phycobiliproteins
Eukaryotic photosynthesis arose in the course of evolution as a result of the incorporation of an unstored cyanobacterium and its transformation into chloroplasts by an ancestral heterotrophic eukaryotic cell. The pigment apparatus of earlier evolved  Archaeplastida algae and other later algal phyla turned out to be arranged in the same way having pigment-protein complexes of photosystem I (PS I), photosystem II (PS II) and antenna complex. PS I and PS II are characterized by uniform structures, while the light-harvesting antennae have undergone a number  of changes.
  • 1.4K
  • 14 Feb 2023
Topic Review
Cathepsin Proteases and Bcl-2 Proteins
Taken with the growing importance of cathepsin-mediated substrate proteolysis in tumor biology and progression, the focus and emphasis placed on therapeutic design and development is coming into fruition. Underpinning this approach is the invariable progression from the direction of fully characterizing cathepsin protease members and their substrate targets, towards targeting such an interaction with tangible therapeutics. The two groups of such substrates that have gained much attention over the years are the pro- and anti- apoptotic protein intermediates from the extrinsic and intrinsic signaling arms of the apoptosis pathway.
  • 1.4K
  • 08 May 2021
Topic Review
High-resolution melt method
HRM (High-resolution melt) analysis is a powerful molecular biology detection method used for the identification of genetic mutations, DNA methylation analysis or species identification. 
  • 1.4K
  • 27 Oct 2020
Topic Review
Non-Amyloidbeta-Tau Biomarkers
Core biomarkers amyloid beta (Aβ) and Tau have been considered as key neuropathological hallmarks of Alzheimer's disease. However, they did not sufficiently reflect clinical severity and therapeutic response, proving the difficulty of the Aβ- and Tau-targeting therapies in clinical trials. Along with these core biomarkers, non-Amyloidbeta-Tau pathophysiological biomarkers (Neurodegeneration-related biomarkers, biomarkers for neuroinflammation and phagocytosis of an innate immune system, lipid metabolism biomarkers) could serve as advanced reporters for early diagnosing AD, predicting AD progression, and monitoring the treatment response.
  • 1.4K
  • 18 Nov 2020
Topic Review
Traveling Across Life Sciences with Acetophenone
Each metabolite, regardless of its molecular simplicity or complexity, has a mission or function in the organism biosynthesizing it.  The biological, allelochemical, and chemical properties of acetophenone, as a metabolite involved in multiple interactions with various (mi-cro)organisms.
  • 1.4K
  • 28 Jan 2023
Topic Review
The IGF1 Signaling Pathway
Insulin-like growth factor 1 (IGF1) is a peptide growth factor with important functions in multiple aspects of growth, development and metabolism. The biological actions of IGF1 are mediated by the IGF1 receptor (IGF1R), a cell-surface protein that is evolutionarily related to the insulin receptor (InsR).
  • 1.4K
  • 12 Oct 2023
Topic Review
CUT Domain Proteins in Cancer
Recent studies revealed that CUT domains function as accessory factors that accelerate DNA repair by stimulating the enzymatic activities of the base excision repair enzymes OGG1, APE1, and DNA pol β. Strikingly, the role of CUT domain proteins in DNA repair is exploited by cancer cells to facilitate their survival. Cancer cells in which the RAS pathway is activated produce an excess of reactive oxygen species (ROS) which, if not counterbalanced by increased production of antioxidants, causes sustained oxidative DNA damage and, ultimately, cell senescence. These cancer cells can adapt by increasing their capacity to repair oxidative DNA damage in part through elevated expression of CUT domain proteins such as CUX1, CUX2, or SATB1. In particular, CUX1 overexpression was shown to cooperate with RAS in the formation of mammary and lung tumors in mice. Conversely, knockdown of CUX1, CUX2, or SATB1 was found to be synthetic lethal in cancer cells exhibiting high ROS levels as a consequence of activating mutations in KRAS, HRAS, BRAF, or EGFR. Importantly, as a byproduct of their adaptation, cancer cells that overexpress CUT domain proteins exhibit increased resistance to genotoxic treatments such as ionizing radiation, temozolomide, and cisplatin.
  • 1.4K
  • 22 Jun 2021
Topic Review
Zinc Signaling in Prostate Cancer
Prostate cancer (PCa) is one of the most common cancers and the second leading cause of cancer-related death among men worldwide. Despite progresses in early diagnosis and therapeutic strategies, prognosis for patients with advanced PCa remains poor. Therefore, it is necessary to develop novel strategies to prevent, diagnose and effectively treat PCa patients in clinic. Noteworthily, a unique feature of healthy prostate is its highest level of zinc content among all soft tissues in the human body, which dramatically decreases during prostate tumorigenesis. Here, we discuss clinical applications of zinc-containing compounds and proteins involved in PCa signaling pathways. Based on currently available studies, we conclude that zinc can serve as a biomarker in PCa diagnosis and therapies.
  • 1.4K
  • 05 Nov 2021
Topic Review
Two phytochrome A Types in Plants
The phytochrome (phy) system of plants with the main phyA and phyB controls their development beginning from seed germination to fruiting and senescence. The regulation reactions are categorized into three modes—the very low and low fluence responses (VLFR and LFR) and the high irradiance responses (HIR). The phyA is unique among the other phytochromes; it is major in etiolated seedlings and light-labile, and mediates all the three photoresponse modes. The phyB is light-stable, dominates in deetiolated plants, and performs the LFR. The phyA is itself heterogeneous which may explain its functional complexity. It comprises two native types, phyA′ and phyA″, the products of post-translational modification of the molecule at the N-terminus, possibly, via serine phosphorylation. This alters chromophore-apoprotein interactions resulting in the different photochemical, phenomenological, and functional properties of the two phyA pools. The phyA′ is major, water-soluble, and light-labile; the phyA″ is minor, amphiphilic, and relatively light-stable. The phyA′ mediates the VLFR whereas the water-soluble fraction of phyA″ is responsible for the HIR and LFR, the processes taking place in the nucleus. The membrane- (protein-) associated fraction of phyA” is likely to participate in the cytoplasmic photoregulation processes. The phyA pools' functions—their mode, intensity and sign—depend on plant's species, genotype and organ/tissue. The evidence of the existence of the two distinct phyA types in a plant, and their physicochemical properties and their role in the phyA functioning are discussed.
  • 1.4K
  • 17 May 2023
Topic Review
The PINK1/Parkin Pathway
The process by which dysfunctional mitochondria are selectively targeted for lysosome-mediated degradation otherwise known as mitophagy, requires the serine/threonine kinase PINK1 and the E3 ubiquitin ligase Parkin to occur. In the last decade the PINK1/Parkin pathway received great attention due to its importance in many physiological and pathological processes. Understanding the mechanisms by which mitochondria are selectively recognized and targeted for degradation is thus fundamental to understand and to develop therapies for many devastating diseases. Here the mechanisms at the basis of the PINK1/Parkin-mediated degradation of dysfunctional mitochondria are described.
  • 1.4K
  • 27 Oct 2020
Topic Review
Bioactivities and Chemical Analysis of Ailanthus altissima(Mill.) Swingle
Many species of the so-called exotic plants coexist with native species in a balanced way, but others thrive very quickly and escape human control, becoming harmful—these are called invasive alien species. In addition to overcoming geographic barriers, these species can defeat biotic and abiotic barriers, maintaining stable populations. Ailanthus altissima is no exception; it is disseminated worldwide and is considered high risk due to its easy propagation and resistance to external environmental factors. Currently, it has no particular use other than ornamental, even though it is used to treat epilepsy, diarrhea, asthma, ophthalmic diseases, and seborrhoea in Chinese medicine. Considering its rich composition in alkaloids, terpenoids, sterols, and flavonoids, doubtlessly, its use in medicine or other fields can be maximised.
  • 1.4K
  • 17 Dec 2021
Topic Review
Benchmarking Data Sets
Developing realistic data sets for evaluating virtual screening methods is a task that has been tackled by the cheminformatics community for many years. Numerous artificially constructed data collections were developed, such as DUD, DUD-E, or DEKOIS. However, they all suffer from multiple drawbacks, one of which is the absence of experimental results confirming the impotence of presumably inactive molecules, leading to possible false negatives in the ligand sets. In light of this problem, the PubChem BioAssay database, an open-access repository providing the bioactivity information of compounds that were already tested on a biological target, is now a recommended source for data set construction. Nevertheless, there exist several issues with the use of such data that need to be properly addressed. In this article, an overview of benchmarking data collections built upon experimental PubChem BioAssay input is provided, along with a thorough discussion of noteworthy issues that one must consider during the design of new ligand sets from this database. The points raised in this review are expected to guide future developments in this regard, in hopes of offering better evaluation tools for novel in silico screening procedures.
  • 1.4K
  • 26 Oct 2020
Topic Review
Xenopus Oocytes to Study Fully-Processed Membrane Proteins
The use of Xenopus oocytes in electrophysiological and biophysical research constitutes a long and successful story, providing major advances to the knowledge of the function and modulation of membrane proteins, mostly receptors, ion channels, and transporters. These cells are capable of correctly expressing heterologous proteins after injecting the corresponding mRNA or cDNA. The Xenopus oocyte has become an outstanding host–cell model to carry out detailed studies on the function of fully-processed foreign membrane proteins after their microtransplantation to the oocyte. 
  • 1.4K
  • 24 Oct 2022
Topic Review
Senile Osteoporosis by BMSCs
Senile osteoporosis has become a worldwide bone disease with the aging of the world population. Unlike postmenopausal osteoporosis which is linked to menopause in women, senile osteoporosis is due to aging, hence, affecting both men and women. Evidence has shown that with age increase, bone marrow stromal cells (BMSCs) differentiate into more adipocytes rather than osteoblasts and undergo senescence, which leads to decreased bone formation and contributes to senile osteoporosis. Therefore, modulating BMSCs to stimulate them either differentiate into more osteoblasts than adipocytes or eliminate their senescence will be wonderful strategies for treating senile osteoporosis. Here, the treatment of senile osteoporosis by aiming at BMSCs is introduced.
  • 1.4K
  • 01 Nov 2020
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