MyMedR

Displaying all 5 publications

Abstract:

Sort:

Fulltext Crown Group Lejeuneaceae and Pleurocarpous Mosses in Early Eocene (Ypresian) Indian Amber

Heinrichs J, Scheben A, Bechteler J, Lee GE, Schäfer-Verwimp A, Hedenäs L, et al.

PLoS One, 2016;11(5):e0156301.
PMID: 27244582 DOI: 10.1371/journal.pone.0156301

Cambay amber originates from the warmest period of the Eocene, which is also well known for the appearance of early angiosperm-dominated megathermal forests. The humid climate of these forests may have triggered the evolution of epiphytic lineages of bryophytes; however, early Eocene fossils of bryophytes are rare. Here, we present evidence for lejeuneoid liverworts and pleurocarpous mosses in Cambay amber. The preserved morphology of the moss fossil is inconclusive for a detailed taxonomic treatment. The liverwort fossil is, however, distinctive; its zig-zagged stems, suberect complicate-bilobed leaves, large leaf lobules, and small, deeply bifid underleaves suggest a member of Lejeuneaceae subtribe Lejeuneinae (Harpalejeunea, Lejeunea, Microlejeunea). We tested alternative classification possibilities by conducting divergence time estimates based on DNA sequence variation of Lejeuneinae using the age of the fossil for corresponding age constraints. Consideration of the fossil as a stem group member of Microlejeunea or Lejeunea resulted in an Eocene to Late Cretaceous age of the Lejeuneinae crown group. This reconstruction is in good accordance with published divergence time estimates generated without the newly presented fossil evidence. Balancing available evidence, we describe the liverwort fossil as the extinct species Microlejeunea nyiahae, representing the oldest crown group fossil of Lejeuneaceae.

Matched MeSH terms: Amber/history
α-Mangostin and its derivatives against estrogen receptor alpha

Mardianingrum R, Yusuf M, Hariono M, Mohd Gazzali A, Muchtaridi M

J Biomol Struct Dyn, 2020 Nov 06.
PMID: 33155528 DOI: 10.1080/07391102.2020.1841031

Estrogen receptor alpha (ERα) acts as the transcription factor and the main therapeutic target against breast cancer. One of the compounds that has been shown to act as an ERα is α-mangostin. However, it still has weaknesses due to its low solubility and low potent activity. In this study, α-mangostin was modified by substituting -OH group at C6 using benzoyl derivatives through a step by step in silico study, namely pharmacokinetic prediction (https://preadmet.bmdrc.kr/adme/), pharmacophore modeling (LigandScout 4.1), molecular docking simulation (AutoDock 4.2), molecular dynamics simulation (AMBER 16) and a binding free energy analysis using MM-PBSA method. From the computational studies, three compounds which are derived from α-mangostin (AMB-1 (-9.84 kcal/mol), AMB-2 (-6.80 kcal/mol) and AMB-10 (-12.42 kcal/mol)) have lower binding free energy than α-mangostin (-1.77 kcal/mol), as evidenced by the binding free energy calculation using the MM-PBSA method. They can then be predicted to have potent activities as ERα antagonists.Communicated by Ramaswamy H. Sarma.

Matched MeSH terms: Amber
Fulltext In silico design of potentially functional artificial metallo-haloalkane dehalogenase containing catalytic zinc

Ang TF, Salleh AB, Normi YM, Leow TC

3 Biotech, 2018 Jul;8(7):314.
PMID: 30023146 DOI: 10.1007/s13205-018-1333-9

Artificial metalloenzymes are unique as they combine the good features of homogeneous and enzymatic catalysts, and they can potentially improve some difficult catalytic assays. This study reports a method that can be used to create an artificial metal-binding site prior to proving it to be functional in a wet lab. Haloalkane dehalogenase was grafted into a metal-binding site to form an artificial metallo-haloalkane dehalogenase and was studied for its potential functionalities in silico. Computational protocols regarding dynamic metal docking were studied using native metalloenzymes and functional artificial metalloenzymes. Using YASARA Structure, a simulation box covering template structure was created to be filled with water molecules followed by one mutated water molecule closest to the metal-binding site to metal ion. A simple energy minimization step was subsequently run using an AMBER force field to allow the metal ion to interact with the metal-binding residues. Long molecular dynamic simulation using YASARA Structure was performed to analyze the stability of the metal-binding site and the distance between metal-binding residues. Metal ions fluctuating around 2.0 Å across a 20 ns simulation indicated a stable metal-binding site. Metal-binding energies were predicted using FoldX, with a native metalloenzyme (carbonic anhydrase) scoring 18.0 kcal/mol and the best mutant model (C1a) scoring 16.4 kcal/mol. Analysis of the metal-binding site geometry was performed using CheckMyMetal, and all scores for the metalloenzymes and mutant models were in an acceptable range. Like native metalloenzymes, the metal-binding site of C1a was supported by residues in the second coordination shell to maintain a more coordinated metal-binding site. Short-chain multihalogenated alkanes (1,2-dibromoethane and 1,2,3-trichloropropane) were able to dock in the active site of C1a. The halides of the substrate were in contact with both the metal and halide-stabilizing residues, thus indicating a better stabilization of the substrate. The simple catalytic mechanism proposed is that the metal ion interacted with halogen and polarized the carbon-halogen bond, thus making the alpha carbon susceptible to attack by nucleophilic hydroxide. The interaction between halogen in the metal ion and halide-stabilizing residues may help to improve the stabilization of the substrate-enzyme complex and reduce the activation energy. This study reports a modified dynamic metal-docking protocol and validation tests to verify the metal-binding site. These approaches can be applied to design different kinds of artificial metalloenzymes or metal-binding sites.

Matched MeSH terms: Amber
First record of the family Pseudochiridiidae (Arachnida, Pseudoscorpiones) from continental South America--a Pseudochiridium from a Brazilian cave

Von Schimonsky DM, Bichuette ME, Mahnert V

Zootaxa, 2014;3889(3):442-6.
PMID: 25544278 DOI: 10.11646/zootaxa.3889.3.6

The small pseudoscorpion family Pseudochiridiidae Chamberlin, 1923 comprises two genera and 12 extant species recorded from Asia (Burma, Christmas Island, Indonesia, India, Nepal, Malaysia, New Guinea, Philippines, Nicobars and Sumba), eastern, central and southern Africa (Chad, D.R. Congo, Kenya, South Africa, Tanzania), Madagascar, Seychelles (Aldabra), North America (Florida) and the Caribbean Islands of Dominican Republic and Cuba (Harvey 2013, Barba & Barroso 2013); one unidentified species is mentioned for the fauna of Mexico (Ceballos 2004). A fossil species has been described from Dominican amber by Judson (2007), who predicted the presence of this family in South America.

Matched MeSH terms: Amber
Self-perceived disease control in childhood eczema

Lam PH, Hon KL, Leung K, Leong KF, Li CK, Leung TF

J Dermatolog Treat, 2020 Sep 22.
PMID: 32962454 DOI: 10.1080/09546634.2020.1826395

BACKGROUND: Atopic eczema (AE) is a common relapsing inflammatory skin disease in children which is often associated with chronicity and poor quality of life. Unlike atopic asthma, control of AE is seldom assessed in therapeutics.
AIM: To investigate the utility of a Traffic Light Control (TLC) system as a measurement/assessment of self-perceived eczema control.
METHODS: This is a prospectively study of all Chinese children (aged 6 to 18 years old) with eczema attending the paediatric dermatology clinic of a tertiary hospital from Jan to June 2020. Eczema control, eczema severity, quality of life and biophysical skin condition of consecutive patients at the paediatric dermatology clinic of a teaching hospital were evaluated with the validated Chinese versions of Depressive, Anxiety, Stress Scales (DASS-21), Patient Oriented Eczema Measure (POEM), transepidermal water loss (TEWL), and stratum corneum skin hydration (SH), respectively. With a visual TLC analogy, patients were asked if their eczema is under control (green light), worsening (yellow) or in flare-up (red light).
RESULTS: Among AE patients (n = 36), self-perceived TLC as green (under control), amber (worsening) and red (flare up) reflected acute and chronic severity (SCORAD, NESS, POEM) and quality of life (CDLQI) (p< 0.0001), but not SH, TEWL or Depression, anxiety and stress.
CONCLUSIONS: Eczema control can be semi-quantified with a child-friendly TLC self-assessment system. AE patients reporting worse eczema control have worse acute and chronic eczema severity, more impairment of quality of life; but not the psychologic symptoms of depression, anxiety and stress or skin hydration or transepidermal water loss. TLC can be linked to an eczema action plan to guide patient management.

Matched MeSH terms: Amber