Investigation of the complexes of EcoRI endonuclease with decanucleotides containing canonical and modified recognition sequences using fluorescence and optical detection of magnetic resonance spectroscopy

The binding of EcoRI endonuclease to the oligonucleotides d(GCGAATTCGC) and d(GCGAA) (5BrdU) (5BrdU) d(CGC) has been investigated to determine whether stacking interactions occur between tryptophan residues and the DNA bases. Fluorescence binding isotherms show that the decamer containing the canonical and that containing the modified recognition sequence bind with comparable affinity. Optically detected magnetic resonance spectra show limited perturbations of the Trp zero-field splitting parameters, which are assigned to electrical field effects. No evidence for Trp stacking interactions has been found.     

Thinner bark increases sensitivity of wetter Amazonian tropical forests to fire

Understory fires represent an accelerating threat to Amazonian tropical forests and can, during drought, affect larger areas than deforestation itself. These fires kill trees at rates varying from < 10 to c. 90% depending on fire intensity, forest disturbance history and tree functional traits. Here, we examine variation in bark thickness across the Amazon. Bark can protect trees from fires, but it is often assumed to be consistently thin across tropical forests. Here, we show that investment in bark varies, with thicker bark in dry forests and thinner in wetter forests. We also show that thinner bark translated into higher fire‐driven tree mortality in wetter forests, with between 0.67 and 5.86 gigatonnes CO₂ lost in Amazon understory fires between 2001 and 2010. Trait‐enabled global vegetation models that explicitly include variation in bark thickness are likely to improve the predictions of fire effects on carbon cycling in tropical forests.     

Polymorphism and genetic diversity of Isospora parnaitatiaiensis Silva,Rodrigues, Lopes,Berto, Luz,Ferreira & Lopes, 2015 (Eimeriidae) from antbirds (Thamnophilidae) in Brazil

Systematic Parasitology - Isospora parnaitatiaiensis Silva, Rodrigues, Lopes, Berto, Luz, Ferreira &amp; Lopes, 2015 was identified from a new host, the plain antvireo Dysithamnus mentalis...     

Molecular Dynamics Study on Protein and it's Water Structure at High Pressure

Abstract

We have performed NPT molecular dynamics simulations (Langevin Piston Method) on two types of solvated proteins-‘denaturation-unfavorable’ protein (insulin) and ‘denaturation-favorable protein’ (ribonuclease A) at high pressure (from 1 bar up to 20 kbar). The method is based on the extended system formalism introduced by Andersen, where the deterministic equations of motion for the piston degree of freedom are replaced by Langevin equation. We report the structural changes of proteins (ribonuclease A and insulin) and water molecules through radius of gyration, solvent accessible surface area, hydrogen bond pattern, and the topology of water clusters connected by the hydrogen bonded circular network. The solvent accessibility of ribonuclease A is mainly decreased by hydrophilic residues rather than hydrophobic residues under high pressure. From the results of hydrogen bond analysis, we have found that α-helix is more stable than β-sheet under high pressure. In addition, from the analysis of the water cluster, we have observed that for ribonuclease A, 5-membered ring structure is more favorable than 6-membered ring at higher pressure. However, for insulin, the ratio of 5 to 6-ring is constant over the pressure ranges for which we have performed MD simulation. This indicates that the water structure around insulin does not change under high pressure.     

A Modified Valley Restrained Monte Carlo Method to Efficiently Search the Low Energy Structures of Peptides

Abstract

A new Monte Carlo sampling scheme, namely the Modified Valley Restrained Monte Carlo procedure, is used to obtain the global energy minimum conformations for polypeptides, such as Met-enkephalin and Melittin. For each peptide, we found close agreement with previous results from both theoretical and experimental studies. The simple idea for controlling the step size according to the Valley Function, provides useful suggestions in searching the global energy minimum structures, and furthermore helps solve the multiple minima problem.     

Six new species of Rhamnocercus Monaco,Wood & Mizelle, 1954 (Monogenea: Diplectanidae) infecting the gills from South American sciaenid fishes

A parasitological survey searching diplectanids (Monogenea: Diplecatnidae) infesting the gills of marine fishes from South America was carried out during the 2019–2020 period. The gills of four sciaenid species, 2 Cheilotrema fasciatum Tschudi, 1 smalleye croaker Nebris microps Cuvier, 2 royal highhat Pareques lanfeari (Barton), and 1 minor stardrum Stellifer minor (Tschudi), were sampled. Six new species of Rhamnocercus Monaco, Wood & Mizelle, 1954 were described: Rhamnocercus chacllae n. sp. and Rhamnocercus chaskae n. sp. from P. lanfeari, Rhamnocercus fasciatus n. sp. from C. fasciatum, Rhamnocercus microps n. sp. from N. microps, and Rhamnocercus rimaci n. sp. and Rhamnocercus tantaleani n. sp. from S. minor. Rhamnocercus chacllae n. sp. can be differentiated from its congeners by its L-shaped male copulatory organ (MCO) and by having an anteromedial slight notch at ventral bar. Rhamnocercus chaskae n. sp. differs from the other species of the genus by its long and straight MCO with bifid distal end and by having haptoral accessory spines at level of ventral bar with quadrifid distal portion. Rhamnocercus fasciatus n. sp. is characterized by possessing a straight and long MCO with truncated distal end, haptoral accessory spines at level of ventral bar with bifid distal portion, dorsal bars with a knob at lateral extremity, and a large vagina with bell-shaped. Rhamnocercus microps n. sp. differs from all congeners mainly by having a short and straight MCO with the distal end of internal tube spatulate and uncovered by external tube. Rhamnocercus rimaci n. sp. is can be distinguished from all other species of Rhamnocercus by having an almost J-shaped MCO with the distal end of external tube slight expanded and the distal end of internal tube narrow and uncovered by external tube. Rhamnocercus tantaleani n. sp. is mainly characterized by its MCO, which is tubular and straight, having the distal end of external tube bifurcated (right branch well-expanded and left branch narrow) and the distal end of internal tube enveloped by left branch of the external tube. This is the first data on the parasites of P. lanfeari, a little known, but popular fish in local markets from Peru. Rhamnocercus microps n. sp. is the first described species of Rhamnocercus in Brazil. The present finding brings to 12, the number of known species of Rhamnocercus. A key to Rhamnocercus species is provided.

     

Temporal and spatial change of the investment in carnivory of the tropical Utricularia foliosa

Investment by bladderwort (Utricularia foliosa L.) in carnivory, in terms of biochemical composition (carbohydrates per bladder), elemental composition (carbon and nitrogen per bladder), and morphology of the bladders (length, depth, size of the trap door, and size of antennae), was estimated in seven plants located in Yahuarcaca creek (Colombian Amazon) five times from March to May 2005. The aims were to determine whether investment in carnivory varies temporally (over the growing season of the plant) and/or spatially, and if this potential change in carnivory investment varies according to nutrient conditions. The main differences in the investment in carnivory (changes in bladder number and bladder size, and changes in the size of the antennae) were among locations and there were not important differences over the growing season of the plant. Nitrogen and not phosphorus, was the element that stimulated the investment in carnivory. In addition to changes in bladder number and bladder size, we observed a new strategy to enhance prey capture under nitrogen limitation: changes in the size of the antennae. The size of the antennae was approximately 1.3 higher in those plants located in sites with low NO₃⁻. However, we did not observed changes in the carbon/nitrogen ratio of the bladders or in the relationship between bladder length with bladder depth or size of the trap door. The amount of carbohydrates per bladder was also 1.8 higher in those plants located in sites with low NO₃⁻ (0.13 μM) than those with higher NO₃⁻ concentration (0.39 μM). However, the amount of carbohydrates in the bladder was related with the abundance of periphyton and, hence, it is not possible to conclude that carbohydrate production was a strategy of the plant to enhance the capture of prey. Therefore, our findings do not support the carbohydrate mucilage lure speculations.     

Plant lectin can target receptors containing sialic Acid, exemplified by podoplanin, to inhibit transformed cell growth and migration

Cancer is a leading cause of death of men and women worldwide. Tumor cell motility contributes to metastatic invasion that causes the vast majority of cancer deaths. Extracellular receptors modified by α2,3-sialic acids that promote this motility can serve as ideal chemotherapeutic targets. For example, the extracellular domain of the mucin receptor podoplanin (PDPN) is highly O-glycosylated with α2,3-sialic acid linked to galactose. PDPN is activated by endogenous ligands to induce tumor cell motility and metastasis. Dietary lectins that target proteins containing α2,3-sialic acid inhibit tumor cell growth. However, anti-cancer lectins that have been examined thus far target receptors that have not been identified. We report here that a lectin from the seeds of Maackia amurensis (MASL) with affinity for O-linked carbohydrate chains containing sialic acid targets PDPN to inhibit transformed cell growth and motility at nanomolar concentrations. Interestingly, the biological activity of this lectin survives gastrointestinal proteolysis and enters the cardiovascular system to inhibit melanoma cell growth, migration, and tumorigenesis. These studies demonstrate how lectins may be used to help develop dietary agents that target specific receptors to combat malignant cell growth.     

Bicentenariella n. g. (Monogenea: Dactylogyridae) including descriptions of three new species and two new combinations from serranid fishes (Actinopterygii: Serranidae: Anthiinae) in the South American Pacific Ocean

Systematic Parasitology - Bicentenariella n. g. is proposed to accommodate three new species of dactylogyrid monogeneans found on the gills of the threadfin bass Pronotogrammus multifasciatus Gill...