A Comparative Study on the Ability of Two Implicit Solvent Lipid Models to Predict Transmembrane Helix Tilt Angles

Free-energy profiles describing the relative orientation of membrane proteins along predefined coordinates can be efficiently calculated by means of umbrella simulations. Such simulations generate reliable orientational distributions but are difficult to converge because of the very long equilibration times of the solvent and the lipid bilayer in explicit representation. Two implicit lipid membrane models are here applied in combination with the umbrella sampling strategy to the simulation of the transmembrane (TM) helical segment from virus protein U (Vpu). The models are used to study both orientation and energetics of this α-helical peptide as a function of hydrophobic mismatch. We observe that increasing the degree of positive hydrophobic mismatch increased the tilt angle of Vpu. These findings agree well with experimental data and as such validate the solvation models used in this study.     

Flow Past a Permeable Stretching/Shrinking Sheet in a Nanofluid Using Two-Phase Model

The steady two-dimensional flow and heat transfer over a stretching/shrinking sheet in a nanofluid is investigated using Buongiorno’s nanofluid model. Different from the previously published papers, in the present study we consider the case when the nanofluid particle fraction on the boundary is passively rather than actively controlled, which make the model more physically realistic. The governing partial differential equations are transformed into nonlinear ordinary differential equations by a similarity transformation, before being solved numerically by a shooting method. The effects of some governing parameters on the fluid flow and heat transfer characteristics are graphically presented and discussed. Dual solutions are found to exist in a certain range of the suction and stretching/shrinking parameters. Results also indicate that both the skin friction coefficient and the local Nusselt number increase with increasing values of the suction parameter.     

Genetic context determines susceptibility to intraocular pressure elevation in a mouse pigmentary glaucoma

Background  

DBA/2J (D2) mice develop an age-related form of glaucoma. Their eyes progressively develop iris pigment dispersion and iris atrophy followed by increased intraocular pressure (IOP) and glaucomatous optic nerve damage. Mutant alleles of the Gpnmb and Tyrp1 genes are necessary for the iris disease, but it is unknown whether alleles of other D2 gene(s) are necessary for the distinct later stages of disease. We initiated a study of congenic strains to further define the genetic requirements and disease mechanisms of the D2 glaucoma.     

Nucleoside diphosphate kinase from human erythrocytes. Structural characterization of the two polypeptide chains responsible for heterogeneity of the hexameric enzyme.

Human erythrocyte nucleoside-diphosphate kinase (NDP kinase) is a hexameric enzyme consisting of two kinds of polypeptide chains, A and B. By random association (A6, A5B...AB5, B6) these polypeptides form isoenzymes differing in their isoelectric point. Chains A and B of NDP kinase were purified by ion-exchange chromatography under denaturing conditions. Upon mixing and renaturation, the isozymic pattern of NDP kinase obtained by conventional methods was restored. Antibodies raised against purified chains showed significant cross-reactivity, both in immunoblot experiments and activity inhibition studies. Sequence determination showed that both chains consisted of 152 amino acid residues corresponding to Mr or 17,143 (chain A) and 17,294 (chain B), respectively. There was high homology between the two sequences (88% identity). The phosphorylation site on the enzyme is located at His-118. Chain A was identical with human Nm23 protein, which has been reported as a potential suppressor protein in tumor metastasis and chain B was identical with Nm23-H2 protein.     

Post‐glacial patterns in vegetation dynamics in Romania: homogenization or differentiation?

Aim This paper examines eight fossil pollen datasets from Romania with the aim of exploring regional and elevational patterns in site similarity throughout the Holocene. In particular, we aim to determine whether there are clear intervals of homogenization/differentiation and to ascertain the potential driving factors. Location Romania. Methods Qualitative (pollen diagrams) and numerical methods including principal components analysis and Bray–Curtis similarity analyses were used. Results We found strong variability in the past vegetation dynamics during the Holocene. Bray–Curtis similarity analyses show large fluctuations in vegetation similarity and distinct periods of homogenization and differentiation throughout the Holocene. The magnitude and length of these periods appear quite variable in time, but the significant ones can be delimited as follows: (1) differentiation between 11,250 and 11,000 cal. yr bp , 10,000 and 9750 cal. yr bp , 6000 and 5750 cal. yr bp , 2500 and 2250 cal. yr bp , and especially over the last 200 years; and (2) homogenization between 9750 and 9500 cal. yr bp , and 2750 and 2500 cal. yr bp , with more stable periods between 9000 and 7750 cal. yr bp , 4750 and 3500 cal. yr bp , and 2000 and 1000 cal. yr bp . Main conclusions First, periods of biotic homogenization that occurred before significant anthropogenic impact on vegetation demonstrate that not all homogenization is a product of anthropogenic change: it can also be driven by natural causes. In fact, recent human impact (over the last 200 years) appears to have resulted in increased regional differentiation and not in homogenization – a result that contradicts most studies based on more modern, short‐term records. Second, both abiotic (climate and disturbance) and biotic factors are likely drivers of intervals of differentiation and homogenization. We suggest that differentiation may be triggered primarily by climate changes and disturbances (mostly natural pre‐2500 cal. yr bp and human‐induced thereafter), whereas homogenization may be driven predominantly by biotic interactions (e.g. immigration and interspecific competition). Third, this long‐term study raises awareness that assessments of pattern in vegetation homogenization/differentiation may depend on the specific time period and length of investigation. Long‐term investigations through multiple generations are likely to yield particularly useful information on the mechanisms and effects of biotic homogenization.     

Nucleoside diphosphate kinase does not directly interact with tubulin nor microtubules.

Nucleoside diphosphate kinase has been shown to play a role in proliferation and development. Microtubules have been evoked as a possible target of NDP kinase action; in particular it was proposed that NDP kinase could regulate the cellular pool of polymerizable GTP-tubulin by direct phosphorylation of tubulin bound GDP. We show that this reaction does not occur in vitro and also that NDP kinase does not bind to microtubules both in the presence and absence of MAPs. Thus, any possible physiological effect of NDP kinase on microtubule dynamics is exerted only by modulating the concentrations of free guanine nucleotides in the vicinity of microtubules.     

Representatives of the genus Triploporella (Dasycladales, calcareous algae) in the Lower Cretaceous limestones of Romania

Recent studies on the Lower Cretaceous deposits located in various areas of the Romanian Carpathians resulted in the identification of several specimens of dasycladalean algae assigned to the genus Triploporella including Triploporella carpatica Bucur, Triploporella cf. praturlonii Barattolo, Triploporella cf. steinmannii Barattolo, Triploporella sp. 1, Triploporella sp. 2, and Triploporella n. sp. This paper provides arguments on their taxonomic assignment, together with discussions on the Triploporella species described in the literature and their paleobiogeographic significance.