Effects of slope aspect and vegetation types on selected soil properties in a dryland Hirmi watershed and adjacent agro‐ecosystem,northern highlands of Ethiopia

This study aimed to determine the spatial variation of topsoil properties as influenced by slope aspects and vegetation types. Three vegetation types and two slope aspects were considered. Disturbed and undisturbed samples were taken from the top soils. A two‐way analysis of variance was used to test significant mean differences (α = 0.05). Results showed that contents of bulk density, total porosity, organic matter and exchangeable magnesium were significantly different with changes in slope aspect (P < 0.05). Textural classes, organic matter, available phosphorus, carbon‐to‐nitrogen ratio, cation‐exchange capacity, per cent base saturation and exchangeable bases demonstrated significant variation among vegetation types (P < 0.05). The south‐facing aspect and the grass vegetation showed higher bulk density but lower organic matter and total porosity. As a remedy for the identified problems, there is a need to undertake plantation of indigenous trees.     

Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment

Background  

Understanding the design logic of living systems requires the understanding and comparison of proteomes. Proteomes define the commonalities between organisms more precisely than genomic sequences. Because uncertainties remain regarding the accuracy of proteomic data, several issues need to be resolved before comparative proteomics can be fruitful.     

Ensuring the quality and specificity of preregistrations

Researchers face many, often seemingly arbitrary, choices in formulating hypotheses, designing protocols, collecting data, analyzing data, and reporting results. Opportunistic use of “researcher degrees of freedom” aimed at obtaining statistical significance increases the likelihood of obtaining and publishing false-positive results and overestimated effect sizes. Preregistration is a mechanism for reducing such degrees of freedom by specifying designs and analysis plans before observing the research outcomes. The effectiveness of preregistration may depend, in part, on whether the process facilitates sufficiently specific articulation of such plans. In this preregistered study, we compared 2 formats of preregistration available on the OSF: Standard Pre-Data Collection Registration and Prereg Challenge Registration (now called “OSF Preregistration,” http://osf.io/prereg/). The Prereg Challenge format was a “structured” workflow with detailed instructions and an independent review to confirm completeness; the “Standard” format was “unstructured” with minimal direct guidance to give researchers flexibility for what to prespecify. Results of comparing random samples of 53 preregistrations from each format indicate that the “structured” format restricted the opportunistic use of researcher degrees of freedom better (Cliff’s Delta = 0.49) than the “unstructured” format, but neither eliminated all researcher degrees of freedom. We also observed very low concordance among coders about the number of hypotheses (14%), indicating that they are often not clearly stated. We conclude that effective preregistration is challenging, and registration formats that provide effective guidance may improve the quality of research.

Researchers face many, often seemingly arbitrary choices in formulating hypotheses, designing protocols, collecting data, analyzing data, and reporting results. A study of two formats of preregistration available on the OSF reveals that the opportunistic use of researcher degrees of freedom aimed at obtaining statistical significance is restricted by using more extensive preregistration guidelines; however, these guidelines should be further improved.     

Continuum electrostatic analysis of irregular ionization and proton allocation in proteins.

Irregular (nonsigmoidal) ionization behavior of titratable groups in proteins is analyzed theoretically, using a computational algorithm designed to count explicitly for tautomers of titratable groups and different locations of polar hydrogens. On the basis of calculations for different model systems (acid-acid, base-base, acid-base pairs, and cluster of three strongly interacting groups), it is demonstrated that the pK values, extracted from nonsigmoidal titration curves by fitting to a sum of Henderson-Hasselbalch equations, do not describe the ionization equilibrium correctly. The conditions for observation of irregular titration curves are derived analytically for the case of arbitrary couple of interacting ionizable groups. A possible relation between irregularly shaped titration curves and tautomerization is also illustrated. The protonation-deprotonation equilibrium of Asp76 in ribonuclease T1 is shown to be coupled to dipole reorientation of a water molecule bound at the protein-solvent interface. This finding provides a new interpretation of the experimentally observed chemical shift of this residue.     

Roles of helicases in translation initiation: A mechanistic view

The goal of this review is to summarize our current knowledge about the helicases involved in translation initiation and their roles in both general and mRNA-specific translation. The main topics covered are the mechanisms of helicase action, with emphasis on the roles of accessory domains and proteins; the functions performed by helicases in translation initiation; and the interplay between direct and indirect effects of helicases that also function in steps preceding translation initiation. Special attention is given to the dynamics of eIF4A binding and dissociation from eIF4F during mRNA unwinding. It is proposed that DHX29, as well as other helicases and translation initiation factors could also cycle on and off the translation initiation complexes, similar to eIF4A. The evidence in favor of this hypothesis and its possible implications for the mechanisms of translation initiation is discussed. This article is part of a Special Issue entitled: The biology of RNA helicases — Modulation for life.     

Position of eukaryotic translation initiation factor eIF1A on the 40S ribosomal subunit mapped by directed hydroxyl radical probing

The universally conserved eukaryotic initiation factor (eIF), eIF1A, plays multiple roles throughout initiation: it stimulates eIF2/GTP/Met-tRNA_i^Met attachment to 40S ribosomal subunits, scanning, start codon selection and subunit joining. Its bacterial ortholog IF1 consists of an oligonucleotide/oligosaccharide-binding (OB) domain, whereas eIF1A additionally contains a helical subdomain, N-terminal tail (NTT) and C-terminal tail (CTT). The NTT and CTT both enhance ribosomal recruitment of eIF2/GTP/Met-tRNA_i^Met, but have opposite effects on the stringency of start codon selection: the CTT increases, whereas the NTT decreases it. Here, we determined the position of eIF1A on the 40S subunit by directed hydroxyl radical cleavage. eIF1A''s OB domain binds in the A site, similar to IF1, whereas the helical subdomain contacts the head, forming a bridge over the mRNA channel. The NTT and CTT both thread under Met-tRNA_i^Met reaching into the P-site. The NTT threads closer to the mRNA channel. In the proposed model, the NTT does not clash with either mRNA or Met-tRNA_i^Met, consistent with its suggested role in promoting the ‘closed’ conformation of ribosomal complexes upon start codon recognition. In contrast, eIF1A-CTT appears to interfere with the P-site tRNA-head interaction in the ‘closed’ complex and is likely ejected from the P-site upon start codon recognition.