A conserved coatomer-related complex containing Sec13 and Seh1 dynamically associates with the vacuole in Saccharomyces cerevisiae

The presence of multiple membrane-bound intracellular compartments is a major feature of eukaryotic cells. Many of the proteins required for formation and maintenance of these compartments share an evolutionary history. Here, we identify the SEA (Seh1-associated) protein complex in yeast that contains the nucleoporin Seh1 and Sec13, the latter subunit of both the nuclear pore complex and the COPII coating complex. The SEA complex also contains Npr2 and Npr3 proteins (upstream regulators of TORC1 kinase) and four previously uncharacterized proteins (Sea1-Sea4). Combined computational and biochemical approaches indicate that the SEA complex proteins possess structural characteristics similar to the membrane coating complexes COPI, COPII, the nuclear pore complex, and, in particular, the related Vps class C vesicle tethering complexes HOPS and CORVET. The SEA complex dynamically associates with the vacuole in vivo. Genetic assays indicate a role for the SEA complex in intracellular trafficking, amino acid biogenesis, and response to nitrogen starvation. These data demonstrate that the SEA complex is an additional member of a family of membrane coating and vesicle tethering assemblies, extending the repertoire of protocoatomer-related complexes.     

An open science pathway for drug marketing authorization—Registered drug approval

Florian Naudet and co-authors propose a pathway involving registered criteria for evaluation and approval of new drugs.

Publisher’s note: This Perspective is one of the two winning Essays of the “Reimagine biomedical research for a healthier future” Essay challenge, launched by the Health Research Alliance in partnership with PLOS. This publication is coordinated with that of the other winning Essay in PLOS Biology. The competition was intended to spark a discussion around the future of biomedical research; publication does not imply endorsement from HRA or PLOS.

     

Effect of Cross-Linking Methods on Structure and Properties of Poly(ε-caprolactone) Stabilized Hydrogels Containing Biopolymers

Different dense and porous biodegradable matrices based on solely atelocollagen, or with different atelocollagen and hyaluronic acid derivative ratios, were obtained by varying feeding formulations, cross-linking reaction parameters, and preparative protocols. The compositions and methods for forming hydrogels through a combination of physical and chemical cross-linking processes are provided. The chemical cross-linking was mainly mediated by a synthetic component, a poly(ε-caprolactone) reactive derivative, aiming the development of new hybrid hydrogels with tailored characteristics by an appropriate use of the advantages offered by the included natural and synthetic components and the selection of the preparative procedure. The structure and morphology of the 3D hybrid materials were comparatively investigated by means of Fourier-transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), X-ray diffraction (XRD), and environmental scanning electron microscopy (ESEM). FTIR and XRD analysis showed no signs of collagen denaturation during the formation of 3D structures. The influence of various factors, such as the chemical composition of the resulted hydrogels and their morphology, on water uptake and water vapor sorption, mechanical behavior, as well as on in vitro degradation characteristics, was systematically investigated. The experimental results point on the advantage offered by the high and modular physicochemical stability of the ternary hydrogels cross-linked by combined approaches. All newly developed materials show no hemolytic effect, which recommends them for potential biomedical applications.     

Exploiting the vitamin B12 pathway to enhance oral drug delivery via polymeric micelles

Vitamin B12 (VB12)-modified dextran-g-polyethyleneoxide cetyl ether (DEX-g-PEO-C16) was synthesized by linking VB12 residues to a DEX-g-PEO-C16 copolymer via a 2,2'-(ethylenedioxy)bis(ethylamine) spacer. The level of VB12 substitution on the DEX-g-PEO-C16 copolymer reached 1.68% (w/w). In aqueous solution, DEX-based copolymers form micelles that can entrap within their hydrophobic core up to 8.5% w/w of cyclosporin A (CsA), a poorly water soluble immunosuppressant. The permeability of Caco-2 cell membranes to CsA incorporated in VB12 modified and unmodified polymeric micelles was monitored in the presence and absence of intrinsic factor (IF). The apical (AP) to basolateral (BL) permeation of CsA through Caco-2 cell monolayers after 24 h of transport was significantly higher (1.8 and 2.3 times in absence and presence of IF, respectively) in the case of CsA loaded in VB12-modified polymeric micelles, compared to CsA in unmodified micelles. The results point to possible improvement in the application of polysaccharide-based polymeric micelles as targeted polymeric drug carriers for the oral delivery of poorly water soluble drugs.     

Fluorescent proteins as proteomic probes

Protein complexes mediate the majority of cellular processes. Knowledge of the localization and composition of such complexes provides key insights into their functions. Although green fluorescent protein (GFP) has been widely applied for in vivo visualization of proteins, it has been relatively little used as a tool for the isolation of protein complexes. Here we describe the use of the standard GFP tag to both visualize proteins in living cells and capture their interactions via a simple immunoaffinity purification procedure. We applied this method to the analysis of a variety of endogenous protein complexes from different eukaryotic cells. We show that efficient isolations can be achieved in 5-60 min. This rapid purification helps preserve protein complexes close to their original state in the cell and minimizes nonspecific interactions. Given the wide use and availability of GFP-tagged protein reagents, the present method should greatly facilitate the elucidation of many cellular processes.     

A survey of biomedical journals to detect editorial bias and nepotistic behavior

Alongside the growing concerns regarding predatory journal growth, other questionable editorial practices have gained visibility recently. Among them, we explored the usefulness of the Percentage of Papers by the Most Prolific author (PPMP) and the Gini index (level of inequality in the distribution of authorship among authors) as tools to identify journals that may show favoritism in accepting articles by specific authors. We examined whether the PPMP, complemented by the Gini index, could be useful for identifying cases of potential editorial bias, using all articles in a sample of 5,468 biomedical journals indexed in the National Library of Medicine. For articles published between 2015 and 2019, the median PPMP was 2.9%, and 5% of journal exhibited a PPMP of 10.6% or more. Among the journals with the highest PPMP or Gini index values, where a few authors were responsible for a disproportionate number of publications, a random sample was manually examined, revealing that the most prolific author was part of the editorial board in 60 cases (61%). The papers by the most prolific authors were more likely to be accepted for publication within 3 weeks of their submission. Results of analysis on a subset of articles, excluding nonresearch articles, were consistent with those of the principal analysis. In most journals, publications are distributed across a large number of authors. Our results reveal a subset of journals where a few authors, often members of the editorial board, were responsible for a disproportionate number of publications. To enhance trust in their practices, journals need to be transparent about their editorial and peer review practices.

Alongside the growing concerns regarding predatory journal growth, other questionable editorial practices have gained visibility recently. This study explores the relationship between hyper-prolific authors and a journal’s editorial team, finding a subset of journals where a few authors, often members of the editorial board, were responsible for a disproportionate number of publications.