The ABCF proteins in Escherichia coli individually cope with 'hard-to-translate' nascent peptide sequences

Organisms possess a wide variety of proteins with diverse amino acid sequences, and their synthesis relies on the ribosome. Empirical observations have led to the misconception that ribosomes are robust protein factories, but in reality, they have several weaknesses. For instance, ribosomes stall during the translation of the proline-rich sequences, but the elongation factor EF-P assists in synthesizing proteins containing the poly-proline sequences. Thus, living organisms have evolved to expand the translation capability of ribosomes through the acquisition of translation elongation factors. In this study, we have revealed that Escherichia coli ATP-Binding Cassette family-F (ABCF) proteins, YheS, YbiT, EttA and Uup, individually cope with various problematic nascent peptide sequences within the exit tunnel. The correspondence between noncanonical translations and ABCFs was YheS for the translational arrest by nascent SecM, YbiT for poly-basic sequence-dependent stalling and poly-acidic sequence-dependent intrinsic ribosome destabilization (IRD), EttA for IRD at the early stage of elongation, and Uup for poly-proline-dependent stalling. Our results suggest that ATP hydrolysis-coupled structural rearrangement and the interdomain linker sequence are pivotal for handling 'hard-to-translate' nascent peptides. Our study highlights a new aspect of ABCF proteins to reduce the potential risks that are encoded within the nascent peptide sequences. Graphical Abstrac

The Japanese Society of Pathology Guidelines on the handling of pathological tissue samples for genomic research: Standard operating procedures based on empirical analyses

Genome research using appropriately collected pathological tissue samples is expected to yield breakthroughs in the development of biomarkers and identification of therapeutic targets for diseases such as cancers. In this connection, the Japanese Society of Pathology (JSP) has developed “The JSP Guidelines on the Handling of Pathological Tissue Samples for Genomic Research” based on an abundance of data from empirical analyses of tissue samples collected and stored under various conditions. Tissue samples should be collected from appropriate sites within surgically resected specimens, without disturbing the features on which pathological diagnosis is based, while avoiding bleeding or necrotic foci. They should be collected as soon as possible after resection: at the latest within about 3 h of storage at 4°C. Preferably, snap‐frozen samples should be stored in liquid nitrogen (about −180°C) until use. When intending to use genomic DNA extracted from formalin‐fixed paraffin‐embedded tissue, 10% neutral buffered formalin should be used. Insufficient fixation and overfixation must both be avoided. We hope that pathologists, clinicians, clinical laboratory technicians and biobank operators will come to master the handling of pathological tissue samples based on the standard operating procedures in these Guidelines to yield results that will assist in the realization of genomic medicine

Comprehensive study of liposome-assisted synthesis of membrane proteins using a reconstituted cell-free translation system

Membrane proteins play pivotal roles in cellular processes and are key targets for drug discovery. However, the reliable synthesis and folding of membrane proteins are significant problems that need to be addressed owing to their extremely high hydrophobic properties, which promote irreversible aggregation in hydrophilic conditions. Previous reports have suggested that protein aggregation could be prevented by including exogenous liposomes in cell-free translation processes. Systematic studies that identify which membrane proteins can be rescued from irreversible aggregation during translation by liposomes would be valuable in terms of understanding the effects of liposomes and developing applications for membrane protein engineering in the context of pharmaceutical science and nanodevice development. Therefore, we performed a comprehensive study to evaluate the effects of liposomes on 85 aggregation-prone membrane proteins from Escherichia coli by using a reconstituted, chemically defined cell-free translation system. Statistical analyses revealed that the presence of liposomes increased the solubility of >90% of the studied membrane proteins, and ultimately improved the yields of the synthesized proteins. Bioinformatics analyses revealed significant correlations between the liposome effect and the physicochemical properties of the membrane proteins

A case of mandibular fracture including coronoid process fracture

The incidence of mandibular fractures is the highest among facial bone fractures. Addi-tionally, most of mandibular fractures occur in the mandibular angle and condylar process. On the other hand, the incidence of fracture of coronoid process is extremely low. We experienced a case of mandibular fractures involving mandibular body, condylar process as well as the coronoid process in a man aged 3₉–years–old who had received strong direct external force to the mandible. Mandibular fractures usually occur in the condylar process and mandibular angle because direct external force is more likely to transmit to these re-gions. Based on the classification of mandibular fractures, the incidence of mandibularfractures involving coronoid process increases with an increased number of fractures lines that means complicated fracture. At the viewpoint of anatomical portion, direct external force dose not transmit to coronoid process; however, it is possible that direct external force may transmit coronoid process in the case of complicated fracture. In this case report, we considered the potential mechanism of fracture of coronoid process by using a three–dimensional finite element model of a human mandible stress distribution analysis

Prebiotic Food Intake May Improve Bone Resorption in Japanese Female Athletes: A Pilot Study

The aim of the present study was to clarify the influence of inulin and lactulose-fortified prebiotic food intakes on bone metabolism turnover among Japanese female athletes. The participants included 29 female athletes aged 18–25 years. They were requested to consume their habitual foods or drinks with one pack of prebiotic food every day for 12 weeks. Dietary intake, training time, body composition, blood sample, and fecal microbiota were assessed during this intervention period. Body composition, total energy intake, and training time of the participants revealed no significant changes during the intervention period. The occupation ratio of Bifidobacterium spp. was significantly increased at 3 and 4 weeks (18.0 ± 8.3% and 17.6 ± 8.5%, respectively) compared to that of pre-intervention (11.7 ± 7.3%) (p = 0.019 and p = 0.035, respectively). The serum TRACP-5b level was significantly decreased at 12 weeks (363 ± 112 mU/dL) compared to that at baseline (430 ± 154 mU/dL) (p = 0.018). These results suggest that the prebiotic food used in this study might have beneficial effects on bone health and gut microbial environment among female athletes. Further studies are warranted to identify the mechanism of the prebiotics–gut–bone axis

SPR Sensing of Bisphenol A Using Molecularly Imprinted Nanoparticles Immobilized on Slab Optical Waveguide with Consecutive Parallel Au and Ag Deposition Bands Coexistent with Bisphenol A-Immobilized Au Nanoparticles

A slab-type optical waveguide (s_OWG)-based microfluidic SPR measurement system for bisphenol A was developed. This s_OWG possesses consecutive parallel gold and silver deposition bands in the line of plasmon flow, allowing two individual SPR signals to be independently obtained as a result of the difference in resonant reflection spectra of these metals. As a molecular recognition element, molecularly imprinted polymer nanoparticles (MIP-Np) were employed and immobilized on the surface of each of the gold and silver deposition bands. The resonant reflection spectra were measured on the MIP-Np-immobilized consecutive parallel gold and silver deposition bands coexistent with BPA-AuNp. The Ag-based SPR spectra showed a red shift (0.7 nm) when free BPA (0.1 mM) was passed over the BPA-AuNp/immobilized MIP-Np complexes formed on the s_OWG, unlike the case for the Au deposition band, while a large excess of BPA induced a blue shift due to the competitive desorption of BPA-AuNp from the immobilized MIP-Np on the s_OWG. By using the proposed detection system, binding events of other small molecules could be monitored in conjunction with the use of MIP-Np and labeled-AuNp

Correction: Novel Lysophospholipid Acyltransferase PLAT1 of Aurantiochytrium limacinum F26-b Responsible for Generation of Palmitate-Docosahexaenoate-Phosphatidylcholine and Phosphatidylethanolamine.

[This corrects the article DOI: 10.1371/journal.pone.0102377.]