Biophysical restriction of growth area using a monodispersed gold sphere nanobarrier prolongs the mitotic phase in HeLa cells

Homogeneous 83 nm gold nanospheres with a human fibronectin-coated substrate surrounding the cells induce biophysical cues which result in a delay in the mitotic phase of the cell cycle.

Complete Genome of Bacillus subtilis subsp. subtilis KCTC 3135T and Variation in Cell Wall Genes of B. subtilis Strains

The type strain Bacillus subtilis subsp. subtilis KCTC 3135^T was deeply sequenced and annotated, replacing a previous draft genome in this study. The tar and tag genes were involved in synthesizing wall teichoic acids (WTAs), and these genes and their products were previously regarded as the distinguishing difference between B. s. subtilis and B. s. spizizenii. However, a comparative genomic analysis of B. subtilis spp. revealed that both B. s. subtilis and B. s. spizizenii had various types of cell walls. These tar and tag operons were mutually exclusive and the tar genes from B. s. spizizenii were very similar to the genes from non-Bacillus bacteria, unlike the tag genes from B. s. subtilis. The results and previous studies suggest that the tar genes and the tag genes are not inherited after subspecies speciation. The phylogenetic tree based on whole genome sequences showed that each subspecies clearly formed a monophyletic group, while the tree based on tar genes showed that monophyletic groups were formed according to the cell wall type rather than the subspecies. These findings indicate that the tar genes and the presence of ribitol as a cell-wall constituent were not the distinguishing difference between the subspecies of B. subtilis and that the description of subspecies B. s. spizizenii should be updated.

Complete genome of Bacillussubtilis subsp. subtilis KCTC 3135T and variation in cell wall genes of B. subtilis strains

The type strain Bacillus subtilis subsp.subtilis KCTC 3135T was deeply sequenced and annotated, replacing a previous draft genome in this study. The tar and tag genes were involved in synthesizing wall teichoic acids (WTAs), and these genes and their products were previously regarded as the distinguishing difference between B. s. subtilis and B. s. spizizenii. However, a comparative genomic analysis of B. subtilis spp. revealed that both B. s. subtilis and B. s. spizizenii had various types of cell walls. These tar and tag operons were mutually exclusive and the tar genes from B. s. spizizenii were very similar to the genes from non-Bacillus bacteria, unlike the tag genes from B. s. subtilis. The results and previous studies suggests that the tar genes and the tag genes are not inherited after subspecies speciation. The phylogenetic tree based on whole genome sequences showed that each subspecies clearly formed a monophyletic group, while the tree based on tar genes showed that monophyletic groups were formed according to the cell wall type rather than the subspecies. These findings indicate that the tar genes and the presence of ribitol as a cell-wall constituent were not the distinguishing difference between the subspecies of B. subtilis and that the description of subspecies B. s. spizizenii should be updated.

Clinical proteomic analysis of scrub typhus infection

Background

Scrub typhus is an acute and febrile infectious disease caused by the Gram-negative α-proteobacterium Orientia tsutsugamushi from the family Rickettsiaceae that is widely distributed in Northern, Southern and Eastern Asia. In the present study, we analysed the serum proteome of scrub typhus patients to investigate specific clinical protein patterns in an attempt to explain pathophysiology and discover potential biomarkers of infection.

Methods

Serum samples were collected from three patients (before and after treatment with antibiotics) and three healthy subjects. One-dimensional sodium dodecyl sulphate–polyacrylamide gel electrophoresis followed by liquid chromatography-tandem mass spectrometry was performed to identify differentially abundant proteins using quantitative proteomic approaches. Bioinformatic analysis was then performed using Ingenuity Pathway Analysis.

Results

Proteomic analysis identified 236 serum proteins, of which 32 were differentially expressed in normal subjects, naive scrub typhus patients and patients treated with antibiotics. Comparative bioinformatic analysis of the identified proteins revealed up-regulation of proteins involved in immune responses, especially complement system, following infection with O. tsutsugamushi, and normal expression was largely rescued by antibiotic treatment.

Conclusions

This is the first proteomic study of clinical serum samples from scrub typhus patients. Proteomic analysis identified changes in protein expression upon infection with O. tsutsugamushi and following antibiotic treatment. Our results provide valuable information for further investigation of scrub typhus therapy and diagnosis.

Electronic supplementary material

The online version of this article (10.1186/s12014-018-9181-5) contains supplementary material, which is available to authorized users.

Proteomic characterization of the outer membrane vesicle of the halophilic marine bacterium Novosphingobium pentaromativorans US6-1

Novosphingobium pentaromativorans US6-1 is a Gram-negative halophilic marine bacterium able to utilize several polycyclic aromatic hydrocarbons such as phenanthrene, pyrene, and benzo[a]pyrene. In this study, using transmission electron microscopy, we confirmed that N. pentaromativorans US6-1 produces outer membrane vesicles (OMVs). N. pentaromativorans OMVs (hereafter OMV_Novo) are spherical in shape, and the average diameter of OMV_Novo is 25-70 nm. Proteomic analysis revealed that outer membrane proteins and periplasmic proteins of N. pentaromativorans are the major protein components of OMV_Novo. Comparative proteomic analysis with the membrane-associated protein fraction and correlation analysis demonstrated that the outer membrane proteins of OMV_Novo originated from the membrane- associated protein fraction. To the best of our knowledge, this study is the first to characterize OMV purified from halophilic marine bacteria.

Expression of microRNA-34a in Alzheimer's disease brain targets genes linked to synaptic plasticity, energy metabolism, and resting state network activity

Polygenetic risk factors and reduced expression of many genes in late-onset Alzheimer's disease (AD) impedes identification of a target(s) for disease-modifying therapies. We identified a single microRNA, miR-34a that is over expressed in specific brain regions of AD patients as well as in the 3xTg-AD mouse model. Specifically, increased miR-34a expression in the temporal cortex region compared to age matched healthy control correlates with severity of AD pathology. miR-34a over expression in patient's tissue and forced expression in primary neuronal culture correlates with concurrent repression of its target genes involved in synaptic plasticity, oxidative phosphorylation and glycolysis. The repression of oxidative phosphorylation and glycolysis related proteins correlates with reduced ATP production and glycolytic capacity, respectively. We also found that miR-34a overexpressed neurons secrete miR-34a containing exosomes that are taken up by neighboring neurons. Furthermore, miR-34a targets dozens of genes whose expressions are known to be correlated with synchronous activity in resting state functional networks. Our analysis of human genomic sequences from the tentative promoter of miR-34a gene shows the presence of NFκB, STAT1, c-Fos, CREB and p53 response elements. Together, our results raise the possibilities that pathophysiology-induced activation of specific transcription factor may lead to increased expression of miR-34a gene and miR-34a mediated concurrent repression of its target genes in neural networks may result in dysfunction of synaptic plasticity, energy metabolism, and resting state network activity. Thus, our results provide insights into polygenetic AD mechanisms and disclose miR-34a as a potential therapeutic target for AD.

Technical Advances in Intracellular Detection Using Immuno-Gold Particles: Simple Cryofixation with Metal Contact Quick Freezing

The preparation of biological specimens using cryofixation techniques ensures excellent visibility of intracellular structures and preserves the antigenic sites of subcellular molecules. Hence, cryofixation is an effective method of preparing samples for analyses using antibodies conjugated to gold nanoparticles that are designed to detect the localization of specific target molecules within cells. However, cryofixation cannot be utilized easily because it requires expensive equipment and skilled technologists, resulting in a high level of expense for researchers. Here, we describe a simple technical approach to cryofixation that uses metal contact quick freezing followed by a modified freeze substitution technique and immuno-gold labeling electron microscopy. Micrograph images of cells prepared using this modified cryofixation method demonstrated its superiority over chemical fixation for high contrast visualization of the morphologies of cellular components and preservation of antigenicity for immuno-gold labeling. This report provides valuable technical information related to the advancement of metal contact quick freezing techniques, which can be used to visualize biomedical events of interest in an easy, simple, and rapid manner.

A new method for segmentation of FDG PET metabolic tumour volume using the peritumoural halo layer and a 10-step colour scale. A study in patients with papillary thyroid carcinoma

AIM

We observed a layer between tumour activity and background on FDG PET/CT with the 10-step colour scale and the window level set properly. We named the layer peritumoral halo layer (PHL). We performed this study to establish the reliability of metabolic tumor volume (MTV) segmentation using PHL (MTV(PHL)) in patients with papillary thyroid carcinoma.

PATIENTS, METHODS

Of a total of 140 papillary thyroid carcinoma (PTC) patients, 70 (50.0%) had FDG-avid PTC. In these patients, MTV(PHL), MTV segmented according to fixed 50% SUVmax (MTV(50%)), and fixed SUV with 2.5 to 4.0 (MTV(2.5) to MTV(4.0)) were compared with pathologic tumour volume (PTV). The absolute percentage difference between MTV(PHL) and PTV was compared in micropapillary carcinoma (MPTC) and non-micropapillary carcinoma (non-MPTC) subgroups. The % SUVmax and SUV thresholds of MTV(PHL) were compared with tumour SUVmax.

RESULTS

Among the MTVs, MTV(50%) was not correlated with PTV (r = -0.16, p = 0.182) and was not reliable according to the Bland-Altman plot. Although MTV(2.5), MTV(3.0), MTV(3.5), and MTV(4.0) correlated with PTV (r = 0.85, 0.86, 0.87, and 0.87, respectively; p < 0.001), these MTVs were not reliable on Bland-Altman analyses. MTV(PHL) was significantly correlated with PTV (r = 0.80, p < 0.001), and the Bland-Altman plot did not show systemic error. The MTV(PHL) was more accurate in non-MPTC than in MPTC (p < 0.001), and the absolute % difference was smaller as PTV became larger (σ = -0.65, p < 0.001). The MTV(PHL) thresholds had correlations with SUVmax (% SUVmax threshold: σ = -0.87, p < 0.001; SUV threshold: r = 0.88, p < 0.001).

CONCLUSIONS

MTV(PHL) was more reliable than MTV(%SUVmax) or MTV(SUV). The reliability of MTV(PHL) improved with larger PTVs. The threshold of the MTV(PHL) was naturally altered by PHL according to SUVmax.

Differential Protein Expression between Type 1 Diabetic Cataract and Age-Related Cataract Patients

Diabetes has become one of the major diseases affecting human health. Diabetic cataracts (DCs) are considered a common complication in diabetic patients. The present study investigated differences in lens proteomic profiles between DCs and age-related cataracts (ACs) to determine the mechanism underlying the formation of DCs. Intrasurgical samples were collected from eight DC patients and 12 AC patients, and lens proteins were extracted by lysis and separated using two-dimensional gel electrophoresis (2-DE). The electrophoretic bands were analysed using PD-Quest software 8.0.1. Differentially expressed proteins were identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and peptide mass fingerprinting combined with protein database searching. In the 2-DE maps, the DC and AC lens proteins migrated in the region of pH 5-9 with a relative molecular weight (RMW) of 14-97 kDa, whereas the RMW of more abundant crystallin was 20-31 kDa. Approximately three protein spots with differential intensity were detected. Two crystallin proteins (αB and βB1) were identified using MALDI-TOF-MS. Proteomic analysis of the crystalline humour is feasible, and the proteins can be well separated; moreover, differentially expressed lens proteins can be analysed using 2-DE and mass spectrometry to compare DC and AC. The present results indicate that the αB and βB1 crystallins may accelerate the development of DCs. These techniques offer new avenues for mechanistic evaluation and future prevention or therapy of DCs.

Correlative microscopy for 3D structural analysis of dynamic interactions

Cryo-electron tomography (cryoET) allows 3D visualization of cellular structures at molecular resolution in a close-to-physiological state(1). However, direct visualization of individual viral complexes in their host cellular environment with cryoET is challenging(2), due to the infrequent and dynamic nature of viral entry, particularly in the case of HIV-1. While time-lapse live-cell imaging has yielded a great deal of information about many aspects of the life cycle of HIV-1(3-7), the resolution afforded by live-cell microscopy is limited (~200 nm). Our work was aimed at developing a correlation method that permits direct visualization of early events of HIV-1 infection by combining live-cell fluorescent light microscopy, cryo-fluorescent microscopy, and cryoET. In this manner, live-cell and cryo-fluorescent signals can be used to accurately guide the sampling in cryoET. Furthermore, structural information obtained from cryoET can be complemented with the dynamic functional data gained through live-cell imaging of fluorescent labeled target. In this video article, we provide detailed methods and protocols for structural investigation of HIV-1 and host-cell interactions using 3D correlative high-speed live-cell imaging and high-resolution cryoET structural analysis. HeLa cells infected with HIV-1 particles were characterized first by confocal live-cell microscopy, and the region containing the same viral particle was then analyzed by cryo-electron tomography for 3D structural details. The correlation between two sets of imaging data, optical imaging and electron imaging, was achieved using a home-built cryo-fluorescence light microscopy stage. The approach detailed here will be valuable, not only for study of virus-host cell interactions, but also for broader applications in cell biology, such as cell signaling, membrane receptor trafficking, and many other dynamic cellular processes.