Description: Objective Despite widespread use of antibiotics for the treatment of life-threatening infections and for research on the role of commensal microbiota, our understanding of their effects on the host is still very limited. Design Using a popular mouse model of microbiota depletion by a cocktail of antibiotics, we analysed the effects of antibiotics by combining intestinal transcriptome together with metagenomic analysis of the gut microbiota. In order to identify specific microbes and microbial genes that influence the host phenotype in antibiotic-treated mice, we developed and applied analysis of the transkingdom network. Results We found that most antibiotic-induced alterations in the gut can be explained by three factors: depletion of the microbiota; direct effects of antibiotics on host tissues and the effects of remaining antibiotic-resistant microbes. Normal microbiota depletion mostly led to downregulation of different aspects of immunity. The two other factors (antibiotic direct effects on host tissues and antibiotic-resistant microbes) primarily inhibited mitochondrial gene expression and amounts of active mitochondria, increasing epithelial cell death. By reconstructing and analysing the transkingdom network, we discovered that these toxic effects were mediated by virulence/quorum sensing in antibiotic-resistant bacteria, a finding further validated using in vitro experiments. Conclusions In addition to revealing mechanisms of antibiotic-induced alterations, this study also describes a new bioinformatics approach that predicts microbial components that regulate host functions and establishes a comprehensive resource on what, why and how antibiotics affect the gut in a widely used mouse model of microbiota depletion by antibiotics.

Description: In this issue, Paul and colleagues' meta-analysis examines the risk for HBV reactivation with and without antiviral prophylaxis and its effectiveness in adults with solid tumors and chronic or resolved HBV infection. The editorialists discuss the findings and their implications for pretreatment HBV screening and prophylaxis.

Description: Lakes are major depositional systems for which the related depositional processes have long been considered relatively simple. Breaking this statement, this study presents a detailed analysis of deposits in Lake Saint-Jean, the third largest natural lake in Québec. In addition to postglacial deltaic and coastal depositional systems fringing the lake, current-controlled features such as a large subaqueous prograding wedge and three sediment drifts have been identified in its central portion based on two-dimensional (2-D) acoustic high-resolution subbottom profiles. The large subaqueous prograding wedge is a 4-km-long and up to 15-m-thick heterolithic shelf-like construction in the southeastern part of the lake. The three sediment drifts are 0.1–0.5-km-long and 2–5-m-thick mud mounds distributed on the lake floor in the central portion of the lake. Diatom analyses and radiocarbon dating show that the development of these current-controlled features occurred during the lacustrine phase, after the disconnection with the postglacial marine Laflamme Gulf at 8.5 cal. k.y. B.P. Depositional facies show evidence of recurrent bottom-current activity. Related deposits alternate with pelagic sedimentation stages characterized by the settling of mud and biogenic accumulations. We investigated the origin of bottom currents using a numerical simulation (SYMPHONIE, an oceanographic model), with the aim of modeling wind-induced lake-scale water circulation. Simulations suggest that the subaqueous prograding wedge and the three sediment drifts result from wind-induced bottom currents generated by storm events having wind speed greater than 10 m s –1 . Such strong winds are able to significantly affect sedimentation in the central portion of Lake Saint-Jean. The resulting wind-induced sedimentary features were integrated into a refined lacustrine depositional model that summarizes the evolution of a group of water bodies referred to as "wind-driven water bodies." This study applies a new tool for lake strata characterization and highlights the potential difficulty in differentiating them from marine deposits in the geological record.

Description: The multifaceted functions of C/EBPα in normal and malignant haematopoiesis Leukemia 30, 767 (April 2016). doi:10.1038/leu.2015.324 Authors: E Ohlsson, M B Schuster, M Hasemann & B T Porse

Description: Intracellular transport is mediated by molecular motors that bind cargo to be transported along the cytoskeleton. Here, we report, for the first time, that peroxisomes (POs), lipid droplets (LDs), and the endoplasmic reticulum (ER) rely on early endosomes (EEs) for intracellular movement in a fungal model system. We show that POs undergo kinesin-3– and dynein-dependent transport along microtubules. Surprisingly, kinesin-3 does not colocalize with POs. Instead, the motor moves EEs that drag the POs through the cell. PO motility is abolished when EE motility is blocked in various mutants. Most LD and ER motility also depends on EE motility, whereas mitochondria move independently of EEs. Covisualization studies show that EE-mediated ER motility is not required for PO or LD movement, suggesting that the organelles interact with EEs independently. In the absence of EE motility, POs and LDs cluster at the growing tip, whereas ER is partially retracted to subapical regions. Collectively, our results show that moving EEs interact transiently with other organelles, thereby mediating their directed transport and distribution in the cell.

Description: About two thirds of laryngeal cancers originate at the vocal cords. Early-stage detection of malignant vocal fold alterations, including a discrimination of premalignant lesions, represents a major challenge in laryngology as precancerous vocal fold lesions and small carcinomas are difficult to distinguish by means of regular endoscopy only. We report a procedure to discriminate between malignant and precancerous lesions by measuring the characteristics of vocal fold dynamics by means of a computerized analysis of laryngeal high-speed videos. Ten patients with squamous cell T1a carcinoma, ten with precancerous lesions with hyperkeratosis, and ten subjects without laryngeal disease underwent high-speed laryngoscopy yielding 4,000 images per second. By means of wavelet-based phonovibrographic analysis, a set of three clinically meaningful vibratory measures was extracted from the videos comprising a total number of 15,000 video frames. Statistical analysis (ANOVA with post hoc two-sided t tests, P 〈 0.05) revealed that vocal fold dynamics is significantly affected in the presence of precancerous lesions and T1a carcinoma. On the basis of the three measures, a discriminating pattern was extracted using a support vector machine-learning algorithm performing an individual classification in respect to the different clinical groups. By applying a leave-one-out cross-validation strategy, we could show that the proposed measures discriminate with a very high performance between precancerous lesions and T1a carcinoma (sensitivity, 100%; specificity, 100%). Although a large-scale study will be necessary to confirm clinical significance, the set of vibratory measures derived in this study may be applicable to improve the accuracy and reliability of noninvasive diagnostics of vocal fold lesions. Cancer Res; 75(1); 31–39. ©2014 AACR.

Description: Key components of the translational apparatus, i.e. ribosomes, elongation factor EF-Tu and most aminoacyl-tRNA synthetases, are stereoselective and prevent incorporation of d -amino acids ( d -aa) into polypeptides. The rare appearance of d -aa in natural polypeptides arises from post-translational modifications or non-ribosomal synthesis. We introduce an in vitro translation system that enables single incorporation of 17 out of 18 tested d -aa into a polypeptide; incorporation of two or three successive d -aa was also observed in several cases. The system consists of wild-type components and d -aa are introduced via artificially charged, unmodified tRNA Gly that was selected according to the rules of ‘thermodynamic compensation’. The results reveal an unexpected plasticity of the ribosomal peptidyltransferase center and thus shed new light on the mechanism of chiral discrimination during translation. Furthermore, ribosomal incorporation of d -aa into polypeptides may greatly expand the armamentarium of in vitro translation towards the identification of peptides and proteins with new properties and functions.

Description: Essential thrombocythemia (ET) and primary myelofibrosis (PMF) are chronic diseases characterized by clonal hematopoiesis and hyperproliferation of terminally differentiated myeloid cells. The disease is driven by somatic mutations in exon 9 of CALR or exon 10 of MPL or JAK2 -V617F in 〉90% of the cases, whereas the remaining cases are termed "triple negative." We aimed to identify the disease-causing mutations in the triple-negative cases of ET and PMF by applying whole-exome sequencing (WES) on paired tumor and control samples from 8 patients. We found evidence of clonal hematopoiesis in 5 of 8 studied cases based on clonality analysis and presence of somatic genetic aberrations. WES identified somatic mutations in 3 of 8 cases. We did not detect any novel recurrent somatic mutations. In 3 patients with clonal hematopoiesis analyzed by WES, we identified a somatic MPL -S204P, a germline MPL -V285E mutation, and a germline JAK2 -G571S variant. We performed Sanger sequencing of the entire coding region of MPL in 62, and of JAK2 in 49 additional triple-negative cases of ET or PMF. New somatic (T119I, S204F, E230G, Y591D) and 1 germline (R321W) MPL mutation were detected. All of the identified MPL mutations were gain-of-function when analyzed in functional assays. JAK2 variants were identified in 5 of 57 triple-negative cases analyzed by WES and Sanger sequencing combined. We could demonstrate that JAK2 -V625F and JAK2 -F556V are gain-of-function mutations. Our results suggest that triple-negative cases of ET and PMF do not represent a homogenous disease entity. Cases with polyclonal hematopoiesis might represent hereditary disorders.

Description: The effects of fluid shear stress (FSS) on the human syncytiotrophoblast and its biological functions have never been studied. During pregnancy, the syncytiotrophoblast is the main source of placental growth factor (PlGF), a proangiogenic factor involved in the placental angiogenesis and the vascular adaptation to pregnancy. The role of FSS in regulating PlGF expression in syncytiotrophoblasts is unknown. We investigated the impact of FSS on the production and secretion of the PlGF by the human syncytiotrophoblasts in primary cell culture. Laminar and continuous FSS (1 dyn cm−2) was applied to human syncytiotrophoblasts cultured in a parallel-plate flow chambers. Secreted levels of PlGF, sFlt-1 (soluble fms-like tyrosin kinase-1), and prostaglandin E2 were tested by immunologic assay. PlGF levels of mRNA and intracellular protein were examined by RT-PCR and Western blot, respectively. Intracellular cAMP levels were examined by time-resolved fluorescence resonance energy transfer cAMP accumulation assay. Production of cAMP and PlGF secretion was significantly increased in FSS conditions compared with static conditions. Western blot analysis of cell extracts exposed to FSS showed an increased phosphorylation of protein kinase A substrates and cAMP response element-binding protein on serine 133. FSS-induced phosphorylation of cAMP response element-binding protein and upregulation of PlGF were prevented by inhibition of protein kinase A with H89 (3 μmol/L). FSS also triggers intracellular calcium flux, which increases the synthesis and release of prostaglandin E2. The enhanced intracellular cAMP in FSS conditions was blocked by COX1/COX2 (cyclooxygenase) inhibitors, suggesting that the increase in prostaglandin E2 production could activate the cAMP/protein kinase A pathway in an autocrine/paracrine fashion. FSS activates the cAMP/protein kinase A pathway leading to upregulation of PlGF in human syncytiotrophoblast.

Description: Cooperation and conflict in microorganisms is being recognized as an important factor in the organization and function of microbial communities. Many of the cooperative behaviors described in bacteria are governed through a cell–cell signaling process generally termed quorum sensing. Communication and cooperation in diverse microorganisms exhibit predictable trends that behave according to social evolutionary theory, notably that public goods dilemmas produce selective pressures for divergence in social phenotypes including cheating. In this review, we relate the general features of quorum sensing and social adaptation in microorganisms to established evolutionary theory. We then describe physiological and molecular mechanisms that have been shown to stabilize cooperation in microbes, thereby preventing a tragedy of the commons. Continued study of the role of communication and cooperation in microbial ecology and evolution is important to clinical treatment of pathogens, as well as to our fundamental understanding of cooperative selection at all levels of life.