Descriptions of the Pain Experience in Adults and Adolescents with Cystic Fibrosis.

Pain Manag Nurs. 2018 Feb 28;:

Authors: Allgood SJ, Kozachik S, Alexander KA, Thaxton A, Vera M, Lechtzin N

Abstract
People living with cystic fibrosis experience pain that is associated with decreased quality of life, poorer health outcomes, and increased mortality. Though pain is highly prevalent as a symptom, it is currently unknown how persons with CF describe their pain experiences or the ways those experiences impact their lives. To explore and describe ways adolescents and adults with CF experience pain. An exploratory descriptive design was implemented to perform interviews with 10 individuals with CF and self-reported moderate to severe pain. The interviews explored their pain experiences within five domains: Pain Characteristics, Activities, Relationships, Work/School Life, and Health Care Team. Transcribed interviews underwent a content analysis with team-based constant comparisons. Individuals with CF identify the disease as being painful; express how pain negatively affects all aspects of their lives, including loss of functionality and productivity; and are able to disclose their pain to those with whom they have relationships. Adolescents feel an emotional toll from the loss of socialization as a result of pain and feel their health care team adequately supports their pain. Adults express a unique emotional pain component to CF and feel stigmatized and unsupported by their health care team when asking for pain management solutions.There are differences in how pain is perceived by adolescents and adults with CF that have otherwise not been reported in the current literature. Further explorations of pain across the lifespan and health care provider attitudes toward pain management are needed to guide the development of effective pain management interventions for those with CF.

PMID: 29501357 [PubMed - as supplied by publisher]

Airway clearance techniques in neuromuscular disorders: A state of the art review.

Respir Med. 2018 Mar;136:98-110

Authors: Chatwin M, Toussaint M, Gonçalves MR, Sheers N, Mellies U, Gonzales-Bermejo J, Sancho J, Fauroux B, Andersen T, Hov B, Nygren-Bonnier M, Lacombe M, Pernet K, Kampelmacher M, Devaux C, Kinnett K, Sheehan D, Rao F, Villanova M, Berlowitz D, Morrow BM

Abstract
This is a unique state of the art review written by a group of 21 international recognized experts in the field that gathered during a meeting organized by the European Neuromuscular Centre (ENMC) in Naarden, March 2017. It systematically reports the entire evidence base for airway clearance techniques (ACTs) in both adults and children with neuromuscular disorders (NMD). We not only report randomised controlled trials, which in other systematic reviews conclude that there is a lack of evidence base to give an opinion, but also include case series and retrospective reviews of practice. For this review, we have classified ACTs as either proximal (cough augmentation) or peripheral (secretion mobilization). The review presents descriptions; standard definitions; the supporting evidence for and limitations of proximal and peripheral ACTs that are used in patients with NMD; as well as providing recommendations for objective measurements of efficacy, specifically for proximal ACTs. This state of the art review also highlights how ACTs may be adapted or modified for specific contexts (e.g. in people with bulbar insufficiency; children and infants) and recommends when and how each technique should be applied.

PMID: 29501255 [PubMed - in process]

Amino acid-level signal-to-noise analysis of incidentally identified variants in genes associated with long QT syndrome during pediatric whole exome sequencing reflects background genetic noise.

Heart Rhythm. 2018 Mar 01;:

Authors: Landstrom AP, Fernandez E, Rosenfeld JA, Yang Y, Dailey-Schwartz AL, Miyake CY, Allen HD, Penny DJ, Kim JJ

Abstract
BACKGROUND: Due to rapid expansion of clinical genetic testing, an increasing number of genetic variants of undetermined significance are being identified in children with unclear diagnostic value. Variants found in genes associated with heritable channelopathies, such as long QT syndrome (LQTS), are particularly difficult to interpret given the risk of sudden cardiac death associated with pathologic mutations.
OBJECTIVE: To determine whether variants in LQTS-associated genes from whole exome sequencing (WES) represent disease-associated biomarkers or background genetic "noise."
METHODS: WES variants from Baylor Genetics Laboratories were obtained for 17 LQTS-associated genes. Rare variants from healthy controls were obtained from the GnomAD database. LQTS case variants were extracted from literature. Amino acid-level mapping and signal-to-noise calculations were conducted. Clinical history and diagnostic studies were analyzed for WES subjects evaluated at our institution.
RESULTS: Variants in LQTS case-associated genes were present in 38.3% of 7,244 WES probands. There was a similar frequency of variants in the WES and healthy cohorts for LQTS1-3 (11.2 and 12.9%, respectively) and LQTS4-17 (27.1 and 38.4%, respectively). WES variants preferentially localized to amino acids altered in control individuals compared to cases. Based on amino acid-level analysis, WES-identified variants are indistinguishable from healthy background variation while LQTS1 and 2 case-identified variants localized to clear pathologic "hot spots." No individuals who underwent clinical evaluation had clinical suspicion for LQTS.
CONCLUSIONS: The prevalence of incidentally identified LQTS-associated variants is ∼38% among WES tests. These variants most likely represent benign healthy background genetic variation rather than disease associated mutations.

PMID: 29501670 [PubMed - as supplied by publisher]

Biochemistry of proinflammatory macrophage activation.

Cell Mol Life Sci. 2018 Mar 03;:

Authors: Nonnenmacher Y, Hiller K

Abstract
In the last decade, metabolism has been recognized as a major determinant of immunological processes. During an inflammatory response, macrophages undergo striking changes in their metabolism. This metabolic reprogramming is governed by a complex interplay between metabolic enzymes and metabolites of different pathways and represents the basis for proper macrophage function. It is now evident that these changes go far beyond the well-known Warburg effect and the perturbation of metabolic targets is being investigated as a means to treat infections and auto-immune diseases. In the present review, we will aim to provide an overview of the metabolic responses during proinflammatory macrophage activation and show how these changes modulate the immune response.

PMID: 29502308 [PubMed - as supplied by publisher]

Comprehensive transcriptome analyses correlated with untargeted metabolome reveal differentially expressed pathways in response to cell wall alterations.

Plant Mol Biol. 2018 Mar 03;:

Authors: Reem NT, Chen HY, Hur M, Zhao X, Wurtele ES, Li X, Li L, Zabotina O

Abstract
KEY MESSAGE: This research provides new insights into plant response to cell wall perturbations through correlation of transcriptome and metabolome datasets obtained from transgenic plants expressing cell wall-modifying enzymes. Plants respond to changes in their cell walls in order to protect themselves from pathogens and other stresses. Cell wall modifications in Arabidopsis thaliana have profound effects on gene expression and defense response, but the cell signaling mechanisms underlying these responses are not well understood. Three transgenic Arabidopsis lines, two with reduced cell wall acetylation (AnAXE and AnRAE) and one with reduced feruloylation (AnFAE), were used in this study to investigate the plant responses to cell wall modifications. RNA-Seq in combination with untargeted metabolome was employed to assess differential gene expression and metabolite abundance. RNA-Seq results were correlated with metabolite abundances to determine the pathways involved in response to cell wall modifications introduced in each line. The resulting pathway enrichments revealed the deacetylation events in AnAXE and AnRAE plants induced similar responses, notably, upregulation of aromatic amino acid biosynthesis and changes in regulation of primary metabolic pathways that supply substrates to specialized metabolism, particularly those related to defense responses. In contrast, genes and metabolites of lipid biosynthetic pathways and peroxidases involved in lignin polymerization were downregulated in AnFAE plants. These results elucidate how primary metabolism responds to extracellular stimuli. Combining the transcriptomics and metabolomics datasets increased the power of pathway prediction, and demonstrated the complexity of pathways involved in cell wall-mediated signaling.

PMID: 29502299 [PubMed - as supplied by publisher]

The role of charge-transfer states in the spectral tuning of antenna complexes of purple bacteria.

Photosynth Res. 2018 Mar 03;:

Authors: Nottoli M, Jurinovich S, Cupellini L, Gardiner AT, Cogdell R, Mennucci B

Abstract
The LH2 antenna complexes of purple bacteria occur, depending on light conditions, in various different spectroscopic forms, with a similar structure but different absorption spectra. The differences are related to point changes in the primary amino acid sequence, but the molecular-level relationship between these changes and the resulting spectrum is still not well understood. We undertook a systematic quantum chemical analysis of all the main factors that contribute to the exciton structure, looking at how the environment modulates site energies and couplings in the B800-850 and B800-820 spectroscopic forms of LH2. A multiscale approach combining quantum chemistry and an atomistic classical embedding has been used where mutual polarization effects between the two parts are taken into account. We find that the loss of hydrogen bonds following amino acid changes can only explain a part of the observed blue-shift in the B850 band. The coupling of excitonic states to charge-transfer states, which is different in the two forms, contributes with a similar amount to the overall blue-shift.

PMID: 29502240 [PubMed - as supplied by publisher]

Suppression of dsRNA response genes and innate immunity following Oct4, Stella, and Nanos2 overexpression in mouse embryonic fibroblasts.

Cytokine. 2018 Mar 01;106:1-11

Authors: Farshchian M, Matin MM, Armant O, Geerts D, Dastpak M, Nakhaei-Rad S, Tajeran M, Jebelli A, Shahriyari M, Bahrami M, Fallah A, Yaghoobi V, Mirahmadi M, Abbaszadegan MR, Bahrami AR

Abstract
The self-renewal capacity of germline derived stem cells (GSCs) makes them an ideal source for research and use in clinics. Despite the presence of active gene network similarities between embryonic stem cells (ESCs) and GSCs, there are unanswered questions regarding the roles of evolutionary conserved genes in GSCs. To determine the reprogramming potential of germ cell- specific genes, we designed a polycistronic gene cassette expressing Stella, Oct4 and Nanos2 in a lentiviral-based vector. Deep transcriptome analysis showed the activation of a set of pluripotency and germ-cell-specific markers and the downregulation of innate immune system. The global shut down of antiviral genes included MHC class I, interferon response genes and dsRNA 2'-5'-oligoadenylate synthetase are critical pathways that has been affected . Individual expression of each factor highlighted suppressive effect of Nanos2 on genes such as Isg15 and Oasl2. Collectively, to our knowledge this is the first report showing that Nanos2 could be considered as an immunosuppressive factor. Furthermore, our results demonstrate suppression of endogenous retrotransposons that harbor immune response but further analysis require to uncover the correlation between transposon suppression and immune response in germ cell development.

PMID: 29501710 [PubMed - as supplied by publisher]

High-throughput quantification of sodium saccharin in foods by ambient flame ionization mass spectrometry.

Talanta. 2018 May 15;182:241-246

Authors: Li Z, Zhang F, Zhao J, Liu X, Chen X, Su Y, Guo Y

Abstract
Ambient flame ionization (AFI) coupled with triple quadrupole tandem mass spectrometry was developed for quantitative analysis of sodium saccharin (SAC) in various food samples. Typically, the micro-flame by the combustion of n-butane provided a heating zone for fast desorption and ionization of analytes in milliseconds. Then high ion abundance of analyte could be produced in a short time, which made AFI-MS possess a very high sensitivity for SAC detection and was particularly appropriate for the quantification in multiple reaction monitor (MRM) mode. Liquid samples were introduced into outer flame using dip-it tips in order to facilitate a rapid and high-throughput analysis. Saccharin-d4 was used as the internal standard to compensate for the variations of the ion intensities. With a minimal sample preparation, a linear range of 4-100 μg/mL was developed with all linear relationships of different matrices (including coke, juice, liquors, sunflower seeds and sweetmeats) greater than 0.992. Recoveries for coke and apple matrices were ranged from 88.4% to 108.9% at the concentration of 5, 20, 80 μg/mL and the limits of detection (LODs) were in the range of 0.12-0.21 μg/mL. Furthermore, the feasibility of this method was exhibited by the quantification analysis of SAC in seventeen real samples. These results indicated that AFI-MS was a valuable strategy for rapid screening detection and precise quantification analysis of SAC in food.

PMID: 29501147 [PubMed - in process]

Funding Opportunity PAR-18-701 from the NIH Guide for Grants and Contracts. This Funding Opportunity Announcement (FOA) invites applications for centers to support transdisciplinary teams of clinical and mental health services researchers, behavioral scientists, social scientists, health information and communications technologists, health systems engineers, decision scientists, and mental health stakeholders (e.g., service users, family members, clinicians, payers) to engage in high-impact studies that will significantly advance clinical practice and generate knowledge that will fuel transformation of mental health care in the United States. Advanced Laboratories for Accelerating the Reach and Impact of Treatments for Youth and Adults with Mental Illness (ALACRITY) Research Centers will support the rapid development, testing, and refinement of novel and integrative approaches for (1) optimizing the effectiveness of therapeutic or preventive interventions for mental disorders within well-defined target populations; (2) organizing and delivering optimized mental health services within real world treatment settings; and (3) continuously improving the quality, impact, and durability of optimized interventions and service delivery within diverse care systems. The ALACRITY Centers program is intended to support research that demonstrates an extraordinary level of synergy across disciplines and has a high potential for increasing the public health impact of existing and emerging mental health interventions and service delivery strategies. The Centers are intended for transdisciplinary projects that could not be achieved using standard research project grant mechanisms. The ALACRITY Centers program is also expected to provide opportunities for graduate students, postdoctoral researchers, and new investigators to participate in transdisciplinary, T2 translational mental health research.

Notice NOT-LM-18-002 from the NIH Guide for Grants and Contracts

Laboratory Diagnosis and Characterization of Fungal Disease in Patients with Cystic Fibrosis (CF): A Survey of Current UK Practice in a Cohort of Clinical Microbiology Laboratories.

Mycopathologia. 2018 Mar 02;:

Authors: Boyle M, Moore JE, Whitehouse JL, Bilton D, Downey DG

Abstract
There is much uncertainty as to how fungal disease is diagnosed and characterized in patients with cystic fibrosis (CF). A 19-question anonymous electronic questionnaire was developed and distributed to ascertain current practice in clinical microbiology laboratories providing a fungal laboratory service to CF centres in the UK. Analyses of responses identified the following: (1) current UK laboratory practice, in general, follows the current guidelines, but the scope and diversity of what is currently being delivered by laboratories far exceeds what is detailed in the guidelines; (2) there is a lack of standardization of fungal tests amongst laboratories, outside of the current guidelines; (3) both the UK CF Trust Laboratory Standards for Processing Microbiological Samples from People with Cystic Fibrosis and the US Cumulative Techniques and Procedures in Clinical Microbiology (Cumitech) Guidelines 43 Cystic Fibrosis Microbiology need to be updated to reflect both new methodological innovations, as well as better knowledge of fungal disease pathophysiology in CF; (4) there is a need for clinical medicine to decide upon a stratification strategy for the provision of new fungal assays that will add value to the physician in the optimal management of CF patients; (5) there is also a need to rationale what assays should be performed at local laboratory level and those which are best served at National Mycology Reference Laboratory level; and (6) further research is required in developing laboratory assays, which will help ascertain the clinical importance of 'old' fungal pathogens, as well as 'emerging' fungal pathogens.

PMID: 29500636 [PubMed - as supplied by publisher]

A Mathematical Model of the Phosphoinositide Pathway.

Sci Rep. 2018 Mar 02;8(1):3904

Authors: Olivença DV, Uliyakina I, Fonseca LL, Amaral MD, Voit EO, Pinto FR

Abstract
Phosphoinositides are signalling lipids that constitute a complex network regulating many cellular processes. We propose a computational model that accounts for all species of phosphoinositides in the plasma membrane of mammalian cells. The model replicates the steady-state of the pathway and most known dynamic phenomena. Sensitivity analysis demonstrates model robustness to alterations in the parameters. Model analysis suggest that the greatest contributor to phosphatidylinositol 4,5-biphosphate (PI(4,5)P2) production is a flux representing the direct transformation of PI into PI(4,5)P2, also responsible for the maintenance of this pool when phosphatidylinositol 4-phosphate (PI(4)P) is decreased. PI(5)P is also shown to be a significant source for PI(4,5)P2 production. The model was validated with siRNA screens that knocked down the expression of enzymes in the pathway. The screen monitored the activity of the epithelium sodium channel (ENaC), which is activated by PI(4,5)P2. While the model may deepen our understanding of other physiological processes involving phosphoinositides, we highlight therapeutic effects of ENaC modulation in Cystic Fibrosis (CF). The model suggests control strategies where the activities of the enzyme phosphoinositide 4-phosphate 5-kinase I (PIP5KI) or the PI4K + PIP5KI + DVL protein complex are decreased and cause an efficacious reduction in PI(4,5)P2 levels while avoiding undesirable alterations in other phosphoinositide pools.

PMID: 29500467 [PubMed - in process]

Ethanolamine phosphotransferase 1 (selenoprotein I) is critical for the neural development and maintenance of plasmalogen in human.

J Lipid Res. 2018 Mar 02;:

Authors: Horibata Y, Elpeleg O, Eran A, Hirabayashi Y, Savitzki D, Tal G, Mandel H, Sugimoto H

Abstract
Ethanolamine phosphotransferase 1 (EPT1), also known as selenoprotein 1 (SELENOI), is an enzyme that transfers phosphoethanolamine from cytidine diphosphate (CDP)-ethanolamine to lipid acceptors to produce ethanolamine glycerophospholipids such as diacyl-linked phosphatidylethanolamine (PE) and ether-linked plasmalogen (plasmenyl-PE). However, to date there has been no analysis of the metabolomic consequence of the mutation of EPT1 on the concentration of ethanolamine glycerophospholipids in mammalian cells. We studied a patient with severe complicated hereditary spastic paraplegia, sensorineural-deafness, blindness, and seizures. Neuroimaging revealed hypomyelination, followed by brain atrophy mainly in the cerebellum and brainstem. Using whole exome sequencing, we identified a novel EPT1 mutation (exon skipping). In vitro EPT activity as well as the rate of biosynthesis of ethanolamine glycerophospholipids was markedly reduced in cultures of the patient's skin fibroblasts. Quantification of phospholipids by LC-MS/MS demonstrated reduced levels of several PE species with polyunsaturated fatty acids, such as 38:6, 38:4, 40:6, 40:5, and 40:4. Notably, most plasmenyl-PE species were significantly decreased in the patient's cells whereas most plasmanyl-choline (plasmanyl-PC) species were increased. Similar findings regarding decreased plasmenyl-PE and increased plasmanyl-PC were obtained using EPT1-KO HeLa cells. Our data demonstrate for the first time the indispensable role of EPT1 in the myelination process and in neurodevelopment, and in the maintenance of normal homeostasis of ether-linked phospholipids in human.

PMID: 29500230 [PubMed - as supplied by publisher]

Compound heterozygous variants in the multiple PDZ domain protein (MPDZ) cause a case of mild non-progressive communicating hydrocephalus.

BMC Med Genet. 2018 Mar 02;19(1):34

Authors: Al-Jezawi NK, Al-Shamsi AM, Suleiman J, Ben-Salem S, John A, Vijayan R, Ali BR, Al-Gazali L

Abstract
BACKGROUND: Congenital hydrocephalus (CH) results from the accumulation of excessive amounts of cerebrospinal fluid (CSF) in the brain, often leading to severe neurological impairments. However, the adverse effects of CH can be reduced if the condition is detected and treated early. Earlier reports demonstrated that some CH cases are caused by mutations in L1CAM gene encoding the neural cell adhesion molecule L1. On the other hand, recent studies have implicated the multiple PDZ domain (MPDZ) gene in some severe forms of CH, inherited in an autosomal recessive pattern.
METHODS: In this study, whole-exome and Sanger sequencing were performed on a 9 months old Emirati child clinically diagnosed by CH. In addition, in silico, cellular, and molecular assays have been conducted to confirm pathogenicity of the identified variants and to establish disease mechanism.
RESULTS: Whole exome sequencing revealed two compound heterozygous novel variants (c.394G > A and c.1744C > G) in the affected child within the MPDZ gene. Segregation analysis revealed that each of the parents is heterozygous for one of the two variants and therefore passed that variant to their child. The outcome of the in silico and bioinformatics analyses came in line with the experimental data, suggesting that the two variants are most likely disease causing.
CONCLUSIONS: The compound heterozygous variants identified in this study are the most likely cause of CH in the affected child. The study further confirms MPDZ as a gene underlying some CH cases.

PMID: 29499638 [PubMed - in process]

Design of Fusion Proteins for Efficient and Soluble Production of Immunogenic Ebola Virus Glycoprotein in Escherichia coli.

Biotechnol J. 2018 Mar 03;:

Authors: Ji Y, Lu Y, Yan Y, Liu X, Su N, Zhang C, Bi S, Xing XH

Abstract
The Ebola hemorrhagic fever caused by Ebola virus is an extremely dangerous disease, and effective therapeutic agents are still lacking. Platforms for the efficient production of vaccines are crucial to ensure quick response against an Ebola virus outbreak. Ebolavirus glycoprotein (EbolaGP) on the virion surface is responsible for membrane binding and virus entry, thus becoming the key target for vaccine development. However, heterologous expression of this protein still faces engineering challenges such as low production levels and insoluble aggregation. Here, we designed and compared various fusion strategies, attaching great importance to the solubility-enhancing effect and tag removal process. It was found that a C-terminal intein-based tag greatly enhanced the solubility of EbolaGP and allowed one-step chromatographic purification of the untagged EbolaGP through thiol-catalyzed self-cleavage. The purified untagged EbolaGP alone or with Freund's adjuvant were highly immunogenic, as confirmed in a mouse model. Consequently, the present study puts forward a new strategy for the efficient and soluble expression of untagged immunogenic EbolaGP. The intein-based protein fusion approach may be of importance for the large-scale production of Ebola virus subunit vaccine.

PMID: 29500882 [PubMed - as supplied by publisher]

Simulating and predicting cellular and in vivo responses of colon cancer to combined treatment with chemotherapy and IAP antagonist Birinapant/TL32711.

Cell Death Differ. 2018 Mar 02;:

Authors: Crawford N, Salvucci M, Hellwig CT, Lincoln FA, Mooney RE, O'Connor CL, Prehn JH, Longley DB, Rehm M

Abstract
Apoptosis resistance contributes to treatment failure in colorectal cancer (CRC). New treatments that reinstate apoptosis competency have potential to improve patient outcome but require predictive biomarkers to target them to responsive patient populations. Inhibitor of apoptosis proteins (IAPs) suppress apoptosis, contributing to drug resistance; IAP antagonists such as TL32711 have therefore been developed. We developed a systems biology approach for predicting response of CRC cells to chemotherapy and TL32711 combinations in vitro and in vivo. CRC cells responded poorly to TL32711 monotherapy in vitro; however, co-treatment with 5-fluorouracil (5-FU) and oxaliplatin enhanced TL32711-induced apoptosis. Notably, cells from genetically identical populations responded highly heterogeneously, with caspases being activated both upstream and downstream of mitochondrial outer membrane permeabilisation (MOMP). These data, combined with quantities of key apoptosis regulators were sufficient to replicate in vitro cell death profiles by mathematical modelling. In vivo, apoptosis protein expression was significantly altered, and mathematical modelling for these conditions predicted higher apoptosis resistance that could nevertheless be overcome by combination of chemotherapy and TL32711. Subsequent experimental observations agreed with these predictions, and the observed effects on tumour growth inhibition correlated robustly with apoptosis competency. We therefore obtained insights into intracellular signal transduction kinetics and their population-based heterogeneities for chemotherapy/TL32711 combinations and provide proof-of-concept that mathematical modelling of apoptosis competency can simulate and predict responsiveness in vivo. Being able to predict response to IAP antagonist-based treatments on the background of cell-to-cell heterogeneities in the future might assist in improving treatment stratification approaches for these emerging apoptosis-targeting agents.

PMID: 29500433 [PubMed - as supplied by publisher]

Next generation sequencing reveals changes of the γδ T cell receptor repertoires in patients with pulmonary tuberculosis.

Sci Rep. 2018 Mar 02;8(1):3956

Authors: Cheng C, Wang B, Gao L, Liu J, Chen X, Huang H, Zhao Z

Abstract
Tuberculosis (TB) is a severe global threat to human health. The immune protection initiated by γδ T cells play an important role in mycobacterial infection. Vaccines for Mycobacterium tuberculosis (Mtb) based on γδ T cells provide a novel approach for TB control. In our previous studies, we found a preponderant complementarity-determining region 3 (CDR3) sequence of the γδ T cell receptor (TCR) in TB patients, and successfully identified a tuberculosis antigen that can effectively activate γδ T cells with a reverse genetic strategy. However, due to the throughput limitation of the method we used, the information we obtained about the γδ TCR repertoire and preponderant CDR3 sequences was limited. In this study, we introduced next generation sequencing (NGS) to study the γδ TCR CDR3 repertoires in TB patients. We found that the CDR3δ tended to be more polyclonal and CDR3γ tended to be longer in TB patients; the γδ T cells expressing CDR3 sequences using a Vγ9-JγP rearrangement expanded significantly during Mtb infection. We also identified new preponderant CDR3 sequences during Mtb infection. This study comprehensively characterized the γδ T cell receptor repertoire changes, and provides useful information for the development of new vaccines and adjuvants against TB.

PMID: 29500378 [PubMed - in process]

Discovery and biosynthesis of the antibiotic bicyclomycin in distant bacterial classes.

Appl Environ Microbiol. 2018 Mar 02;:

Authors: Vior NM, Lacret R, Chandra G, Dorai-Raj S, Trick M, Truman AW

Abstract
Bicyclomycin (BCM) is a clinically promising antibiotic that is biosynthesised by Streptomyces cinnamoneus DSM 41675. BCM is structurally characterized by a core cyclo(L-Ile-L-Leu) 2,5-diketopiperazine (DKP) that is extensively oxidized. Here, we identify the BCM biosynthetic gene cluster, which shows that the core of BCM is biosynthesised by a cyclodipeptide synthase and the oxidative modifications are introduced by five 2-oxoglutarate-dependent dioxygenases and one cytochrome P450 monooxygenase. The discovery of the gene cluster enabled the identification of BCM pathways encoded in the genomes of hundreds of Pseudomonas aeruginosa isolates distributed globally, and heterologous expression of the pathway from P. aeruginosa SCV20265 demonstrated that the product is chemically identical to BCM produced by S. cinnamoneus Overall, putative BCM gene clusters have been found in at least seven genera spanning Actinobacteria and Proteobacteria (Alpha-, Beta- and Gamma-). This represents a rare example of horizontal gene transfer of an intact biosynthetic gene cluster across such distantly related bacteria, and we show that these gene clusters are almost always associated with mobile genetic elements.IMPORTANCE Bicyclomycin is the only natural product antibiotic that selectively inhibits the transcription termination factor Rho. This mechanism of action, combined with its proven biological safety and its activity against clinically relevant Gram-negative bacterial pathogens, makes it a very promising antibiotic candidate. Here, we report the identification of the bicyclomycin biosynthetic gene cluster in the known producing organism Streptomyces cinnamoneus, which will enable the engineered production of new bicyclomycin derivatives. The identification of this gene cluster also led to the discovery of hundreds of bicyclomycin pathways encoded in highly diverse bacteria, including the opportunistic pathogen Pseudomonas aeruginosa This wide distribution of a complex biosynthetic pathway is very unusual, and provides an insight into how a pathway for an antibiotic can be transferred between diverse bacteria.

PMID: 29500259 [PubMed - as supplied by publisher]

Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions.

BMC Syst Biol. 2018 Mar 02;12(1):25

Authors: Kavvas ES, Seif Y, Yurkovich JT, Norsigian C, Poudel S, Greenwald WW, Ghatak S, Palsson BO, Monk JM

Abstract
BACKGROUND: The efficacy of antibiotics against M. tuberculosis has been shown to be influenced by experimental media conditions. Investigations of M. tuberculosis growth in physiological conditions have described an environment that is different from common in vitro media. Thus, elucidating the interplay between available nutrient sources and antibiotic efficacy has clear medical relevance. While genome-scale reconstructions of M. tuberculosis have enabled the ability to interrogate media differences for the past 10 years, recent reconstructions have diverged from each other without standardization. A unified reconstruction of M. tuberculosis H37Rv would elucidate the impact of different nutrient conditions on antibiotic efficacy and provide new insights for therapeutic intervention.
RESULTS: We present a new genome-scale model of M. tuberculosis H37Rv, named iEK1011, that unifies and updates previous M. tuberculosis H37Rv genome-scale reconstructions. We functionally assess iEK1011 against previous models and show that the model increases correct gene essentiality predictions on two different experimental datasets by 6% (53% to 60%) and 18% (60% to 71%), respectively. We compared simulations between in vitro and approximated in vivo media conditions to examine the predictive capabilities of iEK1011. The simulated differences recapitulated literature defined characteristics in the rewiring of TCA metabolism including succinate secretion, gluconeogenesis, and activation of both the glyoxylate shunt and the methylcitrate cycle. To assist efforts to elucidate mechanisms of antibiotic resistance development, we curated 16 metabolic genes related to antimicrobial resistance and approximated evolutionary drivers of resistance. Comparing simulations of these antibiotic resistance features between in vivo and in vitro media highlighted condition-dependent differences that may influence the efficacy of antibiotics.
CONCLUSIONS: iEK1011 provides a computational knowledge base for exploring the impact of different environmental conditions on the metabolic state of M. tuberculosis H37Rv. As more experimental data and knowledge of M. tuberculosis H37Rv become available, a unified and standardized M. tuberculosis model will prove to be a valuable resource to the research community studying the systems biology of M. tuberculosis.

PMID: 29499714 [PubMed - in process]

Ceftriaxone combination therapy versus respiratory fluoroquinolone monotherapy for community-acquired pneumonia: A meta-analysis.

Am J Emerg Med. 2018 Feb 27;:

Authors: Zhang YQ, Zou SL, Zhao H, Zhang MM, Han CL

Abstract
BACKGROUND: The goal of this study was to investigate whether ceftriaxone combination therapy is associated with better clinical outcomes than respiratory fluoroquinolone monotherapy for adults with community-acquired pneumonia (CAP). We conducted a meta-analysis of published studies.
METHODS: Using the PubMed, EMBASE, and Cochrane Library databases, we performed a literature search of available randomized controlled trials (RCTs) published as original articles before September 2017.
RESULTS: Nine RCTs, involving 1520 patients, were included in the meta-analysis. The pooled relative risks (RRs) for the efficacy of ceftriaxone combination therapy versus respiratory fluoroquinolones monotherapy were 0.96 (95% CI: 0.92-1.01), based on clinically evaluable populations, and 0.93 (95% CI: 0.88-0.99) based on intention-to-treat (ITT) populations. No statistically significant differences were observed in microbiological treatment success (pooled RR=0.99, 95% CI: 0.90-1.09), although drug-related adverse events were significantly lower with ceftriaxone combination therapy than with respiratory fluoroquinolones monotherapy (pooled RR=1.27, 95% CI: 1.04-1.55).
CONCLUSIONS: Current evidence showed that the efficacy of ceftriaxone combination therapy was similar to respiratory fluoroquinolone monotherapy for hospitalized CAP patients, and was associated with lower drug-related adverse events.

PMID: 29499898 [PubMed - as supplied by publisher]