bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-molecule imaging of electroporated dye-labelled CheY in liveEscherichia coli
Authors: Di Paolo Diana , Afanzar Oshri , Armitage Judith P. , Berry Richard M. 
Published: September 2016

For the past two decades, the use of genetically fused fluorescent proteins (FPs) has greatly contributed to the study of chemotactic signalling inEscherichia coliincluding the activation of the response regulator protein CheY and its interaction with the flagellar motor. However, this approach suffers from a number of limitations, both biological and biophysical: for example, not all fusions are fully functional when fused to a bulky FP, which can have a similar molecular weight to its fused counterpart; they may interfere with the native interactions of the protein and the chromophores of FPs have low brightness and photostability and fast photobleaching rates. A recently developed technique for the electroporation of fluorescently labelled proteins in live bacteria has enabled us to bypass these limitations and study thein vivobehaviour of CheY at the single-molecule level. Here we show that purified CheY proteins labelled with organic dyes can be internalized intoE. colicells in controllable concentrations and imaged with video fluorescence microscopy. The use of this approach is illustrated by showing single CheY molecules diffusing within cells and interacting with the sensory clusters and the flagellar motors in real time.This article is part of the themed issue ‘The new bacteriology’.
Life: the first two billion years
Authors: Knoll Andrew H. , Bergmann Kristin D. , Strauss Justin V. 
Published: September 2016

Microfossils, stromatolites, preserved lipids and biologically informative isotopic ratios provide a substantial record of bacterial diversity and biogeochemical cycles in Proterozoic (2500–541 Ma) oceans that can be interpreted, at least broadly, in terms of present-day organisms and metabolic processes. Archean (more than 2500 Ma) sedimentary rocks add at least a billion years to the recorded history of life, with sedimentological and biogeochemical evidence for life at 3500 Ma, and possibly earlier; phylogenetic and functional details, however, are limited. Geochemistry provides a major constraint on early evolution, indicating that the first bacteria were shaped by anoxic environments, with distinct patterns of major and micronutrient availability. Archean rocks appear to record the Earth's first iron age, with reduced Fe as the principal electron donor for photosynthesis, oxidized Fe the most abundant terminal electron acceptor for respiration, and Fe a key cofactor in proteins. With the permanent oxygenation of the atmosphere and surface oceanca2400 Ma, photic zone O2limited the access of photosynthetic bacteria to electron donors other than water, while expanding the inventory of oxidants available for respiration and chemoautotrophy. Thus, halfway through Earth history, the microbial underpinnings of modern marine ecosystems began to take shape.This article is part of the themed issue ‘The new bacteriology’.
CRISPR-Cas: biology, mechanisms and relevance
Authors: Hille Frank , Charpentier Emmanuelle 
Published: September 2016

Prokaryotes have evolved several defence mechanisms to protect themselves from viral predators. Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated proteins (Cas) display a prokaryotic adaptive immune system that memorizes previous infections by integrating short sequences of invading genomes—termed spacers—into the CRISPR locus. The spacers interspaced with repeats are expressed as small guide CRISPR RNAs (crRNAs) that are employed by Cas proteins to target invaders sequence-specifically upon a reoccurring infection. The ability of the minimal CRISPR-Cas9 system to target DNA sequences using programmable RNAs has opened new avenues in genome editing in a broad range of cells and organisms with high potential in therapeutical applications. While numerous scientific studies have shed light on the biochemical processes behind CRISPR-Cas systems, several aspects of the immunity steps, however, still lack sufficient understanding. This review summarizes major discoveries in the CRISPR-Cas field, discusses the role of CRISPR-Cas in prokaryotic immunity and other physiological properties, and describes applications of the system as a DNA editing technology and antimicrobial agent.
This article is part of the themed issue ‘The new bacteriology’.
Old concepts, new molecules and current approaches applied to the bacterial nucleotide signalling field
Authors: Gründling Angelika , Lee Vincent T. 
Published: September 2016

Signalling nucleotides are key molecules that help bacteria to rapidly coordinate cellular pathways and adapt to changes in their environment. During the past 10 years, the nucleotide signalling field has seen much excitement, as several new signalling nucleotides have been discovered in both eukaryotic and bacterial cells. The fields have since advanced quickly, aided by the development of important tools such as the synthesis of modified nucleotides, which, combined with sensitive mass spectrometry methods, allowed for the rapid identification of specific receptor proteins along with other novel genome-wide screening methods. In this review, we describe the principle concepts of nucleotide signalling networks and summarize the recent work that led to the discovery of the novel signalling nucleotides. We also highlight current approaches applied to the research in the field as well as resources and methodological advances aiding in a rapid identification of nucleotide-specific receptor proteins.
This article is part of the themed issue ‘The new bacteriology’.
Streptococcus pneumoniae bacteraemia due to parotitis in a patient with systemic sclerosis and secondary Sjögren’s syndrome
Authors: Yii Irene Yuen Lin , Tan Jamie Bee Xian , Fong Warren Weng Seng 
Published: September 2016

Introduction:
Invasive pneumococcal disease is an uncommon and notifiable disease in Singapore. It is often associated with significant morbidity and mortality. We report a rare case of invasive pneumococcal bacteraemia due to parotitis in a patient with systemic sclerosis and secondary Sjögren’s syndrome. We also present a retrospective review of Streptococcus pneumoniae bacteraemia cases in Singapore General Hospital from January 2011 to April 2016.

Case presentation:
A 59-year-old Malay lady with a history of systemic sclerosis with secondary Sjögren’s syndrome presented with fever and left parotid gland swelling. Clinical examination revealed poor salivary pooling and left parotid swelling without fluctuance. Ultrasound of the left parotid gland confirmed acute parotitis without evidence of abscess or sialolithiasis. Blood cultures were positive for S. pneumoniae. She was diagnosed to have invasive pneumococcal bacteraemia secondary to acute parotitis, and treated with intravenous benzylpenicillin with clearance of bacteraemia after 3 days. Upon discharge, her antibiotics were changed to intravenous ceftriaxone to facilitate outpatient parenteral antibiotic therapy for another 2 weeks. She responded favourably to antibiotics at follow-up, with no complications from the bacteraemia. A review of the microbiological records of the Singapore General Hospital revealed 116 cases of pneumococcal bacteraemia, most (80.3 %) of which were due to pneumonia. None were due to parotitis.

Conclusion:

S. pneumoniae parotitis and subsequent bacteraemia is rare. Prompt recognition of the disease and appropriate use of antibiotics are important. This case highlights that close communication between healthcare workers (microbiologist, rheumatologist and infectious disease specialist) is essential in ensuring good clinical outcomes in patients with a potentially fatal disease.
Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset
Authors: Shirts Michael R. , Klein Christoph , Swails Jason M. , Yin Jian , Gilson Michael K. , Mobley David L. , Case David A. , Zhong Ellen D. 
Published: September 2016

We describe our efforts to prepare common starting structures and models for the SAMPL5 blind prediction challenge. We generated the starting input files and single configuration potential energies for the host-guest in the SAMPL5 blind prediction challenge for the GROMACS, AMBER, LAMMPS, DESMOND and CHARMM molecular simulation programs. All conversions were fully automated from the originally prepared AMBER input files using a combination of the ParmEd and InterMol conversion programs.We find that the energy calculations for all molecular dynamics engines for this molecular set agree to a better than 0.1% relative absolute energy for all energy components, and in most cases an order of magnitude better, when reasonable choices are made for different cutoff parameters. However, there are some surprising sources of statistically significant differences. Most importantly, different choices of Coulomb’s constant between programs are one of the largest sources of discrepancies in energies. We discuss the measures required to get good agreement in the energies for equivalent starting configurations between the simulation programs, and the energy differences that occur when simulations are run with program-specific default simulation parameter values. Finally, we discuss what was required to automate this conversion and comparison.
Brain oscillations and connectivity in autism spectrum disorders (ASD): new approaches to methodology, measurement and modelling
Authors: Kessler K. , Seymour R. A. , Rippon G. 
Published: September 2016

AbstractAlthough atypical social behaviour remains a key characterisation of ASD, the presence of sensory and perceptual abnormalities has been given a more central role in recent classification changes. An understanding of the origins of such aberrations could thus prove a fruitful focus for ASD research. Early neurocognitive models of ASD suggested that the study of high frequency activity in the brain as a measure of cortical connectivity might provide the key to understanding the neural correlates of sensory and perceptual deviations in ASD. As our review shows, the findings from subsequent research have been inconsistent, with a lack of agreement about the nature of any high frequency disturbances in ASD brains. Based on the application of new techniques using more sophisticated measures of brain synchronisation, direction of information flow, and invoking the coupling between high and low frequency bands, we propose a framework which could reconcile apparently conflicting findings in this area and would be consistent both with emerging neurocognitive models of autism and with the heterogeneity of the condition.HighlightsSensory and perceptual aberrations are becoming a core feature of the ASD symptom prolife.Brain oscillations and functional connectivity are consistently affected in ASD.Relationships (coupling) between high and low frequencies are also deficient.Novel framework proposes the ASD brain is marked by local dysregulation and reduced top-down connectivityThe ASD brain’s ability to predict stimuli and events in the environment may be affectedThis may underlie perceptual sensitives and cascade into social processing deficits in ASD
Mechanisms for Stable Bump Activity, Winner-Take-All and Group Selection in Neuronal Spiking Networks
Authors: Chen Yanqing 
Published: September 2016

AbstractA major function of central nervous systems is to discriminate different categories or types of sensory input. Neuronal networks accomplish such tasks by learning different sensory maps at several stages of neural hierarchy, such that different neurons fire selectively to reflect different internal or external patterns and states. The exact mechanisms of such map formation processes in the brain are not totally understood. Here we study the mechanism by which a simple recurrent/reentrant neuronal network accomplish group selection and discrimination to different inputs in order to generate sensory maps. We describe the conditions and mechanism of transition from a rhythmic epileptic state (in which all neurons fire synchronized and indiscriminately to any input) to a winner-take-all state in which only a subset of neurons fire for a specific input. We prove an analytic condition under which a stable bump solution and a soft winner-take-all state can emerge from the local recurrent excitation-inhibition interactions in a three-layer spiking network with distinct excitatory and inhibitory populations, and demonstrate the importance of surround inhibitory connection topology on the stability of dynamic patterns in spiking neural network.
Variational Bayesian parameter estimation techniques for the general linear model
Authors: Starke Ludger , Ostwald Dirk 
Published: September 2016

AbstractVariational Bayes (VB), variational maximum likelihood (VML), restricted maximum likelihood (ReML), and maximum likelihood (ML) are cornerstone parametric statistical estimation techniques in the analysis of functional neuroimaging data. However, the theoretical underpinnings of these model parameter estimation techniques are rarely covered in introductory statistical texts. Because of the widespread practical use of VB, VML, ReML, and ML in the neuroimaging community, we reasoned that. a theoretical treatment of their relationships and their application in a basic modelling scenario may be helpful for both neuroimaging novices and practitioners alike. In this technical study, we thus revisit the conceptual and formal underpinnings of VB, VML, ReML, and ML and provide a detailed account of their mathematical relationships and implementational details. We further apply VB, VML, ReML, and ML to the general linear model (GLM) with non-spherical error covariance as commonly encountered in the first-level analysis of fMRI data. To this end, we explicitly derive the corresponding free energy objective functions and ensuing iterative algorithms. Finally, in the applied part of our study, we evaluate the parameter and model recovery properties of VB, VML, ReML, and ML, first in an exemplary setting and then in the analysis of experimental fMRI data acquired from a single participant under visual stimulation.
ImSig: A resource for the identification and quantification of immune signatures in blood and tissue transcriptomics data
Authors: Nirmal Ajit Johnson , Regan Tim , Shih Barbara Bo-Ju , Hume David Arthur , Sims Andrew Harvey , Freeman Tom Charles 
Published: September 2016

AbstractThe outcome of many diseases is commonly correlated with the immune response at the site of pathology. The ability to monitor the status of the immune system in situ provides a mechanistic understanding of disease progression, a prognostic assessment and a guide for therapeutic intervention. Global transcriptomic data can be deconvoluted to provide an indication of the cell types present and their activation state, but the gene signatures proposed to date are either disease-specific or have been derived from data generated from isolated cell populations. Here we describe an improved set of immune gene signatures,ImSig, derived based on their co-expression in blood and tissue datasets.ImSigincludes validated lists of marker genes for the main immune cell types and a number of core pathways. When used in combination with network analysis,ImSigis an accurate and easy to use approach for monitoring immune phenotypes in transcriptomic data derived from clinical samples.
Scrounging by foragers can resolve the paradox of enrichment
Authors: Toyokawa Wataru 
Published: September 2016

AbstractTheoretical models of predator-prey system predict that sufficient enrichment of prey can generate large amplitude limit cycles, paradoxically causing a high risk of extinction (the paradox of enrichment). While real ecological communities contain many gregarious species whose foraging behaviour should be influenced by socially transmitted information, few theoretical studies have examined the possibility that social foraging might be a resolution of the paradox. I considered a predator population in which individuals play the producer-scrounger foraging game both in a one-prey-one-predator system and a two-prey-one-predator system. I analysed the stability of a coexisting equilibrium point in the former one-prey system and that of non-equilibrium dynamics of the latter two-prey system. The result showed that social foraging can stabilise both systems and thereby resolves the paradox of enrichment when scrounging behaviour is prevalent in predators. This suggests a previously neglected mechanism underlying a powerful effect of group-living animals on sustainability of ecological communities.
An Electrochemistry Study of Cryoelectrolysis in Frozen Physiological Saline
Authors: Manuel Thomas J. , Munnangi Pujita , Rubinsky Boris 
Published: September 2016

AbstractThis is the first quantitative study on the fundamental physical and electrochemical processes that occur during cryoelectrolysis. Cryoelectrolysis is a new minimally invasive tissue ablation surgical technique that combines the processes of electrolysis and solid/liquid phase transformation (freezing). We measured the pH front propagation and the changes in resistance in a tissue simulant made of physiological saline gel with a pH dye as a function of the sample temperature in the high subzero range above the eutectic. Results demonstrate that effective electrolysis can occur in a high subzero freezing milieu and that the propagation of the pH front is only weakly dependent on temperature. These observations are consistent with a mechanism involving ionic movement through the concentrated saline solution channels between ice crystals at subfreezing temperatures above the eutectic. The Joule heating in these microchannel may cause local microscopic melting, the observed weak dependence of pH front propagation on temperature, and the large changes in resistance with time. In addition, we observed that the pH front propagation from the anode is more rapid than from the cathode. The explanation is the electro-osmotic flow from the cathode to the anode. The findings in this paper may be of fundamental value for designing future cryoelectrolytic ablation surgery protocols.
A pyrethroïd-treated bed net increases host attractiveness forAnopheles gambiae s.s.carrying thekdrallele in a dual-choice olfactometer
Authors: Porciani Angélique , Diop Malal , Moiroux Nicolas , Kadoke-Lambi Tatiana , Cohuet Anna , Chandre Fabrice , Dormont Laurent , Pennetier Cédric 
Published: September 2016

AbstractThe use of long lasting insecticide nets (LLINs) treated with pyrethroïd is known for its major contribution in malaria control. However, LLINs are suspected to induce behavioral changes in malaria vectors, which may in turn drastically affect their efficacy againstPlasmodium sp. transmission. In sub Saharan Africa, where malaria imposes the heaviest burden, the main malaria vectors are widely resistant to pyrethroïds, the insecticide family used on LLINs, which also threatens LLIN efficiency. There is therefore a crucial need for deciphering how insecticide-impregnated materials might affect the host-seeking behavior of malaria vectors in regards to insecticide resistance. In this study, we explored the impact of permethrin-impregnated net on the host attractiveness forAnopheles gambiaemosquitoes, either susceptible to insecticides, or carrying the insecticide resistance conferring allelekdr. Groups of female mosquitoes were released in a dual-choice olfactometer and their movements towards an attractive odor source (a rabbit) protected by insecticide-treated (ITN) or untreated nets (UTN) were monitored.Kdrhomozygous mosquitoes, resistant to insecticides, were more attracted by a host behind an ITN than an UTN, while the presence of insecticide on the net did not affect the choice of susceptible mosquitoes. These results suggest that permethrin-impregnated net is detectable by malaria vectors and that thekdrmutation impacts their response to a LLIN protected host. We discuss the implication of these results for malaria vector control.
A statistical framework for mapping risk genes fromde novomutations in whole-genome sequencing studies
Authors: Liu Yuwen , Liang Yanyu , Cicek A. Ercument , Li Zhongshan , Li Jinchen , Muhle Rebecca , Krenzer Martina , Mei Yue , Wang Yan , Knoblauch Nicholas , Morrison Jean , Zhao Siming , Jiang Yi , Geller Evan , Ionita-Laza Iuliana , Wu Jinyu , Xia Kun , Noonan James , Sun Zhong Sheng , He Xin 
Published: September 2016

AbstractAnalysis ofde novomutations (DNMs) from sequencing data of nuclear families has identified risk genes for many complex diseases, including multiple neurodevelopmental and psychiatric disorders. Most of these efforts have focused on mutations in protein-coding sequences. Evidence from genome-wide association studies (GWAS) strongly suggests that variants important to human diseases often lie in non-coding regions. Extending DNM-based approaches to non-coding sequences is, however, challenging because the functional significance of non-coding mutations is difficult to predict. We propose a new statistical framework for analyzing DNMs from whole-genome sequencing (WGS) data. This method, TADA-Annotations (TADA-A), is a major advance of the TADA method we developed earlier for DNM analysis in coding regions. TADA-A is able to incorporate many functional annotations such as conservation and enhancer marks, learn from data which annotations are informative of pathogenic mutations and combine both coding and non-coding mutations at the gene level to detect risk genes. It also supports meta-analysis of multiple DNM studies, while adjusting for study-specific technical effects. We applied TADA-A to WGS data of ∼300 autism family trios across five studies, and discovered several new autism risk genes. The software is freely available for all research uses.
Natural Antimicrobial Edible Coatings for Microbial Safety and Food Quality Enhancement
Authors: Aloui Hajer , Khwaldia Khaoula 
Published: September 2016

AbstractNatural antimicrobial agents have been investigated as alternatives to synthetic ones for ensuring food safety and quality. However, the practical use of these preservatives in the food industry is limited due to their negative impact on the odor and taste of food products, as well as the early loss of functionality due to their rapid diffusion and interaction with food components. The incorporation of natural antimicrobial agents into edible coatings has been investigated to control diffusion of active compounds and maintain their concentrations at a critical level on a food surface. Recently, nanoencapsulating and multilayered/nanolaminate delivery systems have emerged as promising tools to enhance the functionality of edible coatings. This review highlights the potential use of polymeric edible coatings for the incorporation of natural antimicrobial agents and the improvement of their controlled release in food systems. The methods used to assess the antimicrobial activity of encapsulated natural antimicrobial agents and the most recent findings regarding the application of nanoencapsulating and multilayered/nanolaminate delivery systems in food products are also discussed.