bluuebunny/crossref_metadata_2025 huggingface dataset:
Combining Inferred Regulatory and Reconstructed Metabolic Networks Enhances Phenotype Prediction in Yeast
Authors: Wang Zhuo , Danziger Samuel A. , Heavner Benjamin D. , Ma Shuyi , Smith Jennifer J. , Li Song , Herricks Thurston , Simeonidis Evangelos , Baliga Nitin S. , Aitchison John D. , Price Nathan D.
Published: November 2016

Gene regulatory and metabolic network models have been used successfully in many organisms, but inherent differences between them make networks difficult to integrate. Probabilistic Regulation Of Metabolism (PROM) provides a partial solution, but it does not incorporate network inference and underperforms in eukaryotes. We present an Integrated Deduced REgulation And Metabolism (IDREAM) method that combines statistically inferred Environment and Gene Regulatory Influence Network (EGRIN) models with the PROM framework to create enhanced metabolic-regulatory network models. We used IDREAM to predict phenotypes and genetic interactions between transcription factors and genes encoding metabolic activities in the eukaryote,Saccharomyces cerevisiae.IDREAM models contain many fewer interactions than PROM and yet produce significantly more accurate growth predictions. IDREAM consistently outperformed PROM using any of three popular yeast metabolic models and across three experimental growth conditions. Importantly, IDREAM’s enhanced accuracy makes it possible to identify subtle synthetic growth defects. With experimental validation, these novel genetic interactions involving the pyruvate dehydrogenase complex suggested a new role for fatty acid-responsive factor Oaf1 in regulating acetyl-CoA production in glucose grown cells.

Author Summary

The integration of gene regulatory and metabolic network models is an important goal in computational biology, in order to develop methods that can identify the underlying mechanistic links in biological networks and advance metabolic engineering techniques. In this paper, we develop a framework called Integrated Deduced REgulation And Metabolism (IDREAM) that can improve our ability to predict phenotypes of microorganisms, and particularly it can address the challenges in evaluating phenotypic consequence of perturbing transcriptional regulation of metabolism in a eukaryotic cell. We compare the predictive performance of an IDREAMS. cerevisiaemodel with a PROM model using a TRN available from the YEASTRACT database. IDREAM outperforms PROM using any of three popular yeast metabolic models and across three experimental growth conditions, making it possible to identify subtle synthetic growth defects, and a new role for Oaf1 in the regulation of acetyl-CoA biosynthesis.
Ensembl Core Software Resources: storage and programmatic access for DNA sequence and genome annotation
Authors: Ruffier Magali , Kähäri Andreas , Komorowska Monika , Keenan Stephen , Laird Matthew R. , Longden Ian , Proctor Glenn , Steve Searle , Staines Daniel , Taylor Kieron , Vullo Alessandro , Yates Andrew , Zerbino Daniel , Flicek Paul
Published: November 2016

The Ensembl software resources are a stable infrastructure to store, access and manipulate genome assemblies and their functional annotations. The Ensembl “Core” database and Application Programming Interface (API) was our first major piece of software infrastructure and remains at the centre of all of our genome resources. Since its initial design more than fifteen years ago, the number of publicly available genomic, transcriptomic and proteomic datasets has grown enormously, accelerated by continuous advances in DNA sequencing technology. Initially intended to provide annotation for the reference human genome, we have extended our framework to support the genomes of all species as well as richer assembly models. Cross-referenced links to other informatics resources facilitate searching our database with a variety of popular identifiers such as UniProt and RefSeq. Our comprehensive and robust framework storing a large diversity of genome annotations in one location serves as a platform for other groups to generate and maintain their own tailored annotation. Our databases and APIs are publicly available and all of our source code is released with a permissive Apache v2.0 licence athttp://github.com/Ensembl.
Eavesdropping and crosstalk between secreted quorum sensing peptide signals that regulate bacteriocin production inStreptococcus pneumoniae
Authors: Miller Eric L. , Kjos Morten , Abrudan Monica I. , Roberts Ian S. , Veening Jan-Willem , Rozen Daniel E.
Published: November 2016

Quorum sensing (QS), where bacteria secrete and respond to chemical signals to coordinate population-wide behaviors, has revealed that bacteria are highly social. Here, we investigate how diversity in QS signals and receptors can modify social interactions controlled by the QS system regulating bacteriocin secretion inStreptococcus pneumoniae, encoded by theblpoperon (bacteriocin-likepeptide). Analysis of 4 096 pneumococcal genomes detected nineblpQS signals (BlpC) and five QS receptor groups (BlpH). Imperfect concordance between signals and receptors suggested widespread social interactions between cells, specifically eavesdropping (where cells respond to signals that they do not produce) and crosstalk (where cells produce signals that non-clones detect). This was confirmedin vitroby measuring the response of reporter strains containing each of six differentblpQS receptors to cognate and non-cognate peptides. Assays between pneumococcal colonies grown adjacent to one another provided further evidence that crosstalk and eavesdropping occur at endogenous levels of signal secretion. Finally, simulations of QS strains producing bacteriocins revealed that eavesdropping can be evolutionarily beneficial even when the affinity for non-cognate signals is very weak. Our results highlight that social interactions can mediate intraspecific competition among bacteria and reveal that competitive interactions can be modified by polymorphic QS systems.
An annotated draft genome for Radix auricularia (Gastropoda, Mollusca)
Authors: Schell Tilman , Feldmeyer Barbara , Schmidt Hanno , Greshake Bastian , Tills Oliver , Truebano Manuela , Rundle Simon D. , Paule Juraj , Ebersberger Ingo , Pfenninger Markus
Published: November 2016

Molluscs are the second most species-rich phylum in the animal kingdom, yet only eleven genomes of this group have been published so far. Here, we present the draft genome sequence of the pulmonate freshwater snail Radix auricularia. Six whole genome shotgun libraries with different layouts were sequenced. The resulting assembly comprises 4,823 scaffolds with a cumulative length of 910 Mb and an overall read coverage of 72x. The assembly contains 94.6 % of a metazoan core gene collection, indicating an almost complete coverage of the coding fraction. The discrepancy of ~690 Mb compared to the estimated genome size of R. auricularia (1.6 Gb) results from a high repeat content of 70 % mainly comprising DNA transposons. The annotation of 17,338 protein coding genes was supported by the use of publicly-available transcriptome data. This draft will serve as starting point for further genomic and population genetic research in this scientifically important phylum.
Network activity influences the subthreshold and spiking visual responses of pyramidal neurons in a three-layer cortex
Authors: Wright Nathaniel C. , Wessel Ralf
Published: November 2016

A primary goal of systems neuroscience is to understand cortical function, which typically involves studying spontaneous and sensory-evoked cortical activity. Mounting evidence suggests a strong and complex relationship between the ongoing and evoked state. To date, most work in this area has been based on spiking in populations of neurons. While advantageous in many respects, this approach is limited in scope; it records the activities of a minority of neurons, and gives no direct indication of the underlying subthreshold dynamics. Membrane potential recordings can fill these gaps in our understanding, but are difficult to obtainin vivo. Here, we record subthreshold cortical visual responses in theex vivoturtle eye-attached whole-brain preparation, which is ideally-suited to such a study. In the absence of visual stimulation, the network is “synchronous”; neurons display network-mediated transitions between low- and high-conductance membrane potential states. The prevalence of these slow-wave transitions varies across turtles and recording sessions. Visual stimulation evokes similar high-conductance states, which are on average larger and less reliable when the ongoing state is more synchronous. Responses are muted when immediately preceded by large, spontaneous high-conductance events. Evoked spiking is sparse, highly variable across trials, and mediated by concerted synaptic inputs that are in general only very weakly correlated with inputs to nearby neurons. Together, these results highlight the multiplexed influence of the cortical network on the spontaneous and sensory-evoked activity of individual cortical neurons.
Problem‐based learning in internal medicine: virtual patients or paper‐based problems?
Authors: Sobocan Monika , Turk Neja , Dinevski Dejan , Hojs Radovan , Pecovnik Balon Breda
Published: November 2016

Background

Teaching using paper problem‐based learning (p‐PBL) sessions has left some students fatigued with the learning process. Therefore, attempts have been made to replace p‐PBL with digitally enhanced, decision‐making PBL in the form of virtual patients (VP). Student enthusiasm for substituting p‐PBL with VP has not been quantitatively evaluated on the intended educational effects.

Aim

To determine the educational effects of substituting p‐PBL sessions with VP on undergraduate medical students in their internal medicine course.

Methods

We conducted a randomised controlled study on 34 third‐year undergraduate medical students in the academic year 2015–2016. Student performance after an intervention substituting p‐PBL sessions with VP was analysed. The educational outcomes were measured with knowledge exams and the Diagnostic Thinking Inventory.

Results

There was no difference in exam performance between groups (P > 0.833) immediately after the intervention, or in long term. Nor was there a significant difference in improvement of diagnostic thinking between groups (P > 0.935 and P > 0.320).

Conclusions

Our study showed no significant improvement in diagnostic thinking abilities or knowledge exam results with the use of VP. Educators can add VP to sessions to motivate students, but a significant improvement to educational outcome should not be expected.
Direct observation of individual dislocation interaction processes with grain boundaries
Authors: Kondo Shun , Mitsuma Tasuku , Shibata Naoya , Ikuhara Yuichi
Published: November 2016

In situ electron microscopy reveals the dynamic processes of individual dislocation interaction with grain boundaries.
In vivo characterization of distinct modality-specific subsets of somatosensory neurons using GCaMP
Authors: Emery Edward C. , Luiz Ana P. , Sikandar Shafaq , Magnúsdóttir Rán , Dong Xinzhong , Wood John N.
Published: November 2016

In vivo imaging shows that the great majority of somatosensory neurons are modality-specific.
Critical enhancement of thermopower in a chemically tuned polar semimetal MoTe
2
Authors: Sakai Hideaki , Ikeura Koji , Bahramy Mohammad Saeed , Ogawa Naoki , Hashizume Daisuke , Fujioka Jun , Tokura Yoshinori , Ishiwata Shintaro
Published: November 2016

Unusual enhancement of cryogenic thermopower manifests itself around the critical point of polar order in a metal.
Human Oral Buccal Microbiomes Are Associated with Farmworker Status and Azinphos-Methyl Agricultural Pesticide Exposure
Authors: Stanaway Ian B. , Wallace James C. , Shojaie Ali , Griffith William C. , Hong Sungwoo , Wilder Carly S. , Green Foad H. , Tsai Jesse , Knight Misty , Workman Tomomi , Vigoren Eric M. , McLean Jeffrey S. , Thompson Beti , Faustman Elaine M.
Published: November 2016

In a longitudinal agricultural community cohort sampling of 65 adult farmworkers and 52 adult nonfarmworkers, we investigated agricultural pesticide exposure-associated changes in the oral buccal microbiota. We found a seasonally persistent association between the detected blood concentration of the insecticide azinphos-methyl and the taxonomic composition of the buccal swab oral microbiome. Blood and buccal samples were collected concurrently from individual subjects in two seasons, spring/summer 2005 and winter 2006. Mass spectrometry quantified blood concentrations of the organophosphate insecticide azinphos-methyl. Buccal oral microbiome samples were 16S rRNA gene DNA sequenced, assigned to the bacterial taxonomy, and analyzed after “centered-log-ratio” transformation to handle the compositional nature of the proportional abundances of bacteria per sample. Nonparametric analysis of the transformed microbiome data for individuals with and without azinphos-methyl blood detection showed significant perturbations in seven common bacterial taxa (>0.5% of sample mean read depth), including significant reductions in members of the common oral bacterial genus
Streptococcus
. Diversity in centered-log-ratio composition between individuals' microbiomes was also investigated using principal-component analysis (PCA) to reveal two primary PCA clusters of microbiome types. The spring/summer “exposed” microbiome cluster with significantly less bacterial diversity was enriched for farmworkers and contained 27 of the 30 individuals who also had azinphos-methyl agricultural pesticide exposure detected in the blood.

IMPORTANCE
In this study, we show in human subjects that organophosphate pesticide exposure is associated with large-scale significant alterations of the oral buccal microbiota composition, with extinctions of whole taxa suggested in some individuals. The persistence of this association from the spring/summer to the winter also suggests that long-lasting effects on the commensal microbiota have occurred. The important health-related outcomes of these agricultural community individuals' pesticide-associated microbiome perturbations are not understood at this time. Future investigations should index medical and dental records for common and chronic diseases that may be interactively caused by this association between pesticide exposure and microbiome alteration.
Microdiversification of a Pelagic Polynucleobacter Species Is Mainly Driven by Acquisition of Genomic Islands from a Partially Interspecific Gene Pool
Authors: Hoetzinger Matthias , Schmidt Johanna , Jezberová Jitka , Koll Ulrike , Hahn Martin W.
Published: November 2016

Microdiversification of a planktonic freshwater bacterium was studied by comparing 37
Polynucleobacter asymbioticus
strains obtained from three geographically separated sites in the Austrian Alps. Genome comparison of nine strains revealed a core genome of 1.8 Mb, representing 81% of the average genome size. Seventy-five percent of the remaining flexible genome is clustered in genomic islands (GIs). Twenty-four genomic positions could be identified where GIs are potentially located. These positions are occupied strain specifically from a set of 28 GI variants, classified according to similarities in their gene content. One variant, present in 62% of the isolates, encodes a pathway for the degradation of aromatic compounds, and another, found in 78% of the strains, contains an operon for nitrate assimilation. Both variants were shown in ecophysiological tests to be functional, thus providing the potential for microniche partitioning. In addition, detected interspecific horizontal exchange of GIs indicates a large gene pool accessible to
Polynucleobacter
species. In contrast to core genes, GIs are spread more successfully across spatially separated freshwater habitats. The mobility and functional diversity of GIs allow for rapid evolution, which may be a key aspect for the ubiquitous occurrence of
Polynucleobacter
bacteria.

IMPORTANCE
Assessing the ecological relevance of bacterial diversity is a key challenge for current microbial ecology. The polyphasic approach which was applied in this study, including targeted isolation of strains, genome analysis, and ecophysiological tests, is crucial for the linkage of genetic and ecological knowledge. Particularly great importance is attached to the high number of closely related strains which were investigated, represented by genome-wide average nucleotide identities (ANI) larger than 97%. The extent of functional diversification found on this narrow phylogenetic scale is compelling. Moreover, the transfer of metabolically relevant genomic islands between more distant members of the
Polynucleobacter
community provides important insights toward a better understanding of the evolution of these globally abundant freshwater bacteria.
Identification of a New Phosphatase Enzyme Potentially Involved in the Sugar Phosphate Stress Response in Pseudomonas fluorescens
Authors: Maleki Susan , Hrudikova Radka , Zotchev Sergey B. , Ertesvåg Helga
Published: November 2016

The alginate-producing bacterium
Pseudomonas fluorescens
utilizes the Entner-Doudoroff (ED) and pentose phosphate (PP) pathways to metabolize fructose, since the upper part of its Embden-Meyerhof-Parnas pathway is defective. Our previous study indicated that perturbation of the central carbon metabolism by diminishing glucose-6-phosphate dehydrogenase activity could lead to sugar phosphate stress when
P. fluorescens
was cultivated on fructose. In the present study, we demonstrate that PFLU2693, annotated as a haloacid dehalogenase-like enzyme, is a new sugar phosphate phosphatase, now designated Spp, which is able to dephosphorylate a range of phosphate substrates, including glucose 6-phosphate and fructose 6-phosphate,
in vitro
. The effect of
spp
overexpression on growth and alginate production was investigated using both the wild type and several mutant strains. The results obtained suggested that sugar phosphate accumulation caused diminished growth in some of the mutant strains, since this was partially relieved by
spp
overexpression. On the other hand, overexpression of
spp
in fructose-grown alginate-producing strains negatively affected both growth and alginate production. The latter implies that Spp dephosphorylates the sugar phosphates, thus depleting the pool of these important metabolites. Deletion of the
spp
gene did not affect growth of the wild-type strain on fructose, but the gene could not be deleted in the alginate-producing strain. This indicates that Spp is essential for relieving the cells of sugar phosphate stress in
P. fluorescen
s actively producing alginate.

IMPORTANCE
In enteric bacteria, the sugar phosphate phosphatase YigL is known to play an important role in combating stress caused by sugar phosphate accumulation. In this study, we identified a sugar phosphate phosphatase, designated Spp, in
Pseudomonas fluorescens
. Spp utilizes glucose 6-phosphate, fructose 6-phosphate, and ribose 5-phosphate as substrates, and overexpression of the gene had a positive effect on growth in
P. fluorescens
mutants experiencing sugar phosphate stress. The gene was localized downstream of
gnd
and
zwf-2
, which encode enzymes involved in the pentose phosphate and Entner-Doudoroff pathways. Genes encoding Spp homologues were identified in similar genetic contexts in some bacteria belonging to several phylogenetically diverse families, suggesting similar functions.
Zn
2+
-Inducible Expression Platform for Synechococcus sp. Strain PCC 7002 Based on the
smtA
Promoter/Operator and
smtB
Repressor
Authors: Pérez Adam A. , Gajewski John P. , Ferlez Bryan H. , Ludwig Marcus , Baker Carol S. , Golbeck John H. , Bryant Donald A.
Published: November 2016

Synechococcus
sp. strain PCC 7002 has been gaining significance as both a model system for photosynthesis research and for industrial applications. Until recently, the genetic toolbox for this model cyanobacterium was rather limited and relied primarily on tools that only allowed constitutive gene expression. This work describes a two-plasmid, Zn
2+
-inducible expression platform that is coupled with a
zurA
mutation, providing enhanced Zn
2+
uptake. The control elements are based on the metal homeostasis system of a class II metallothionein gene (
smtA
7942
) and its cognate SmtB
7942
repressor from
Synechococcus elongatus
strain PCC 7942. Under optimal induction conditions, yellow fluorescent protein (YFP) levels were about half of those obtained with the strong, constitutive phycocyanin (
cpcBA
6803
) promoter of
Synechocystis
sp. strain PCC 6803. This metal-inducible expression system in
Synechococcus
sp. strain PCC 7002 allowed the titratable gene expression of YFP that was up to 19-fold greater than the background level. This system was utilized successfully to control the expression of the
Drosophila melanogaster
β-carotene 15,15′-dioxygenase, NinaB, which is toxic when constitutively expressed from a strong promoter in
Synechococcus
sp. strain PCC 7002. Together, these properties establish this metal-inducible system as an additional useful tool that is capable of controlling gene expression for applications ranging from basic research to synthetic biology in
Synechococcus
sp. strain PCC 7002.

IMPORTANCE
This is the first metal-responsive expression system in cyanobacteria, to our knowledge, that does not exhibit low sensitivity for induction, which is one of the major hurdles for utilizing this class of genetic tools. In addition, high levels of expression can be generated that approximate those of established constitutive systems, with the added advantage of titratable control. Together, these properties establish this Zn
2+
-inducible system, which is based on the
smtA
7942
operator/promoter and
smtB
7942
repressor, as a versatile gene expression platform that expands the genetic toolbox of
Synechococcus
sp. strain PCC 7002.
Production of 2-Hydroxyisobutyric Acid from Methanol by Methylobacterium extorquens AM1 Expressing (
R
)-3-Hydroxybutyryl Coenzyme A-Isomerizing Enzymes
Authors: Rohde Maria-Teresa , Tischer Sylvi , Harms Hauke , Rohwerder Thore
Published: November 2016

The biotechnological production of the methyl methacrylate precursor 2-hydroxyisobutyric acid (2-HIBA) via bacterial poly-3-hydroxybutyrate (PHB) overflow metabolism requires suitable (
R
)-3-hydroxybutyryl coenzyme A (CoA)-specific coenzyme B
12
-dependent mutases (RCM). Here, we characterized a predicted mutase from
Bacillus massiliosenegalensis
JC6 as a mesophilic RCM closely related to the thermophilic enzyme previously identified in
Kyrpidia tusciae
DSM 2912 (M.-T. Weichler et al., Appl Environ Microbiol 81:4564–4572, 2015,
https://doi.org/10.1128/AEM.00716-15
). Using both RCM variants, 2-HIBA production from methanol was studied in fed-batch bioreactor experiments with recombinant
Methylobacterium extorquens
AM1. After complete nitrogen consumption, the concomitant formation of PHB and 2-HIBA was achieved, indicating that both sets of RCM genes were successfully expressed. However, although identical vector systems and incubation conditions were chosen, the metabolic activity of the variant bearing the RCM genes from strain DSM 2912 was severely inhibited, likely due to the negative effects caused by heterologous expression. In contrast, the biomass yield of the variant expressing the JC6 genes was close to the wild-type performance, and 2-HIBA titers of 2.1 g liter
−1
could be demonstrated. In this case, up to 24% of the substrate channeled into overflow metabolism was converted to the mutase product, and maximal combined 2-HIBA plus PHB yields from methanol of 0.11 g g
−1
were achieved. Reverse transcription-quantitative PCR analysis revealed that metabolic genes, such as methanol dehydrogenase and acetoacetyl-CoA reductase genes, are strongly downregulated after exponential growth, which currently prevents a prolonged overflow phase, thus preventing higher product yields with strain AM1.

IMPORTANCE
In this study, we genetically modified a methylotrophic bacterium in order to channel intermediates of its overflow metabolism to the C
4
carboxylic acid 2-hydroxyisobutyric acid, a precursor of acrylic glass. This has implications for biotechnology, as it shows that reduced C
1
substrates, such as methanol and formic acid, can be alternative feedstocks for producing today's commodities. We found that product titers and yields depend more on host physiology than on the activity of the introduced heterologous function modifying the overflow metabolism. In addition, we show that the fitness of recombinant strains substantially varies when they express orthologous genes from different origins. Further studies are needed to extend the overflow production phase in methylotrophic microorganisms for the implementation of biotechnological processes.
Three-Dimensional Structure of the Ultraoligotrophic Marine Bacterium “Candidatus Pelagibacter ubique”
Authors: Zhao Xiaowei , Schwartz Cindi L. , Pierson Jason , Giovannoni Stephen J. , McIntosh J. Richard , Nicastro Daniela
Published: November 2016

SAR11 bacteria are small, heterotrophic, marine alphaproteobacteria found throughout the oceans. They thrive at the low nutrient concentrations typical of open ocean conditions, although the adaptations required for life under those conditions are not well understood. To illuminate this issue, we used cryo-electron tomography to study “
Candidatus
Pelagibacter ubique” strain HTCC1062, a member of the SAR11 clade. Our results revealed its cellular dimensions and details of its intracellular organization. Frozen-hydrated cells, which were preserved in a life-like state, had an average cell volume (enclosed by the outer membrane) of 0.037 ± 0.011 μm
3
. Strikingly, the periplasmic space occupied ∼20% to 50% of the total cell volume in log-phase cells and ∼50% to 70% in stationary-phase cells. The nucleoid occupied the convex side of the crescent-shaped cells and the ribosomes predominantly occupied the concave side, at a relatively high concentration of 10,000 to 12,000 ribosomes/μm
3
. Outer membrane pore complexes, likely composed of PilQ, were frequently observed in both log-phase and stationary-phase cells. Long filaments, most likely type IV pili, were found on dividing cells. The physical dimensions, intracellular organization, and morphological changes throughout the life cycle of “
Ca.
Pelagibacter ubique” provide structural insights into the functional adaptions of these oligotrophic ultramicrobacteria to their habitat.

IMPORTANCE
Bacterioplankton of the SAR11 clade (
Pelagibacterales
) are of interest because of their global biogeochemical significance and because they appear to have been molded by unusual evolutionary circumstances that favor simplicity and efficiency. They have adapted to an ecosystem in which nutrient concentrations are near the extreme limits at which transport systems can function adequately, and they have evolved streamlined genomes to execute only functions essential for life. However, little is known about the actual size limitations and cellular features of living oligotrophic ultramicrobacteria. In this study, we have used cryo-electron tomography to obtain accurate physical information about the cellular architecture of “
Candidatus
Pelagibacter ubique,” the first cultivated member of the SAR11 clade. These results provide foundational information for answering questions about the cell architecture and functions of these ultrasmall oligotrophic bacteria.
Development of a High-Efficiency Transformation Method and Implementation of Rational Metabolic Engineering for the Industrial Butanol Hyperproducer Clostridium saccharoperbutylacetonicum Strain N1-4
Authors: Herman Nicolaus A. , Li Jeffrey , Bedi Ripika , Turchi Barbara , Liu Xiaoji , Miller Michael J. , Zhang Wenjun
Published: November 2016

While a majority of academic studies concerning acetone, butanol, and ethanol (ABE) production by
Clostridium
have focused on
Clostridium acetobutylicum
, other members of this genus have proven to be effective industrial workhorses despite the inability to perform genetic manipulations on many of these strains. To further improve the industrial performance of these strains in areas such as substrate usage, solvent production, and end product versatility, transformation methods and genetic tools are needed to overcome the genetic intractability displayed by these species. In this study, we present the development of a high-efficiency transformation method for the industrial butanol hyperproducer
Clostridium saccharoperbutylacetonicum
strain N1-4 (HMT) ATCC 27021. Following initial failures, we found that the key to creating a successful transformation method was the identification of three distinct colony morphologies (types S, R, and I), which displayed significant differences in transformability. Working with the readily transformable type I cells (transformation efficiency, 1.1 × 10
6
CFU/μg DNA), we performed targeted gene deletions in
C. saccharoperbutylacetonicum
N1-4 using a homologous recombination-mediated allelic exchange method. Using plasmid-based gene overexpression and targeted knockouts of key genes in the native acetone-butanol-ethanol (ABE) metabolic pathway, we successfully implemented rational metabolic engineering strategies, yielding in the best case an engineered strain (
Clostridium saccharoperbutylacetonicum
strain N1-4/pWIS13) displaying an 18% increase in butanol titers and 30% increase in total ABE titer (0.35 g ABE/g sucrose) in batch fermentations. Additionally, two engineered strains overexpressing aldehyde/alcohol dehydrogenases (encoded by
adh11
and
adh5
) displayed 8.5- and 11.8-fold increases (respectively) in batch ethanol production.

IMPORTANCE
This paper presents the first steps toward advanced genetic engineering of the industrial butanol producer
Clostridium saccharoperbutylacetonicum
strain N1-4 (HMT). In addition to providing an efficient method for introducing foreign DNA into this species, we demonstrate successful rational engineering for increasing solvent production. Examples of future applications of this work include metabolic engineering for improving desirable industrial traits of this species and heterologous gene expression for expanding the end product profile to include high-value fuels and chemicals.
Efficiency and productivity measurement of rural township hospitals in China: a bootstrapping data envelopment analysis
Authors: Cheng Zhaohui , Cai Miao , Tao Hongbing , He Zhifei , Lin Xiaojun , Lin Haifeng , Zuo Yuling
Published: November 2016

Objective

Township hospitals (THs) are important components of the three-tier rural healthcare system of China. However, the efficiency and productivity of THs have been questioned since the healthcare reform was implemented in 2009. The objective of this study is to analyse the efficiency and productivity changes in THs before and after the reform process.

Setting and participants

A total of 48 sample THs were selected from the Xiaogan Prefecture in Hubei Province from 2008 to 2014.

Outcome measures

First, bootstrapping data envelopment analysis (DEA) was performed to estimate the technical efficiency (TE), pure technical efficiency (PTE) and scale efficiency (SE) of the sample THs during the period. Second, the bootstrapping Malmquist productivity index was used to calculate the productivity changes over time.

Results

The average TE, PTE and SE of the sample THs over the 7-year period were 0.5147, 0.6373 and 0.7080, respectively. The average TE and PTE increased from 2008 to 2012 but declined considerably after 2012. In general, the sample THs experienced a negative shift in productivity from 2008 to 2014. The negative change was 2.14%, which was attributed to a 23.89% decrease in technological changes (TC). The sample THs experienced a positive productivity shift from 2008 to 2012 but experienced deterioration from 2012 to 2014.

Conclusions

There was considerable space for TE improvement in the sample THs since the average TE was relatively low. From 2008 to 2014, the sample THs experienced a decrease in productivity, and the adverse alteration in TC should be emphasised. In the context of healthcare reform, the factors that influence TE and productivity of THs are complex. Results suggest that numerous quantitative and qualitative studies are necessary to explore the reasons for the changes in TE and productivity.
Feasibility study and pilot cluster-randomised controlled trial of the GoActive intervention aiming to promote physical activity among adolescents: outcomes and lessons learnt
Authors: Corder Kirsten , Brown Helen E , Schiff Annie , van Sluijs Esther M F
Published: November 2016

Objectives

Assess the feasibility of implementing the GoActive intervention in secondary schools, to identify improvements, test study procedures, determine preliminary effectiveness to increase moderate-to-vigorous physical activity (MVPA), and inform power calculations to establish programme effectiveness.

Setting

Feasibility study (1 school) and pilot cluster-randomised controlled trial (CRCT; 2 intervention; 1 control school(s)).

Participants

460 participants (46.6% female; 13.2 (0.4) years old).

Interventions

8-week intervention (2013) involved: classes choosing weekly activities encouraged by mentors (older adolescents) and in-class peer leaders. Students gain points for trying activities which are entered into an intramural competition.

Primary and secondary outcome measures

Planned quantitative (questionnaire) and qualitative (focus groups) process evaluation addressed enjoyment, confidence, participation, suggested improvements. Outcomes were assessed at baseline and follow-up (week 8) in pilot CRCT and included accelerometer-assessed MVPA; adolescent-reported activity type, well-being, peer support, shyness, sociability. Analysis of covariance was used to assess preliminary effectiveness as change in MVPA adjusted for baseline.

Results

All year 9 students in intervention schools were exposed to the intervention; over all schools 77% of eligible students were measured. 71% boys and 74% girls found GoActive ‘fun’; 38% boys and 32% girls said it increased confidence, and 64% boys and 59% girls said they would continue with a GoActive activity. Suggested improvements included more mentorship; improved training; streamlined points recording. Pilot results indicated potential effectiveness ((adjusted mean difference (95% CI) p value; MVPA mins; 5.1 (1.1 to 9.2) p=0.014)) and suggest recruitment of 16 schools (2400 adolescents) for a full trial. Compared with control, intervention students reported greater peer support 0.5 (0.1 to 0.9) p=0.03, well-being 1.8 (0.1 to 3.4) p=0.04 but no difference in shyness/sociability. Participation in activity types approached significance (intervention group 2.3 (−0.2 to 4.7) p=0.07 more activity types).

Conclusions

Results suggest feasibility and indicate potential effectiveness of GoActive to increase MVPA and support a fully powered evaluation of effectiveness and cost-effectiveness. Process evaluation data were used to refine GoActive prior to a full trial.

Trial registration number

ISRCTN31583496; pre-results.
Assessment of cardiac resynchronisation therapy in patients with wide QRS and non-specific intraventricular conduction delay: rationale and design of the multicentre randomised NICD-CRT study
Authors: Eschalier Romain , Ploux Sylvain , Pereira Bruno , Clémenty Nicolas , Da Costa Antoine , Defaye Pascal , Garrigue Stéphane , Gourraud Jean-Baptiste , Gras Daniel , Guy-Moyat Benoît , Leclercq Christophe , Mondoly Pierre , Bordachar Pierre
Published: November 2016

Introduction

Cardiac resynchronisation therapy (CRT) was initially developed to treat patients with left bundle branch block (LBBB). However, many patients with heart failure have a widened QRS but neither left-BBB nor right-BBB; this is called non-specific intraventricular conduction delay (NICD). It is unclear whether CRT is effective in this subgroup of patients.

Methods and analysis

The NICD-CRT study is a prospective, double-blind, randomised (1:1), parallel-arm, multicentre trial comparing the effects of CRT in patients with heart failure, a reduced left ventricular ejection fraction (LVEF <35%) and NICD, who have been implanted with a device (CRT-pacemaker or CRT-defibrillator) that has or has not been activated. Enrolment began on 15 July 2015 and should finish within 3 years; 40 patients have already been randomised and 11 centres have agreed to participate. The primary end point is the comparison of the proportion of patients improved, unchanged or worsened over the subsequent 12 months. 100 patients per group are required to demonstrate a difference between groups with a statistical power of 90%, a type I error of 0.05% (two-sided) and a loss to follow-up of 10%. This trial will add substantially to the modest amount of existing data on CRT in patients with NICD and should reduce uncertainty for guidelines and clinical practice when added to the pool of current information.

Ethics and dissemination

Local ethics committee authorisations have been obtained since May 2015. We will publish findings from this study in a peer-reviewed scientific journal and present results at national and international conferences.

Trial registration number

NCT02454439; pre-results.
Framing of research question using the PICOT format in randomised controlled trials of venous ulcer disease: a protocol for a systematic survey of the literature
Authors: Abbade Luciana P F , Wang Mei , Sriganesh Kamath , Mbuagbaw Lawrence , Thabane Lehana
Published: November 2016

Introduction

Although venous ulcers have a great social and economic impact, there is a lack of evidence from randomised controlled trials (RCTs) to support appropriate management for this disease. Framing the research question using the Population; Intervention; Comparator; Outcome; Time frame (PICOT) format in RCTs can improve the quality of the research design.

Objectives

To evaluate how the PICOT format is used to frame a research question in reports of RCTs of venous ulcer disease and to determine the factors associated with better adherence to the PICOT format in framing the research question.

Methods and analyses

We will conduct a systematic survey of RCTs on venous ulcers published in the National Institute of Health, PubMed database between January 2009 and May 2016. We will include all RCTs addressing therapeutic intervention for venous ulcer disease involving human subjects, and published in the English language. The selection process will be carried out in duplicate by two independent investigators. First, titles and abstracts will be screened, then full-text articles. We will examine whether the five elements of the PICOT format are used in formulating the research question and give a score between 0 and 5. The primary outcome will be the proportion of studies that have adequately reported all five PICOT elements.

Dissemination

This will be the first survey to assess how the PICOT format is used to frame research questions on the management of venous ulcers in reports of RCTs. On completion, this review will be submitted to a peer-reviewed biomedical journal for publication and the findings will also be presented at scientific conferences.
Inter-rater reliability of the Shoulder Symptom Modification Procedure in people with shoulder pain
Authors: Lewis Jeremy S , McCreesh Karen , Barratt Eva , Hegedus Eric J , Sim Julius
Published: November 2016

Background

Musculoskeletal conditions involving the shoulder are common and, because of the importance of the upper limb and hand in daily function, symptoms in this region are commonly associated with functional impairment in athletic and non-athletic populations. Deriving a definitive diagnosis as to the cause of shoulder symptoms is fraught with difficulty. Limitations have been recognised for imaging and for orthopaedic special tests. 1 solution is to partially base management on the response to tests aimed at reducing the severity of the patient's perception of symptoms. 1 (of many) such tests is the Shoulder Symptom Modification Procedure (SSMP). The reliability of this procedure is unknown.

Methods

37 clinician participants independently watched the videos of 11 patient participants undergoing the SSMP and recorded each patient's response as improved (partially or completely), no change or worse. Inter-rater reliability was assessed by Krippendorff's α, which ranges from 0 to 1.

Results

Krippendorff's α was found to range from 0.762 to 1.000, indicating moderate to substantial reliability. In addition, short (3-hour) and longer (1-day) durations of training were associated with similar levels of reliability across the techniques.

Conclusions

Deriving a definitive structural diagnosis for a person presenting with a musculoskeletal condition involving the shoulder is difficult. The findings of the present study suggest that the SSMP demonstrates a high level of reliability. More research is needed to better understand the relevance of such procedures.

Trial registration number

ISRCTN95412360.
Single-nucleotide polymorphism array (SNP-A) improves the identification of chromosomal abnormalities by metaphase cytogenetics in myelodysplastic syndrome
Authors: da Silva Fernanda Borges , Machado-Neto João Agostinho , Bertini Virginia Helena Leira Lipoli , Velloso Elvira Deolinda Rodrigues Pereira , Ratis Cristina Alonso , Calado Rodrigo T , Simões Belinda Pinto , Rego Eduardo Magalhães , Traina Fabiola
Published: November 2016

Aims

The myelodysplastic syndromes (MDS) are a heterogeneous group of clonal haematopoietic stem cell disorders characterised by inefficient haematopoiesis and risk of progression to acute myeloid leukaemia. Metaphase cytogenetics is an extremely valuable clinical tool in the management of haematological malignancies. However, metaphase cytogenetics requires cellular proliferation, its sensitivity and resolution depends on the proportion of clonal cells in the sample and size of the lesion, respectively. Single-nucleotide polymorphism array (SNP-A) does not depend on the presence of dividing cells, is able to detect copy number variations with a high resolution and to detect copy number neutral loss of heterozygosity or uniparental disomy (UPD). The aim of this study was to illustrate that the use of SNP-A can cover cryptic chromosomal lesions not identified by metaphase cytogenetics in patients with MDS.

Methods

Metaphase cytogenetics was performed on bone marrow aspirate using standard methods. Genomic DNA from total bone marrow cells were submitted to SNP-A using Affymetrix Genome-Wide Human SNP CytoScan HD.

Results

In our cohort of 15 patients with a diagnosis of MDS and related diseases, chromosomal abnormalities were found in 47% of the cases by SNP-A and in 33% by metaphase cytogenetics. SNP-A detected all lesions identified by metaphase cytogenetics, except a balanced translocation and a marker chromosome. Notably, SNP-A detected a total of 30 new lesions: 1 (3%) gain, 17 (57%) losses and 12 (40%) UPDs in 5 patients with MDS.

Conclusions

SNP-A may complement metaphase cytogenetics to improve the detection of chromosomal abnormalities in myeloid neoplasms.
Treatment dilemmas in Guillain-Barré syndrome
Authors: Verboon Christine , van Doorn Pieter A , Jacobs Bart C
Published: November 2016

Guillain-Barré syndrome (GBS) is an acute polyradiculoneuropathy with a highly variable clinical course and outcome. Intravenous immunoglobulin (IVIg) and plasma exchange are proven effective treatments, but the efficacy has been demonstrated mainly on motor improvement in adults with a typical and severe form of GBS. In clinical practice, treatment dilemmas may occur in patients with a relatively mild presentation, variant forms of GBS, or when the onset of weakness was more than 2 weeks ago. Other therapeutic dilemmas may arise in patients who do not improve or even progress after initial treatment. We provide an overview of the current literature about therapeutic options in these situations, and additionally give our personal view that may serve as a basis for therapeutic decision-making.
Treatment of posterior circulation non-saccular aneurysms with flow diverters: a single-center experience and review of 56 patients
Authors: Bhogal P , Pérez M Aguilar , Ganslandt O , Bäzner H , Henkes H , Fischer S
Published: November 2016

Background and purpose

Non-saccular aneurysms of the posterior fossa are an uncommon pathology with no clear treatment strategy. The use of flow-diverting stents (FDS) has had mixed results. We sought to evaluate our experience of FDS for the treatment of this pathology.

Methods

We retrospectively reviewed our database of prospectively collected information for all patients treated only with flow diversion for an unruptured non-saccular aneurysm of the posterior circulation between February 2009 and April 2016. The aneurysms were classified as dolichoectasia, fusiform or transitional, and imaging characteristics including maximal diameter, disease vessel segment, MRI features (intra-aneurysmal thrombus, T1 hyperintensity in the aneurysmal wall, infarctions in the territory of the posterior circulation, and mass effect) were recorded alongside clinical and follow-up data.

Results

We identified 56 patients (45 men) with 58 aneurysms. The average age of the patients was 63.5 years. Twenty-two patients were symptomatic from the aneurysms at presentation. The majority of the lesions were vertebrobasilar in location (44.8%) with isolated vertebral lesions representing 29.3% of aneurysms. Transitional aneurysms were the most common (48.2%). The mean maximal diameter of the aneurysms was 11 mm. Angiographic exclusion of the aneurysms was seen in 57.4% of aneurysms with follow-up (n=47). During the follow-up period nine patients died.

Conclusions

Treatment of non-saccular aneurysms of the posterior fossa is technically possible. Early treatment, particularly of the fusiform and transitional subtypes, is recognized, as is treatment prior to the development of symptoms. A ‘watch and wait’ strategy with regular imaging follow-up could be employed for asymptomatic dolichoectasia.
Teiichi Kobayashi: his life and works, with an emphasis on his contribution to the history of the geosciences in Japan
Authors: Sato T. , Yamada T. , Yajima M.
Published: November 2016

Teiichi Kobayashi (1901–96), a major figure in the history of Japanese geology and palaeontology, was one of the founding members of INHIGEO. He is best known for his work on the Sakawa orogenic cycle and its bearing on the origin of the Japanese islands, which was published in 1941. He researched the geology and palaeontology of the Palaeozoic in East and SE Asia between 1964 and 1984 and published work on cephalopods and trilobites in Asia. During his research, he always recognized the importance of the history of the geological sciences. In 1972, he proposed and organized a committee dedicated to the history of the Japanese geosciences. Based on his awareness of the social significance of the geosciences and their history in Japan, he also contributed to the promotion of
Chigaku
(earth science) education in high schools and in universities.
A look into the history of geology in France
Authors: Taquet Philippe
Published: November 2016

The history of geology in France benefited from a renewal of interest after the creation of the French Committee for the History of Geology in 1976. This initiative, which was led by F. Ellenberger, resulted in the organization of numerous meetings, symposia and publications that have characterized the last decade of work in the history of the earth sciences in France.
Progression of instrument use and practice in mineralogy and petrology, 1750–1950
Authors: Newcomb Sally
Published: November 2016

Although laboratory practice has changed enormously over the last two centuries, it is more a matter of the addition of instruments and methods than their replacement. Balances, microscopes, thermometers and methods of applying pressure are still used. The analysis and characterization of the constituents of rocks and minerals continue to be of basic and necessary interest. Some methods have changed and others, previously unavailable, are now accessible. Each natural philosopher–mineralogist–geologist made use of the instrumentation available, often extending its use or improving it to meet their needs.