bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extensive transcriptional changes in the aphid speciesMyzus cerasiunder different host environments associated with detoxification genes
Authors: Thorpe Peter , Escudero-Martinez Carmen M. , den Akker Sebastian Eves-van , Bos Jorunn I.B. 
Published: July 2018

AbstractAphids are phloem-feeding insects that cause yield losses to crops globally. These insects feature complex life cycles, which in the case of many agriculturally important species involves the use of primary and secondary host plant species. Whilst host alternation between primary and secondary host can occur in the field depending on host availability and the environment, aphid populations maintained as laboratory stocks generally are kept under conditions that allow asexual reproduction by parthenogenesis on secondary hosts. Here, we usedMyzus cerasi(black cherry aphid) to assess aphid transcriptional differences between populations collected from primary hosts in the field and those adapted to secondary hosts under controlled environment conditions. Adaptation experiments ofM. cerasicollected from local cherry tress to reported secondary host species resulted in low survival rates. Moreover, aphids were unable to survive on secondary host Land cress, unless first adapted to another secondary host, cleavers. Transcriptome analyses of populations collected from primary host cherry in the field and the two secondary host plant species in a controlled environment showed extensive transcriptional plasticity to a change in host environment, with predominantly genes involved in redox reactions differentially regulated. Most of the differentially expressed genes across theM. cerasipopulations from the different host environments were duplicated and we found evidence for differential exon usage. In contrast, we observed only limited transcriptional to a change in secondary host plant species.
Exploring the effects of BCG vaccination in patients diagnosed with tuberculosis: observational study using the Enhanced Tuberculosis Surveillance system
Authors: Abbott Sam , Christensen Hannah , Lalor Maeve K , Zenner Dominik , Campbell Colin , Ramsay Mary , Brooks-Pollock Ellen 
Published: July 2018

ABSTRACTBackgroundBacillus Calmette–Guérin (BCG) is one of the most widely-used vaccines worldwide. BCG primarily reduces the progression from infection to disease, however there is evidence that BCG may provide additional benefits. We aimed to investigate whether there is evidence in routinely-collected surveillance data that BCG vaccination impacts outcomes for tuberculosis (TB) cases in England.MethodsWe obtained all TB notifications for 2009–2015 in England from the Enhanced Tuberculosis surveillance system. We considered five outcomes: All-cause mortality, death due to TB (in those who died), recurrent TB, pulmonary disease, and sputum smear status. We used logistic regression, with complete case analysis, to investigate each outcome with BCG vaccination, years since vaccination and age at vaccination, adjusting for potential confounders. All analyses were repeated using multiply imputed data.ResultsWe found evidence of an association between BCG vaccination and reduced all-cause mortality (aOR:0.76 (95%CI 0.64 to 0.89), P:0.001) and weak evidence of an association with reduced recurrent TB (aOR:0.90 (95%CI 0.81 to 1.00), P:0.056). Analyses using multiple imputation suggested that the benefits of vaccination for all-cause mortality were reduced after 10 years.ConclusionsWe found that BCG vaccination was associated with reduced all-cause mortality in people with TB although this benefit was less pronounced more than 10 years after vaccination. There was weak evidence of an association with reduced recurrent TB.HighlightsFound evidence of an association between BCG vaccination and reduced all-cause mortality in TB cases.Weaker evidence of an association between BCG vaccination and reduced repeat TB episodes in TB cases.There was little evidence of an association with other TB outcomes.We explored the identified associations by age and time since vaccination.
Interspecies interactions mediated by conductive minerals in the sediments of the ferruginous Lake La Cruz, Spain
Authors: Rotaru Amelia-Elena , Posth Nicole R. , Löscher Carolin R. , Miracle Maria R. , Vicente Eduardo , Cox Raymond P. , Thompson Jennifer , Poulton Simon W. , Thamdrup Bo 
Published: July 2018

AbstractLake La Cruz is considered a biogeochemical analogue to early Earth marine environments because its water column is depleted in sulfate, but rich in methane and iron, similar to conditions envisaged for much of the Precambrian. In this early Earth analogue environment, we show that conductive particles establish a tight metabolic coupling between electroactive microbial clades. We propose that mineral-based syntrophy is of potential relevance for the evolution of Earth’s earliest complex life forms. We show that the anoxic sediment of Lake La Cruz, which is rich in biogeochemically ‘reactive’ iron minerals, harbors known electroactive species such asGeobacterandMethanothrix,in addition to other groups which have not been previously associated with an electroactive lifestyle. Slurry incubations on various substrates in the presence of conductive particles showed significant methanogenic activity, whereas incubations with non-conductive glass beads resulted in low methanogenic rates similar to slurries without added particles. In the absence of conductive particles, all tested substrates were metabolized to acetate, which accumulated to ∼10 mM. Similar to a previous study on iron-rich Baltic Sea sediments, we observed that conductive mineral additions to La Cruz slurries enabled acetate oxidation, thus preventing acetate accumulation. Acetate oxidation coupled to high methanogenic activity was only maintained in successive mud-free enrichments when these were amended with conductive minerals. In serial mud-free transfers, conductive particles conserved a consortium ofYoungiibacter-Methanothrix,whereasYoungiibacterspp. died off in the absence of conductive particles. In contrast, mud-free enrichments without conductive particles ceased any metabolic activity during the second transfers. Syntrophic consortia from this early Earth analogue environment only survived in the presence of conductive particles. Mineral-mediated syntrophy could be one of the earliest evolutionary interspecies associations. Conductive minerals might have fueled metabolic exchange between cells via intercellular electron transfer prompting tight cell-to-cell associations and possibly eukaryogenesis.
Processivity, velocity and universal characteristics of nucleic acid unwinding by helicases
Authors: Chakrabarti Shaon , Jarzynski Christopher , Thirumalai D. 
Published: July 2018

AbstractHelicases that act as motors and unwind double stranded nucleic acids are broadly classified as either active or passive, depending on whether or not they directly destabilize the double strand. By using this description in a mathematical framework, we derive analytic expressions for the velocity and run-length of a general model of finitely processive helicases. We show that, in contrast to the helicase unwinding velocity, the processivity exhibits a universal increase in response to external force. We use our results to analyze velocity and processivity data from single molecule experiments on the superfamily-4 ring helicase T7, and establish quantitatively that T7 is a weakly active helicase. We predict that compared to single-strand translocation, there is almost a two orders-of-magnitude increase in the back-stepping probability of T7 while unwinding double-stranded DNA. Our quantitative analysis of T7 suggests that the tendency of helicases to take frequent back-steps may be more common than previously anticipated, as was recently shown for the XPD helicase. Finally, our results suggest the intriguing possibility of a single underlying physical principle governing the experimentally observed increase in unwinding efficiencies of helicases in the presence of force, oligomerization or partner proteins like single strand binding proteins. The clear implication is that helicases may have evolved to maximize processivity rather than speed.
Feasibility of Functional MRI at Ultralow Magnetic Field via Changes in Cerebral Blood Volume
Authors: Buckenmaier Kai , Pedersen Anders , SanGiorgio Paul , Scheffler Klaus , Clarke John , Inglis Ben 
Published: July 2018

AbstractWe investigate the feasibility of performing functional MRI (fMRI) at ultralow field (ULF) with a Superconducting QUantum Interference Device (SQUID), as used for detecting magnetoencephalography (MEG) signals from the human head. While there is negligible magnetic susceptibility variation to produce blood oxygenation level-dependent (BOLD) contrast at ULF, changes in cerebral blood volume (CBV) may be a sensitive mechanism for fMRI given the five-fold spread in spin-lattice relaxation time (T1) values across the constituents of the human brain. We undertook simulations of functional signal strength for a simplified brain model involving activation of a primary cortical region in a manner consistent with a blocked task experiment. Our simulations involve measured values of T1 at ULF and experimental parameters for the performance of an upgraded ULFMRI scanner. Under ideal experimental conditions we predict a functional signal-to-noise ratio of between 3.1 and 7.1 for an imaging time of 30 minutes, or between 1.5 and 3.5 for a blocked task experiment lasting 7.5 minutes. Our simulations suggest it may be feasible to perform fMRI using a ULFMRI system designed to perform MRI and MEG in situ.
The many nuanced evolutionary consequences of duplicated genes
Authors: Teufel Ashley I. , Johnson Mackenzie M. , Laurent Jon M. , Kachroo Aashiq H. , Marcotte Edward M. , Wilke Claus O. 
Published: July 2018

AbstractGene duplication is seen as a major source of structural and functional divergence in genome evolution. Under the conventional models of sub- or neofunctionalizaton, functional changes arise in one of the duplicates after duplication. However, we suggest here that the presence of a duplicated gene can result in functional changes to its interacting partners. We explore this hypothesis byin-silicoevolution of a heterodimer when one member of the interacting pair is duplicated. We examine how a range of selection pressures and protein structures leads to differential patterns of evolutionary divergence. We find that a surprising number of distinct evolutionary trajectories can be observed even in a simple three member system. Further, we observe that selection to correct dosage imbalance can affect the evolution of the initial function in several unexpected ways. For example, if a duplicate is under selective pressure to avoid binding its original binding partner, this can lead to changes in the binding interface of a non-duplicated interacting partner to exclude the duplicate. Hence, independent of the fate of the duplicate, its presence can impact how the original function operates. Additionally, we introduce a conceptual framework to describe how interacting partners cope with dosage imbalance after duplication. Contextualizing our results within this framework reveals that the evolutionary path taken by a duplicate’s interacting partners is highly stochastic in nature. Consequently, the fate of duplicate genes may not only be controlled by their own ability to accumulate mutations but also by how interacting partners cope with them.
Acinetobacter baumanniidetected on mCCDA medium in a waste stabilisation pond
Authors: Sheludchenko Maxim , Padovan Anna , Katouli Mohammad , Roiko Anne , Stratton Helen 
Published: July 2018

AbstractAcinetobacter baumanniisurvives for prolonged periods under a wide range of environmental conditions. In a larger study investigating the efficacy of pathogen removal in a waste stabilization ponds (WSP), we cultivated microbes from wastewater samples on mCCDA agar containing selective and recommended supplements for the growth ofCampylobacter. This bacterium is a recommended reference pathogen for the verification and validation of water recycling schemes in Australia and other parts of the world. A high number of colonies characteristic ofCampylobactergrew on the selective media but this did not correlate with qPCR data. Using primers targeting the16S rRNA gene, and additional confirmatory tests such as detection of VS1,ompA, blaOXA-51-like, blaOXA-23-likegenes, we tested eight random colonies from eight samples (64 colonies in total) and identified them asA. baumannii. Wastewater grab samples taken three times over 6 months throughout the WSP system showed removal ofA. baumanniiin the WSP atrates similar toE. coli. In contrast, further intensive sampling from the inlet and the outlet of the WSP using a refrigerated auto-sampler showed that the number ofA. baumanniiin most sampling rounds did not differ significantly between the inlet and outlet of the WSP and that there was high variation between replicates at the outlet only. Resistance genes were detected in mostA. baumanniiisolated from the waste stabilisation pond and may potentially be a source of antibiotic resistance for environmental strains.
Lineage tracing using a Cas9-deaminase barcoding system targeting endogenous L1 elements
Authors: Hwang Byungjin , Lee Wookjae , Yum Soo-Young , Jeon Yujin , Cho Namjin , Jang Goo , Bang Duhee 
Published: July 2018

ABSTRACTDetermining cell lineage and function is critical to understanding human physiology and pathology. Although advances in lineage tracing methods have provided new insight into cell fate, defining cellular diversity at the mammalian level remains a challenge. Here, we developed a genome editing strategy using a cytidine deaminase fused with inactive Cas9 (dCas9) to specifically target endogenous interspersed repeat regions in mammalian cells. The resulting mutation patterns served as a genetic barcode, which was induced by targeted mutagenesis with single-guide RNA (sgRNA), leveraging substitution events, and subsequent read out by a single primer pair. By analyzing interspersed mutation signatures, we show the accurate reconstruction of cell lineage using both bulk cell and single-cell data. We envision that our genetic barcode system will enable fine-resolution mapping of organismal development in healthy and diseased mammalian states.
The Biological Basis of Mathematical Beauty
Authors: Zeki Semir , Chén Oliver Y. , Romaya John Paul 
Published: July 2018

AbstractThrough our past studies of the neurobiology of beauty, we have come to divide aesthetic experiences into two broad categories: biological and artifactual. The aesthetic experience of biological beauty is dictated by inherited brain concepts, which are resistant to change even in spite of extensive experience. The experience of artifactual beauty on the other hand is determined by post-natally acquired concepts, which are modifiable throughout life by exposure to different experiences (Zeki, 2009). Hence, in terms of aesthetic rating, biological beauty (in which we include the experience of beautiful faces or human bodies) is characterized by less variability between individuals belonging to different ethnic origins and cultural backgrounds or the same individual at different times. Artifactual beauty (in which we include the aesthetic experience of human artifacts such as buildings and cars) is characterized by greater variability between individuals belonging to different ethnic and cultural groupings and by the same individual at different times. In this paper, we present results to show that the experience of mathematical beauty (Zeki et al 2014), even though it constitutes an extreme example of beauty that is dependent upon (mathematical) culture and learning, belongs to the biological category and obeys one of its characteristics, namely a lesser variability in terms of the aesthetic ratings given to mathematical formulae experienced as beautiful.
The creation of sexual dimorphism in Drosophila gonad stem cell niches
Authors: Camara Nicole , Whitworth Cale , Van Doren Mark 
Published: July 2018

SUMMARYSex-specific development of the gonads is a key aspect of sexual dimorphism that is regulated by Doublesex/Mab3 Related Transcription Factors (DMRTs) in diverse animals species. We find that in mutants forDrosophila dsx, important components of the male and female gonad stem cell niches (hubs and terminal filaments/cap cells, respectively) still form. Initially, gonads in alldsxmutants (both XX and XY) initiate the male program of development, but later half of these gonads switch to form female stem cell niche structures. One individual can have both male-type and female-type gonad niches, however male and female niches are usually not observed in the same gonad, indicating that cells make a “group decision” about which program to follow. We conclude thatdsxdoes not act in an instructive manner to regulate male vs. female niche formation, as these structures form in the absence ofdsxfunction. Instead,dsxacts to “tip the balance” between the male or female programs, which are then executed independent ofdsx. We show thatbric a bracacts downstream ofdsxto control the male vs. female niche decision. These results indicate that, in both flies and mammals, the sexual fate of the somatic gonad is remarkably plastic and is controlled by a combination of autonomous and non-autonomous cues.
Differential metabolic activity and discovery of therapeutic targets using summarized metabolic pathway models
Authors: Çubuk Cankut , Hidalgo Marta R. , Amadoz Alicia , Rian Kinza , Salavert Francisco , Pujana Miguel A. , Mateo Francesca , Herranz Carmen , Carbonell-Caballero Jose , Dopazo Joaquín 
Published: July 2018

AbstractBackgroundin spite of the increasing availability of genomic and transcriptomic data, there is still a gap between the detection of perturbations in gene expression and the understanding of their contribution to the molecular mechanisms that ultimately account for the phenotype studied. Alterations in the metabolism are behind the initiation and progression of many diseases, including cancer. The wealth of available knowledge on metabolic processes can therefore be used to derive mechanistic models that link gene expression perturbations to changes in metabolic activity that provide relevant clues on molecular mechanisms of disease and drug modes of action (MoA). In particular, pathway modules, which recapitulate the main aspects of metabolism, are especially suitable for this type of modeling.Resultswe present Metabolizer, a web-based application that offers an intuitive, easy-to-use interactive interface to analyze differences in pathway module metabolic activities that can also be used for class prediction and in silico prediction of Knock-Out (KO) effects. Moreover, Metabolizer can automatically predict the optimal KO intervention for restoring a diseased phenotype. We provide different types of validations of some of the predictions made by Metabolizer.ConclusionsMetabolizer is a web tool that allows understanding molecular mechanisms of disease or the MoA of drugs within the context of the metabolism by using gene expression measurements. In addition, this tool automatically suggests potential therapeutic targets for individualized therapeutic interventions.Metabolizer can be found at:http://metabolizer.babelomics.org.
Olive fruit fly rearing procedures affect the vertical transmission of the bacterial symbiontCandidatusErwinia dacicola
Authors: Sacchetti Patrizia , Pastorelli Roberta , Bigiotti Gaia , Guidi Roberto , Ruschioni Sara , Viti Carlo , Belcari Antonio 
Published: July 2018

AbstractBackground: The symbiosis between the olive fruit fly,Bactrocera oleae, andCandidatusErwinia dacicola has been demonstrated as essential for the fly’s larval development and adult physiology. The mass rearing of the olive fruit fly has been hindered by several issues, including problems which could be related to the lack of the symbiont, presumably due to preservatives and antibiotics currently used in the laboratory. To better understand the mechanisms underlying symbiont removal or loss during the rearing of lab colonies of the olive fruit fly, we performed experiments that focused on bacterial transfer from wild female flies to their eggs. In this research, eggs laid by wild females were treated with propionic acid solution, which is often used as an antifungal agent, a mixture of sodium hypochlorite and Triton X, or water (as a control). The presence of the bacterial symbiont on eggs was evaluated by real-time PCR and scanning electron microscopy.Results: DGGE analysis showed a clear band with the same migration behavior present in all DGGE profiles but with a decreasing intensity. Molecular analyses performed by real-time PCR showed a significant reduction inCa. E. dacicola abundance in eggs treated with propionic acid solution or a mixture of sodium hypochlorite and Triton X compared to those treated with water. In addition, the removal of bacteria from the surfaces of treated eggs was highlighted by scanning electron microscopy.Conclusions: The results clearly indicate how the first phases of the colony-establishment process are important in maintaining the symbiont load in laboratory populations and suggest that the use of products with antimicrobial activity should be avoided. The results also suggest that alternative rearing procedures for the olive fruit fly should be investigated.
Corticospinal neuroplasticity and sensorimotor recovery in rats treated by infusion of neurotrophin-3 into disabled forelimb muscles started 24 h after stroke
Authors: Duricki Denise A. , Drndarski Svetlana , Bernanos Michel , Wood Tobias , Bosch Karen , Chen Qin , Shine H. David , Simmons Camilla , Williams Steven C.R. , McMahon Stephen B. , Begley David J. , Cash Diana , Moon Lawrence D.F. 
Published: July 2018

AbstractStroke often leads to arm disability and reduced responsiveness to stimuli on the other side of the body. Neurotrophin-3 (NT3) is made by skeletal muscle during infancy but levels drop postnatally and into adulthood. It is essential for the survival and wiring-up of sensory afferents from muscle. We have previously shown that gene therapy delivery of human NT3 into the affected triceps brachii forelimb muscle improves sensorimotor recovery after ischemic stroke in adult and elderly rats. Here, to move this therapy one step nearer to the clinic, we set out to test the hypothesis that intramuscular infusion of NT3 protein could improve sensorimotor recovery after ischemic cortical stroke in adult rats. To simulate a clinically-feasible time-to-treat, twenty-four hours later rats were randomized to receive NT3 or vehicle by infusion into triceps brachii for four weeks using implanted minipumps. NT3 increased the accuracy of forelimb placement during walking on a horizontal ladder and increased use of the affected arm for lateral support during rearing. NT3 also reversed sensory deficits on the affected forearm. There was no evidence of forepaw sensitivity to cold stimuli after stroke or NT3 treatment. MRI confirmed that treatment did not induce neuroprotection. Functional MRI during low threshold electrical stimulation of the affected forearm showed an increase in peri-infarct BOLD signal with time in both stroke groups and indicated that neurotrophin-3 did not further increase peri-infarct BOLD signal. Rather, NT3 induced spinal neuroplasticity including sprouting of the spared corticospinal and serotonergic pathways. Neurophysiology showed that NT3 treatment increased functional connectivity between the corticospinal tracts and spinal circuits controlling muscles on the treated side. After intravenous injection, radiolabelled NT3 crossed from bloodstream into the brain and spinal cord in adult mice with or without strokes. Our results show that delayed, peripheral infusion of neurotrophin-3 can improve sensorimotor function after ischemic stroke. Phase I and II clinical trials of NT3 (for constipation and neuropathy) have shown that peripheral, high doses are safe and well tolerated, which paves the way for NT3 as a therapy for stroke.