bluuebunny/crossref_metadata_2025_split huggingface dataset:
From proteins to polysaccharides: lifestyle and genetic evolution of Coprothermobacter proteolyticus
Authors: Kunath Benoit J , Delogu Francesco , Naas Adrian E , Arntzen Magnus Ø , Eijsink Vincent G H , Henrissat Bernard , Hvidsten Torgeir R , Pope Phillip B 
Published: October 2018

Abstract
Microbial communities that degrade lignocellulosic biomass are typified by high levels of species- and strain-level complexity, as well as synergistic interactions between both cellulolytic and non-cellulolytic microorganisms. Coprothermobacter proteolyticus frequently dominates thermophilic, lignocellulose-degrading communities with wide geographical distribution, which is in contrast to reports that it ferments proteinaceous substrates and is incapable of polysaccharide hydrolysis. Here we deconvolute a highly efficient cellulose-degrading consortium (SEM1b) that is co-dominated by Clostridium (Ruminiclostridium) thermocellum and multiple heterogenic strains affiliated to C. proteolyticus. Metagenomic analysis of SEM1b recovered metagenome-assembled genomes (MAGs) for each constituent population, whereas in parallel two novel strains of C. proteolyticus were successfully isolated and sequenced. Annotation of all C. proteolyticus genotypes (two strains and one MAG) revealed their genetic acquisition of carbohydrate-active enzymes (CAZymes), presumably derived from horizontal gene transfer (HGT) events involving polysaccharide-degrading Firmicutes or Thermotogae-affiliated populations that are historically co-located. HGT material included a saccharolytic operon, from which a CAZyme was biochemically characterized and demonstrated hydrolysis of multiple hemicellulose polysaccharides. Finally, temporal genome-resolved metatranscriptomic analysis of SEM1b revealed expression of C. proteolyticus CAZymes at different SEM1b life stages as well as co-expression of CAZymes from multiple SEM1b populations, inferring deeper microbial interactions that are dedicated toward community degradation of cellulose and hemicellulose. We show that C. proteolyticus, a ubiquitous population, consists of closely related strains that have adapted via HGT to presumably degrade both oligo- and longer polysaccharides present in decaying plants and microbial cell walls, thus explaining its dominance in thermophilic anaerobic digesters on a global scale.
N-acetylcysteine add-on treatment leads to an improvement of fornix white matter integrity in early psychosis: a double-blind randomized placebo-controlled trial
Authors: Klauser Paul , Xin Lijing , Fournier Margot , Griffa Alessandra , Cleusix Martine , Jenni Raoul , Cuenod Michel , Gruetter Rolf , Hagmann Patric , Conus Philippe , Baumann Philipp S. , Do Kim Q. 
Published: October 2018

AbstractMechanism-based treatments for schizophrenia are needed, and increasing evidence suggests that oxidative stress may be a target. Previous research has shown that N-acetylcysteine (NAC), an antioxidant and glutathione (GSH) precursor almost devoid of side effects, improved negative symptoms, decreased the side effects of antipsychotics, and improved mismatch negativity and local neural synchronization in chronic schizophrenia. In a recent double-blind randomized placebo-controlled trial by Conus et al., early psychosis patients received NAC add-on therapy (2700 mg/day) for 6 months. Compared with placebo-treated controls, NAC patients showed significant improvements in neurocognition (processing speed) and a reduction of positive symptoms among patients with high peripheral oxidative status. NAC also led to a 23% increase in GSH levels in the medial prefrontal cortex (GSHmPFC) as measured by 1H magnetic resonance spectroscopy. A subgroup of the patients in this study were also scanned with multimodal MR imaging (spectroscopy, diffusion, and structural) at baseline (prior to NAC/placebo) and after 6 months of add-on treatment. Based on prior translational research, we hypothesized that NAC would protect white matter integrity in the fornix. A group × time interaction indicated a difference in the 6-month evolution of white matter integrity (as measured by generalized fractional anisotropy, gFA) in favor of the NAC group, which showed an 11% increase. The increase in gFA correlated with an increase in GSHmPFC over the same 6-month period. In this secondary study, we suggest that NAC add-on treatment may be a safe and effective way to protect white matter integrity in early psychosis patients.
The dark side of centromeres: types, causes and consequences of structural abnormalities implicating centromeric DNA
Authors: Barra V. , Fachinetti D. 
Published: October 2018

AbstractCentromeres are the chromosomal domains required to ensure faithful transmission of the genome during cell division. They have a central role in preventing aneuploidy, by orchestrating the assembly of several components required for chromosome separation. However, centromeres also adopt a complex structure that makes them susceptible to being sites of chromosome rearrangements. Therefore, preservation of centromere integrity is a difficult, but important task for the cell. In this review, we discuss how centromeres could potentially be a source of genome instability and how centromere aberrations and rearrangements are linked with human diseases such as cancer.
The architecture of EGFR’s basal complexes reveals autoinhibition mechanisms in dimers and oligomers
Authors: Zanetti-Domingues Laura C. , Korovesis Dimitrios , Needham Sarah R. , Tynan Christopher J. , Sagawa Shiori , Roberts Selene K. , Kuzmanic Antonija , Ortiz-Zapater Elena , Jain Purvi , Roovers Rob C. , Lajevardipour Alireza , van Bergen en Henegouwen Paul M. P. , Santis George , Clayton Andrew H. A. , Clarke David T. , Gervasio Francesco L. , Shan Yibing , Shaw David E. , Rolfe Daniel J. , Parker Peter J. , Martin-Fernandez Marisa L. 
Published: October 2018

AbstractOur current understanding of epidermal growth factor receptor (EGFR) autoinhibition is based on X-ray structural data of monomer and dimer receptor fragments and does not explain how mutations achieve ligand-independent phosphorylation. Using a repertoire of imaging technologies and simulations we reveal an extracellular head-to-head interaction through which ligand-free receptor polymer chains of various lengths assemble. The architecture of the head-to-head interaction prevents kinase-mediated dimerisation. The latter, afforded by mutation or intracellular treatments, splits the autoinhibited head-to-head polymers to form stalk-to-stalk flexible non-extended dimers structurally coupled across the plasma membrane to active asymmetric tyrosine kinase dimers, and extended dimers coupled to inactive symmetric kinase dimers. Contrary to the previously proposed main autoinhibitory function of the inactive symmetric kinase dimer, our data suggest that only dysregulated species bear populations of symmetric and asymmetric kinase dimers that coexist in equilibrium at the plasma membrane under the modulation of the C-terminal domain.
Substantiating freedom from parasitic infection by combining transmission model predictions with disease surveys
Authors: Michael Edwin , Smith Morgan E. , Katabarwa Moses N. , Byamukama Edson , Griswold Emily , Habomugisha Peace , Lakwo Thomson , Tukahebwa Edridah , Miri Emmanuel S. , Eigege Abel , Ngige Evelyn , Unnasch Thomas R. , Richards Frank O. 
Published: October 2018

AbstractStopping interventions is a critical decision for parasite elimination programmes. Quantifying the probability that elimination has occurred due to interventions can be facilitated by combining infection status information from parasitological surveys with extinction thresholds predicted by parasite transmission models. Here we demonstrate how the integrated use of these two pieces of information derived from infection monitoring data can be used to develop an analytic framework for guiding the making of defensible decisions to stop interventions. We present a computational tool to perform these probability calculations and demonstrate its practical utility for supporting intervention cessation decisions by applying the framework to infection data from programmes aiming to eliminate onchocerciasis and lymphatic filariasis in Uganda and Nigeria, respectively. We highlight a possible method for validating the results in the field, and discuss further refinements and extensions required to deploy this predictive tool for guiding decision making by programme managers.
In silico proteomic and phylogenetic analysis of the outer membrane protein repertoire of gastric Helicobacter species
Authors: Bauwens Eva , Joosten Myrthe , Taganna Joemar , Rossi Mirko , Debraekeleer Ayla , Tay Alfred , Peters Fanny , Backert Steffen , Fox James , Ducatelle Richard , Remaut Han , Haesebrouck Freddy , Smet Annemieke 
Published: October 2018

AbstractHelicobacter (H.) pylori is an important risk factor for gastric malignancies worldwide. Its outer membrane proteome takes an important role in colonization of the human gastric mucosa. However, in zoonotic non-H. pylori helicobacters (NHPHs) also associated with human gastric disease, the composition of the outer membrane (OM) proteome and its relative contribution to disease remain largely unknown. By means of a comprehensive survey of the diversity and distribution of predicted outer membrane proteins (OMPs) identified in all known gastric Helicobacter species with fully annotated genome sequences, we found genus- and species-specific families known or thought to be implicated in virulence. Hop adhesins, part of the Helicobacter-specific family 13 (Hop, Hor and Hom) were restricted to the gastric species H. pylori, H. cetorum and H. acinonychis. Hof proteins (family 33) were putative adhesins with predicted Occ- or MOMP-family like 18-stranded β-barrels. They were found to be widespread amongst all gastric Helicobacter species only sporadically detected in enterohepatic Helicobacter species. These latter are other members within the genus Helicobacter, although ecologically and genetically distinct. LpxR, a lipopolysaccharide remodeling factor, was also detected in all gastric Helicobacter species but lacking as well from the enterohepatic species H. cinaedi, H. equorum and H. hepaticus. In conclusion, our systemic survey of Helicobacter OMPs points to species and infection-site specific members that are interesting candidates for future virulence and colonization studies.
The Competition of Homophily and Popularity in Growing and Evolving Social Networks
Authors: Liu Yezheng , Li Lingfei , Wang Hai , Sun Chunhua , Chen Xiayu , He Jianmin , Jiang Yuanchun 
Published: October 2018

AbstractPrevious studies have used several models to investigate the mechanisms for growing and evolving real social networks. These models have been widely used to simulate large networks in many applications. In this paper, based on the evolutionary mechanisms of homophily and popularity, we propose a new generation model for growing and evolving social networks, namely, the Homophily-Popularity model. In this new model, new links are added, and old links are deleted based on the link probabilities between every node pair. The results of our simulation-based experimental studies provide evidence that the proposed model is capable of modelling a variety of real social networks.
Differential incorporation of one-carbon substrates among microbial populations identified by stable isotope probing from the estuary to South China Sea
Authors: Deng Wenchao , Peng Lulu , Jiao Nianzhi , Zhang Yao 
Published: October 2018

AbstractMethanol (MOH) and monomethylamine (MMA) are two typical one-carbon (C1) compounds found in natural environments. They play an important role in marine and atmospheric chemistry, cloud formation, and global climate. The main biological sink of MOH and MMA is rapid consumption by marine microbes. Here, field-based time-series incubations with supplemental 13C-labelled MOH and MMA and isotope ratio analyses were performed. A substantial difference in the MOH and MMA incorporation rates and bacterial taxa were observed between the South China Sea (SCS) and the Pearl River estuary. C1 substrates were assimilated more quickly in the estuary than the SCS shelf where MOH and MMA had similar bio-availability. However, microbial responses to MMA may be faster than to MOH in the coastal and basin surface water of the SCS despite similar active bacterial populations. Three ecological types of bacteria, in terms of response to supplemented MOH and MMA, were identified: rapid incorporation (I, dominant C1-incorporating group), slow incorporation (II, minor C1-incorporating group), and no incorporation (III, C1-non-incorporating group). Members of the families Methylophilaceae (β-Proteobacteria) and Piscirickettsiaceae (γ-Proteobacteria) belonged to type I and actively incorporated substrates in the estuary and SCS, respectively. Diverse MOH and MMA-incorporating type II bacteria were identified by stable isotope probing in the SCS, and could play a more important role in the transformation of C1 compounds in marine environments than hitherto assumed.
Regulatory elements in vectors containing the ctEF-1α first intron and double enhancers for an efficient recombinant protein expression system
Authors: Lee Chi-Pin , Ko Albert Min-Shan , Chiang Shang-Lun , Lu Chi-Yu , Tsai Eing-Mei , Ko Ying-Chin 
Published: October 2018

AbstractTo establish a stable and scalable transient protein production system, we modified the EF-1 first intron size and verified the order of two recombinant enhancers downstream of the SV40 polyA sequence. This new vector was named pHH-Gemini (pHH-GM1) and was used to express alpha kinase 1 (ALPK1) and various other proteins, NLRP3, F-actin, Camodulin, PP2A, URAT1, Rab11a and myosin IIA. The results showed that, compared with six commercial plasmids, pHH-GM1 significantly enhanced His-HA-ALPK1 expression in a western blot analysis of transfected HEK293T cells. The expression of various other genes was also successful using the pHH-GM1 vector. In addition, we inserted turbo green florescence protein (tGFP) into the pHH-GM1 vector, and an improvement in fluorescence intensity was observed after transient transfection of HEK293T cells. For large-scale production, protein production was tested by standard supplementation with one volume of medium, and volumetric yields of 2 and 2.3 mg/L were achieved with pHH-GM1-ALPK1 in HEK293-F and CHO-S cells, respectively. We found that cell viability was more than 70% 11 days after cells were transfected with the pHH-GM1 vector. The pHH-GM1 vector with the ctEF-1α first intron and double enhancers, Simian virus 40 and Cytomegalovirus (SV40 and CMV) is an efficient CMV promoter-based gene expression system that can potentially be applied to study genes of interest and improve protein production.
Nighttime activities and peripheral clock oscillations depend on Wolbachia endosymbionts in flies
Authors: Morioka Eri , Oida Minami , Tsuchida Tsutomu , Ikeda Masayuki 
Published: October 2018

AbstractWolbachia are ubiquitous bacterial endosymbionts of arthropods and affect host gene expression. Although Wolbachia infections were suggested to modulate sleep in flies, their influence on the circadian clock remained obscure. Here, we screened bacterial symbionts in a laboratory Drosophila melanogaster colony, and observed widespread infections of wMel strain Wolbachia. We established a Wolbachia-free strain from a clock gene reporter strain, period-luciferase (per-luc). Temperature (19–29 °C)-compensated free-running periods were detected regardless of infections which may reflect the lack of wMel infections in central circadian pacemaker neurons. However, locomotor activity levels during the night or subjective night were significantly amplified in uninfected flies. Moreover, the behavioral phenotype of F1 offspring of an uninfected female and infected male resembled that of uninfected flies. This trait is consistent with maternal transmission of Wolbachia infection. Interestingly, per-luc activities in headless bodies, as an index of peripheral circadian oscillators, were severely damped in uninfected flies. Additionally, circadian amplitudes of PER immunoreactivities in Malpighian tubules were reduced in uninfected flies. These results demonstrate that Wolbachia boost fly peripheral clock oscillations and diurnal behavioral patterns. Genetic mechanisms underlying behavioral rhythms have been widely analyzed using mutant flies whereas screening of Wolbachia will be necessary for future studies.
The role of functional and structural interhemispheric auditory connectivity for language lateralization - A combined EEG and DTI study
Authors: Steinmann Saskia , Amselberg Rom , Cheng Bastian , Thomalla Götz , Engel Andreas K. , Leicht Gregor , Mulert Christoph 
Published: October 2018

AbstractInterhemispheric connectivity between auditory areas is highly relevant for normal auditory perception and alterations are a major factor for the development of auditory verbal hallucinations. Surprisingly, there is no combined EEG-DTI study directly addressing the role of functional and structural connectivity in the same group of subjects. Accordingly, nothing is known about the relationship between functional connectivity such as gamma-band synchrony, structural integrity of the interhemispheric auditory pathways (IAPs) and language lateralization as well as whether the gamma-band synchrony is configured on the backbone of IAPs. By applying multimodal imaging of 64-channel EEG and DTI tractography, we investigated in 27 healthy volunteers the functional gamma-band synchrony between either bilateral primary or secondary auditory cortices from eLORETA source-estimation during dichotic listening, as well as the correspondent IAPs from which fractional anisotropy (FA) values were extracted. Correlation and regression analyses revealed highest values for gamma-band synchrony, followed by FA for secondary auditory cortices, which were both significantly related to a reduced language lateralization. There was no such association between the white-matter microstructure and gamma-band synchrony, suggesting that structural connectivity might also be relevant for other (minor) aspects of information transfer in addition to gamma-band synchrony, which are not detected in the present coupling analyses. The combination of multimodal EEG-DTI imaging provides converging evidence of neural correlates by showing that both stronger pathways and increased gamma-band synchrony within one cohort of subjects are related to a reduced leftward-lateralization for language.
Nocturnal spawning as a way to avoid egg exposure to diurnal predators
Authors: Šmejkal Marek , Souza Allan T. , Blabolil Petr , Bartoň Daniel , Sajdlová Zuzana , Vejřík Lukáš , Kubečka Jan 
Published: October 2018

AbstractAnimals that do not provide parental care have to secure the survival of their offspring by ensuring a safe reproductive environment or smart timing tactics. Nocturnal spawning behaviour of many fish species is an example of the latter behaviour in the animal kingdom and is hypothesized to provide a survival advantage to the eggs spawned during the night. In order to test the efficiency of the smart timing tactics in a freshwater fish, a study was carried out of the interaction of the rheophilic spawner (asp Leuciscus aspius) and the predator of its drifting eggs (bleak Alburnus alburnus) using passive telemetry. According to a model based on acquired data, asp laid 63% of its eggs at night, while vision-oriented bleak was present in 92% of the time during the day. This study gives support to the predator avoidance hypothesis, which expects animals to reproduce in a period when the probability of offspring predation is at its lowest.
Characteristics of phantom upper limb mobility encourage phantom-mobility-based prosthesis control
Authors: Touillet Amélie , Peultier-Celli Laetitia , Nicol Caroline , Jarrassé Nathanaël , Loiret Isabelle , Martinet Noël , Paysant Jean , De Graaf Jozina B 
Published: October 2018

AbstractThere is an increasing need to extend the control possibilities of upper limb amputees over their prosthetics, especially given the development of devices with numerous active joints. One way of feeding pattern recognition myoelectric control is to rely on the myoelectric activities of the residual limb associated with phantom limb movements (PLM). This study aimed to describe the types, characteristics, potential influencing factors and trainability of upper limb PLM. Seventy-six below- and above-elbow amputees with major amputation underwent a semi-directed interview about their phantom limb. Amputation level, elapsed time since amputation, chronic pain and use of prostheses of upper limb PLM were extracted from the interviews. Thirteen different PLM were found involving the hand, wrist and elbow. Seventy-six percent of the patients were able to produce at least one type of PLM; most of them could execute several. Amputation level, elapsed time since amputation, chronic pain and use of myoelectric prostheses were not found to influence PLM. Five above-elbow amputees participated in a PLM training program and consequently increased both endurance and speed of their PLM. These results clearly encourage further research on PLM-associated muscle activation patterns for future PLM-based modes of prostheses control.
Effect of diversity on growth, mortality, and loss of resilience to extreme climate events in a tropical planted forest experiment
Authors: Hutchison Chantal , Gravel Dominique , Guichard Frédéric , Potvin Catherine 
Published: October 2018

AbstractA pressing question is whether biodiversity can buffer ecosystem functioning against extreme climate events. However, biodiversity loss is expected to occur due to climate change with severe impacts to tropical forests. Using data from a ca. 15 year-old tropical planted forest, we construct models based on a bootstrapping procedure to measure growth and mortality among different species richness treatments in response to extreme climate events. In contrast to higher richness mixtures, in one-species plots we find growth is strongly regulated by climate events and we also find increasingly higher mortality during a consecutive three year dry event. Based on these results together with indicators of loss of resilience, we infer an effect of diversity on critical slowing down. Our work generates new methods, concepts, and applications for global change ecology and emphasises the need for research in the area of biodiversity-ecosystem functioning along environmental stress gradients.