bluuebunny/crossref_metadata_2025_split huggingface dataset:
Visual plasticity and exercise revisited: no evidence for a “cycling lane”
Authors: Finn Abigail E , Baldwin Alex S , Reynaud Alexandre , Hess Robert F 
Published: October 2018

AbstractExperiments using enriched environments have shown that physical exercise modulates visual plasticity in rodents. A recent study (Lunghi & Sale, 2015, doi: 10.1016/j.cub.2015.10.026) investigated whether exercise also affects visual plasticity in adult humans. The plastic effect they measured was the shift in ocular dominance caused by 2 hours of monocular deprivation (e.g. by an eye patch). They used a binocular rivalry task to measure this shift. They found that the magnitude of the shift was increased by exercise during the deprivation period. This effect of exercise was later disputed by a study that used a different behavioural task (Zhouet al., 2017, doi: 10.1155/2017/4780876). Our goal was to determine whether the difference in task was responsible for that study’s failure to find an exercise effect. We set out to replicate Lunghi & Sale (2015). We measured ocular dominance with a rivalry task before and after 2 hours of deprivation. We measured data from two conditions in 30 subjects. On two separate days they either performed exercise or rested during the deprivation period. Contrary to the previous study, we find no significant effect of exercise. We hypothesise that exercise may affect rivalry dynamics in a way that interacts with the measurement of the deprivation effect.
Local vulnerability and global connectivity jointly shape neurodegenerative disease propagation
Authors: Zheng Ying-Qiu , Zhang Yu , Yau Yvonne , Zeighami Yahar , Larcher Kevin , Misic Bratislav , Dagher Alain 
Published: October 2018

AbstractIt is becoming increasingly clear that brain network organization shapes the course and expression of neurodegenerative diseases. Parkinson’s disease (PD) is marked by progressive spread of atrophy from the midbrain to subcortical structures and eventually, to the cerebral cortex. Recent discoveries suggest that the neurodegenerative process involves the misfolding and prion-like propagation of endogenous α-synuclein via axonal projections. However, the mechanisms that translate local “synucleinopathy” to large-scale network dysfunction and atrophy remain unknown. Here we use an agent-based epidemic spreading model to integrate structural connectivity, functional connectivity and gene expression, and to predict sequential volume loss due to neurodegeneration. The dynamic model replicates the spatial and temporal patterning of empirical atrophy in PD and implicates the substantia nigra as the disease epicenter. We reveal a significant role for both connectome topology and geometry in shaping the distribution of atrophy. The model also demonstrates that SNCA and GBA transcription influence α-synuclein concentration and local regional vulnerability. Functional co-activation further amplifies the course set by connectome architecture and gene expression. Altogether, these results support the theory that the progression of PD is a multifactorial process that depends on both cell-to-cell spreading of misfolded proteins and regional vulnerability.
Prediction of Algal Blooms in the Great Lakes through a Convolution Neural Network of Remote Sensing Data
Authors: Srinivasan Karthik , Duvvur Vikram , Hess Daniel 
Published: October 2018

AbstractHarmful algal blooms (HABs) are the proliferation of algae due to eutrophication and have severe repercussions to the ecological balance in many water bodies, due to the toxins the algae produce. Additionally, the identification and prediction of these HABs has been a challenge in the scientific community due to the interactions between both biological and physical processes that cause the HABs. Here, we used remote sensing data to bypass these issues; remote sensing data provides significant information about the coverage of chlorophyll which can be used to locate HABs. Using this indicator of HABs, we trained a Convolution Neural Network (CNN) to identify nine types of algal blooms, using 25 epochs of 900 images, which can predict algal bloom shapes with an 80 percent accuracy. This approach of HAB identification can easily be applied to other aquatic ecosystems where remote sensing data is present.
The global diversity of the major parasitic nematodeHaemonchus contortusis shaped by human intervention and climate
Authors: Sallé G. , Doyle S.R. , Cortet J. , Cabaret J. , Berriman M. , Holroyd N. , Cotton J.A 
Published: October 2018

AbstractThe gastrointestinal parasiteHaemonchus contortusis an haematophagous parasitic nematode of veterinary interest and a model for the study of drug resistance mechanisms or host-parasite interactions. To understand its evolutionary history, and its ability to adapt in the face of climatic and drug pressure, we have performed an extensive survey of genome-wide diversity using single-worm whole genome sequencing of 223 individuals sampled from 19 isolates spanning five continents. The pattern of global diversity is driven by an African origin for the species, together with contemporary dispersal that is consistent with modern human movement, with evidence for parasites spreading during the transatlantic slave trade and colonisation of Australia presented. Strong selective sweeps were identified in independent populations each surrounding the β-tubulin locus, a target of benzimidazole anthelmintic drug treatment used widely to controlH. contortusinfections. These signatures of selection were further supported by signals of diversifying selection enriched in genes involved in response to drugs, as well as other anthelmintic-associated biological functions including pharyngeal pumping and oviposition. From these analyses, we identify some known, and previously undescribed, candidate genes that may play a role in ivermectin resistance. Finally, we describe genetic signatures of climate-driven adaptation, revealing a gene acting as an epigenetic regulator and components of thedauerpathway may play a role in adaptation in the face of climatic fluctuations. These results begin to define genetic adaptation to climate for the first time in a parasitic nematode, and provides insight into the ongoing expansion in the range ofHaemonchus contortus, which may have consequences for the management of this parasite.
Single nucleotide polymorphisms of the c-MYC gene’s relationship with formation of Burkitt’s lymphoma using bioinformatics analysis
Authors: Sati Anfal Osama Mohamed , Osman Weaam Anwer , Ahmedon Enas Abdalla Mohammed , Yousif Safa Hamed Elneel , Khairi Enas Dawoud , Hassan Alaa Ibrahim Mohammed , Elsammani Moshtaha Ali Ibrahim , Salih Mohamed Ahmed 
Published: October 2018

AbstractBurkitt’s lymphoma (BL) is an aggressive form of non-Hodgkin lymphoma, originates from germinal center B cells, MYC gene (MIM ID 190080) is an important proto-oncogene transcriptional factor encoding a nuclear phosphoprotein for central cellular processes. Dysregulated expression or function of c-MYC is one of the most common abnormalities in BL. This study focused on the investigation of the possible role of single nucleotide polymorphisms (SNPs) in MYC gene associated with formation of BL.MYC SNPs were obtained from NCBI database. SNPs in the coding region that are non-synonymous (nsSNPs) were analysed by multiple programs such as SIFT, Polyphen2, SNPs&GO, PHD-SNP and I-mutant. In this study, a total of 286 Homo sapiens SNPs were found. Roughly, forty-eight of them were deleterious and were furtherly investigated.Eight SNPs were considered most disease causing [rs4645959 (N26S), rs4645959 (N25S), rs141095253 (P396L), rs141095253 (P397L), rs150308400 (C233Y), rs150308400 (C147Y), rs150308400 (C147Y), rs150308400 (C148Y)] according to the four softwares used. Two of which have not been reported previously [rs4645959 (N25S), rs141095253 (P396L)]. SNPs analysis helps is a diagnostic marker which helps in diagnosing and consequently, finding therapeutics for clinical diseases. This is through SNPs genotyping arrays and other techniques. Thus, it is highly recommended to confirm the findings in this study in vivo and in vitro.
Antigen-specific T-cell receptor signatures of cytomegalovirus infection
Authors: Huth Alina , Liang Xiaoling , Krebs Stefan , Blum Helmut , Moosmann Andreas 
Published: October 2018

AbstractCytomegalovirus (CMV) is a prevalent human pathogen. The virus cannot be eliminated from the body, but is kept in check by CMV-specific T cells. Patients with an insufficient T-cell response, such as transplant recipients, are at high risk of developing CMV disease. However, the CMV-specific T-cell repertoire is complex, and is not yet clear which T cells protect best against virus reactivation and disease. Here we present a highly resolved characterization of CMV-specific CD8+ T cells based on enrichment by specific peptide stimulation and mRNA sequencing of their T-cell receptor β chains (TCRβ). Our analysis included recently identified T-cell epitopes restricted through HLA-C, whose presentation is resistant to viral immunomodulation, and well-studied HLA-B-restricted epitopes. In 8 healthy virus carriers, we identified a total of 1052 CMV-specific TCRβ chains. HLA-C-restricted, CMV-specific TCRβ clonotypes theex vivoT-cell response, and contributed the highest-frequency clonotype of the entire repertoire in 2 of 8 donors. We analyzed sharing and similarity of CMV-specific TCRβ sequences and identified 63 public or related sequences belonging to 17 public TCRβ families. In our cohort and in an independent cohort of 352 donors, the cumulative frequency of these public TCRβ family members was a highly discriminatory indicator of carrying both CMV infection and the relevant HLA type. Based on these findings, we propose CMV-specific TCRβ signatures as a biomarker for an antiviral T-cell response to identify patients in need of treatment and to guide future development of immunotherapy.
AGEpy: a Python package for computational biology
Authors: Metge Franziska , Sehlke Robert , Boucas Jorge 
Published: October 2018

AbstractSummary:AGEpy is a Python package focused on the transformation of interpretable data into biological meaning. It is designed to support high-throughput analysis of pre-processed biological data using either local Python based processing or Python based API calls to local or remote servers. In this application note we describe its different Python modules as well as its command line accessible toolsaDiff,abed,blasto,david, andobo2tsv.Availability:The open source AGEpy Python package is freely available at:https://github.com/mpg-age-bioinformatics/AGEpy.Contact:jorge.boucas@age.mpg.de
Silencing cathepsin L expression reduces Myzus persicae protein content and the nutritional value as prey for Coccinella septempunctata
Authors: Rauf Imran , Asif Muhammad , Amin Imran , Naqvi Rubab Zahra , Umer Noroza , Mansoor Shahid , Jander Georg 
Published: October 2018

AbstractGut-expressed aphid genes, which may be more easily inhibited by RNA interference (RNAi) constructs, are attractive targets for pest control efforts involving transgenic plants. Here we show that expression of cathepsin L, a cysteine protease that functions in aphid guts, can be reduced by expression of an RNAi construct in transgenic tobacco. The effectiveness of this approach is demonstrated by up to 80% adult mortality, reduced fecundity, and delayed nymph production of Myzus persicae (green peach aphids) when cathepsin L expression was reduced by plant-mediated RNAi. Consistent with the function of cathepsin L as a gut protease, M. persicae fed on the RNAi plants had a lower protein content in their bodies and excreted more protein in their honeydew. Larvae of Coccinella septempunctata (seven-spotted ladybugs) grew more slowly on aphids having reduced cathepsin L expression, suggesting that prey insect nutritive value, and not just direct negative effects of the RNAi construct, needs to be considered when producing transgenic plants for RNAi-mediated pest control.HighlightsSilencing expression of cathepsin L by RNA interference reduces protein content of Myzus persicae (green peach aphid) bodies.Honeydew of aphids with cathepsin L silenced contains elevated protein.Cathepsin L is required for efficient protein uptake from phloem sap.Aphids with cathepsin L expression silenced have increased mortality and fewer offspring.Coccinella septempunctata (seven-spotted ladybugs) grow more slowly on aphids with expression of cathepsin L silenced.
CFP-1 interacts with HDAC1/2 complexes inC. elegansdevelopment
Authors: Pokhrel Bharat , Chen Yannic , Biro Jonathan Joseph 
Published: October 2018

AbstractCFP-1 (CXXC finger binding protein 1) is an evolutionarily conserved protein that binds to non-methylated CpG-rich promoters in humans andC. elegans. This conserved epigenetic regulator is a part of the COMPASS complex that contains the H3K4me3 methyltransferase SET1 in mammals and SET-2 inC. elegans. Previous studies have indicated the importance ofcfp-1in embryonic stem cell differentiation and cell fate specification. However, neither the function nor the mechanism of action ofcfp-1is well understood at the organismal level. To further investigate the function of CFP-1, we have characterisedC. elegansCOMPASS mutantscfp-1(tm6369)andset-2(bn129). We found that bothcfp-1andset-2play an important role in the regulation of fertility and development of the organism. Furthermore, we found that bothcfp-1andset-2are required for H3K4 trimethylation and play a repressive role in the expression of heat shock and salt-inducible genes. Interestingly, we found thatcfp-1but notset-2genetically interacts with Histone Deacetylase (HDAC1/2) complexes to regulate fertility, suggesting a function of CFP-1 outside of the COMPASS complex. Additionally we found thatcfp-1andset-2acts on a separate pathways to regulate fertility and development ofC. elegans. Our results suggest that CFP-1 genetically interacts with HDAC1/2 complexes to regulate fertility, independent of its function within COMPASS complex. We propose that CFP-1 could cooperate with COMPASS complex and/or HDAC1/2 in a context dependent manner.
Self-Organized Critical Control of Genome Expression: Novel Scenario on Cell-Fate Decision
Authors: Tsuchiya Masa , Giuliani Alessandro , Yoshikawa Kenichi 
Published: October 2018

AbstractIn our current studies on whole genome expression in several biological processes, we have demonstrated the actual existence of self-organized critical control (SOC) of gene expression at both population and single cell level. SOC allows for cell-fate change by critical transition encompassing the entire genome expression that, in turn, is partitioned into distinct response domains (critical states).In this paper, we go more in depth into the elucidation of SOC control of genome expression focusing on the determination of critical point (CP) and associated distinct critical states in single-cell genome expression. This leads us to the proposal of a potential universal model with genome-engine mechanism for cell-fate change. Our findings suggest that the CP is fixed point in terms of temporal expression variance, where the CP (set of critical genes) becomes active (ON) for cell-fate change (‘super-critical’ in genome-state) or else inactive (OFF) state (‘sub-critical’ in genome-state); this may lead to a novel scenario of the cell-fate control through activating or inactivating CP.
Somatic Evolution Introduces Distinctive Changes in Proteome Composition in Cancer Types
Authors: Tsuber Viktoriia 
Published: October 2018

AbstractOn the proteome level, somatic evolution in cancer is asymmetric, with several amino acids being irreversibly lost and the others gained across cancer types. However, though the gains and losses of amino acids are consistent in multiple cancer types, their magnitudes and prevalences differ. Here, we analyzed data on circa three million amino acid substitutions in the Catalogue of Somatic Mutations in Cancer (COSMIC) database to investigate profiles of gains and losses of amino acids in 23 human cancer types. We found characteristic differences in amino acid gain/loss profiles in the cancer types, with several of them demonstrating very specific profiles of proteome alterations associated with distinct endogenous or exogenous factors.
Genetic characterization of chytrids isolated from larval amphibians collected in central and east Texas
Authors: Marshall Thomas L. , Baca Carlos R. , Correa Decio T. , Forstner Michael R. J. , Hahn Dittmar , Rodriguez David 
Published: October 2018

ABSTRACTChytridiomycosis, an emerging infectious disease caused by the fungal pathogenBatrachochytrium dendrobatidis(Bd), has caused amphibian population declines worldwide.Bdwas first described in the 1990s and there are still geographic gaps in the genetic analysis of this globally distributed pathogen. Relatively few genetic studies have focused on regions whereBdexhibits low virulence, potentially creating a bias in our current knowledge of the pathogen’s genetic diversity. Disease-associated declines have not been recorded in Texas (USA), yetBdhas been detected on amphibians in the state. These strains have not been isolated and characterized genetically; therefore, we isolated, cultured, and genotypedBdfrom central Texas and compared isolates to a panel of previously genotyped strains distributed across the Western Hemisphere. We also isolated other chytrids not known to infect amphibians from east Texas. To identify larval amphibian hosts, we sequenced part of the COI gene. Among 37Bdisolates from Texas, we detected 19 unique multi-locus genotypes, but found no genetic structure associated with host species, Texas localities, or across North America. Isolates from central Texas exhibit high diversity and genetically cluster withBd-GPL isolates from the western U.S. that have caused amphibian population declines. This study genetically characterizes isolates ofBdfrom the south central U.S. and adds to the global knowledge ofBdgenotypes.
The impact of data reduction and lossy image formats on electron microscope images
Authors: Eng Edward T. , Kopylov Mykhailo , Negro Carl J. , Dallaykan Sarkis , Rice William J. , Jordan Kelsey D. , Kelley Kotaro , Carragher Bridget , Potter Clinton S. 
Published: October 2018

AbstractRecent advances in instrumentation and software for cryoEM have increased the applicability and utility of this method. Coupled with the adoption of automated pipelines, significant infrastructure support is required to sustain high throughput workflows. In particular, data generation rates may outpace the ability to deploy data storage and archival solutions. We have investigated what effects data compression and conversion to different file formats have on the ability to obtain high resolution cryoEM reconstructions. Standard lossless data compression strategies have a high impact on reducing the size of direct detector electron counting movie stacks, but provide more modest gains for aligned summed images. We show that EM images can be compressed using standard lossy methods to reduce file storage to 5–10% of the size of the original aligned sum or movie stack file and yet still retain enough information such that modern image processing pipelines will provide sub-2Å reconstructions from the compressed data.
Integrated in vivo quantitative proteomics and nutrient tracing reveals age-related metabolic rewiring of pancreatic β-cell function
Authors: Wortham Matthew , Benthuysen Jacqueline R. , Wallace Martina , Savas Jeffrey N. , Mulas Francesca , Divakaruni Ajit S. , Liu Fenfen , Albert Verena , Taylor Brandon L. , Sui Yinghui , Saez Enrique , Murphy Anne N. , Yates John R. , Metallo Christian M. , Sander Maike 
Published: October 2018

SummaryPancreatic β-cell physiology changes substantially throughout life; yet, the mechanisms that drive these changes are poorly understood. Here, we performed comprehensive in vivo quantitative proteomic profiling of pancreatic islets from adolescent and one-year-old mice. The analysis revealed striking differences in abundance of enzymes controlling glucose metabolism. We show that these changes in protein abundance are associated with higher activities of glucose metabolic enzymes involved in coupling factor generation as well as increased activity of the coupling factor-dependent amplifying pathway of insulin secretion. Nutrient tracing and targeted metabolomics demonstrated accelerated accumulation of glucose-derived metabolites and coupling factors in islets from one-year-old mice, indicating that age-related changes in glucose metabolism contribute to improved glucose-stimulated insulin secretion with age. Together, our study provides the first in-depth characterization of age-related changes in the islet proteome and establishes metabolic rewiring as an important mechanism for age-associated changes in β-cell function.
Lipid unsaturation properties govern the sensitivity of membranes to photo-induced oxidative stress
Authors: Bour A. , Kruglik S. G. , Chabanon M. , Rangamani P. , Puff N. , Bonneau S. 
Published: October 2018

ABSTRACTUnsaturated lipid oxidation is a fundamental process involved in different aspects of cellular bioenergetics; dysregulation of lipid oxidation is often associated with cell aging and death. In order to study how lipid oxidation affects membrane biophysics, we used a chlorin photosensitizer to oxidize vesicles of various lipid compositions and degree of unsaturation in a controlled manner. We observed different shape transitions that can be interpreted as an increase in the area of the targeted membrane followed by a decrease. These area modifications induced by the chemical modification of the membrane upon oxidation, were followed in situ by Raman Tweezers Microspectroscopy (RTM). We found that the membrane area increase corresponds to the lipids peroxidation and is initiated by the delocalization of the targeted double bonds in the tails of the lipids. The subsequent decrease of membrane area can be explained by the formation of cleaved secondary products. As a result of these area changes, we observe vesicle permeabilization after a time lag that is characterized in relation with the level of unsaturation. The evolution of photosensitized vesicle radius was measured and yields an estimation of the mechanical changes of the membrane over oxidation time. The membrane is both weakened and permeabilized by the oxidation. Interestingly, the effect of unsaturation level on the dynamics of vesicles undergoing photooxidation is not trivial and thus carefully discussed. Our findings shed light on the fundamental dynamic mechanisms underlying the oxidation of lipid membranes, and highlight the role of unsaturations on their physical and chemical properties
A Thermodynamic Limit on the Role of Self-Propulsion in Enhanced Enzyme Diffusion
Authors: Feng Mudong , Gilson Michael K. 
Published: October 2018

AbstractA number of enzymes reportedly exhibit enhanced diffusion in the presence of their substrates, with a Michaelis-Menten-like concentration dependence. Although no definite explanation of this phenomenon has emerged, a physical picture of enzyme self-propulsion using energy from the catalyzed reaction has been widely considered. Here, we present a kinematic and thermodynamic analysis of enzyme self-propulsion that is independent of any specific propulsion mechanism. Using this theory, along with biophysical data compiled for all enzymes so far shown to undergo enhanced diffusion, we show that the propulsion speed required to generate experimental levels of enhanced diffusion exceeds the speeds of well-known active biomolecules, such as myosin, by several orders of magnitude. Furthermore, the minimum power dissipation required to account for enzyme enhanced diffusion by self-propulsion markedly exceeds the chemical power available from enzyme-catalyzed reactions. Alternative explanations for the observation of enhanced enzyme diffusion therefore merit stronger consideration.