bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unfolding and identification of membrane proteins in situ
Authors: Galvanetto Nicola , Ye Zhongjie. , Marchesi Arin , Mortal Simone , Maity Sourav , Laio Alessandro , Torre Vincent 
Published: August 2019

AbstractSingle-molecule force spectroscopy (SMFS) uses the cantilever tip of an AFM to apply a force able to unfold a single protein. The obtained force-distance curve encodes the unfolding pathway, and from its analysis it is possible to characterize the folded domains. SMFS has been mostly used to study the unfolding of purified proteins, in solution or reconstituted in a lipid bilayer. Here, we describe a pipeline for analyzing membrane proteins based on SMFS, that involves the isolation of the plasma membrane of single cells and the harvesting of force-distance curves directly from it. We characterized and identified the embedded membrane proteins combining, within a Bayesian framework, the information of the shape of the obtained curves, with the information from Mass Spectrometry and proteomic databases. The pipeline was tested with purified/reconstituted proteins and applied to five cell types where we classified the unfolding of their most abundant membrane proteins. We validated our pipeline by overexpressing 4 constructs, and this allowed us to gather structural insights of the identified proteins, revealing variable elements in the loop regions. Our results set the basis for the investigation of the unfolding of membrane proteins in situ, and for performing proteomics from a membrane fragment.
Parallel genomic architecture underlies repeated sexual signal divergence in HawaiianLaupalacrickets
Authors: Blankers Thomas , Oh Kevin P. , Shaw Kerry L. 
Published: August 2019

ABSTRACTWhen the same phenotype evolves repeatedly, we can explore the predictability of genetic changes underlying phenotypic evolution. Theory suggests that genetic parallelism is less likely when phenotypic changes are governed by many small-effect loci compared to few of major effect, because different combinations of genetic changes can result in the same quantitative outcome. However, some genetic trajectories might be favored over others, making a shared genetic basis to repeated polygenic evolution more likely. To examine this, we studied the genetics of parallel male mating song evolution in the Hawaiian cricketLaupala. We compared quantitative trait loci (QTL) underlying song divergence in three species pairs varying in phenotypic distance. We tested whether replicated song divergence between species involves the same QTL and the likelihood that sharing QTL is related to phenotypic effect sizes. Contrary to theoretical predictions, we find substantial parallelism in polygenic genetic architectures underlying repeated song divergence. QTL overlapped more than expected based on simulated QTL analyses. Interestingly, QTL effect size did not predict QTL sharing, but did correlate with magnitude of phenotypic divergence. We highlight potential mechanisms driving these constraints on cricket song evolution and discuss a scenario that consolidates empirical quantitative genetic observations with micro-mutational theory.
Correlation of Infinium HumanMethylation450K and MethylationEPIC BeadChip arrays in cartilage
Authors: Cheung Kathleen , Burgers Marjolein J. , Young David A. , Cockell Simon , Reynard Louise N. 
Published: August 2019

AbstractBackgroundDNA methylation of CpG sites is commonly measured using Illumina Infinium BeadChip platforms. The Infinium MethylationEPIC array has replaced the Infinium Methylation450K array. The two arrays use the same technology, with the EPIC array assaying 865859 CpG sites, almost double the number of sites present on the 450K array. In this study, we compare DNA methylation values of shared CpGs of the same human cartilage samples assayed using both platforms.MethodsDNA methylation was measured in 21 human cartilage samples using the Illumina Infinium Methylation450K BeadChip and the Infinium methylationEPIC array. Additional matched 450K and EPIC data in whole tumour and whole blood were downloaded from GEO GSE92580 and GSE86833 respectively. Data were processed using the Bioconductor package Minfi. Additionally, DNA methylation of six CpG sites was validated for the same 21 cartilage samples by use of pyrosequencing.ResultsIn cartilage samples, overall sample correlations between methylation values generated by the two arrays were high (Pearson correlation coefficient r > 0.96). However, 50.5% of CpG sites showed poor correlation (r < 0.2) between arrays. Sites with limited variance and with either very high or very low methylation levels in cartilage exhibited lower correlation values, corroborating prior studies in whole blood. Bisulfite pyrosequencing did not highlight one array as generating more accurate methylation values that the other. For a specific CpG site, the array methylation correlation coefficient differed between cartilage, tumour and whole blood, reflecting the difference in methylation variance between cell types. These patterns can be observed across different tissues with different CpG site variances. When performing differential methylation analysis, the mean probe correlation co-efficient increased with increasing Δβ threshold used.ConclusionCpG sites with low variability within a tissue showed poor reproducibility between arrays. However, variance and thus reproducibility differs across different tissue types. Therefore, researchers should be cautious when analysing methylation of CpG sites that show low methylation variance within the cell type of interest, regardless of platform or method used to assay methylation.
Cellular contractile forces are non-mechanosensitive
Authors: Feld Lea , Kellerman Lior , Mukherjee Abhishek , Livne Ariel , Bouchbinder Eran , Wolfenson Haguy 
Published: August 2019

AbstractCells’ ability to apply contractile forces to their environment and to sense its mechanical properties (e.g. rigidity) are among their most fundamental features. Yet, the interrelations between contractility and mechanosensing, in particular whether contractile force generation depends on mechanosensing, are not understood. We use theory and extensive experiments to study the time evolution of cellular contractile forces and show that they are generated by time-dependent actomyosin contractile displacements that are independent of the environment’s rigidity. Consequently, contractile forces are non-mechanosensitive. We further show that the force-generating displacements are directly related to the evolution of the actomyosin network, most notably to the time-dependent concentration of F-actin. The emerging picture of force generation and mechanosensitivity offers a unified framework for understanding contractility.One Sentence SummaryCellular contractile forces are generated by rigidity-independent displacements that are determined by the time evolution of F-actin assembly.
The potentials and pitfalls of a human cervical organoid model including Langerhans cells
Authors: Jackson Robert , Lukacs Jordan D , Zehbe Ingeborg 
Published: August 2019

AbstractThree-dimensional cell culturing to capture a life-like experimental environment has become a versatile tool for basic and clinical research. Mucosal and skin tissues can be grown as “organoids” in a petri dish and serve a wide variety of research questions. Here, we report our experience with human cervical organoids which could also include an immune component, e.g. Langerhans cells. We employ commercially available human cervical keratinocytes and fibroblasts as well as a myeloid cell line matured and purified into langerin-positive Langerhans cells. These are then seeded on a layer of keratinocytes with underlying dermal equivalent. Using about 10-fold more than the reported number in healthy cervical tissue (1–3%), we obtain differentiated cervical epithelium after 14 days with ~ 1% being Langerhans cells. We provide a detailed protocol for interested researchers to apply the described “aseptic” organoid model for all sorts of investigations—with or without Langerhans cells.
Defects in the assembly of ribosomes selected for β-amino acid incorporation
Authors: Ward Fred R. , Watson Zoe L. , Ad Omer , Schepartz Alanna , Cate Jamie H. D. 
Published: August 2019

AbstractRibosome engineering has emerged as a promising field in synthetic biology, particularly concerning the production of new sequence-defined polymers. Mutant ribosomes have been developed that improve the incorporation of several non-standard monomers including D-amino acids, dipeptides, and β-amino acids into polypeptide chains. However, there remains little mechanistic understanding of how these ribosomes catalyze incorporation of these new substrates. Here we probed the properties of a mutant ribosome–P7A7–evolved for betterin vivoβ-amino acid incorporation throughin vitrobiochemistry and cryo-electron microscopy. Although P7A7 is a functional ribosomein vivo, it is inactivein vitro, and assembles poorly into 70S complexes. Structural characterization revealed large regions of disorder in the peptidyltransferase center and nearby features, suggesting a defect in assembly. Comparison of RNA helix and ribosomal protein occupancy with other assembly intermediates revealed that P7A7 is stalled at a late stage in ribosome assembly, explaining its weak activity. These results highlight the importance of ensuring efficient ribosome assembly during ribosome engineering towards new catalytic abilities.
Accounting for Gene Flow from Unsampled ‘Ghost’ Populations while Estimating Evolutionay History under the Isolation with Migration Model
Authors: Sethuraman Arun , Lynch Melissa 
Published: August 2019

AbstractUnsampled or extinct ‘ghost’ populations leave signatures on the genomes of individuals from extant, sampled populations, especially if they have exchanged genes with them over evolutionary time. This gene flow from ‘ghost’ populations can introduce biases when estimating evolutionary history from genomic data, often leading to data misinterpretation and ambiguous results. Here we assess these biases while accounting, or not accounting for gene flow from ‘ghost’ populations under the Isolation with Migration (IM) model. We perform extensive simulations under five scenarios with no gene flow (Scenario A), to extensive gene flow to- and from- an unsampled ‘ghost’ population (Scenarios B, C, D, and E). Estimates of evolutionary history across all scenarios A-E (effective population sizes, divergence times, and migration rates) indicate consistent a) under-estimation of divergence times between sampled populations, (b) over-estimation of effective population sizes of sampled populations, and (c) under-estimation of migration rates between sampled populations, with increased gene flow from the unsampled ‘ghost’ population. Without accounting for an unsampled ‘ghost’, summary statistics likeFSTare under-estimated, andπis over-estimated with increased gene flow from the‘ghost’. To show this persistent issue in empirical data, we use a 355 locus dataset from African Hunter-Gatherer populations and discuss similar biases in estimating evolutionary history while not accounting for unsampled ‘ghosts’. Considering the large effects of gene flow from these ‘ghosts’, we propose a multi-pronged approach to account for the presence of unsampled ‘ghost’ populations in population genomics studies to reduce erroneous inferences.
A molecular switch for Cdc48 activity and localization during oxidative stress and aging
Authors: Radzinski Meytal , Yogev Ohad , Yesharim Yarden , Brielle Esther S. , Israeli Ran , Fassler Rosi , Melamed-Book Naomi , Shai Nadav , Arkin Isaiah T. , Pick Elah , Ravid Tommer , Schuldiner Maya , Reichmann Dana 
Published: August 2019

SummaryControl over a healthy proteome begins with the birth of the polypeptide chain and ends with coordinated protein degradation. One of the major players in eukaryotic protein degradation is the essential and highly conserved ATPase, Cdc48 (p97/VCP in mammals). Cdc48 mediates clearance of misfolded proteins from the nucleus, cytosol, ER, mitochondria, and more. Here we dissect the crosstalk between cellular oxidation and Cdc48 activity by identification of a redox-sensitive site, Cys115. By integrating proteomics, biochemistry, microscopy, and bioinformatics, we show that removal of Cys115’s redox-sensitive thiol group leads to accumulation of Cdc48 in the nucleus and consequently, results in severe defects in the oxidative stress response, mitochondrial fragmentation, and a decrease in ERAD and sterol biogenesis. We have thus identified a unique redox switch in Cdc48, which may provide a clearer picture of the importance of Cdc48’s localization in maintaining a “healthy” proteome during oxidative stress and chronological aging in yeast.
Estimation of Global and Local Complexities of Brain Networks: A Random Walks Approach
Authors: Sotero Roberto C. , Sanchez-Rodriguez Lazaro M. , Moradi Narges 
Published: August 2019

AbstractThe complexity of brain activity has been observed at many spatial scales and there exists increasing evidence supporting its use in differentiating between mental states and disorders. Here we proposed a new measure of network (global) complexity that is constructed as the sum of the complexities of its nodes (i.e, local complexity). The local complexity of each node is regarded as an index that compares the sample entropy of the time series generated by the movement of a random walker on the network resulting from removing the node and its connections, with the sample entropy of the time series obtained from a regular lattice (the ordered state) and an Erdös-Renyi network (disordered state). We studied the complexity of fMRI-based resting-state functional networks. We found that positively correlated, or “pos”, network comprising only the positive functional connections has higher complexity than the anticorrelation (“neg”) network (comprising the negative functional connections) and the network consisting of the absolute value of all connections (“abs”). We also found a significant correlation between complexity and the strength of functional connectivity. For the pos network this correlation is significantly weaker at the local scale compared to the global scale, whereas for the neg network the link is stronger at the local scale than at the global scale, but still weaker than for the pos network. Our results suggest that the pos network is related to the information processing in the brain and should be used for functional connectivity analysis instead of the abs network as is usually done.
Differences in Early and Late Pattern-Onset Visual-Evoked Potentials between Self-Reported Migraineurs and Controls
Authors: Fong Chun Yuen , Crystal Law Wai Him , Braithwaite Jason , Mazaheri Ali 
Published: August 2019

AbstractStriped patterns have been shown to induce strong visual illusions and discomforts to migraineurs in the literature. Previous research has suggested that those unusual visual symptoms be linked with the hyperactivity on the visual cortex of migraine sufferers. The present study searched for evidence supporting this hypothesis by comparing the visual evoked potentials (VEPs) elicited by striped patterns of specific spatial frequencies (0.5, 3, and 13 cycles) between a group of 29 migraineurs (17 with aura/12 without) and 31 non-migraineurs. In addition, VEPs to the same stripped patterns were compared between non-migraineurs who were classified as hyperexcitable versus non-hyperexcitable using a previously established behavioural pattern glare task. We found that the migraineurs had a significantly increased N2 amplitude for stimuli with 13 cpd gratings but an attenuated late negativity (LN: 400 – 500 ms after the stimuli onset) for all the spatial frequencies. Interestingly, non-migraineurs who scored as hyperexcitable appeared to have similar response patterns. We proposed that the enhanced N2 could reflect disruption of the balance between parvocellular and magnocellular pathway, which is in support of a grating-induced cortical hyperexcitation mechanism on migraineurs. On the other hand, the attenuation of the late negativity could reflect a top-down feedback mechanism to suppress visual processing of an aversive stimulus.
Homeoprotein ENGRAILED-1 promotes motoneuron survival and motor functions
Authors: Vargas Abonce Stephanie E. , Lebœuf Mélanie , Moya Kenneth L. , Prochiantz Alain 
Published: August 2019

ABSTRACTMotoneuron degeneration leads to skeletal muscle denervation and impaired motor functions, yet the signals involved remain poorly understood. We find that extracellular ENGRAILED-1, a homeoprotein expressed in spinal cord V1 interneurons that synapse on α-motoneurons, has non-cell autonomous activity. Mice heterozygote for Engrailed-1 develop muscle weakness, abnormal spinal reflex and partial neuromuscular junction denervation. A single intrathecal injection of ENGRAILED-1 restores innervation, limb strength, extensor reflex and prevents lumbar α-motoneuron death for several months. The autophagy gene p62, which was found to network with Engrailed-1 and amyotrophic lateral sclerosis genes, is misregulated in Engrailed-1 heterozygote mice α-motoneurons and is rescued following ENGRAILED-1 injection. These results identify ENGRAILED-1 as an α-motoneuron trophic factor with long-lasting protective activity.
Identification ofEscherichia coliClpAP in regulating susceptibility to type VI secretion system-mediated attack byAgrobacterium tumefaciens
Authors: Lin (林筱涵) Hsiao-Han , Yu (余文廸) Manda , Sriramoju Manoj Kumar , Hsu (徐尚德) Shang-Te Danny , Liu (劉啟德) Chi-Te , Lai (賴爾珉) Erh-Min 
Published: August 2019

AbstractType VI secretion system (T6SS) is an effector delivery system used by gram-negative bacteria to kill other bacteria or eukaryotic host to gain fitness. InAgrobacterium tumefaciens, T6SS has been shown to kill other bacteria such asEscherichia coli. Interestingly, theA. tumefaciensT6SS killing efficiency differs when using differentE. colistrains as recipient cells. Thus, we hypothesize that a successful T6SS killing not only relies on attacker T6SS activity but also depends on recipient factors. A high-throughput interbacterial competition assay was employed to test the hypothesis by screening for mutants with reduced killing outcomes caused byA. tumefaciensstrain C58. From the 3909E. coliKeio mutants screened, 16 candidate mutants were filtered out. One strain, ΔclpP::Kan, showed ten times more resistant to T6SS-mediating killing but restored its susceptibility when complemented withclpP in trans. ClpP is a universal and highly conserved protease that exists in both prokaryotes and eukaryotic organelles. InE. coli, ClpP uses either ClpA or ClpX as an adaptor for substrate specificity. Therefore, the susceptibility of the ΔclpA::Kan and ΔclpX::Kan was also tested. The T6SS attack susceptibility of ΔclpA::Kan is at the same level as ΔclpP::Kan, while ΔclpX::Kan showed no difference as compared to that of wild-typeE. coliBW25113. The data also suggest that ClpA-ClpP interaction, rather than its protease activity, is responsible for enhancing susceptibility to T6SS killing. This study highlights the importance of recipient factors in determining the outcome of T6SS killing.
Low rate of follow-up colonoscopy after positive results of colorectal cancer screening in a Chinese urban core district
Authors: Guo Yawen , Jiang Qingwu , Tanimoto Tetsuya , Kami Masahiro , Peng Peng , He Yongpin , Yang Xiaoming , Zhang Xin , Gao Wenjun , Wang Yanming , Chu Xiaoting , Wang Yunhui , Kato Shigeaki , Ding Xiaocao 
Published: August 2019

AbstractColorectal cancer (CRC) is one of the most common cancers in China. In 2003, a systematic CRC registry that enables the determination of CRC incidence and mortality and a CRC screening project were introduced in the Jing’an district of Shanghai by the municipal government. This study assessed the registry data to determine the status of CRC and CRC screening rates in the core district of an urban area of China. Data were retrieved from the Official registry information systems of Jing’an district Shanghai Cance. The incidence and mortality of CRC, as well as population-based CRC screening rates, were analysed. Individuals who screened positive for CRC based upon results of a high-risk factor questionnaire (HRFQ) and a faecal immunochemical test (FIT) were selected for follow-up colonoscopy (CSPY). From the registry data collected between 2003 and 2013, the standardized incidence rate was 26.44/105, with a significant gender difference. The CRC standardized mortality rate was 10.08/105. In 2013, 17,866 individuals (21.6%) enrolled for CRC screening among the 82,602 candidate residents. The positive screening rate was 16.28% (2909/17866). Among the 2909 positives, 508 (17.5%) underwent follow-up CSPY. In 41.3% of these individuals (210/508), abnormal lesions were detected. Of these, 8 (1.57%) lesions were diagnosed as CRC, and 142 (28.0%) were identified as precancerous lesions. During the assessment period, both the incidence and mortality of CRC in the Jing’an district were determined in the area of high CRC prevalence in Chin. Nevertheless, the rate of participation in CRC screening was low (21.6%), and the rate of participation in follow-up CSPY for individuals who screened positive was only 17.5%. Improved participation in CRC screening and follow-up CSPY is expected to lower the incidence and mortality of CRC significantly in the rural areas of China. (288)
Epicuticular wax lipid composition of endemic European Betula species and its application to chemotaxonomy and paleobotany
Authors: Weber J. , Schwark L. 
Published: August 2019

AbstractPlants, in particular trees with specific habitat demands are excellent indicators of climate state. Vegetation successions in subrecent and deep geologic time is recorded in fossil macro-remains or pollen accumulating in geological archives like limnic and marine sediments, peat bogs and mires. Birch trees in Europe form a major part in plant successions and constitute the dwarf species Betula nana and Betula humilis representing cold-adapted habitats or climates and two tree birches, Betula pubescens and Betula pendula characteristic for temperate habitats or climates. These birch species exhibit highly similar pollen shape and size, preventing their unambiguous application as paleoclimate/paleovegetation proxies. We here present a chemotaxonomic differentiation of the four European birch species based on their epicuticular wax lipids. The dominating lipid classes in epicuticular birch waxes were found to be n-alkanes (in the range of n-C23 to n-C33), straight-chain primary alcohols and fatty acids (in the range of n-C20 to n-C32), and long-chain wax ester (in the range of n-C38 to n-C46) in variable amounts and distributions. When preserved in geological archives these lipids may serve in paleovegetation/paleoclimate reconstruction. Long-chain wax esters are susceptible to hydrolysis and upon diagenesis the release of ester-bound alcohols and fatty acids may modify the distribution pattern of the corresponding primary free lipids. Quantitative analysis of the hydrolyzable wax ester proportion revealed primary distribution patterns of birch lipids not to change substantially upon release of bound analogues. The specific composition and abundance of epicuticular wax lipids facilitates unambiguous chemotaxonomic separation of the four European birch species. Wax lipid-based discrimination in field application, however, is complicated by mixing of alkyl lipids derived from different birch species and contribution of wax lipids from other plants. In cases, where palynology indicates a high contribution of Betula species to European vegetation associations, wax lipids may serve for differentiation of the species contributing.