bluuebunny/crossref_metadata_2025_split huggingface dataset:
Independent Control of the Thermodynamic and Kinetic Properties of Aptamer Switches
Authors: Wilson Brandon D. , Hariri Amani A. , Thompson Ian A.P. , Eisenstein Michael , Soh H. Tom 
Published: July 2019

AbstractMolecular switches that change their conformation upon target binding offer powerful capabilities for biotechnology and synthetic biology. In particular, aptamers have proven useful as molecular switches because they offer excellent binding properties, undergo reversible folding, and can be readily engineered into a wide range of nanostructures. Unfortunately, the thermodynamic and kinetic properties of the aptamer switches developed to date are intrinsically coupled, such that high temporal resolution (i.e., switching time) can only be achieved at the cost of lower sensitivity or high background. Here, we describe a general design strategy that decouples the thermodynamic and kinetic behavior of aptamer switches to achieve independent control of sensitivity and temporal resolution. We used this strategy to generate an array of aptamer switches with effective dissociation constants (KD) ranging from 10 μM to 40 mM and binding kinetics ranging from 170 ms to 3 s—all generated from the same parent ATP aptamer. Our strategy is broadly applicable to other aptamers, enabling the efficient development of switches with characteristics suitable for diverse range of biotechnology applications.
Decoupling gene knockout effects from gene functions by evolutionary analyses
Authors: Liu Li , Liu Mengdi , Zhang Di , Deng Shanjun , Chen Piaopiao , Yang Jing , Xie Yunhan , He Xionglei 
Published: July 2019

AbstractGenic functions have long been confounded by pleiotropic mutational effects. To understand such genetic effects, we examine HAP4, a well-studied transcription factor inSaccharomyces cerevisiaethat functions by forming a tetramer with HAP2, HAP3, and HAP5. Deletion of HAP4 results in highly pleiotropic gene expression responses, some of which are clustered in related cellular processes (clustered effects) while most are distributed randomly across diverse cellular processes (distributed effects). Strikingly, the distributed effects that account for much of HAP4 pleiotropy tend to be non-heritable in a population, suggesting they have little evolutionary consequences. Indeed, these effects are poorly conserved in closely related yeasts. We further show substantial overlaps of clustered effects, but not distributed effects, among the four genes encoding the HAP2/3/4/5 tetramer. This pattern holds for other biochemically characterized yeast protein complexes or metabolic pathways. Examination of a set of cell morphological traits of the deletion lines yields consistent results. Hence, only some gene deletion effects support related biochemical understandings with the rest being pleiotropic and evolutionarily decoupled from the gene’s normal functions.
Partners in health? Investigating social genetic effects for married and cohabiting couples
Authors: Mandemakers Jornt , Otten Kasper 
Published: July 2019

Abstract‘Social contagion’ research suggests that health behaviors (BMI, smoking, drinking, etc.) spread through social networks, including dyadic ties such as between married/cohabiting partners. However, separating contagion from assortative mating (‘like seeks like’) and shared environmental factors remains notoriously difficult in observational studies. It is not possible to obtain exogenous variation in long-term partnerships (‘random mating’), but genetic approaches can offer a novel way to examine partner similarity and the role of social contagion. This paper explores possible social genetic effects among partners, i.e., effects of the partner’s genes on one’s own behavior. We use the longitudinal Health and Retirement Study with data on health behavior and genomic data for both ego and his/her partner to examine social genetic effects for BMI, drinking, and smoking behavior. For each outcome, we find support for social genetic effects. Americans of European descent were more overweight if they had partners with higher polygenic scores for BMI net of their own polygenic score. Similar findings were found for the number of drinks per week and cigarettes per day. Longitudinal analyses that conditioned on past health behavior of both spouses confirmed these findings. We further explored whether susceptibility to the partner’s influence differed between men and women, but did not find consistent differences across outcomes. Findings are further discussed in the light of ramifications of social genetic effects for the social and biological sciences.
Bayesian-Maximum-Entropy reweighting of IDP ensembles based on NMR chemical shifts
Authors: Crehuet Ramon , Buigues Pedro J. , Salvatella Xavier , Lindorff-Larsen Kresten 
Published: July 2019

AbstractBayesian and Maximum Entropy approaches allow for a statistically sound and systematic fitting of experimental and computational data. Unfortunately, assessing the relative confidence in these two types of data remains difficult as several steps add unknown error. Here we propose the use of a validation-set method to determine the balance, and thus the amount of fitting. We apply the method to synthetic NMR chemical shift data of an intrinsically disordered protein. We show that the method gives consistent results even when other methods to assess the amount of fitting cannot be applied. Finally, we also describe how the errors in the chemical shift predictor can lead to an incorrect fitting and how using secondary chemical shifts could alleviate this problem.
Lake overturn as a key driver for methane oxidation
Authors: Zimmermann M. , Mayr M. J. , Bouffard D. , Eugster W. , Steinsberger T. , Wehrli B. , Brand A. , Bürgmann H. 
Published: July 2019

AbstractMany seasonally stratified lakes accumulate substantial amounts of the greenhouse gas methane in the anoxic zone. Methane oxidizing bacteria in the water column act as a converter, oxidizing methane into carbon dioxide and biomass before it reaches the atmosphere. Current observations and estimates of this methane oxidation efficiency are diverging, especially for the lake overturn period. Here we combine a model of turbulent mixing, gas exchange and microbial growth with a comprehensive data set for autumn mixing to quantify the relevant physical and microbial processes. We show that the microbial methane converter is effectively transforming the increased methane flux during the overturn period. Only rare events of pronounced surface cooling in combination with persistently strong wind can trigger substantial outgassing. In the context of climate change, these results suggest that changes in the frequency of storms may be even more important for methane emissions from temperate lakes than gradual warming.
Evaluating the ecological impacts of pesticide seed treatments on arthropod communities in a grain crop rotation
Authors: Dubey Aditi , Lewis Margaret T. , Dively Galen P. , Hamby Kelly A. 
Published: July 2019

AbstractWhile many studies have investigated non-target impacts of neonicotinoid seed treatments (NSTs), they usually take place within a single crop and focus on specific pest or beneficial arthropod taxa.We compared the impacts of three seed treatments to an untreated control: imidacloprid + fungicide products, thiamethoxam + fungicide products, and fungicide products alone in a three-year crop rotation of full-season soybean, winter wheat, double-cropped soybean and maize. Specifically, we quantified neonicotinoid residues in the soil and in weedy winter annual flower buds and examined treatment impacts on soil and foliar arthropod communities, and on plant growth and yield.Trace amounts of insecticide were found in winter annual flowers of one species in one site year, which did not correspond with our treatments. Although low levels of insecticide residues were present in the soil, residues were not persistent. Residues were highest in the final year of the study, suggesting some accumulation.We observed variable impacts of NSTs on the arthropod community; principle response curve analysis, diversity and evenness values exhibited occasional community disturbances, and treatments impacted the abundance of various taxa. Overall, imidacloprid had a greater effect than thiamethoxam, with the fungicide only treatment also occasionally impacting communities and individual taxa.Pest pressure was low throughout the study, and although pest numbers were reduced by the insecticides no corresponding increases in yield were observed. However, the fungicide products contributed to higher yields in wheat.Synthesis and applications. Pesticide seed treatments can disturb arthropod communities, even when environmental persistence and active ingredient concentrations are low. The foliar community in wheat and maize exhibited a trend of increasing disturbance throughout the sampling period, suggesting that recovery from the impacts of NSTs is not always rapid. Our study is among the first to demonstrate that seed applied fungicides alone can disrupt arthropod communities in agroecosystems and highlights the need for further investigation into the impacts of seed applied fungicides.
Effects of nicotine on the thermodynamics of the DPPC phase coexistence region
Authors: Vieira Ernanni D. , Costa-Filho A. J. , Basso Luis. G. M. 
Published: July 2019

ABSTRACTPhase separation plays critical roles in several membrane functions, and reduction or disappearance of phase coexistence by action of membrane-interacting molecules have been implicated in membrane function impairment. Here, we applied differential scanning calorimetry, electron paramagnetic resonance (EPR), and non-linear least-squares (NLLS) spectral simulations to study the effects of nicotine, a parasympathomimetic drug, on the two-phase coexistence of dipalmitoyl phosphatidylcholine (DPPC) lipid membrane. The thermodynamic quantities describing the DPPC phase coexistence are temperature dependent, giving rise to non-linear van’t Hoff behavior. Our results showed that nicotine preferentially binds to the fluid phase and modifies the enthalpy and entropy changes of the DPPC heat capacity profile, while marginally perturbing the homogeneous gel and fluid phases. An EPR/NLLS/van’t Hoff analysis of the DPPC phase coexistence revealed that nicotine significantly modified the temperature dependence of the free energy change of the two-phase equilibrium from a cubic to a parabolic behavior, resulting in an alteration of the thermodynamical driving force and the balance of the non-covalent interactions of the lipids in equilibrium. The thermotropic behavior of the enthalpy, entropy, and heat capacity changes, as determined by EPR, indicated that nicotine modified the relative contributions of hydrogen-bonding, electrostatic interactions, and conformational entropy of the lipids to the thermodynamics of the phase coexistence. The predominantly entropically-driven gel-fluid transition in nicotine-free DPPC changes to a temperature-triggered entropically-driven or enthalpically-driven process in nicotine-bound DPPC. Further applications of this thermodynamic EPR/NLLS/van’t Hoff analysis are discussed.
Delineating the site of interaction on the intracellular domain of 5-HT3A receptors with the chaperone protein RIC-3
Authors: Pirayesh Elham , Stuebler Antonia G. , Pandhare Akash , Jansen Michaela 
Published: July 2019

ABSTRACTThe serotonin type 3A (5-HT3A) receptor is a homopentameric cation-selective member of the pentameric ligand-gated ion channel (pLGIC) superfamily. Members of this superfamily assemble from five subunits, each of which consists of three domains, extracellular (ECD), transmembrane (TMD), and intracellular domain (ICD). Previously, we have also demonstrated that 5-HT3A-ICD is required and sufficient for the interaction between 5-HT3A and RIC-3. Additionally, we have shown that 5-HT3A-ICD fused to maltose binding protein (MBP) directly interacts with the chaperone protein resistance to inhibitors of choline esterase (RIC-3), without the involvement of other protein(s). To elucidate the molecular determinants of this interaction we developed different MBP-fused 5-HT3A-ICD constructs by deletion of large portions of its amino acid sequence. We have expressed seven mutants in Escherichia coli and purified them to homogeneity. Using a RIC-3 affinity pull-down assay, the interaction of MBP-5HT3A-ICD constructs and RIC-3 is investigated. Furthermore, we co-expressed 5-HT3A and 5-HT3AB, a heteromeric form of 5-HT3Rs, with RIC-3 in Xenopus oocytes to compare their interaction with RIC-3 in-vivo by two electrode voltage clamp (TEVC) recordings. Full-length 5-HT3A-and 5-HT3AB mediated currents are significantly reduced when RIC-3 is co-expressed in either condition. In summary, we identify a 24-amino acid long segment of the 5-HT3A-ICD as a molecular determinant for the interaction between the 5-HT3A-ICD and RIC-3.Statement of SignificanceThe chaperone protein RIC-3 is known to modulate the functional surface expression of cation-conducting pentameric ligand-gated ion channels. Previously we have demonstrated that the intracellular domain of serotonin channels mediates this effect. Here we provide experimental evidence for a 24-amino acid long segment within the 115-amino acid long intracellular domain as a determinant for RIC-3 interaction. Recently it was found experimentally that the identified segment contains an alpha helix that has been observed or predicted to be present in other cation-conducting channels. The present work provides novel insights into protein-protein interactions that are likely also relevant for other cation-conducting members of this large ion channel family that includes nACh and 5-HT3 receptors.
Metal bridge in S4 segment supports helix transition inShakerchannel
Authors: Bassetto Carlos A Z , Carvalho-de-Souza João Luis , Bezanilla Francisco 
Published: July 2019

ABSTRACTVoltage-gated ion channels play important roles in physiological processes, especially in excitable cells, where they shape the action potential. In S4-based voltage sensors voltage-gated channels, a common feature is shared: the transmembrane segment 4 (S4) contains positively charged residues intercalated by hydrophobic residues. Although several advances have been made in understating how S4 moves through a hydrophobic plug upon voltage changes, possible helix transition from α-to 310-helix in S4 during activation process is still unresolved. Here, we have mutated several hydrophobic residues from I360 to F370 in the S4 segment into histidine, ini, i+3andi, i+6ori, i+4andi, i+7pairs, to favor 310- or α-helical conformations, respectively. We have taken advantage that His can be coordinated by Zn+2to promote metal ion bridges and we have found that the histidine introduced at position 366 (L366H) can interact with the introduced histidine at position 370 (stabilizing that portion of the S4 segment in α-helical conformation). In presence of 20 μM of Zn+2, the activation currents of L366H:F370H channels were slowed down by a factor of 3.5, the voltage-dependence is shifted by 10 mV towards depolarized potentials with no change on the deactivation time constant. Our data supports that by stabilizing a region of the S4 segment in α-helical conformation a closed(resting or intermediate)state is stabilized rather than destabilizing the open (active)state. Taken together, our data indicates that the S4 undergoes α-helical conformation to a short-lived different secondary structure transiently before reaching theactivestate in the activation process.STATEMENT OF SIGNIFICANCEConformational transitions between α-helix and 310-helix in the S4 segment ofShakerpotassium channel during gating has been under debate. The present study shows the coordination by Zn2+of a pair of engineered histidine residues (L366H:F370H) in the intermediate region of S4 in Shaker, favoring α-helical conformation. In presence of 20μM of Zn+2the activation currents of L366H:F370H channels become slower, with 10 mV positive shift in the voltage-dependence and no effects on deactivation time constants suggesting a stabilization of a closed state rather than destabilization the open(active)state. Collectively, our data indicate that S4 undergoes secondary structure changes, including a short-lived secondary structure transition, when S4 moves from therestingto theactivestate during activation.
Testis single-cell RNA-seq reveals the dynamics ofde novogene transcription and germline mutational bias inDrosophila
Authors: Witt Evan , Benjamin Sigi , Svetec Nicolas , Zhao Li 
Published: July 2019

SummaryThe testis is a peculiar tissue in many respects. It shows patterns of rapid gene evolution and provides a hotspot for the origination of genetic novelties such asde novogenes, duplications and mutations. To investigate the expression patterns of genetic novelties across cell types, we performed single-cell RNA-sequencing of adultDrosophilatestis. We found that new genes were expressed in various cell types, the patterns of which may be influenced by their mode of origination. In particular, lineage-specificde novogenes are commonly expressed in early spermatocytes, while young duplicated genes are often bimodally expressed. Analysis of germline substitutions suggests that spermatogenesis is a highly reparative process, with the mutational load of germ cells decreasing as spermatogenesis progresses. By elucidating the distribution of genetic novelties across spermatogenesis, this study provides a deeper understanding of how the testis maintains its core reproductive function while being a hotbed of evolutionary innovation.
A novel metric reveals previously unrecognized distortion in dimensionality reduction of scRNA-seq data
Authors: Cooley Shamus M. , Hamilton Timothy , Aragones Samuel D. , Ray J. Christian J. , Deeds Eric J. 
Published: July 2019

AbstractHigh-dimensional data are becoming increasingly common in nearly all areas of science. Developing approaches to analyze these data and understand their meaning is a pressing issue. This is particularly true for single-cell RNA-seq (scRNA-seq), a technique that simultaneously measures the expression of tens of thousands of genes in thousands to millions of single cells. The emerging consensus for analysis workflows significantly reduces the dimensionality of the dataset before performing downstream analysis, such as assignment of cell types. One problem with this approach is that dimensionality reduction can introduce substantial distortion into the data; consider the familiar example of trying to represent the three-dimensional earth as a two-dimensional map. It is currently unclear if such distortion affects analysis of scRNA-seq data. Here, we introduce a straightforward approach to quantifying this distortion by comparing the local neighborhoods of points before and after dimensionality reduction. We found that popular techniques like t-SNE and UMAP introduce substantial distortion even for relatively simple simulated data sets. For scRNA-seq data, we found the distortion in local neighborhoods was often greater than 95% in the representations typically used for downstream analyses. This level of distortion can introduce errors into cell type identification, pseudotime ordering, and other analyses. We found that principal component analysis can generate accurate embeddings, but only when using dimensionalities that are much higher than typically used in scRNA-seq analysis. Our work suggests the need for a new generation of dimensional reduction algorithms that can accurately embed high dimensional data in its true latent dimension.
Alcohol preferring P rats exhibit aversion resistant drinking of alcohol adulterated with quinine
Authors: Timme Nicholas M. , Linsenbardt David , Timm Maureen , Galbari Taylor , Cornwell Ethan , Lapish Christopher 
Published: July 2019

AbstractUnderstanding why some people continue to drink alcohol despite negative consequences and others do not is a central problem in the study of alcohol use disorder (AUD). In this study, we used alcohol preferring P rats (a strain bred to prefer to drink alcohol, a model for genetic risk for AUD) and Wistars (control) to examine drinking despite negative consequences in the form of an aversive bitter taste stimuli produced by quinine. Animals were trained to consume 10% ethanol in a simple Pavlovian conditioning task that paired alcohol access with an auditory stimulus. When the alcohol was adulterated with quinine (0.1 g/L), P rats continued to consume alcohol+quinine at the same rate as unadulterated alcohol, despite a demonstrated aversion to quinine adulterated alcohol when given a choice between adulterated and unadulterated alcohol in the home cage. Conversely, Wistars decreased consumption of quinine adulterated alcohol in the task, but continued to try the alcohol+quinine solution at similar rates to unadulterated alcohol. These results indicate that following about 8 weeks of alcohol consumption P rats exhibit aversion resistant drinking. This model could be used in future work to explore how biological basis of alcohol consumption and genetic risk for excessive drinking lead to drinking that is resistant to devaluation.
Genomic risk score offers predictive performance comparable to clinical risk factors for ischaemic stroke
Authors: Abraham Gad , Malik Rainer , Yonova-Doing Ekaterina , Salim Agus , Wang Tingting , Danesh John , Butterworth Adam , Howson Joanna , Inouye Michael , Dichgans Martin 
Published: July 2019

AbstractRecent genome-wide association studies in stroke have enabled the generation of genomic risk scores (GRS) but the predictive power of these GRS has been modest in comparison to established stroke risk factors. Here, using a meta-scoring approach, we developed a metaGRS for ischaemic stroke (IS) and analysed this score in the UK Biobank (n=395,393; 3075 IS events by age 75). The metaGRS hazard ratio for IS (1.26, 95% CI 1.22-1.31 per standard deviation increase of the score) doubled that of previous GRS, enabling the identification of a subset of individuals at monogenic levels of risk: individuals in the top 0.25% of metaGRS had a three-fold increased risk of IS. The metaGRS was similarly or more predictive when compared to established risk factors, such as family history, blood pressure, body mass index and smoking status. For participants within accepted guideline levels for established stroke risk factors, we found substantial variation in incident stroke rates across genomic risk backgrounds. We further estimated combinations of reductions needed in modifiable risk factors for individuals with different levels of genomic risk and suggest that, for individuals with high metaGRS, achieving currently recommended risk factor levels may be insufficient to mitigate risk.