bluuebunny/crossref_metadata_2025_split huggingface dataset:
Backstepping mechanism of kinesin-1
Authors: Toleikis Algirdas , Carter Nicholas J. , Cross Robert A. 
Published: November 2019

AbstractKinesin-1 is an ATP-driven molecular motor that transports cellular cargo along microtubules. At low loads, kinesin-1 almost always steps forwards, towards microtubule plus ends, but at higher loads, it can also step backwards. Backsteps are usually 8 nm, but can be larger. These larger backwards events of 16 nm, 24 nm or more are thought to be slips rather than steps, because they are too fast to consist of multiple, tightly-coupled 8 nm steps. Here we propose that not just these larger backsteps, but all kinesin-1 backsteps, are slips. We show firstly that kinesin waits before forward steps for less time than before backsteps and detachments; secondly that kinesin waits for the same amount of time before backsteps and detachments and thirdly that by varying the microtubule type we can change the ratio of backsteps to detachments, without affecting forward stepping. Our findings indicate that backsteps and detachments originate from the same state and that this state arises later in the mechanochemical cycle than the state that gives rise to forward steps. To explain our data, we propose that in each cycle of ATP turnover, forward kinesin steps can only occur before Pi release, whilst backslips and detachments can only occur after Pi release. In the scheme we propose, Pi release gates access to a weak binding K.ADP-K.ADP state that can slip back along the microtubule, re-engage, release ADP and try again to take an ATP-driven forward step. We predict that this rescued detachment pathway is key to maintaining kinesin processivity under load.Significance statementKinesin-1 molecular motors are ATP-driven walking machines that typically step forward, towards microtubule plus ends. But they can also step backwards, especially at high load. Backsteps are currently thought to occur by directional reversal of forwards walking. To the contrary, we propose here that kinesin backsteps are not steps, but slips. We show that backwards translocations originate from a different and later state in the kinesin mechanism than the state that generates forward steps. To explain this, we propose that following ATP binding, kinesin molecules that fail to step forward within a load-dependent time window convert to a state that can slip back, rebind to the microtubule, and try again to step forward.
Covert spatial attention speeds target individuation
Authors: Foster Joshua J. , Bsales Emma M. , Awh Edward 
Published: November 2019

AbstractCovert spatial attention has long been thought to speed visual processing. Psychophysics studies have shown that target information accrues faster at attended locations than at unattended locations. However, with behavioral evidence alone, it is difficult to determine whether attention speeds visual processing of the target, or subsequent post-perceptual stages of processing (e.g. decision making and response selection). Moreover, while many studies have shown that that attention can boost the amplitude of visually-evoked neural responses, no effect has been observed on the latency of those neural responses. Here, we offer new evidence that may reconcile the neural and behavioral findings. Our study focused on the N2pc, an EEG marker of visual selection that has been linked with object individuation – the formation of an object representation that is distinct from the background and from other objects. In two experiments, we manipulated whether or not covert attention was precisely deployed to the location of an impending search target. We found that the target-evoked N2pc onset approximately 20 ms earlier when the target location was cued than when it was not cued. Thus, although attention may not speed the earliest stages of sensory processing, attention does speed the critical transition between raw sensory encoding and the formation of individuated object representations.Significance StatementCovert spatial attention improves processing at attended locations. Past behavioral studies have shown that information about visual targets accrues faster at attended than at unattended locations. However, it has remained unclear whether attention speeds perceptual analysis or subsequent post-perceptual stages of processing. Here we present robust evidence that attention speeds the N2pc, an electrophysiological signal that indexes the formation of individuated object representations. Our findings show that attention speeds a relatively early stage of perceptual processing, while also elucidating the specific perceptual process that is speeded.
Suramin potently inhibits binding of the mammalian high mobility group protein AT-hook 2 to DNA
Authors: Su Linjia , Bryan Nadezda , Battista Sabrina , Freitas Juliano , Garabedian Alyssa , D’Alessio Federica , Romano Miriam , Falanga Fabiana , Fusco Alfredo , Kos Lidia , Chambers Jeremy , Fernandez-Lima Francisco , Chapagain Prem P. , Vasile Stefan , Smith Layton , Leng Fenfei 
Published: November 2019

AbstractThe mammalian high mobility group protein AT-hook 2 (HMGA2) is a multi-functional DNA-binding protein which plays important roles in tumorigenesis and adipogenesis. Previous results showed that HMGA2 is a potential therapeutic target of anticancer and anti-obesity drugs by inhibiting its DNA-binding activities. Here we report the development of a miniaturized, automated AlphaScreen high throughput screening (HTS) assay to identify inhibitors targeting HMGA2-DNA interactions. After screening the LOPAC1280 compound library, we discovered that suramin, a negatively charged antiparasitic drug potently inhibits the HMGA2-DNA interaction. Our results also show that the inhibition is through suramin binding to the AT-hooks of HMGA2, therefore blocking its DNA binding capacity. Furthermore, we demonstrate that suramin can induce brain tumor stem cells differentiation into cells with neurite-like structures, a process triggered by disrupting HMGA2-DNA interactions. Since suramin has strong antitumor and anti-metastasis activities, our discovery suggests that HMGA2 and HMGA2-like proteins may be the cellular target of this century-old drug.
Molecular and Circuit Architecture of Social Hierarchy
Authors: Nelson Adam C. , Kapoor Vikrant , Vaughn Eric , Gnanasegaram Jeshurun A. , Rubinstein Nimrod D. , Murthy Venkatesh N , Dulac Catherine 
Published: November 2019

SUMMARYSocial hierarchy is a common organizational structure of animal groups, in which an individual’s social status generates an adaptive behavioral state that facilitates interactions with other group members. Although generally stable, the social status of an animal can change, underscoring the plasticity of the underlying neural circuits. Here, we uncover the molecular and biophysical properties of a cortico-thalamic circuit that supports the emergence of hierarchy in mice. We established a robust behavioral paradigm to explore the establishment of hierarchy among groups of unfamiliar males, and identified the mediodorsal thalamus (MDT) and the caudal part of anterior cingulate area (cACC) as brain areas that are differentially activated between dominants and subordinates. Glutamatergic MDT neurons project to inhibitory parvalbumin interneurons of the cACC, and activity levels of both cell types control competitive performance. Synaptic inputs and excitability of MDT neurons undergo dramatic changes according to the animal social status, and single nucleus sequencing identified increased transcription of the voltage gated ion channelTrpm3in dominant mice, leading to enhanced excitatory transmission in the MDT-cACC circuit. Our data suggest a model in which cellular, molecular and biophysical plasticity in a thalamocortical circuit controls the expression of social status.
Sex identification of ancient pinnipeds using the dog genome
Authors: Bro-Jørgensen Maiken Hemme , Keighley Xénia , Ahlgren Hans , Scharff-Olsen Camilla Hjorth , Rosing-Asvid Aqqalu , Dietz Rune , Ferguson Steven H. , Gotfredsen Anne Birgitte , Jordan Peter , Glykou Aikaterini , Lidén Kerstin , Olsen Morten Tange 
Published: November 2019

AbstractDetermining the male and female representation in zooarchaeological material from hunted animal species is essential, to fully investigate the effects and means of prehistoric hunting practices, and may further provide valuable biological information on past animal life-history, behaviour and demography. However, the fragmented nature of the zooarchaeological record and a lack of clear diagnostic skeletal markers, often prevents such inference. Here, we test the usability of the dog nuclear genome (CanFam3.1) for sex identification of pinnipeds. First, a contemporary sample set (n=72) of ringed seals (Pusa hispida), with known sex was used to test the genetic sex identification method. By quantifying the proportion of X chromosome reads, as the chrX/chr1 ratio, the ratios clustered in two clearly distinguishable sex groups. Of the 72 individuals, 69 were identified to the accurate sex, which proves a high reliability of the genetic method. Second, random down sampling of a subset of the ringed seal samples to different read number, suggests at least 5000 DNA sequence reads mapped to the reference genome as the lower limit for which this method is applicable. Finally, applying this standard, sex identification was successfully carried out on a broad set of ancient pinniped samples, including walruses (Odobenus rosmarus), grey seals (Halichoerus grypus) and harp seals (Pagophilus groenlandicus), which all showed clearly distinct male and female chrX/chr1 ratio groups.
Development of microsatellite markers for the threatened speciesColeocephalocereus purpureus(Cactaceae) using next-generation sequencing
Authors: Fraga Daphne Amaral , de Carvalho Anderson Figueiredo , Santana Ricardo Souza , Machado Marlon Câmara , Lacorte Gustavo Augusto 
Published: November 2019

AbstractTen microsatellite loci were developed and validated for the endangered cactus speciesColeocephalocereus purpureus. The markers were obtained from sequences generated by whole genome shotgun sequencing approaches. A testing group of 36 specimens of the main grouping were genotyped and all described markers presented suitable outcomes to population genetic studies, showing polymorphic status forC. purpureustesting group with clean and reproducible amplification. No evidence for scoring errors, null alleles or linkage disequilibrium was detected. Number of alleles per locus ranged from 3 to 6 and expected heterozygosity ranged from 0.78 to 0.99. These new microsatellite loci are suitable to be used in future diversity and structure population studies ofC. purpureus.
The effect of proximity on the function and energy transfer capability of fluorescent protein pairs
Authors: Pope Jacob R. , Johnson Rachel L. , Jamieson W. David , Worthy Harley L , Kailasam Senthilkumar D. , Auhim Husam Sabah , Watkins Daniel W. , Rizkallah Pierre , Castell Oliver , Jones D. Dafydd 
Published: November 2019

AbstractFluorescent proteins (FPs) are commonly used in pairs to monitor dynamic biomolecular events through changes in their proximity via distance dependent processes such as Förster resonance energy transfer (FRET). Many FPs have a tendency to oligomerise, which is likely to be promoted through attachment to associating proteins through increases in local FP concentration. We show here that on association of FP pairs, the inherent function of the FPs can alter. Artificial dimers were constructed using a bioorthogonal Click chemistry approach that combined a commonly used green fluorescent protein (superfolder GFP) with itself, a yellow FP (Venus) or a red FP (mCherry). In each case dimerisation changes the inherent fluorescent properties, including FRET capability. The GFP homodimer demonstrated synergistic behaviour with the dimer being brighter than the sum of the two monomers. The structure of the GFP homodimer revealed that a water-rich interface is formed between the two monomers, with the chromophores being in close proximity with favourable transition dipole alignments. Dimerisation of GFP with Venus results in a complex displaying ∼86% FRET efficiency, which is significantly below the near 100% efficiency predicted. When GFP is complexed with mCherry, FRET and mCherry fluorescence itself is essentially lost. Thus, the simple assumptions used when monitoring interactions between proteins via FP FRET may not always hold true, especially under conditions whereby the protein-protein interactions promote FP interaction.Abstract Figure
Eliciting priors and relaxing the single causal variant assumption in colocalisation analyses
Authors: Wallace Chris 
Published: November 2019

AbstractHorizontal integration of summary statistics from different GWAS traits can be used to evaluate evidence for their shared genetic causality. One popular method to do this is a Bayesian method, coloc, which is attractive in requiring only GWAS summary statistics and no linkage disequilibrium estimates and is now being used routinely to perform thousands of comparisons between traits.Here we show that while most users do not adjust default software values, misspecification of prior parameters can substantially alter posterior inference. We suggest data driven methods to derive sensible prior values, and demonstrate how sensitivity analysis can be used to assess robustness of posterior inference.The flexibility of coloc comes at the expense of an unrealistic assumption of a single causal variant per trait. This assumption can be relaxed by stepwise conditioning, but this requires external software and an LD matrix aligned to study alleles. We have now implemented conditioning within coloc, and propose a new alternative method, masking, that does not require LD and approximates conditioning when causal variants are independent. Importantly, masking can be used in combination with conditioning where allelically aligned LD estimates are available for only a single trait.We have implemented these developments in a new version of coloc which we hope will enable more informed choice of priors and overcome the restriction of the single causal variant assumptions in coloc analysis.Author SummaryDetermining whether two traits share a genetic cause can be helpful to identify mechanisms underlying genetically-influenced risk of disease or other traits. One method for doing this is “coloc”, which updates prior knowledge about the chance of two traits sharing a causal variant with observed genetic association data in a Bayesian statistical framework. To do this using only summary genetic association data that is commonly shared, the method makes certain assumptions, in particular about the number of genetic causal variants that may underly each measured trait in a genomic region.We walk through several data-driven approaches to summarise the prior knowledge required for this technique, and propose sensitivity analysis as a means of checking that inference is robust to uncertainty about that prior knowledge. We also show how the assumptions about number of causal variants in a region may be relaxed, and that this improves inferential accuracy.
Synapsin is required for dense core vesicle capture and cAMP-dependent neuropeptide release
Authors: Yu Szi-chieh , Steuer Costa Wagner , Liewald Jana F. , Shao Jiajie , Gottschalk Alexander 
Published: November 2019

ABSTRACTRelease of neuropeptides from dense core vesicles (DCVs) is important for neuromodulation. By optogenetics, behavioral analysis, electrophysiology, and electron microscopy, we show that synapsin SNN-1 is required for cAMP-dependent neuropeptide release inCaenorhabditis eleganscholinergic motor neurons. In synapsin mutants, behaviors induced by the photoactivated adenylyl cyclase bPAC, which we previously showed to depend on acetylcholine and neuropeptides, are altered like in animals with reduced cAMP. While synapsin mutants have slight alterations in synaptic vesicle distribution, DCVs were affected much more: DCVs were ~30% reduced in synaptic terminals, and not released following bPAC stimulation. Imaging axonal DCV trafficking, also in genome-engineered mutants in the serine-9 protein kinase A phosphorylation site, showed that synapsin captures DCVs at synapses, making them available for release. In non-phosphorylatable SNN-1B(S9A) mutants, DCVs traffic less and accumulate, likely by enhanced tethering to the actin cytoskeleton. Our work establishes synapsin as a key mediator of neuropeptide release.
6mer seed toxicity in viral microRNAs
Authors: Murmann Andrea E. , Bartom Elizabeth T. , Schipma Matthew J. , Vilker Jacob , Chen Siquan , Peter Marcus E. 
Published: November 2019

SUMMARYMicro(mi)RNAs are short double stranded noncoding RNAs (19-23nts) that regulate gene expression by suppressing mRNAs through RNA interference. Targeting is determined by the seed sequence (position 2-7/8) of the mature miRNA. A minimal G-rich seed of just 6 nucleotides is highly toxic to cells by targeting genes essential for cell survival. A screen of 215 miRNAs encoded by 17 human pathogenic viruses (v-miRNAs) now suggests that a number of v-miRNAs can kill cells through a G-rich 6mer sequence embedded in their seed. Specifically, we demonstrate that miR-K12-6-5p, an oncoviral mimic of the tumor suppressive miR-15/16 family encoded by human Kaposi’s sarcoma-associated herpes virus, harbors a noncanonical toxic 6mer seed (position 3-8) and that v-miRNAs are more likely than cellular miRNAs to utilize a noncanonical 6mer seed. Our data suggest that during evolution viruses evolved to use 6mer seed toxicity to kill cells.
Adhesion modulates cell morphology and migration within dense fibrous networks
Authors: Moreira-Soares Maurício , Cunha Susana P. , Bordin José Rafael , Travasso Rui D. M. 
Published: November 2019

AbstractOne of the most fundamental abilities required for the sustainability of complex life forms is active cell migration, since it is essential in diverse processes from morphogenesis to leukocyte chemotaxis in immune response. The movement of a cell is the result of intricate mechanisms, that involve the coordination between mechanical forces, biochemical regulatory pathways and environmental cues. In particular, epithelial cancer cells have to employ mechanical strategies in order to migrate through the tissue’s basement membrane and infiltrate the bloodstream during the invasion stage of metastasis. In this work we explore how mechanical interactions such as spatial restriction and adhesion affect migration of a self-propelled droplet in dense fibrous media. We have performed a systematic analysis using a phase-field model and we propose a novel approach to simulate cell migration with Dissipative Particle Dynamics (DPD) modelling. With this purpose we have measured the cell’s velocity and quantified its morphology as a function of the fibre density and of its adhesiveness to the matrix fibres. Furthermore, we have compared our results to a previous in vitro migration assay of fibrosacorma cells in fibrous matrices. The results are model independent and show good agreement between the two methodologies and experiments in the literature, which indicates that these minimalist descriptions are able to capture the main features of the system. Our results indicate that adhesiveness is critical for cell migration, by modulating cell morphology in crowded environments and by enhancing cell velocity. In addition, our analysis suggests that matrix metalloproteinases (MMPs) play an important role as adhesiveness modulators. We propose that new assays should be carried out to address the role of adhesion and the effect of different MMPs in cell migration under confined conditions.
Cross-kingdom signalling regulates spore germination in the moss Physcomitrella patens
Authors: Vesty Eleanor F. , Whitbread Amy L. , Needs Sarah , Tanko Wesal , Jones Kirsty , Halliday Nigel , Ghaderiardakani Fatemeh , Liu Xiaoguang , Cámara Miguel , Coates Juliet C. 
Published: November 2019

ABSTRACTPlants live in close association with microorganisms that can have beneficial or detrimental effects. The activity of bacteria in association with flowering plants has been extensively analysed. Bacteria use quorum-sensing as a way of monitoring their population density and interacting with their environment. A key group of quorum sensing molecules in Gram-negative bacteria are the N-acylhomoserine lactones (AHLs), which are known to affect the growth and development of both flowering plants, including crops, and marine algae. Thus, AHLs have potentially important roles in agriculture and aquaculture. Nothing is known about the effects of AHLs on the earliest-diverging land plants, thus the evolution of AHL-mediated bacterial-plant- and algal interactions is unknown. In this paper, we show that AHLs can affect spore germination in a representative of the earliest plants on land, the Bryophyte moss Physcomitrella patens. Furthermore, we demonstrate that sporophytes of wild isolates of Physcomitrella patens are associated with AHL-producing bacteria.
Design to Data for mutants of β-glucosidase B from Paenibacillus polymyxa: M319C, T431I, and K337D
Authors: Huang Peishan , Contreras Stephanie C. , Bloomfield Eliana , Schmitz Kristine , Arredondo Augustine , Siegel Justin B. 
Published: November 2019

ABSTRACTThe use of computational tools has become an increasingly popular tool for engineering protein function. While there are numerous examples of computational tools enabling the design of novel protein functions, there remains room for improvement in both prediction accuracy and success. To improve algorithms for functional and stability predictions, we have initiated the development of a data set designed to be used for training new computational algorithms for enzyme design. To date our dataset is composed of over 129 mutants with associated expression levels, kinetic data, and thermal stability for the enzyme β-glucosidase B (BglB) from Paenibacillus polymyxa. In this study, we introduced three new variants (M319C, T431I, and K337D) to our existing dataset with the goal of cultivating a larger dataset to train new design algorithms and more broadly explore structure-function relationships in BglB.