bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversity, dynamics and effects of LTR retrotransposons in the model grassBrachypodium distachyon
Authors: Stritt C , Wyler M , Gimmi EL , Pippel M , Roulin AC 
Published: July 2019

SummaryTransposable elements (TEs) are the main reason for the high plasticity of plant genomes, where they occur as communities of diverse evolutionary lineages. Because research has typically focused on single abundant families or summarized TEs at a coarse taxonomic level, our knowledge about how these lineages differ in their effects on genome evolution is still rudimentary.Here we investigate the community composition and dynamics of 32 long terminal repeat retrotransposon (LTR-RT) families in the 272 Mb genome of the Mediterranean grassBrachypodium distachyon.We find that much of the recent transpositional activity in theB. distachyongenome is due to centromericGypsyfamilies andCopiaelements belonging to the Angela lineage. With a half-life as low as 66 ky, the latter are the most dynamic part of the genome and an important source of within-species polymorphisms. Second, GC-richGypsyelements of the Retand lineage are the most abundant TEs in the genome. Their presence explains more than 20 percent of the genome-wide variation in GC content and is associated to higher methylation levels.Our study shows how individual TE lineages change the genetic and epigenetic constitution of the host beyond simple changes in genome size.
Parallel ecological and evolutionary responses to selection in a natural bacterial community
Authors: Hesse Elze , Luján Adela M. , O’Brien Siobhan , Newbury Arthur , McAvoy Terence , Pascual Jesica Soria , Bayer Florian , Hodgson Dave J. , Buckling Angus 
Published: July 2019

AbstractEvolution can occur over ecological timescales, suggesting a potentially important role for rapid evolution in shaping community trait distributions. However, evidence of concordant eco-evolutionary dynamics often comes fromin vitrostudies of highly simplified communities, and measures of ecological and evolutionary dynamics are rarely directly comparable. Here, we quantified how ecological species sorting and rapid evolution simultaneously shape community trait distributions by tracking within and between-species changes in a key trait in a complex bacterial community. We focused on the production of siderophores; bacteria use these costly secreted metabolites to scavenge poorly soluble iron and to detoxify environments polluted with toxic non-ferrous metals. We found that responses to copper-imposed selection within and between species were ultimately the same – intermediate siderophore levels were favored – and occurred over similar timescales. Despite being a social trait, this level of siderophore production was selected regardless of whether species evolved in isolation or in a community context. Our study suggests that evolutionary selection can play a pivotal role in shaping community trait distributions within natural, highly complex, bacterial communities. Furthermore, trait evolution may not always be qualitatively affected by interactions with other community members.SignificanceBacterial communities possess remarkable taxonomic and metabolic diversity and play a key role in nearly every biogeochemical process on Earth. Rapid evolution (occurring over ecological time scales) can in principle shape these processes, yet we have little understanding of its importance in natural communities. Here, we quantified how the production of metal-detoxifying siderophores is driven by species compositional changes and evolution in a compost community in response to copper stress. We found that siderophore production converged at intermediate levels, with evolutionary and ecological changes occurring at similar rates. Understanding how ecological and evolutionary processes contribute to shaping trait distributions will improve our ability to predict ecosystem responses to global change, and aid in the engineering of microbial consortia.
Addressing lipid structural diversity in signalling: Photochemical probes for live-cell lipid biochemistry
Authors: Schuhmacher Milena , Grasskamp Andreas T. , Wagner Nicolai , Lombardot Benoit , Schuhmacher Jan S. , Sala Pia , Lohmann Annett , Henry Ian , Shevchenko Andrej , Coskun Ünal , Walter Alexander M. , Nadler André 
Published: July 2019

SummaryEvery cell produces thousands of distinct lipid species, but methodology for studying the biological roles of individual lipids is insufficient. Using the example of diacylglycerols, prominent second messengers, we here investigate whether lipid chemical diversity can provide a basis for cellular signal specification. We developed novel photo-caged lipid probes, which allow acute manipulation of distinct diacylglycerol species in the plasma membrane. Combining uncaging experiments with mathematical modelling enabled the determination of binding constants for diacylglycerol-protein interactions and kinetic parameters for diacylglycerol transbilayer movement and turnover in quantitative live-cell experiments. Strikingly, we find that affinities and kinetics vary by orders of magnitude due to diacylglycerol structural diversity. These differences are sufficient to explain differential recruitment of diacylglycerol binding proteins and thus differing downstream phosphorylation patterns. Our approach represents a generally applicable method for elucidating the biological function of single lipid species on subcellular scales.
Heat dissipation capacity influences reproductive performance in an aerial insectivore
Authors: Tapper Simon , Nocera Joseph J. , Burness Gary 
Published: July 2019

AbstractClimatic warming will likely increase the frequency of extreme weather events, which may reduce an individual’s capacity for sustained activity due to thermal limits. We tested whether the risk of overheating may limit parental provisioning of an aerial insectivorous bird in population decline. For many seasonally breeding birds, parents are thought to operate close to an energetic ceiling during the 2-3 week chick-rearing period. The factors determining the ceiling remain unknown, although it may be set by an individual’s capacity to dissipate body heat (the heat dissipation limitation hypothesis). To test this hypothesis, over two breeding seasons we experimentally trimmed the ventral feathers of female tree swallows (Tachycineta bicolor) to provide a thermal window. We then monitored maternal provisioning rates, nestling growth rates, and fledging success. We found the effect of our experimental treatment was context-dependent and varied with environmental conditions. Females with trimmed plumage fed their nestlings at higher rates than controls when conditions were hot and non-windy, but the reverse was true under cool and windy conditions. On average, nestlings of trimmed females were heavier than controls, and had a higher probability of fledging. We suggest that removal of a thermal constraint allowed females to increase provisioning rates, but additionally provided nestlings with a thermal advantage via increased heat transfer during maternal brooding. Our data provide partial support for the heat dissipation limitation hypothesis, and suggest that depending on weather patterns, heat dissipation capacity can influence reproductive success in aerial insectivores.
The most common RNF43 mutant G659Vfs41 is fully functional in inhibiting Wnt signaling and unlikely to play a role in tumorigenesis
Authors: Tu Jianghua , Park Soohyun , Yu Wangsheng , Zhang Sheng , Wu Ling , Carmon Kendra , Liu Qingyun J. 
Published: July 2019

AbstractRNF43 is an E3 ligase that inhibits Wnt signaling by ubiquitinating Wnt receptors for degradation. It is mutated in various cancer types with the most recurrent mutation being the frameshift G659Vfs41 with frequencies of ~5-8% in colon, stomach and endometrial cancers. The mutation has always been assumed to be loss-of-function that would lead to increased Wnt signaling and tumorigenesis, yet no functional characterization has been reported. We analyzed the distribution of the G659Vfs41 mutation and its association with other cancer gene mutations, and found that the mutation occurred nearly exclusively in tumors with low expression of the DNA mismatch repair gene MLH1. Mutant RNF43-G659Vfs41 was no different from wild type RNF43 in expression, localization, R-spondin binding, promotion of Wnt receptor degradation, inhibition of Wnt signaling. We also found that colon tumors with RNF43-G659Vfs41 had low expression of Wnt/β-catenin signaling markers and were frequently mutated in BRAF. A colon cancer cell line with RNF43-G659Vfs41 and BRAF-V600E mutations was uniquely sensitively to activation of Wnt/β-catenin signaling. These findings indicate that RNF43-G659Vfs41 is likely a passenger mutation in MLH1-down regulated tumors, not a loss-of-function driver mutation that facilitates tumorigenesis. Tumors with RNF43-G659Vfs41 and BRAF-V600E may be susceptible to activators of Wnt signaling.
Modelling of pH-dependence to develop a strategy for stabilising mAbs at acidic steps in production
Authors: Hebditch Max , Kean Ryan , Warwicker Jim 
Published: July 2019

AbstractEngineered proteins are increasingly being required to function or pass through environmental stresses for which the underlying protein has not evolved. A major example in health are antibody therapeutics, where a low pH step is used for purification and viral clearance. In order to develop a computational model for analysis of pH-stability, predictions are compared with experimental data for the relative pH-sensitivities of antibody domains. The model is then applied to proteases that have evolved to be functional in an acid environment, showing a clear signature for low pH-dependence of stability in the neutral to acidic pH region, largely through reduction of saltbridges. Interestingly, an extensively acidic protein surface can maintain contribution to structural stabilisation at acidic pH through replacement of basic sidechains with polar, hydrogen-bonding groups. These observations form a design principle for engineering acid-stable proteins.
Force-exerting lateral protrusions in fibroblastic cell contraction
Authors: Padhi Abinash , Singh Karanpreet , Franco-Barraza Janusz , Marston Daniel J. , Cukierman Edna , Hahn Klaus M. , Kapania Rakesh K. , Nain Amrinder S. 
Published: July 2019

ABSTRACTAligned extracellular matrix fibers enable fibroblasts to undergo myofibroblastic activation and lead to elongated cell morphology. The fibroblasts in turn contract to cause alignment of the extracellular matrix. This feedback process is critical in pathological occurrences such as desmoplasia and is not well understood. Using engineered fiber networks that serve as force sensors, we identify lateral protrusions with specific functions and morphology that are induced by elongated fibroblastic cells and which apply extracellular fiber-deflecting contractile forces. Lateral projections, named twines, produce twine bridges upon interacting with neighboring parallel fibers. These mature into “perpendicular lateral protrusions” (PLPs) that enable cells to spread laterally and effectively contract. Using quantitative microscopy, we show that the twines originate from the stratification of cyclic actin waves traversing the entire length of the cell. The primary twines swing freely in 3D and engage neighboring extracellular fibers. Once engaged, a lamellum extends from the primary twine and forms a second twine, which also engages with the neighboring fiber. As the lamellum fills in the space between the two twines, a sheet-like PLP is formed to contract effectively. By controlling the geometry of extracellular networks we confirm that anisotropic fibrous environments enable PLP formation, and these force-generating PLPs are oriented perpendicular to the parent cell body. PLP formation kinetics indicated mechanisms analogous to other/known actin-based structures. Our identification of force-exerting PLPs in anisotropic fibrous environments suggests an explanation for cancer-associated desmoplastic expansion at single-cell resolution, providing possible new clinical intervention opportunities.
Disulfide chaperone knock-outs enable in-vivo double spin-labeling of an outer-membrane transporter
Authors: Nilaweera T. D. , Nyenhuis D. A. , Nakamoto R. K. , Cafiso D. S. 
Published: July 2019

AbstractRecent advances in the application of EPR spectroscopy have demonstrated that it is possible to obtain structural information on bacterial outer-membrane proteins in intact cells from extracellularly labeled cysteines. However, in the Escherichia coli outer-membrane vitamin B12 transport protein, BtuB, the double labeling of many cysteine pairs is not possible in a wild-type K12-derived E. coli strain. It has also not yet been possible to selectively label single or paired cysteines that face the periplasmic space. Here we demonstrate that the inability to produce reactive cysteine residues in pairs is a result of the disulfide bond formation system, which functions to oxidize pairs of free-cysteine residues. Mutant strains that are dsbA or dsbB null facilitate labeling pairs of cysteines. Moreover, we demonstrate that the double labeling of sites on the periplasmic facing surface of BtuB is possible using a dsbA null strain. BtuB is found to exhibit different structures and structural changes in the cell than it does in isolated outer membranes or reconstituted systems, and the ability to label and perform EPR in cells is expected to be applicable to a range of other bacterial outer-membrane proteins.Statement of SignificanceEPR spectroscopy is an important method to characterize the structure and dynamics of membrane proteins, and recent efforts demonstrate that pulse EPR can be used to examine the extracellular surface of outer membrane proteins in live bacteria. In the present work, we show that pairs of cysteine residues in the Escherichia coli vitamin B12 transporter, BtuB, cannot be spin-labeled in wild-type strains, but can be labeled with the use of certain null mutants in the periplasmic disulfide bond formation, Dsb, system. These mutants also facilitate efficient spin-labeling of cysteines located on the periplasmic surface of BtuB. Distance measurements using pulse EPR provide evidence that the behavior of BtuB is different in the bacterial cell than it is in purified systems.
Genetic risk for Alzheimer’s disease predicts hippocampal volume through the lifespan
Authors: Walhovd Kristine B , Fjell Anders M. , Sørensen Øystein , Mowinckel Athanasia Monica , Reinbold Céline Sonja , Idland Ane-Victoria , Watne Leiv Otto , Franke Andre , Dobricic Valerijia , Kilpert Fabian , Bertram Lars , Wang Yunpeng 
Published: July 2019

AbstractINTRODUCTIONIt is unknown whether genetic risk for Alzheimer’s disease (AD) represents a stable influence on the brain from early in life, or whether effects are age-dependent. It is critical to characterize the effects of genetic risk factors on the primary neural substrate of AD, the hippocampus, throughout life.METHODSRelations of polygenic risk score (PGS) for AD, including variants in Apolipoprotein E (APOE) with hippocampal volume and its change were assessed in a healthy longitudinal lifespan sample (n = 1181, 4-95 years), followed for up to 11 years with a total of 2690 MRI scans.RESULTSAD-PGS showed a significant negative effect on hippocampal volume. Offset effects of AD-PGS andAPOEε4 were present in hippocampal development, and interactions between age and genetic risk on volume change were not consistently observed. DISCUSSION: Endophenotypic manifestation of polygenic risk for AD may be seen across the lifespan in healthy persons.HighlightsGenetic risk for AD affects the hippocampus throughout the lifespanAPOEε4 carriers have smaller hippocampi in developmentDifferent effects of genetic risk at different ages were not consistently observedGenetic factors increasing risk for AD impact healthy persons throughout lifeA broader population and age range are relevant targets for attempts to prevent AD
Functional annotation of rare structural variation in the human brain
Authors: Han Lide , Zhao Xuefang , Benton Mary Lauren , Perumal Thaneer , Collins Ryan L. , Hoffman Gabriel E. , Johnson Jessica S. , Sloofman Laura , Wang Harold Z. ,   CommonMind Consortium, Brennand Kristen J. , Brand Harrison , Sieberts Solveig K. , Marenco Stefano , Peters Mette A. , Lipska Barbara K. , Roussos Panos , Capra John A. , Talkowski Michael , Ruderfer Douglas M. 
Published: July 2019

AbstractStructural variants (SVs) contribute substantially to risk of many brain related disorders including autism and schizophrenia. However, annotating the potential contribution of SVs to disease remains a major challenge. Here, we integrated high resolution SV calling from genome-sequencing in 755 human post-mortem brains with dorsal lateral prefrontal cortex RNA-sequencing from a subset of 629 samples to quantify the dosage and regulatory effects of SVs. We show that genic (p = 5.44×10−9) and regulatory SVs (enhancer p = 3.22×10−23, CTCF p = 3.86×10−18) are present at significantly lower frequencies than intergenic SVs after correcting for SV length. Copy number variants (CNVs)—deletions and duplications—exhibit a significant quantitative and directional relationship between the proportion of genic and regulatory content altered and gene expression, and the size of the effect is inversely correlated with the loss-of-function intolerance of the gene. We trained a joint linear model that leverages genic and regulatory annotations to predict expression effects of rare CNVs in independent samples (R2= 0.21-0.41). We further developed a regulatory disruption score for each CNV that aggregates the predicted expression across all affected genes weighted by the genes’ intolerance score and applied it to an independent set of SVs from 14,891 genome-sequenced individuals. Pathogenic deletions implicated in neurodevelopmental disorders by ClinGen had significantly more extreme regulatory disruption scores than the rest of the SVs. Rank ordering based on the most extreme regulatory disruption scores prioritized pathogenic deletions that would not have been prioritized by frequency or length alone. This work points to the deleteriousness of regulatory SVs, particularly those altering CTCF sites. We further provide a simple approach for functionally annotating the regulatory effects of SVs in the human brain that has potential to be useful in larger SV studies and should improve as more regulatory annotation data is generated.
Contrast invariant tuning in human perception of image content
Authors: Fruend Ingo , Patel Jaykishan , Stalker Elee D. 
Published: July 2019

AbstractHigher levels of visual processing are progressively more invariant to low-level visual factors such as contrast. Although this invariance trend has been well documented for simple stimuli like gratings and lines, it is difficult to characterize such invariances in images with naturalistic complexity. Here, we use a generative image model based on a hierarchy of learned visual features—a Generative Adversarial Network—to constrain image manipulations to remain within the vicinity of the manifold of natural images. This allows us to quantitatively characterize visual discrimination behaviour for naturalistically complex, non-linear image manipulations. We find that human tuning to such manipulations has a factorial structure. The first factor governs image contrast with discrimination thresholds following a power law with an exponent between 0.5 and 0.6, similar to contrast discrimination performance for simpler stimuli. A second factor governs image content with approximately constant discrimination thresholds throughout the range of images studied. These results support the idea that human perception factors out image contrast relatively early on, allowing later stages of processing to extract higher level image features in a stable and robust way.
Residue-Residue Mutual Work Analysis of Retinal-Opsin Interaction in Rhodopsin: Implications for Protein-Ligand Binding
Authors: Li Wenjin 
Published: July 2019

AbstractEnergetic contributions at single-residue level to retinal-opsin interaction in rhodopsin were studied by combining molecular dynamics simulations, transition path sampling, and a newly developed energy decomposition approach. The virtual work at an infinitesimal time interval was decomposed into the work components on one residue due to its interaction with another residue, which were then averaged over the transition path ensemble along a proposed reaction coordinate. Such residue-residue mutual work analysis on 62 residues within the active center of rhodopsin resulted in a very sparse interaction matrix, which is generally not symmetric but anti-symmetric to some extent. 14 residues were identified to be major players in retinal relaxation, which is in excellent agreement with an existing NMR study. Based on the matrix of mutual work, a comprehensive network was constructed to provide detailed insights into the chromophore-protein interaction from a viewpoint of energy flow.
Improving the specificity of adenine base editor using high-fidelity Cas9
Authors: Hong Ruisha , Ma Sidi , Wang Feng 
Published: July 2019

ABSTRACTAdenine base editor (ABE) mediates the conversion of A to G in genomic DNA. In human, approximately 47.8% of known pathogenic SNPs can be corrected by A to G conversion, indicating that ABE have tremendous potential in gene therapy. However, the off-target activity of ABE limits its clinical application. ABE off-target activity in DNA is depended on the bonding of Streptococcus pyogenes Cas9 (SpCas9) on off-target sites [1, 2]. Therefore, using high-fidelity Cas9 should be able to improve the specificity of ABE. Based on this, we replaced the wild-type SpCas9 in ABE7.10 with four high-fidelity Cas9s to improve its specificity. The analysis of target deep sequencing data demonstrate that the specificity of e-ABE is substantially improved compared to conventional ABE7.10 in four test sites. But the broad editing window of ABE hampers its application, ABE needs to be optimized to get variants with narrow editing window.