bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plan-based generalization shapes local implicit adaptation to opposing visuomotor transformations
Authors: Schween Raphael , Taylor Jordan , Hegele Mathias 
Published: July 2018

AbstractThe human ability to use different tools demonstrates our capability of forming and maintaining multiple, context specific motor memories. Experimentally, this ability has been investigated in dual adaptation, where participants adjust their reaching movements to opposing visuomotor transformations. Adaptation in these paradigms occurs by distinct processes, i.e. the development of explicit aiming strategies for each transformation and/or the implicit acquisition of distinct visuomotor mappings. The presence of distinct, transformation-dependent aftereffects has been interpreted as support for the latter. Alternatively, however, distinct aftereffects could reflect adaptation of a single visuomotor map, which is locally adjusted in different regions of the workspace. Indeed, recent studies suggest that explicit aiming strategies direct where in the workspace implicit adaptation occurs.Disentangling these possibilities is critical to understanding how humans acquire and maintain separate motor memories for different skills and tools. We therefore investigated generalization of explicit and implicit adaptation to different directions after participants practiced two opposing cursor rotations, which were associated with separate visual workspaces. Whereas participants learned to compensate opposing rotations by explicit strategies that were specific to the visual workspace cue, aftereffects were not sensitive to visual workspace cues. Instead, aftereffects displayed bimodal generalization patterns that appeared to reflect locally limited learning of both transformations. By varying target arrangements and instructions, we show that these generalization patterns are consistent with implicit adaptation that generalizes locally around (explicit) movement plans associated with opposing visuomotor transformations. Our findings show that strategies can shape implicit adaptation in a complex manner.New & NoteworthyVisuomotor dual adaptation experiments have identified contextual cues that enable learning of separate visuomotor mappings, but little is known about the underlying representations of learning. We report that visual workspace separation as a contextual cue enables participants to compensate opposing cursor rotations by a combination of explicit and implicit processes: Learners developed context-dependent explicit aiming strategies while an implicit visuomotor map represented dual adaptation independent from context by local adaptation around the explicit movement plan.
A migration-associated supergene reveals loss of biocomplexity in Atlantic cod
Authors: Kess Tony , Bentzen Paul , Lehnert Sarah J. , Sylvester Emma V.A. , Lien Sigbjørn , Kent Matthew P. , Sinclair-Waters Marion , Morris Corey , Regular Paul , Fairweather Robert , Bradbury Ian R. 
Published: July 2018

AbstractIntraspecific phenotypic diversity is integral to ecological resilience and the provision of ecosystem services1. Chromosome structural variation may underpin intraspecific diversity and complex phenotypes2 by reducing recombination within supergenes containing linked, co-adapted alleles. Connecting ecologically-relevant phenotypes to genomic variation can enable more precise conservation of exploited marine species by protecting important genetic diversity3,4. Here, using genome-wide association analysis of a 12K single nucleotide polymorphism (SNP) array we confirm that an ancient, derived chromosomal rearrangement consisting of two adjacent inversions is strongly associated with migratory phenotype and individual-level genetic structure in Atlantic cod (Gadus morhua) across the Northwest Atlantic. The presence of all identified migration-associated loci within this rearrangement indicates that pervasive variation in migration phenotype is in part controlled by a recombination-resistant supergene, facilitating fine-scale individual phenotypic variation within Northern cod. Furthermore, we reconstruct trends in effective population size over the last century, and find genomic signatures of population collapse, and different patterns of population expansion and decline among individuals based on supergene alleles. We demonstrate declines in effective population size consistent with the onset of industrialized harvest (post 1950) and substantially reduced effective size of individuals homozygous for the derived chromosomal rearrangement relative to heterozygous individuals or those homozygous for the ancestral version of this chromosomal region. These results illustrate how chromosomal structural diversity can mediate fine-scale genetic and phenotypic variation in a highly connected marine species, and suggest a loss of biocomplexity from a migration-associated supergene within Northern cod by overfishing.
Fluorescence Multiplexing with Spectral Imaging and Combinatorics
Authors: Holzapfel Hadassa Y. , Stern Alan D. , Bouhaddou Mehdi , Anglin Catilin M. , Putur Danielle , Comer Sarah , Birtwistle Marc R. 
Published: July 2018

ABSTRACTUltraviolet-to-infrared fluorescence is a versatile and accessible assay modality, but is notoriously hard to multiplex due to overlap of wide emission spectra. We present an approach for fluorescence multiplexing using spectral imaging and combinatorics (MuSIC). MuSIC consists of creating new independent probes from covalently-linked combinations of individual fluorophores, leveraging the wide palette of currently available probes with the mathematical power of combinatorics. Probe levels in a mixture can be inferred from spectral emission scanning data. Theory and simulations suggest MuSIC can increase fluorescence multiplexing ~4-5 fold using currently available dyes and measurement tools. Experimental proof-of-principle demonstrates robust demultiplexing of nine solution-based probes using ~25% of the available excitation wavelength window (380-480 nm), consistent with theory. The increasing prevalence of white lasers, angle filter-based wavelength scanning, and large, sensitive multi-anode photo-multiplier tubes make acquisition of such MuSIC-compatible datasets increasingly attainable.
Architecture and organization of mouse posterior parietal cortex relative to extrastriate areas
Authors: Hovde Karoline , Gianatti Michele , Witter Menno P. , Whitlock Jonathan R. 
Published: July 2018

ABSTRACTThe posterior parietal cortex (PPC) is a multifaceted region of cortex, contributing to several cognitive processes including sensorimotor integration and spatial navigation. Although recent years have seen a considerable rise in the use of rodents, particularly mice, to investigate PPC and related networks, a coherent anatomical definition of PPC in the mouse is still lacking. To address this, we delineated the mouse PPC using cyto- and chemoarchitectural markers from Nissl-, parvalbumin- and muscarinic acetylcholine receptor M2-staining. Additionally, we performed bilateral triple anterograde tracer injections in primary visual cortex (V1) and prepared flattened tangential sections from one hemisphere and coronal sections from the other, allowing us to co-register the cytoarchitectural features of PPC with V1 projections. In charting the location of extrastriate areas and the architectural features of PPC in the context of each other, we reconcile different, widely used conventions for demarcating PPC in the mouse. Furthermore, triple anterograde tracer injections in PPC showed strong projections to associative thalamic nuclei as well as higher visual areas, orbitofrontal, cingulate and secondary motor cortices. Retrograde circuit mapping with rabies virus further showed that all cortical connections were reciprocal. These combined approaches provide a coherent definition of mouse PPC that incorporates laminar architecture, extrastriate projections, thalamic, and cortico-cortical connections.
HIV-1 vaccine design through minimizing envelope metastability
Authors: He Linling , Kumar Sonu , Allen Joel D. , Huang Deli , Lin Xiaohe , Mann Colin J. , Saye-Francisco Karen L. , Copps Jeffrey , Sarkar Anita , Blizard Gabrielle S. , Ozorowski Gabriel , Sok Devin , Crispin Max , Ward Andrew B. , Nemazee David , Burton Dennis R. , Wilson Ian A. , Zhu Jiang 
Published: July 2018

SUMMARYOvercoming envelope metastability is crucial to trimer-based HIV-1 vaccine design. Here, we present a coherent vaccine strategy by minimizing metastability. For ten strains across five clades, we demonstrate that gp41 ectodomain (gp41ECTO) is the main source of envelope metastability by replacing wild-type gp41ECTOwith BG505 gp41ECTOof the uncleaved prefusion-optimized (UFO) design. These gp41ECTO-swapped trimers can be produced in CHO cells with high yield and high purity. Crystal structure of a gp41ECTO-swapped trimer elucidates how a neutralization-resistant tier 3 virus evades antibody recognition of the V2 apex. UFO trimers of transmitted/founder (T/F) viruses and UFO trimers containing a consensus-based ancestral gp41ECTOsuggest an evolutionary root of the metastability. Gp41ECTO-stabilized trimers can be readily displayed on 24- and 60-meric nanoparticles, with incorporation of additional T cell help illustrated for a hyperstable 60-mer. In mice and rabbits, gp140 nanoparticles induced more effective tier 2 neutralizing antibody response than trimers with statistical significance.HIGHLIGHTSgp41 is the main source of HIV-1 envelope metastabilityBG505 gp41 of the UFO design stabilizes gp140 trimers of diverse subtypesgp41 stabilization facilitates gp140 nanoparticle assembly and improves productionNanoparticles elicit tier 2 neutralizing antibodies more effectively than trimers
Regulatory networks of gene expression in maize (Zea mays) under drought stress and re-watering
Authors: Cao Liru , Lu Xiaomin , Zhang Pengyu , Ku Lixia , Wang Guorui , Yuan Zhen , Zhang Xin , Cui Jingyu , Han Jingli , Liu Ying , Cao Yangyong , Wei Li , Wang Tongchao 
Published: July 2018

AbstractDrought can severely limit plant growth and production. However, few studies have investigated gene expression profiles in maize during drought/re-watering. We compared drought-treated and water-sufficient maize plants by measuring their leaf relative water content, superoxide dismutase and peroxidase activities, proline content, and leaf gas exchange parameters (photosynthetic rates, stomatal conductance, and transpiration rates). We conducted RNA sequencing analyses to elucidate gene expression profiles and identify miRNAs that might be related to drought resistance. A GO enrichment analysis showed that the common DEGs (differently expressed genes) between drought-treated and control plants were involved in response to stimulus, cellular process, metabolic process, cell part, and binding and catalytic activity. Analyses of gene expression profiles revealed that 26 of the DEGs under drought encoded 10 enzymes involved in proline synthesis, suggesting that increased proline synthesis was a key part of the drought response. We also investigated cell wall-related genes and transcription factors regulating abscisic acid-dependent and -independent pathways. The expression profiles of the miRNAs miR6214-3p, miR5072-3p, zma-miR529-5p, zma-miR167e-5p, zma-miR167f-5p, and zma-miR167j-5p and their relevant targets under drought conditions were analyzed. These results provide new insights into the molecular mechanisms of drought tolerance, and may identify new targets for breeding drought-tolerant maize lines.Abbreviationsleaf relative water content: RWC, superoxide dismutase activity: SOD, peroxidase activity: POD, proline content: Pro, photosynthetic rates: Pn, stomatal conductance: Cond, transpiration rates: Tr.; quantitative real-time polymerase chain reaction: qPCR; abscisic acid; ABA; polyethylene glycol :PEG; Principal component analysis :PCA; polyacrylamide gel electrophoresis :PAGEHighlightThe study of physiology and molecular mechanism of maize laid a theoretical foundation for drought resistance breeding under drought stress and re-watering.
DrosophilaDNA/RNA methyltransferase contributes to robust host defense in ageing animals by regulating sphingolipid metabolism
Authors: Abhyankar Varada , Kaduskar Bhagyashree , Kamat Siddhesh S. , Deobagkar Deepti , Ratnaparkhi Girish 
Published: July 2018

ABSTRACTDrosophilamethyltransferase (Mt2) has been implicated in methylation of both DNA and tRNA. In this study, we demonstrate that loss ofMt2activity leads to an age dependent decline of immune function in the adult fly. A newly eclosed adult has mild immune defects that exacerbate in a fifteen-day oldMt2−/−fly. The age dependent effects appear to be systemic, including disturbances in lipid metabolism, changes in cell shape of hemocytes and significant fold changes in levels of transcripts related to host defense. Lipid imbalance, as measured by quantitative lipidomics, correlates with immune dysfunction with high levels of immunomodulatory lipids, sphingosine-1phosphate (S1P) and ceramides, along with low levels of storage lipids. Activity assays on fly lysates confirm the age dependent increase in S1P and concomitant reduction of S1P lyase activity. We hypothesize thatMt2functions to regulate genetic loci such as S1P lyase and this regulation is essential for robust host defense as the animal ages. Our study uncovers novel links between age dependentMt2function, innate immune response and lipid homeostasis.
Population genomics supports clonal reproduction and multiple gains and losses of parasitic abilities in the most devastating nematode plant pest
Authors: Koutsovoulos Georgios D. , Marques Eder , Arguel Marie-Jeanne , Duret Laurent , Machado Andressa C.Z. , Carneiro Regina M.D.G. , Kozlowski Djampa K. , Bailly-Bechet Marc , Castagnone-Sereno Philippe , Albuquerque Erika V.S. , Danchin Etienne G.J. 
Published: July 2018

ABSTRACTThe most devastating nematodes to worldwide agriculture are the root-knot nematodes withMeloidogyne incognitabeing the most widely distributed and damaging species. This parasitic and ecological success seem surprising given its supposed obligatory clonal reproduction. Clonal reproduction has been suspected based on cytological observations but, so far, never confirmed by population genomics data. At the species level,M. incognitais highly polyphagous with thousands of host plants. However, the host range varies among differentM. incognitaisolates that may present distinct and more restricted host compatibilities. Historically, four ‘host races’ had been defined as a function of ranges of compatible and incompatible plants. We sequenced the genomes of 11 isolates across Brazil, covering these four distinct races to assess (i) how clonal reproduction is and (ii) how the level of genome variability associates with biological traits such as the host races, affected agronomic culture, and geographical distribution. By aligning the genomic reads of the isolates to theM. incognitareference genome assembly, we identified SNV and small-scale insertions/deletions. Analysis of linkage disequilibrium and 4-gametes test, showed no sign of recombination, confirming the clonal mode of reproduction ofM. incognita.We showed that there are relatively few point variations between the different isolates, and these variations show no significant association with either the host races, the geographical origin of the samples or the host plant on which they have been collected. Due to the lack of phylogenetic signal underlying their existence, we recommend the discontinuation of the terminology ‘race’. Overall, these results suggest that multiple gains and losses of parasitic abilities and adaptations to different environmental conditions account for the broad host spectrum and wide geographic distribution ofM. incognita. Hence, this nematode constitutes a model species to study adaptability without sexual recombination and overall low genomic variations in animals.
Using the Weibull accelerated failure time regression model to predict time to health events
Authors: Liu Enwu , Lim Karen 
Published: July 2018

AbstractWe describe a statistical method protocol to use a Weibull accelerated failure time (AFT) model to predict time to a health-related event. This prediction method is quite common in engineering reliability research but rarely used for medical predictions such as survival time. A worked example for how to perform the prediction using a published dataset is included.
Mate choice and gene expression signatures associated with nutritional adaptation in the medfly (Ceratitis capitata)
Authors: Nash Will , Mohorianu Irina , Chapman Tracey 
Published: July 2018

AbstractEvolutionary responses to nutrition are key to understanding host shifts and the potential for reproductive isolation. Previously, experimental evolution was used to describe responses of the medfly (Ceratitis capitata) to divergent larval diets. Within 30 generations there was divergence in larval development time, egg to adult survival and adaptation in adult body size. In this study, the gene expression signatures associated with these changes were examined, using mRNA-seq on males following 60 generations of nutritional selection. Variation in gene expression was also validated using qRT-PCR. The results showed observed an over-representation of differential expression in metabolism, oxidative phosphorylation and proteolysis genes. In addition, at generations 60 and 90, we tested whether these evolved patterns (differences in gene expression) were associated with mate choice. We found evidence for assortative mating by diet at generation 60, but not in mating tests within and between replicate lines at generation 90. Hence, there was no consistent evidence for assortative mating by diet, which emphasises the importance of replicate tests of evolutionary responses over time. Overall, the study provides the first genome-wide survey of the putative mechanisms underpinning evolved responses to nutritional adaptation.
The Enzymes that beyond Non-Oxidative Glycolysis
Authors: Xu Zixiang , Wu Qiaqing , Zhu Dunming 
Published: July 2018

AbstractHigh yield is an important objective of cell factory. One or several genes cloned into the bacterial may make the synthetic pathway much more optimal, so can increase the yield. But the global benefit enzymes are rare, which can increase the yields of many chemical products for a cell factory such as E.coli. Two of these kinds of global benefit enzymes are the famous enzymes, D-fructose-6-phosphate D-erythrose-4-phosphate-lyase and D-Xylulose 5-phosphate D-glyceraldehyde-3-phosphate-lyase, of non-oxidative glycolysis (NOG) published in Nature, which can improve the utilization ratio of carbon. We expect to find other global benefit enzymes. We use an integrated model, which integrated in silico model of E.coli and KEGG. By computation, we analyze the effect of adding each reaction from KEGG on the theoretical yields of several products with E.coli and find 83 enzymes that may be potentially global benefit enzymes. By comparison, we find about 30 of the 83 enzymes are better in improving the theoretical yields than the two enzymes of NOG.In order to compare the global benefit enzymes with NOG, as an example, we select “Glycerol:NADP+ oxidoreductase” (GNO) which can increase the supply of NADPH in E.coli. But To increase the supply of reducing power, such as NADPH will probably increase the yield of chemicals in a cell factory. We use flux balance analysis method to testify our assumption. By comparing the maximum yields of 80 products produced by E.coli with respectively using GNO and NOG, we find GNO has better performance in the product production of E.coli. So GNO is a global benefit enzyme which can increase the yields of many chemical products in E.coli.
Protein Deacetylase CobB Interplays with c-di-GMP
Authors: Xu Zhaowei , Zhang Hainan , Zhang Xingrun , Liu Chengxi , Jiang Hewei , Wu Fanlin , Qian Lili , Czajkowsky Daniel M. , Guo Shujuan , Bi Lijun , Wang Shihua , Li Haitao , Tan Minjia , Feng Lei , Hou Jingli , Tao Sheng-ce 
Published: July 2018

AbstractAs a ubiquitous bacterial secondary messenger, c-di-GMP plays key regulatory roles in processes such as bacterial motility and transcription regulation. CobB is the Sir2 family protein deacetylase that controls energy metabolism, chemotaxis and DNA supercoiling in many bacteria. Using anE.coliproteome microarray, we found that c-di-GMP strongly binds to CobB. Protein deacetylation assays showed that c-di-GMP inhibits CobB activity and thereby modulates the biogenesis of acetyl-CoA. Through mutagenesis studies, residues R8, R17 and E21 of CobB were shown to be required for c-di-GMP binding. Next, we found that CobB is an effective deacetylase of YdeH, a major diguanylate cyclase (DGC) ofE.colithat is endogenously acetylated. Mass spectrometry analysis identified YdeH K4 as the major site of acetylation, and it could be deacetylated by CobB. Interestingly, deacetylation of YdeH enhances its stability and cyclase activity in c-di-GMP production. Thus, our work establishes a novel negative feedback loop linking c-di-GMP biogenesis and CobB-mediated protein deacetylation.
Human back-tracking behaviour is associated with suppression of default-mode region activity and enhanced dorsal anterior cingulate activity
Authors: Javadi Amir-Homayoun , Patai Eva Zita , Marin-Garcia Eugenia , Margois Aaron , Tan Heng-Ru M. , Kumaran Dharshan , Nardini Marko , Penny Will , Duzel Emrah , Dayan Peter , Spiers Hugo J. 
Published: July 2018

AbstractCentral to the concept of the ‘cognitive map’ is that it confers behavioural flexibility, allowing animals to take efficient detours, exploit shortcuts and realise the need to back-track rather than persevere on a poorly chosen route. The neural underpinnings of such naturalistic and flexible behaviour remain unclear. During fMRI we tested human subjects on their ability to navigate to a set of goal locations in a virtual desert island riven by lava, which occasionally shifted to block selected paths (necessitating detours) or receded to open new paths (affording shortcuts). We found that during self-initiated back-tracking, activity increased in frontal regions and the dorsal anterior cingulate cortex, while activity in regions associated with the core default-mode network was suppressed. Detours activated a network of frontal regions compared to shortcuts. Activity in right dorsolateral prefrontal cortex specifically increased when participants encountered new plausible shortcuts but which in fact added to the path (false shortcuts). These results help inform current models as to how the brain supports navigation and planning in dynamic environments.Significance StatementAdaptation to change is important for survival. Although real-world spatial environments are prone to continual change, little is known about how the brain supports navigation in dynamic environments where flexible adjustments to route plans are needed. Here, we used fMRI to examine the brain activity elicited when humans took forced detours, identified shortcuts and spontaneously back-tracked along their recent path. Both externally and internally generated changes in the route activated the fronto-parietal attention network, whereas only internally generated changes generated increased activity in the dorsal anterior cingulate cortex with a concomitant disengagement in regions associated with the default-mode network. The results provide new insights into how the brain plans and re-plans in the face of a changing environment.