bluuebunny/crossref_metadata_2025_split huggingface dataset:
Context information supports serial dependence of multiple visual objects across memory episodes
Authors: Fischer Cora , Czoschke Stefan , Peters Benjamin , Rahm Benjamin , Kaiser Jochen , Bledowski Christoph 
Published: June 2019

AbstractVisual perception operates in an object-based manner, by integrating associated features via attention. Working memory allows a flexible access to a limited number of currently relevant objects, even when they are occluded or physically no longer present. Recently, it has been shown that we compensate for small changes of an object’s feature over memory episodes, which can support its perceptual stability. This phenomenon was termed ‘serial dependence’ and has mostly been studied in situations that comprised only a single relevant object. However, since we are typically confronted with situations where several objects have to be perceived and held in working memory, the central question of how we selectively create temporal stability of several objects has remained unsolved. As different objects can be distinguished by their accompanying context features, like their color or temporal position, we tested whether serial dependence is supported by the congruence of context features across memory episodes. Specifically, we asked participants to remember the motion directions of two sequentially presented colored dot fields per trial. At the end of a trial one motion direction was cued for continuous report either by its color (Experiment 1) or serial position (Experiment 2). We observed serial dependence, i.e., an attractive bias of currently toward previously memorized objects, between current and past motion directions that was clearly enhanced when items had the same color or serial position across trials. This bias was particularly pronounced for the context feature that was used for cueing and for the target of the previous trial. Together, these findings demonstrate that coding of current object representations depends on previous representations, especially when they share similar content and context features. Apparently the binding of content and context features is not completely erased after a memory episode, but it is carried over to subsequent episodes. As this reflects temporal dependencies in natural settings, the present findings reveal a mechanism that integrates corresponding bundles of content and context features to support stable representations of individualized objects over time.
Global analysis of Two Component System (TCS) member of chickpea and other legume genomes implicates its role in enhanced nodulation
Authors: Tiwari Manish , Yadav Manisha , Singh Baljinder , Pandey Vimal , Nawaz Kashif , Bhatia Sabhyata 
Published: June 2019

AbstractNodule organogenesis is governed primarily by phytohormone cytokinin. We observed the significant nodulation in chickpea at particular cytokinin concentration (2.5×10−7) which indicated the importance of cytokinin in nodule development. Cytokinin signaling is mediated through the Two Component System (TCS) which comprises of sensor histidine kinases (HKs), histidine phosphotransfer proteins (HPs), and response regulators (RRs). Therefore, we analyzed the interconnection of cytokinin with TCS molecules during root nodule development through global analysis of TCS candidates in legumes with special consideration to cytokinin receptor and Type-B RR member. We have conducted an in depth global analysis of TCS family members in chickpea and other legumes, Medicago and pigeon pea. Higher number of TCS genes were found in Medicago (96), followed by pigeonpea (75) and chickpea (67). A good correlation between TCS members with their corresponding total number of genes were observed in all three-legume species. Collinearity analysis of TCS revealed phylogenetically closer proximity of Cicer to Medicago followed by Glycine than Cajanus. Comprehensive analysis of 3-dimensional structure, genomic organisation and domain arrangement showed a conservation of TCS members within species. In depth investigation showed that HKs were mainly conserved among TCS members in legumes and non-legumes while divergence occurred at level of RRs. Further, Type-B RRs were functionally most diversified in RRs based on phylogeny, syntenic and transcript analysis. Few numbers of segmentally duplicated pair of TCS showed difference in their transcriptional regulation suggesting the functional evolution. For functional characterization the cre1 mutants of (Medicago) were complemented with chickpea cytokinin responsive HKs and nodulation deficient phenotype of mutants were restored. A synchronous cytokinin-induced expression of chickpea cytokinin receptor HKs and CaNIN provides strong relation of cytokinin signaling during nodulation. Furthermore, interesting potential candidate CaRR13 was selected to deduce the underlying molecular mechanism of nodulation, chickpea in specific and legumes in general.
Epithelium intrinsic vitamin A signaling co-ordinates pathogen clearance in the gut via IL-18
Authors: Iyer Namrata , Grizotte-Lake Mayara , Gordon Sarah R. , Palmer Ana C. S. , Calvin Crystle , Vaishnava Shipra 
Published: June 2019

AbstractIntestinal epithelial cells (IECs) are at the forefront of host-pathogen interactions, coordinating a cascade of immune responses to confer protection against pathogens. Here we show that IEC-intrinsic vitamin A signaling restricts pathogen invasion early in the infection and subsequently activates immune cells to promote pathogen clearance. Mice blocked for retinoic acid receptor (RAR) signaling selectively in IECs (stopΔIEC) showed significantly higherSalmonellaburden in colonic tissues early in the infection associated with higher luminal and systemic loads of the pathogen at later stages. Higher susceptibility of stopΔIECmice correlated with attenuated mucosal interferon gamma (IFNγ) production by underlying immune cells. We found that, at homeostasis, the intestinal epithelium of stopΔIECmice produced significantly lower amounts of interleukin 18 (IL-18), a potent inducer of IFNγ. Regulation of IL-18 by vitamin A was also observed in a dietary model of vitamin A supplementation. IL-18 reconstitution in stopΔIECmice restored resistance toSalmonellaby promoting epithelial cell shedding to eliminate infected cells and limit pathogen invasion early in infection. Further, IL-18 augmented IFNγ production by underlying immune cells to restrict pathogen burden and systemic spread. Our work uncovers a critical role for vitamin A in coordinating a biphasic immune response toSalmonellainfection by regulating IL-18 production by IECs.Author SummaryEpithelial cells line the intestinal lumen, forming a barrier between the body and dietary and microbial contents in the lumen. Apart from absorbing nutrients from diet, these epithelial cells help mediate a stable, symbiotic relationship between microbes in the gut and the immune cells. During infection, they help co-ordinate the immune response to counter the infection. How dietary micronutrients, such as vitamin A, inform epithelial cell function during infection is poorly understood. Using a model where epithelial cells in the gut cannot respond to vitamin A signals, we find that epithelial vitamin A signaling promotes resistance toSalmonellainfection. We show that, vitamin A increases the production of a key cytokine, interleukin 18, by epithelial cells. IL-18 promotes shedding of infected epithelial cells to reduce the pathogen invasion while also inducing the production of interferon gamma by immune cells to mediate pathogen clearance. Thus, epithelial cells dynamically respond to dietary vitamin A to regulate interleukin 18 production and potentiate resistance to infection.
Wampa is a dynein subunit required for axonemal assembly and male fertility inDrosophila
Authors: Bauerly Elisabeth , Yi Kexi , Gibson Matthew C. 
Published: June 2019

AbstractAxonemal dyneins are motor proteins that form the inner and outer arms of the axoneme in cilia and flagella. Defects in dynein arms are the leading cause of primary ciliary dyskinesia (PCD), which is characterized by chronic respiratory infections, situs inversus, and sterility. Despite current understanding of pathological features associated with PCD, many of their causative genes still remain elusive. Here we analyze genetic requirements forwampa(wam), a previously uncharacterized component of the outer dynein arm that is essential for male fertility. In addition to a role in outer dynein arm formation, we uncovered additional requirements during spermatogenesis, including regulation of remodeling events for the mitochondria and the nucleus. Due to the conserved nature of axonemal dyneins and their essential role in both PCD and fertility, this study advances our understanding of the pathology of PCD, as well as the functional role of dyneins in axonemal formation and spermatogenesis.
The Eya1 phosphatase mediates Shh-driven symmetric cell division of cerebellar granule cell precursors
Authors: Merk Daniel J. , Zhou Pengcheng , Cohen Samuel M. , Pazyra-Murphy Maria F. , Hwang Grace H. , Rehm Kristina J. , Alfaro Jose , Zhao Xuesong , Park Eunyoung , Xu Pin-Xian , Chan Jennifer A. , Eck Michael J. , Nazemi Kellie J. , Segal Rosalind A. 
Published: June 2019

AbstractDuring neural development, stem and precursor cells can divide either symmetrically or asymmetrically. The transition between symmetric and asymmetric cell divisions is a major determinant of precursor cell expansion and neural differentiation, but the underlying mechanisms that regulate this transition are not well understood. Here, we identify the Sonic hedgehog (Shh) pathway as a critical determinant regulating the mode of division of cerebellar granule cell precursors (GCPs). Using partial gain and loss of function mutations within the Shh pathway, we show that pathway activation determines spindle orientation of GCPs, and that mitotic spindle orientation directly correlates with the mode of division. Mechanistically, we show that the phosphatase Eya1 is essential for implementing Shh-dependent GCP spindle orientation. We identify atypical protein kinase C (aPKC) as a direct target of Eya1 activity and show that Eya1 dephosphorylates Threonine (T410) in the activation loop of this polarity complex component. Thus, Eya1 inactivates the cell polarity complex, resulting in reduced phosphorylation of Numb and other components that regulate the mode of division. This Eya1-dependent cascade is critical in linking spindle orientation, cell cycle exit and terminal differentiation. Together these findings demonstrate that a Shh-Eya1 regulatory axis selectively promotes symmetric cell divisions during cerebellar development by coordinating spindle orientation and cell fate determinants.Summary statementBiological responses to Shh signaling are specified by the magnitude of pathway activation and the cellular context. This study shows that potent Shh signaling regulates mitotic orientation and symmetric division of cerebellar granule cell precursors in a process that requires the phosphatase Eya1 and unequal distribution of cell fate determinants to daughter cells.
A chromosome-level assembly of the Atlantic herring – detection of a supergene and other signals of selection
Authors: Pettersson Mats E. , Rochus Christina M. , Han Fan , Chen Junfeng , Hill Jason , Wallerman Ola , Fan Guangyi , Hong Xiaoning , Xu Qiwu , Zhang He , Liu Shanshan , Liu Xin , Haggerty Leanne , Hunt Toby , Martin Fergal J. , Flicek Paul , Bunikis Ignas , Folkvord Arild , Andersson Leif 
Published: June 2019

ABSTRACTThe Atlantic herring is a model species for exploring the genetic basis for ecological adaptation, due to its huge population size and extremely low genetic differentiation at selectively neutral loci. However, such studies have so far been hampered because of a highly fragmented genome assembly. Here, we deliver a chromosome-level genome assembly based on a hybrid approach combining ade novoPacBio assembly with Hi-C-supported scaffolding. The assembly comprises 26 autosomes with sizes ranging from 12.4 to 33.1 Mb and a total size, in chromosomes, of 726 Mb. The development of a high-resolution linkage map confirmed the global chromosome organization and the linear order of genomic segments along the chromosomes. A comparison between the herring genome assembly with other high-quality assemblies from bony fishes revealed few interchromosomal but frequent intrachromosomal rearrangements. The improved assembly makes the analysis of previously intractable large-scale structural variation more feasible; allowing, for example, the detection of a 7.8 Mb inversion on chromosome 12 underlying ecological adaptation. This supergene shows strong genetic differentiation between populations from the northern and southern parts of the species distribution. The chromosome-based assembly also markedly improves the interpretation of previously detected signals of selection, allowing us to reveal hundreds of independent loci associated with ecological adaptation in the Atlantic herring.
Cross-linked RNA Secondary Structure Analysis using Network Techniques
Authors: Fischer-Hwang Irena , Lu Zhipeng , Zou James , Weissman Tsachy 
Published: June 2019

AbstractNext generation sequencing and biochemical cross-linking methods have been combined into powerful tools to probe RNA secondary structure. One such method, known as PARIS, has been used to produce near base-pair maps of long-range and alternative RNA structures in living cells. However, the procedure for generating these maps typically relies on laborious manual analysis. We developed an automated method for producing RNA secondary structure maps using network analysis techniques. We produced an analysis pipeline, dubbed cross-linked RNA secondary structure analysis using network techniques (CRSSANT), which automates the grouping of gapped RNA sequencing reads produced using the PARIS assay, and tests the validity of secondary structures implied by the groups. We validated the clusters and secondary structures produced by CRSSANT using manually-produced grouping maps and known secondary structures. We implemented CRSSANT in Python using the network analysis package NetworkX and RNA folding software package ViennaRNA. CRSSANT is fast and efficient, and is available as Python source code at https://github.com/ihwang/CRSSANT.
The identification of mecciRNAs and their roles in mitochondrial entry of proteins
Authors: Liu Xu , Wang Xiaolin , Li Jingxin , Hu Shanshan , Deng Yuqi , Yin Hao , Bao Xichen , Zhang Qiangfeng Cliff , Wang Geng , Wang Baolong , Shi Qinghua , Shan Ge 
Published: June 2019

AbstractMammalian mitochondria have small genomes encoding very limited numbers of proteins. Over one thousand proteins and noncoding RNAs encoded by nuclear genome have to be imported from the cytosol into the mitochondria. Here we report the identification of hundreds of circular RNAs (mecciRNAs) encoded by mitochondrial genome. We provide both in vitro and in vivo evidence to show that mecciRNAs facilitate mitochondrial entry of nuclear-encoded proteins by serving as molecular chaperones in the folding of imported proteins. Known components of mitochondrial protein and RNA importation such as TOM40 and PNPASE interact with mecciRNAs and regulate protein entry. Expression of mecciRNAs is regulated, and these transcripts are critical for mitochondria in adapting to physiological conditions and diseases such as stresses and cancers by modulating mitochondrial protein importation. mecciRNAs and their associated physiological roles add categories and functions to eukaryotic circular RNAs, and shed novel lights on communication between mitochondria and nucleus.
Diversity of Microarthropods in Different Habitats: An Ecological Perspective
Authors: Abbas Mohammad Jalaluddin , Parwez Hina 
Published: June 2019

AbstractSoil biological communities are influenced by several factors like edaphic factors, environmental variables, soil nutrients availability and anthropogenic changes including urban development and agricultural practices.Edaphic factors exert the conditions directly to influence microarthropods populations. To test this hypothesis, a question has been addressed; how factors regulate the ecosystem functions in contemporary a combined fashion? We observed, vegetation and habitat conditions both have close relationship and profoundly affect microarthropods populations particularly affect on local scale, resulted microclimatic influence of edaphic matrix which is generally system oriented. It is further discussed in this paper, on what attempt possible for better functional use of microarthropods which is important for conservation and for better output as a result of soil productivity in contemporary harsh climatic conditions with minimum use of amendments. It has been concluded in this study that diverse species found in structurally diverse habitats where they often appear to specialized conditions in native agricultural ecosystem.
Environmental Triggers oflrgAExpression inStreptococcus mutans
Authors: Ishkov Ivan , Ahn Sang-Joon , Rice Kelly C. , Hagen Stephen J. 
Published: June 2019

AbstractThelrgABandcidABoperons ofStreptococcus mutansencode proteins that are structurally similar to the bacteriophage lambda family of holin-antiholin proteins, which are believed to facilitate cell death in other bacterial species. Although their precise function is not known,cidABandlrgABare linked to multiple virulence traits ofS. mutans, including oxidative stress tolerance, biofilm formation, and autolysis. The regulation ofcidABandlrgABis still not understood, as these operons show opposite patterns of expression as well as a complex dependence on growth conditions. We have used a microfluidic approach, together with single-cell imaging of a fluorescent gene reporter, to identify with greater precision the cues that triggerlrgAexpression and characterize cell-to-cell heterogeneity inlrgAactivity.lrgAactivates very abruptly at stationary phase, with a high degree of synchrony across the population. We find this activation is controlled by a small number of inputs that are sensitive to growth phase: Extracellular pyruvate, glucose, and molecular oxygen. Further, activation oflrgAappears to be self-limiting, so thatlrgAis strongly expressed only for a very short interval of time. Consequently,lrgAis programmed to switch on briefly at the end of exponential growth, as glucose and molecular oxygen are exhausted and extracellular pyruvate is available. Our findings are consistent with studies showing that homologs oflrgABare linked, together withlytST, to the reimport of pyruvate for anaerobic fermentative growth.ImportanceThe function and regulation ofcidABandlrgABin Streptococcus mutans is not understood, although these operons have been clearly linked to stress responses and they show a complex dependence on environmental inputs and growth phase. Identifying specific environmental cues that trigger activation oflrgABhas been difficult owing to the cells’ own modification of key inputs such as glucose and oxygen: InS. mutansthelrgABoperon is strongly upregulated at the end of exponential phase, where growth conditions in a bulk culture become poorly defined. Here we have used microfluidics to apply precise control of environmental inputs toS. mutansand identify specific chemical cues that activatelrgAB. We find that rigorously anaerobic conditions and the presence of extracellular pyruvate are sufficient to inducelrgABexpression, suggesting thatlrgABis timed to activate just as pyruvate fermentation becomes favorable.
Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains
Authors: Kentepozidou Elissavet , Aitken Sarah J , Feig Christine , Stefflova Klara , Ibarra-Soria Ximena , Odom Duncan T , Roller Maša , Flicek Paul 
Published: June 2019

ABSTRACTCTCF binding contributes to the establishment of higher order genome structure by demarcating the boundaries of large-scale topologically associating domains (TADs). We have carried out an experimental and computational study that exploits the natural genetic variation across five closely related species to assess how CTCF binding patterns stably fixed by evolution in each species contribute to the establishment and evolutionary dynamics of TAD boundaries. We performed CTCF ChIP-seq in multiple mouse species to create genome-wide binding profiles and associated them with TAD boundaries. Our analyses reveal that CTCF binding is maintained at TAD boundaries by an equilibrium of selective constraints and dynamic evolutionary processes. Regardless of their conservation across species, CTCF binding sites at TAD boundaries are subject to stronger sequence and functional constraints compared to other CTCF sites. TAD boundaries frequently harbor rapidly evolving clusters containing both evolutionary old and young CTCF sites as a result of repeated acquisition of new species-specific sites close to conserved ones. The overwhelming majority of clustered CTCF sites colocalize with cohesin and are significantly closer to gene transcription start sites than nonclustered CTCF sites, suggesting that CTCF clusters particularly contribute to cohesin stabilization and transcriptional regulation. Overall, CTCF site clusters are an apparently important feature of CTCF binding evolution that are critical the functional stability of higher order chromatin structure.
Influence of fats, carotenoids and POPs on the reproduction of the leatherback turtle
Authors: De Andrés E. , Negro Balmaseda Juan José , Navarro Juan Carlos , Marco Adolfo 
Published: June 2019

ABSTRACTThis study provides baseline data on fatty acid profiles and carotenoids in eggs of the leatherback sea turtle, Dermochelys coriacea. Correlations among such compounds, persistent organic pollutants, and reproductive parameters are also investigated. A number of 18 clutches were evaluated during June and August of 2008 at Reserva Pacuare Beach, in the Caribbean side of Costa Rica. Viability and fertility were calculated for each nest. Concentration levels of saturated and unsaturated fatty acids (SFAs and PUFAs), carotenoids and different congeners of persistent organic pollutants (POPs) were determined from egg-yolk samples. Mean ± SD values were calculated for each compound and for each clutch. Correlations were performed searching for interactions among different compounds and for potential effects on reproductive parameters, thus all the studied compounds were related to each other and to any of the reproductive parameters. Low carotenoid levels characterized all eggs of this species, and a positive relationship between carotenoid concentrations and the viability rate was found. POPs and PUFA were positive and strongly correlated, suggesting molecular interactions. PUFAs appeared to increase fertility rate and hatchling length. This study provides potential evidences of PUFA enhancing fertility and hatchling size, and of carotenoids limiting vitellogenesis. The positive correlation found between POPs and PUFAs may indicate that harmful effects of these contaminants on the reproduction of leatherback turtles could be masked.