bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide quantitative trait loci mapping on Verticillium wilt resistance in 300 chromosome segment substitution lines from Gossypium hirsutum × Gossypium barbadense
Authors: Rashid Md Harun or , Li Peng-tao , Chen Tingting , Palanga Koffi Kibalou , Gong Wan-kui , Ge Qun , Gong Ju-wu , Liu Ai-ying , Lu Quan-wei , Diouf Latyr , Sarfraz Zareen , Jamshed Muhammad , Shi Yu-zhen , Yuan You-lu 
Published: October 2019

AbstractCotton Verticillium wilt (VW) is a devastating disease seriously affecting fiber yield and quality, and the most effective and economical prevention measure at present is selection and extension of Gossypium varieties harboring high resistant VW. However, multiple attempts to improve the VW resistance of the most widely cultivated Upland cotton have brought in little significant progress, and it seems necessary and urgent to develop Chromosome segment substitution lines (CSSLs) for merging the superior genes related with high yield and wide adaptation from G. hirsutum and VW resistance and excellent fiber quality from G. barbadense. In this study, 300 CSSLs were chosen from the developed BC5F3:5 CSSLs constructed by G. hirsutum CCRI36 and G. barbadense Hai1 to conduct quantitative trait locus (QTL) mapping on VW resistance, and a total of 53 QTLs relevant to VW disease index (DI) were identified together with the phenotypic data of 2 years investigations in two fields with two replications per year. All the QTLs were distributed on 20 chromosomes with phenotypic variation of 3.74-11.89%, of which 29 stable ones were consistent in at least two environments. Based on Meta-analysis on the 53 QTLs, 43 novel ones were identified, while 10 ones consistent to previously identified QTLs. Meanwhile, 32 QTL hotspot regions were detected, including 15 ones were novel. This study concentrates on QTL identification and screening hotspot region related with VW in the 300 CSSLs, which lay a solid platform not only for revealing the genetic and molecular mechanisms of VW resistance, but also for further fine mapping, gene cloning and molecular designing in breeding program for resistant cotton varieties.
Genomic Competition for Noise Reduction Shaped Evolutionary Landscape of Mir-4673
Authors: Farahani Ramin M , Rezaei-Lotfi Saba , Hunter Neil 
Published: October 2019

AbstractThe genomic platform that informs evolution of microRNA cascades remains unknown. Here we capitalized on the recent evolutionary trajectory of hominin-specific miRNA-4673 (Dokumcu et al., 2018) encoded in intron 4 of notch-1 to uncover the identity of one such precursor genomic element and the selective forces acting upon it. The miRNA targets genes that regulate Wnt/β-catenin signalling cascade. Primary sequence of the microRNA and its target region in Wnt modulating genes evolved from homologous signatures mapped to homotypic cis-clusters recognised by TCF3/4 and TFAP2A/B/C families. Integration of homologous TFAP2A/B/C cis-clusters (short range inhibitor of β-catenin (Li and Dashwood, 2004)) into the transcriptional landscape of Wnt cascade genes can reduce noise in gene expression (Blake et al., 2003). Probabilistic adoption of miRNA secondary structure by one such cis-signature in notch-1 reflected selection for superhelical curvature symmetry of precursor DNA to localize a nucleosome that overlapped the latter cis-cluster. By replicating the cis-cluster signature, non-random interactions of the miRNA with key Wnt modulator genes expanded the transcriptional noise buffering capacity via a coherent feed-forward loop mechanism (Hornstein and Shomron, 2006). In consequence, an autonomous transcriptional noise dampener (the cis-cluster/nucleosome) evolved into a post-transcriptional one (the miRNA). The findings suggest a latent potential for remodelling of transcriptional landscape by miRNAs that capitalize on non-random distribution of genomic cis-signatures.
Isolation and Characterization of aRhizobiumBacterium Associated with the Toxic DinoflagellateGambierdiscus balechii
Authors: Wu Zhen , Yang Xiaohong , Lin Senjie , Lee Wai Hin , Lam Paul K.S. 
Published: October 2019

ABSTRACTAlgae-bacteria associations are increasingly being recognized to be important in shaping the growth of both algae and bacteria. Bacteria belonging to order Rhizobiales are important symbionts of legumes often developing as nodules on plant roots, but have not been widely documented in association with algae. Here, we detected, isolated, and characterized aRhizobiumspecies from the toxic benthic dinoflagellateGambierdiscusculture. The sequence of 16S rDNA showed 99% identity with that ofRhizobium rosettiformans. To further characterize the bacterium, we amplified and sequenced a cell wall hydrolase (CWH)-encoding gene; phylogenetic analysis indicated that this sequence was similar to the homologs ofMartellelasp. andHoefleasp, of order Rhizobiales. We performed PCR usingnifH primers to determine whether this bacterium can fix N2; however, the results of sequencing analysis showed that it was closer to chlorophyllideareductase-encoding gene (bchX), which is similar tonifH. Results of 16S rDNA qPCR showed that compared to that in the early exponential phase, the abundance of this bacterium increased during the late exponential growth phase ofGambierdiscus. When the dinoflagellate culture was subjected to N limitation, the abundance of the bacterium represented by both 16S rDNA and CWH increased. Based on these results and published literature, it is apparent that thisRhizobiumbacterium benefits from the association withGambierdiscusby hydrolyzing and utilizing the extracellular organic matter exudates released by the dinoflagellate. This is the first report ofRhizobiumspecies being associated with dinoflagellates, which will shed light on the algae-bacteria relationships.IMPORTANCEPhytoplankton are the undisputed primary producers in the aquatic ecosystems and contribute approximately half of the global net primary productivity.Dinoflagellates are one of the most important phytoplankton in the marine ecosystems. Commonly, they do not exist autonomously in the marine environment but rather co-live with many bacteria that interact with dinoflagellates, producing a dynamic microbial ecosystem. Their interactions play a major role in important processes such as carbon fluxes and nutrient regeneration in the ocean, ultimately influencing the global carbon cycle and the climate. Hence, there is a need to understand the association and relationships between dinoflagellates and bacteria. Here, we tried to elucidate these interactions through isolating and characterizing a bacterium from a benthic toxic dinoflagellate culture. Our study is the first report of such bacterium being recorded to be associated with a dinoflagellate in this genus, providing new insights into the dinoflagellate-bacteria association for future research.
Spatially explicit ecological modeling improves empirical characterization of dispersal
Authors: Karisto Petteri , Suffert Frédéric , Mikaberidze Alexey 
Published: October 2019

AbstractDispersal is a key ecological process, but remains difficult to measure. By recording numbers of dispersed individuals at different distances from the source one can acquire a dispersal gradient. Although dispersal gradients contain information on dispersal, they are influenced by the spatial extent of the source. How can we separate the two contributions to extract knowledge on dispersal?One could use a small, point-like source for which a dispersal gradient represents a dispersal kernel, which quantifies the probability of an individual dispersal event from a source to a destination point. However, the validity of this approximation cannot be established before conducting measurements.We formulated a theory that incorporates the spatial extent of sources to estimate dispersal kernels from dispersal gradients. We re-analyzed published dispersal gradients for three major plant pathogens. We also demonstrated using simulations that this approach provides more accurate estimates of dispersal kernels across biologically plausible scenarios. We concluded that the three plant pathogens disperse over substantially shorter distances compared to conventional estimates. Using this method, a significant proportion of published dispersal gradients can be re-analyzed to improve our knowledge about spatial scales of dispersal. Thus, our results can boost progress in characterization of dispersal across taxa.
The roles ofhox 13genes in newt limb development and regeneration
Authors: Takeuchi Takashi , Minamitani Fumina , Koriyama Kazuki , Satoh Yukio , Suzuki Ken-ichi , Shigenobu Shuji , Inoue Takeshi , Agata Kiyokazu , Hayashi Toshinori 
Published: October 2019

ABSTRACTPosteriorHoxgenes play crucial roles in limb development and specify regions in the proximal-distal (PD) axis of limbs. However, there is no direct genetic evidence thatHoxgenes are essential for limb regeneration. Moreover, if essential, it is totally unknown whichHoxgenes have the same or distinct functions between development and regeneration. Here, we mutatedhox13using an efficient CRISPR/Cas9 system in newts (Pleurodeles waltl), which have strong regenerative capacities in various tissues. Triple or double mutants ofhox13paralogs lost their digit and metacarpal/metatarsal bones. Limb regeneration progressed but regenerates lacked the same autopod region. These results showed thathox13paralogs have the same functions in limb development and regeneration.
Looking for mimicry in a snake assemblage using deep learning
Authors: de Solan Thomas , Renoult Julien Pierre , Geniez Philippe , David Patrice , Crochet Pierre-Andre 
Published: October 2019

AbstractBatesian mimicry, with its highly colorful species and astonishing mimic-model resemblance, is a canonical example of evolution by natural selection. However, Batesian mimicry could also occur in inconspicuous species and rely on subtle resemblance. Although potentially widespread, such instances have been rarely investigated, such that the real frequency of Batesian mimicry has remained largely unknown. To fill this gap, we developed a new approach using deep learning to quantify the resemblance between putative mimics and models from photographs. We applied this method to quantify the frequency of Batesian mimicry in Western Palearctic snakes. Potential mimics were revealed by an excess of resemblance with sympatric venomous snakes compared to random expectations. We found that 8% of the non-venomous species were potential mimics, among which all were imperfect mimics. This study is the first to quantify the frequency of Batesian mimicry in a whole community of vertebrates, and shows that even concealed species can be reliably identified as potential models. Our approach should prove useful to detect mimicry in other communities, and more generally it highlights the benefits of deep learning for quantitative studies of phenotypic resemblance.
Differential Effects of SUMO1/2 on Circadian Protein PER2 Stability and Function
Authors: Chen Ling-Chih , Hsieh Yung-Lin , Kuo Tai-Yun , Chou Yu-Chi , Hsu Pang-Hung , Hwang-Verslues Wendy W. 
Published: October 2019

AbstractPosttranslational modification (PTM) of core circadian clock proteins, including Period2 (PER2), is required for proper circadian regulation. PER2 function is regulated by casein kinase 1 (CK1)-mediated phosphorylation and ubiquitination but little is known about other PER2 PTMs or their interaction with PER2 phosphorylation. We found that PER2 can be SUMOylated by both SUMO1 and SUMO2; however, SUMO1 versus SUMO2 conjugation had different effects on PER2 turnover and transcriptional suppressor function. SUMO2 conjugation facilitated PER2-β-TrCP interaction leading to PER2 proteasomal degradation. In contrast, SUMO1 conjugation, mediated by E3 SUMO-protein ligase RanBP2, enhanced CK1-mediated PER2S662 phosphorylation and increased PER2 transcriptional suppressor function. PER2 K736 was critical for both SUMO1- and SUMO2-conjugation. A PER2K736R mutation was sufficient to alter circadian periodicity and reduce PER2-mediated transcriptional suppression. Together, our data revealed SUMO1 versus SUMO2 conjugation acts as an upstream determinant of PER2 phosphorylation and thereby affects the circadian regulatory system and circadian periodicity.
CtIP promotes the motor activity of DNA2 to accelerate long-range DNA end resection
Authors: Ceppi Ilaria , Howard Sean M. , Kasaciunaite Kristina , Pinto Cosimo , Anand Roopesh , Seidel Ralf , Cejka Petr 
Published: October 2019

SummaryBLM or WRN helicases function with the DNA2 helicase-nuclease to resect DNA doublestrand breaks and initiate homologous recombination. Upon DNA unwinding by BLM/WRN, RPA directs the DNA2 nuclease to degrade the 5’-strand, revealing the 3’ overhang needed for recombination. RPA bound to ssDNA also represents a barrier, explaining the need for the motor activity of DNA2 to displace RPA prior to resection. Using ensemble and single molecule biochemistry, we show that phosphorylated CtIP dramatically stimulates the ATP hydrolysis driven motor activity of DNA2. This activation in turn strongly promotes the degradation of RPA-coated ssDNA by DNA2. The domains of CtIP required to stimulate DNA2 are separable from those that regulate the MRN complex. These results establish that CtIP couples both MRE11-dependent short and DNA2-dependent long-range resection, and show how the motor activity of DNA2 promotes resection. Our data explain the less severe resection defects of MRE11 nuclease-deficient cells compared to those lacking CtIP.HighlightsPhosphorylated CtIP stimulates the motor activity of DNA2The activated DNA2 translocase facilitates degradation of RPA-coated ssDNACtIP promotes both MRN and DNA2 nucleases coupling short and long-range resectionThe CtIP domains required to promote DNA2 and MRN are distinct and fully separable
Metabolic remodeling by TIGAR overexpression is a therapeutic target in esophageal squamous-cell carcinoma
Authors: Chu Jiahui , Niu Xiangjie , Chang Jiang , Shao Mingming , Peng Linna , Xi Yiyi , Lin Ai , Wang Chengcheng , Cui Qionghua , Luo Yingying , Fan Wenyi , Chen Yamei , Sun Yanxia , Guo Wenjia , Tan Wen , Lin Dongxin , Wu Chen 
Published: October 2019

SummaryWhole-genome sequencing has identified many amplified genes in esophageal squamous-cell carcinoma (ESCC); however, their roles and the clinical relevance have yet elucidated. Here we show TP53-induced glycolysis and apoptosis regulator (TIGAR) is a major player in ESCC progression and chemoresistance. TIGAR reprograms glucose metabolism from glycolysis to the glutamine pathway through AMP-activated kinase, and its overexpression is correlated with poor disease outcomes. Tigar knockout mice have reduced ESCC growth and tumor burden. Treatment of TIGAR-overexpressed ESCC cell xenografts and patient-derived tumor xenografts in mice with combination of glutaminase inhibitor and chemotherapeutic agents achieves significant more efficacy than chemotherapy alone. These findings shed light on an important role of TIGAR in ESCC and provide evidence for targeted treatment of TIGAR-overexpressed ESCC.SignificanceEffective and target therapies are required for ESCC, one of the most common types of digestive OR cancer. Little has been known about the biology of ESCC progression or potential molecular targets OR for treatment. Whole-genome sequencing and RNA sequencing studies in ESCC have identified OR many recurrent copy number gain genes; however, the roles and druggable relevance of these OR genes remains poorly understood. Herein we demonstrate that TIGAR overexpression leads to OR metabolic remodeling, promoting ESCC progression and resistance to chemotherapeutic agents. OR Inhibiting the glutamine pathway significantly represses TIGAR-overexpressing ESCC growth and OR enhances tumor cell sensitization to cytotoxic agents. These findings might provide the rationale OR for clinical trials testing glutamine pathway inhibitors in combination with chemotherapy in OR TIGAR-expressing ESCC.
Genetic diversity and multiplicity of infection in Fasciola gigantica isolates of Pakistani livestock
Authors: Rehman Zia Ur , Zahid Osama , Rashid Imran , Ali Qasim , Akbar Muhammad Haroon , Oneeb Muhammad , Shehzad Wasim , Ashraf Kamran , Sargison Neil D. , Chaudhry Umer 
Published: October 2019

AbstractFasciola gigantica liver flukes are responsible for over 3 billion US dollars of production loss annually in farmed livestock and cause widespread zoonotic disease. Nevertheless, the understating of the emergence and spread of the trematode species is poor. The multiplicity of F. gigantica infection and its spread is potentially influenced by multiple factors, including the abundance of suitable intermediate hosts, climatic conditions favoring the completion of the parasite’s lifecycle, and translocation of infected animals or free-living parasite stages between regions. Here we describe the development of a ‘tremabiome’ metabarcoding sequencing method to explore the numbers of F. gigantica genotypes per infection and patterns of parasite spread, based on genetic characteristics of the mitochondrial NADH dehydrogenase 1 (mt-ND-1) locus. We collected F. gigantica from three abattoirs in the Punjab and Balochistan provinces of Pakistan, and our results show a high level of genetic diversity in 20 F. gigantica populations derived from small and large ruminants consigned to slaughter in both provinces. This implies that F. gigantica can reproduce in its definitive hosts through meiosis involving cross- and self-breeding, as described in the closely related species, Fasciola hepatica. The genetic diversity between the 20 populations derived from different locations also illustrates the impact of animal movements on gene flow. Our results demonstrate the predominance of single haplotypes, consistent with a single introduction of F. gigantica infection in 85% of the hosts from which the parasite populations were derived. This is consistent with clonal reproduction in the intermediate snail hosts.
Time-Space Fourier κώ Filter for Motion Artifacts Compensation during Transcranial Fluorescence Brain Imaging
Authors: Molodij Guillaume , Meglinski Igor , Sdobnov Anton , Kuznetsov Yuri , Harmelin Alon , Kalchenko Vyacheslav 
Published: October 2019

AbstractIntravital imaging of brain vasculature through the intact craniumin vivois based on the evolution of the fluorescence intensity and provides an ability to characterize various physiological processes in the natural context of cellular resolution. The involuntary motions of the examined subjects often limitin vivonon-invasive functional optical imaging. Conventional imaging diagnostic modalities encounter serious difficulties in correction of artificial motions, associated with the rapid structural variations and fast high dynamics of the intensity values in the collected image sequences, when a common reference cannot be provided. In current report, we introduce an alternative solution that utilizes a Fourier Kappa-Omega filtering approach. We demonstrate that the proposed approach is effective for image stabilization of fast dynamic image sequences. The validation of the Fourier Kappa-Omega filtering was performed on the images obtaining during mouse transcranial brain imaging using fluorescent microscope as well as on the simulated sequences of images. The proposed technique can be used autonomously without supervision and assignation of a reference image.
Neurobiological successor features for spatial navigation
Authors: de Cothi William , Barry Caswell 
Published: October 2019

AbstractThe hippocampus has long been observed to encode a representation of an animal’s position in space. Recent evidence suggests that the nature of this representation is somewhat predictive and can be modelled by learning a successor representation (SR) between distinct positions in an environment. However, this discretisation of space is subjective making it difficult to formulate predictions about how some environmental manipulations should impact the hippocampal representation. Here we present a model of place and grid cell firing as a consequence of learning a SR from a basis set of known neurobiological features – boundary vector cells (BVCs). The model describes place cell firing as the successor features of the SR, with grid cells forming a low-dimensional representation of these successor features. We show that the place and grid cells generated using the BVC-SR model provide a good account of biological data for a variety of environmental manipulations, including dimensional stretches, barrier insertions, and the influence of environmental geometry on the hippocampal representation of space.
The effect of Rosovitine on mPSM explants: a real time analysis
Authors: Moya Lucas J. Morales , Bailey Charlotte S. L. , Dale J. Kim , Murray Philip J. 
Published: October 2019

AbstractPreviously we showed, using fixed tissue techniques, that treatment of chick embryos with a family of pharmacological inhibitors yields increased levels of NICD, an increased NICD half life and longer segments (Wiederman et al., 2015). Here we measure the effect of one of the pharmacological perturbations (Roscovtine) using a real time reporter of the somitogenesis clock. After processing the reporter signal using empirical mode decomposition, we measure the oscillator period in mPSM explants and find, in agreement with the previous study, that the period of the segmentation clock increases upon Roscovitine treatment. However, we also make the novel discovery that the differentiation rate of the mPSM tissue also increases upon Roscovitine treatment. Returning to the previous study, we find that the measured increases in somite size and oscillator period are only consistent with the clock and wavefront model if the wavefront velocity also increased.
β-cell dedifferentiation is associated with epithelial-mesenchymal transition triggered by miR-7-mediated repression of mSwi/Snf complex
Authors: Mak Tracy CS , von Ohlen Yorrick , Wang Yi Fang , Kane Eva , Jurgaityte Kaste , Ervilha Pedro , Chabosseau Pauline , Distaso Walter , Salem Victoria , Tomas Alejandra , Stoffel Markus , Marchetti Piero , Shapiro A.M. James , Rutter Guy A. , Latreille Mathieu 
Published: October 2019

Abstractβ-cell dedifferentiation has been revealed as a pathological mechanism underlying pancreatic dysfunction in diabetes. However, little is known on the genetic and epigenetic changes linked with the dedifferentiation of β-cells. We now report that β-cell dedifferentiation is associated with epithelial to mesenchymal transition (EMT) triggered by miR-7-mediated repression of Smarca4/Brg1 expression, a catalytic subunit of the mSwi/Snf chromatin remodeling complexes essential for β-cell transcription factors (β-TFs) activity. miR-7-mediated repression of Brg1 expression in diabetes causes an overall compaction of chromatin structure preventing β-TFs from accessing and transactivating genes maintaining the functional and epithelial identity of β-cells. Concomitantly, loss of β-cell identity impairs the ability of β-TFs Pdx1, Nkx6-1, Neurod1 to repress non-β-cell genes enriched selectively in mesenchymal cells leading to EMT, change in islet microenvironment, and fibrosis. Remarkably, anti-EMT agents normalized glucose tolerance of diabetic mice, thus revealing mesenchymal reprogramming of β-cells as a novel therapeutic target in diabetes. This study sheds light on the genetic signature of dedifferentiated β-cells and highlights how loss of mSwi/Snf activity in diabetes initiating a step-wise remodeling of epigenetic landscapes of β-cells leading to the induction of an EMT process reminiscent of a response to tissue injury.