bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Effect of Gelling agent, medium pH and silver nitrate on adventitious shoot regeneration inSolanum tuberosum
Authors: Kaur Amanpreet , Kumar Anil 
Published: January 2020

AbstractVegetative propagation of potato makes the crop vulnerable to many seed borne diseases. The importance of the crop in attainment of food security makes it an important candidate for in vitro propagation and genetic manipulations. To undertake crop improvement programmes, development of an efficient regeneration protocol is a pre-requisite. Therefore, the present report was focussed to study various factors affecting shoot organogenesis in potato cultivar ‘Kufri Chipsona 1’. The incorporation of silver nitrate (10 µM) to the regeneration medium (MS medium supplemented with BA and GA3) was found to induce shoot organogenesis in 32.11% of leaf and 59.99% of internodal explants. An increase in mean number of shoots regenerated per leaf (5.31) and internodal (8.67) explant was also observed upon addition of silver nitrate to the medium. Similarly, solidification of medium with clarigel and its adjustment to pH 5.8 was found optimum for increasing shoot organogenesis frequency in potato. Among the two types of explants tested, a better response was observed from internodes in comparison with leaf explants. The regenerated shoots were tested for clonal fidelity using PCR based molecular markers [Random Amplified Polymorphic DNA (RAPD) and Inter-Simple Sequence Repeats (ISSR)] and were found true to type.
Measuring Historical and Compositional Signals in Phylogenetic Data
Authors: Jermiin Lars S , Misof Bernhard 
Published: January 2020

AbstractMost commonly-used molecular phylogenetic methods assume that the sequences evolved on a single bifurcating tree and that the evolutionary processes operating at the variable sites are Markovian. Typically, it is also assumed that these evolutionary processes were stationary, reversible and homogenous across the edges of the tree and that the multiple substitutions at variable sites occurred so infrequently that the historical signal (i.e., the signal in DNA that is due to the order and time of divergence event) in phylogenetic data has been retained, allowing for accurate phylogenetic estimates to be obtained from the data. Here, we present two metrics,λandδCFS, to quantify the strength of the historical and compositional signals in phylogenetic data.λquantifiesloss of historical signal, withλ= 0.0 indicating evidence of a strong historical signal andλ= 1.0 indicating evidence of a fully eroded historical signal.δCFSquantifiescompositional distancefrom full symmetry of a divergence matrix generated by comparing two sequences, withδCFS= 0.0 indicating no evidence of evolution under dissimilar conditions andδCFS> 0.0 indicating increasing evidence of lineages diverging under different conditions. The metrics are implemented in methods intended for use after multiple sequence alignment and before model selection and phylogenetic analysis. Results generated using these methods allow users of phylogenetic tools to select phylogenetic data more wisely than it previously was possible. The merits of these metrics and methods are illustrated using simulated data and multi-gene alignments obtained from 144 insect genomes.
Accurate reconstruction of bacterial pan- and core- genomes with PEPPAN
Authors: Zhou Zhemin , Charlesworth Jane , Achtman Mark 
Published: January 2020

AbstractBacterial genomes can contain traces of a complex evolutionary history, including extensive homologous recombination, gene loss, gene duplications and horizontal gene transfer. In order to reconstruct the phylogenetic and population history of a set of multiple bacteria, it is necessary to examine their pan-genome, the composite of all the genes in the set. Here we introduce PEPPAN, a novel pipeline that can reliably construct pan-genomes from thousands of genetically diverse bacterial genomes that represent the diversity of an entire genus. PEPPAN outperforms existing pan-genome methods by providing consistent gene and pseudogene annotations extended by similarity-based gene predictions, and identifying and excluding paralogs by combining tree- and synteny-based approaches. The PEPPAN package additionally includes PEPPAN_parser, which implements additional downstream analyses including the calculation of trees based on accessory gene content or allelic differences between core genes. In order to test the accuracy of PEPPAN, we implemented SimPan, a novel pipeline for simulating the evolution of bacterial pan-genomes. We compared the accuracy and speed of PEPPAN with four state-of-the-art pan-genome pipelines using both empirical and simulated datasets. PEPPAN was more accurate and more specific than any of the other pipelines and was almost as fast as any of them. As a case study, we used PEPPAN to construct a pan-genome of ~40,000 genes from 3052 representative genomes spanning at least 80 species ofStreptococcus. The resulting gene and allelic trees provide an unprecedented overview of the genomic diversity of the entireStreptococcusgenus.
Tools for the genetic manipulation ofHerpetomonas muscarum
Authors: Sloan Megan A. , Ligoxygakis Petros 
Published: January 2020

AbstractTrypanosomatid parasites are causative agents of important human and animal diseases such as sleeping sickness and leishmaniasis. Most trypanosomatids are transmitted to their mammalian hosts by insects, often belonging to Diptera (or true flies). With resistance to both vector-targeted pesticides and trypanocidal drugs being reported, there is a need for novel transmission blocking strategies to be developed. Studies using the blood-feeding vectors themselves are not broadly accessible, as such, new model systems are being developed to unpick insect-trypanosmatids interactions. One such case is the interactions between the model dipteranDrosophila melanogasterand its natural trypanosomatidHerpetomonas muscarum. Our previous work has found that much of the transcriptomic changes triggered inH. muscarumafter ingestion byDrosophilareflect what is known for disease-causing trypanosomatids. Here we describe a set of tools to genetically manipulate the parasite and therefore create a truly tractable insect-parasite interaction system from both sides of this association. These include transgenic fluorescently tagged parasites to follow infection dynamics in the fly gut as well as iterations of plasmids that can be used for generating knock-in and knock-out strains. The tools presented in this short report will facilitate further characterisation of trypanosomatid establishment in a model dipteran.
Disruption ofNAP1genes supresses thefas1mutant phenotype and enhances genome stability
Authors: Kolářová Karolína , Dadejová Martina Nešpor , Loja Tomáš , Sýkorová Eva , Dvořáčková Martina 
Published: January 2020

ABSTRACTHistone chaperones mediate assembly and disassembly of nucleosomes and participate in essentially all DNA-dependent cellular processes. InArabidopsis thaliana,loss-of-functions of FAS1 or FAS2 subunits of the H3-H4 histone chaperone complex CHROMATIN ASSEMBLY FACTOR 1(CAF-1) has a dramatic effect on plant morphology, growth and overall fitness. Altered chromatin compaction, systematic loss of repetitive elements or increased DNA damage clearly demonstrate the severity of CAF-1 dysfunction. How histone chaperone molecular networks change without a functional CAF-1 remains elusive. Here we present an intriguing observation that disruption of the H2A-H2B histone chaperone NUCLEOSOME ASSEMBLY PROTEIN 1 (NAP1) supressesFAS1loss-of function. The quadruple mutantfas1nap1;1-3shows wild-type growth and decreased sensitivity to genotoxic stress. Chromatin offas1nap1;1-3plants is less accessible to micrococcal nuclease and progressive loss of telomeres and 45S rDNA is supressed. Interestingly, the strong genetic interaction betweenFAS1andNAP1does not occur via direct protein-protein interaction. We propose that NAP1;1-3 play an essential role in nucleosome assembly infas1,thus their disruption abolishesfas1defects. Our data altogether reveal a novel function of NAP1 proteins, unmasked by CAF-1 dysfunction. It emphasizes the importance of a balanced composition of chromatin and shed light on the histone chaperone molecular network.
Restoring the pattern of proteoglycan sulphation in perineuronal nets corrects age-related memory loss
Authors: Yang Sujeong , Gigout Sylvain , Molinaro Angelo , Naito-Matsui Yuko , Hilton Sam , Foscarin Simona , Nieuwenhuis Bart , Verhaagen Joost , Pizzorusso Tommaso , Saksida Lisa M. , Bussey Timothy M. , Kitagawa Hiroshi , Kwok Jessica C.F. , Fawcett James W. 
Published: January 2020

AbstractMemory loss is a usual consequence of ageing and aged mice show progressive deficits in memory tasks. In aged brains, perineuronal nets (PNNs), which are implicated in plasticity and memory, become inhibitory due to decreased 6-sulphation of their glycan chains (C6S). Removal of PNNs or digestion of their glycosaminoglycans rescued age-related memory loss. Premature reduction of permissive C6S by transgenic deletion of chondroitin 6-sulfotransferase led to very early memory loss. However, restoring C6S levels in aged animals by AAV delivery or transgenic expression of 6-sulfotransferase restored memory. Low C6S levels caused loss of cortical long-term potentiation, which was restored by AAV-mediated 6-sulfotransferase delivery. The study shows that loss of C6S in the aged brain leads to declining memory and cognition. Age-related memory impairment was restored by C6S replacement or other interventions targeting perineuronal nets
Identification of a novel HIF-1α-αMβ2Integrin-NETosis axis in fibrotic interstitial lung disease
Authors: Khawaja Akif A. , Chong Deborah L.W. , Sahota Jagdeep , Pericleous Charis , Ripoll Vera M. , Booth Helen L. , Khan Saif , Rodriguez-Justo Manuel , Giles Ian P. , Porter Joanna C. 
Published: January 2020

AbstractNeutrophilic inflammation correlates with mortality in fibrotic interstitial lung disease (ILD) however, the underlying mechanisms remain unclear. We aimed to determine whether aberrant neutrophil activation is a feature of ILD and the relative role of hypoxia. We used lung biopsies and bronchoalveolar lavage (BAL) from ILD patients to investigate the extent of hypoxia and neutrophil activation in lungs of patients with ILD. We complemented these findings withex vivofunctional studies of neutrophils from healthy volunteers to determine the effects of hypoxia. We demonstrate for the first time HIF-1α staining in neutrophils and endothelial cells in ILD lung biopsies. Hypoxia enhanced both spontaneous and phorbol 12-myristate 13-acetate (PMA)-induced neutrophil extracellular trap (NET) release (NETosis), neutrophil adhesion, and trans-endothelial migration. Hypoxia also increased neutrophil expression of the αMand αXintegrin subunits. Interestingly, NETosis was induced by αMβ2integrin activation and prevented by cation chelation. Finally, NETs were demonstrated in the BAL from ILD patients, and quantification showed significantly increased cell-free DNA content and MPO-citrullinated histone H3 complexes in ILD patients compared to non-ILD controls. Our work indicates that HIF-1α upregulation may augment neutrophil recruitment and activation within the lung interstitium through activation of β2integrins. Our results identify a novel HIF-1α-Integrin-NETosis axis for future exploration in therapeutic approaches to fibrotic ILD.
miR-206 knockout shows it is critical for myogenesis and directly regulates newly identified target mRNAs
Authors: Salant Georgiana M. , Tat Kimngan L. , Goodrich James A. , Kugel Jennifer F. 
Published: January 2020

AbstractThe muscle specific miRNA, miR-206, is important for the process of myogenesis; however, studying the function of miR-206 in muscle development and differentiation still proves challenging because the complement of mRNA targets it regulates remains undefined. In addition, miR-206 shares close sequence similarity to miR-1, another muscle specific miRNA, making it hard to study the impact of miR-206 alone in cell culture models. Here we used CRISPR/Cas9 technology to knockout miR-206 in C2C12 muscle cells. We show that knocking out miR-206 significantly impairs and delays differentiation and myotube formation, revealing that miR-206 alone is important for myogenesis. In addition, we use an experimental affinity purification technique to identify new mRNA targets of miR-206 in C2C12 cells. We identified over one hundred mRNAs as putative miR-206 targets. Functional experiments on six putative targets indicate that Adam19, Bgn, Cbx5, Smarce1, and Spg20 are direct miR-206 targets in C2C12 cells. Our data show a unique and important role for miR-206 in myogenesis.
Conditional Antibody Expression to Avoid Central B Cell Deletion in a Humanized HIV-1 Vaccine Mouse Models
Authors: Tian Ming , McGovern Kelly , Cheng Hwei-Ling , Waddicor Peyton , Rieble Lisa , Dao Mai , Chen Yiwei , Kimble Michael T. , Cantor Elizabeth , Manfredonia Nicole , Judson Rachael , Chapdelaine-Williams Aimee , Cain Derek W. , Haynes Barton F. , Alt Frederick W. 
Published: January 2020

AbstractHIV-1 vaccine development aims to elicit broadly neutralizing antibodies (bnAbs) against diverse viral strains. In some HIV-1 infected individuals, bnAbs evolve from precursor antibodies through affinity maturation. To induce bnAbs, a vaccine must mediate a similar process of antibody maturation. One way to test vaccination strategies is to immunize mouse models that express human bnAb precursors. Such immunization experiments can assess whether the vaccine can convert precursor antibody into bnAb. A major problem with such mouse models is that bnAb expression often hinders B cell development in the bone marrow. Such developmental blocks may be attributed to unusual properties of bnAb variable regions, such as poly-reactivity and long antigen-binding loops, which are often under negative selection during primary B cell development. To address this problem, we devised a method to circumvent B cell developmental block by expressing bnAbs conditionally in mature B cells. We validated this method by expressing the unmutated common ancestor (UCA) of the human VRC26 bnAb in transgenic mice. Constitutive expression of combined immunoglobulin heavy and light chains of VRC26UCA led to developmental arrest of B cell progenitors in the bone marrow; poly-reactivity of VRC26UCA and poor pairing of VRC26UCA IgH chain with mouse surrogate light chain may contribute to the phenotype. The conditional expression strategy circumvented this developmental impediment, allowing the VRC26UCA to be expressed in mature peripheral B cells. This method should be generally applicable for expressing other antibodies that are under negative selection during B cell development.Significance statementMouse models can provide fast and cost-effective systems to test HIV-1 vaccine candidates at the pre-clinical stage. To serve this purpose, mouse models are engineered to express the precursors of human bnAbs against diverse HIV-1 strains. Immunization of such mouse models can evaluate the ability of vaccines to mature the precursor antibodies into bnAbs. However, due to unusual properties of bnAbs, mouse models expressing their precursors often have B cell developmental defects. In this study, we devised and validated a strategy to address this problem. This method could also facilitate the expression of other clinically relevant antibodies in mature B cells in transgenic mice; immunization of such mice could be used to generate novel antibodies with desirable properties.
Opportunities for prioritizing and expanding conservation enterprise in India using carnivores as flagships
Authors: Srivathsa Arjun , Majgaonkar Iravatee , Sharma Sushma , Singh Priya , Punjabi Girish Arjun , Chawla Malaika Mathew , Banerjee Aditya 
Published: January 2020

AbstractConservation interventions in developing countries are frequently thwarted by socio-economic agendas, severely limiting the scope and rigor of biodiversity and habitat conservation. Very few ecological assessments incorporate human interests in conservation prioritization, creating asynchrony between planning and implementation. For conservation actions to be logistically feasible, multiple criteria including ecological, social, economic and administrative aspects must be considered. Understanding how these different dimensions interact spatially is also important for gauging the potential for conservation success. Here, we use a guild of select mammalian carnivores (wild canids and hyenas) in India to (i) generate distribution maps at the spatial scale of administrative sub-districts, that is relevant to management, (ii) examine ecological, social and biogeographic factors associated with their distribution, quantify key threats, and identify areas important for their conservation, (iii) use prioritization tools for balancing habitat conservation, human needs and economic growth, and (iv) evaluate the spatial congruence between areas with high conservation potential, and areas currently in focus for protection efforts, conservation investments, and infrastructure development. We find that the current Protected Area system does not adequately cover or represent diverse habitats, that there is immense potential for States to increase financial investments towards alternative conservation strategies, and, most infrastructure projects may be jeopardizing important carnivore habitats. Our framework allowed for identifying locations where conservation investments would lead to the highest dividends for flagship carnivores and associated species across habitats. We make a case for re-evaluating how large-scale prioritization assessments are made, and for broadening the purview of conservation policies in India and other developing countries.
Dual-localized enzymatic components that constitute the mitochondrial and plastidial fatty acid synthase systems
Authors: Guan Xin , Okazaki Yozo , Zhang Rwisdom , Saito Kazuki , Nikolau Basil J 
Published: January 2020

ABSTRACTWe report the identification and characterization of genes encoding three enzymes that are shared between the mitochondrial and plastidial-localized Type II fatty acid synthase systems (mtFAS and ptFAS, respectively). Two of these enzymes, β-ketoacyl-ACP reductase (pt/mtKR) and enoyl-ACP reductase (pt/mtER) catalyze two of the reactions that constitute the core, 4-reaction cycle of the FAS system, which iteratively elongate the acyl-chain by 2-carbon atoms per cycle. The third enzyme, malonyl-CoA:ACP transacylase (pt/mtMCAT) catalyzes the reaction that loads the mtFAS system with substrate, by malonylating the phosphopantetheinyl cofactor of acyl carrier protein (ACP). GFP-transgenic experiments determined the dual localization of these enzymes, which were validated by the characterization of mutant alleles, which were transgenically rescued by transgenes that were singularly retargeted to either plastids or mitochondria. The singular retargeting of these proteins to plastids rescued the embryo-lethality associated with disruption of the essential ptFAS system, but these rescued plants display phenotypes typical of the lack of mtFAS function. Specifically, these phenotypes include reduced lipoylation of the H subunit of the glycine decarboxylase complex, the hyperaccumulation of glycine, and reduced growth; all these traits are reversible by growing these plants in an elevated CO2atmosphere, which suppresses mtFAS-associated, photorespiration-dependent chemotypes.
Early enforcement of cell identity by a functional component of the terminally differentiated state
Authors: Bahrami-Nejad Zahra , Chen Tinghuan , Tholen Stefan , Zhang Zhi-Bo , Rabiee Atefeh , Zhao Michael L. , Kraemer Fredric B. , Teruel Mary N. 
Published: January 2020

ABSTRACTHow progenitor cells can attain a distinct differentiated cell identity is a challenging problem given that critical transcription factors are often not unique to a differentiation process and the fluctuating signaling environment in which cells exist. Here we test the hypothesis that a unique differentiated cell identity can result from a core component of the differentiated state doubling up as a signaling protein that also drives differentiation. Using live single-cell imaging in the adipocyte differentiation system, we show that progenitor fat cells (preadipocytes) can only commit to terminally differentiate after upregulating FABP4, a lipid buffer that is highly enriched in mature adipocytes. Upon induction of adipogenesis, we show that after a long delay, cells first abruptly start to engage a positive feedback between CEBPA and PPARG before then engaging, after a second delay, a positive feedback between FABP4 and PPARG. These sequential positive feedbacks both need to engage in order to drive PPARG levels past the threshold for irreversible differentiation. In the last step before commitment, PPARG transcriptionally increases FABP4 expression while fatty-acid loaded FABP4 binds to and increases PPARG activity. Together, our study suggests a control principle for robust cell identity whereby a core component of the differentiated state also promotes differentiation from its own progenitor state.HIGHLIGHTSFatty-acid loaded FABP4 binds to and increases PPARG expression, thereby turning on PPARG positive feedback loops that further increase PPARG expression.FABP4 critically controls the second phase of adipogenesis between activation of the feedback loops and reaching the threshold to differentiate.Only a small fraction (∼10%) of the FABP4 levels typically attained in mature fat cells is needed to commit cells to the differentiated state, thus providing an explanation for why maintenance of the mature adipocyte state is so robust.
Epigenetic regulation of Wnt7b expression by thecis-acting long noncoding RNA lnc-Rewind in muscle stem cells
Authors: Cipriano Andrea , Macino Martina , Buonaiuto Giulia , Santini Tiziana , Biferali Beatrice , Peruzzi Giovanna , Colantoni Alessio , Mozzetta Chiara , Ballarino Monica 
Published: January 2020

ABSTRACTSkeletal muscle possesses an outstanding capacity to regenerate upon injury due to the adult muscle stem cells (MuSCs) activity. This ability requires the proper balance between MuSCs expansion and differentiation which is critical for muscle homeostasis and contributes, if deregulated, to muscle diseases. Here, we functionally characterize a novel chromatin-associated lncRNA, lnc-Rewind, which is expressed in murine MuSCs and conserved in human. We find that, in mouse, lnc-Rewind acts as an epigenetic regulator of MuSCs proliferation and expansion by influencing the expression of skeletal muscle genes and several components of the WNT (Wingless-INT) signalling pathway. Among them, we identified the nearbyWnt7bgene as a direct lnc-Rewind target. We show that lnc-Rewind interacts with the G9a histone lysine methyltransferase and mediates thein cisrepression ofWnt7bby H3K9me2 deposition. Overall, these findings provide novel insights into the epigenetic regulation of adult muscle stem cells fate by lncRNAs.