bluuebunny/crossref_metadata_2025 huggingface dataset:
Mutational analysis of the structure and function of the chaperone domain of UNC-45B
Authors: Gaziova I. , Moncrief T. , Christian C. J. , White M. , Villarreal M. , Powell S. , Qadota H. , Benian G. M. , Oberhauser A. F.
Published: January 2020

UNC-45B is a multidomain molecular chaperone that is essential for the proper folding and assembly of myosin into muscle thick filamentsin vivo. We have previously demonstrated that its UCS domain is responsible for the chaperone-like properties of UNC-45B. In order to better understand the chaperoning function of the UCS domain we engineered mutations designed to: i) disrupt chaperone-client interactions by removing and altering the structure of the putative client-interacting loop and ii) disrupt chaperone-client interactions by changing highly conserved residues in the putative client-binding groove. We tested the effect of these mutations by using a novel combination of complementary biophysical (circular dichroism, intrinsic tryptophan fluorescence, chaperone activity, and SAXS) andin vivotools (C. eleganssarcomere structure). Removing the client-holding loop had a pronounced effect on the secondary structure, thermal stability, solution conformation and chaperone function of the UCS domain. These results are consistent with previousin vivofindings that this mutation neither rescue the defect inC. eleganssarcomere organization nor bind to myosin. We found that mutating several conserved residues in the client-binding groove do not affect UCS domain secondary structure or structural stability but reduced its chaperoning activity. We found that these groove mutations also significantly altered the structure and organization of the worm sarcomeres. We also tested the effect of R805W, a mutation distant from the client-binding region. Ourin vivodata show that, to our surprise, the R805W mutation appeared to have the most drastic effect on the structure and organization of the worm sarcomeres. In humans, the R805W mutation segregates with human congenital/infantile cataract, indicating a crucial role of R805 in UCS domain stability and/or client interaction. Hence, our experimental approach combining biophysical and biological tools facilitates the study of myosin/chaperone interactions in mechanistic detail.

Statement of Significance

The folding of myosin and the assembly of a functional sarcomere requires the chaperone UNC-45B. The molecular mechanism(s) for how UNC-45B assist in this assembly process or prevent stress-induced aggregation states are presently unknown. Answering this question is a problem at the core of muscle development and function. Here we developed a novel approach that combines biophysical and biological tools to study UNC-45B/myosin interactions in mechanistic detail. Our approach may provide critical insights into the molecular nature of the pathogenesis of many muscle disorders stemming from mutations in sarcomeric proteins including skeletal myopathies and cardiomyopathies, and possibly the age-associated decline in muscle mass and function found in the elderly known as sarcopenia.
AnArabidopsislong noncoding RNA modulates the transcriptome through interactions with a network of splicing factors
Authors: Rigo Richard , Bazin Jérémie , Romero-Barrios Natali , Moison Michaël , Lucero Leandro , Christ Aurélie , Benhamed Moussa , Blein Thomas , Huguet Stéphanie , Charon Céline , Crespi Martin , Ariel Federico
Published: January 2020

Alternative splicing (AS) is a major source of transcriptome and proteome diversity in higher organisms. Long noncoding RNAs (lncRNAs) have emerged as regulators of AS through a range of molecular mechanisms. InArabidopsis thaliana, the AS regulators NSRa and b, which affect auxin-driven lateral root formation, can interact with theALTERNATIVE SPLICING COMPETITOR (ASCO)lncRNA. Here, we analyzed the effect of the knockdown and overexpression ofASCOat genome-wide level and found a high number of deregulated and differentially spliced genes, related to flagellin responses and biotic stress. In agreement, roots fromASCO-knocked down plants are more sensitive to flagellin. Surprisingly, only a minor subset of genes overlapped with the AS defects of thensra/bdouble mutant. Using biotin-labelled oligonucleotides for RNA-mediated ribonucleoprotein purification, we found thatASCObinds to the highly conserved core spliceosome component PRP8a.ASCOderegulation impairs the recognition of specific flagellin-related transcripts by PRP8a and SmD1b, another spliceosome component, suggesting thatASCOfunction regulates AS through the interaction with multiple splicing factors. Hence, lncRNAs may interact in a dynamic network with many splicing factors to modulate transcriptome reprogramming in eukaryotes.
The Effect of Gelling agent, medium pH and silver nitrate on adventitious shoot regeneration inSolanum tuberosum
Authors: Kaur Amanpreet , Kumar Anil
Published: January 2020

Vegetative 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

Most 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.
Dscamgene triplication causes neocortical overinhibition in Down syndrome
Authors: Liu H , Caballero-Florán RN , Yang T , Hull JM , Pan G , Li R , Veling MW , Isom LL , Kwan KY , Huang ZJ , Fuerst PG , Jenkins PM , Ye B
Published: January 2020

A growing number of molecules have been identified as regulators of inhibitory synapse development, but whether dysregulated expression of these molecules contribute to brain disorders is poorly understood. Here we show that Down syndrome cell adhesion molecule (Dscam) regulates the inhibition of neocortical pyramidal neurons (PyNs) in a level-dependent fashion. Loss ofDscamimpairs inhibitory neuron development and function. In the Ts65Dn mouse model for Down syndrome, whereDscamis overexpressed, GABAergic innervation of cortical PyNs by chandelier and basket cells is increased. Genetic normalization ofDscamexpression rescues the excessive GABAergic innervation and the increased inhibition of PyNs. These findings demonstrate excessive GABAergic innervation and inhibition in the neocortex of Down syndrome mouse model and identifyDscamoverexpression as the cause. They also implicate dysregulatedDscamlevels as a potential pathogenic driver in related neurological disorders.
Accurate reconstruction of bacterial pan- and core- genomes with PEPPAN
Authors: Zhou Zhemin , Charlesworth Jane , Achtman Mark
Published: January 2020

Bacterial 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

Trypanosomatid 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

Histone 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

Memory 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

Neutrophilic 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.
Plasmodium falciparumpopulation genetic complexity influences transcriptional profile and immune recognition of highly related genotypic clusters
Authors: Bei Amy K. , Larremore Daniel B. , Miura Kazutoyo , Diouf Ababacar , Baro Nicholas K. , Daniels Rachel F. , Griggs Allison , Moss Eli L. , Neafsey Daniel E. , Deme Awa B. , Sy Mouhamad , Schaffner Stephen , Ahouidi Ambroise D. , Ndiaye Daouda , Dieye Tandakha , Mboup Souleymane , Buckee Caroline O. , Volkman Sarah K. , Long Carole A. , Wirth Dyann F.
Published: January 2020

As transmission intensity has declined in Senegal, so has the genetic complexity of circulatingPlasmodium falciparumparasites, resulting in specific genotypes emerging and persisting over years. We address whether changes in parasite genetic signatures can alter the immune repertoire to variant surface antigens, and whether such responses can influence the expansion or contraction of specific parasite genotypes in the population. We characterize parasites within genotypic clusters, defined as identical by a 24-SNP molecular barcode and a haplotype identifier for other highly polymorphic loci; we measure expression of variant surface antigens (VSA) such as PfEMP-1 by transcript expression typing and expressedvarDBL1αsequencing in ex vivo and short-term adapted RNA samples; and we measure IgG responses against VSAs from short-term adapted parasites. We find that parasites within genotypic clusters are genetically identical at other highly polymorphic loci. These parasites express similar Upsvarclasses and largely the same dominantvarDBL1αsequences ex vivo. These parasites are recognized similarly by anti-VSA antibodies after short-term adaptation to culture; however, antibody responses do not correlate with genotype frequencies over time. Both genotype-specific and multiple genotype-reactive surface IgG responses are observed in this population. Parasites with identical genomes are extremely similar in their expression and host antibody recognition of VSAs. Monitoring changes in population-level parasite genomics and transmission dynamics is critical, as fluctuations will influence the breadth of resulting host immune responses to circulating parasite genotypes. These findings suggest shared immune recognition of genetically similar parasites, which has implications for both our understanding of immunity and vaccine development strategies in malaria elimination settings.
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

The 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

HIV-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 statement

Mouse 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.
Tree crowns as meeting points of diversity generating mechanisms – a test with epiphytic lichens in a temperate forest
Authors: Patzak R. , Richter R. , Engelmann R.A. , Wirth C.
Published: January 2020

Forest canopies are hotspots of biodiversity even in temperate forests but which and how many ecological mechanisms contribute to the high diversity remains elusive. This biodiversity is not distributed evenly throughout the complex fractal structures formed by individual tree crowns. They are non-stationary, constantly expose new surface habitat via growth, and create contrasting abiotic conditions. These features give rise to a range of vertical gradients in habitat optimality, heterogeneity, available surface area and time for succession - all known to be mechanisms shaping diversity patterns. Using a canopy crane facility and epiphytic lichens on Fraxinus excelsior and Quercus robur as model system, we aim to assess the relative importance as well as the interplay of these mechanisms in shaping biodiversity patterns within tree canopies by detecting their distinct mechanistic fingerprints. Lichen species richness exhibited a hump-shaped vertical pattern, skewed towards the top of the crown. This pattern was observable at both the level of individual plots and that of aggregate height layers and it was correlated with lichen cover. Also, a vertical gradient in species composition was found and could be related to species traits known to reflect successional niches such as dispersal mode and growth form. Habitat heterogeneity and available surface area have been found to have little effect on vertical lichen diversity patterns. We conclude that the vertical lichen diversity patterns in the tree crown are mainly shaped by the successional accumulation of species along a branch age gradient and a pronounced vertical gradient in environmental optimality from harshly exposed young branches at the top crown over suitable habitats with a balance in light and humidity towards the limiting light conditions in the dim understory. At the level of the whole canopy, successional and environmental niche dynamics jointly operate to generate lichen diversity.
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

Conservation 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

We 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

How 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.

HIGHLIGHTS

Fatty-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

Skeletal 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.
A test of community assembly rules using foliar endophytes from a tropical forest canopy
Authors: Donald Julian , Roy Mélanie , Suescun Uxue , Iribar Amaia , Manzi Sophie , Péllissier Léonie , Gaucher Philippe , Chave Jérôme
Published: January 2020

Community assembly theory assumes that ecological communities are spatially delimited into patches. Within these patches, coexistence results from environmental filtering, competition and immigration. Truly delineated communities exist in laboratory studies of microbial cultures in Petri dishes, yet empirical tests conducted in continuous environments often use patches defined by convention as opposed to realized boundaries.

Here we perform a test of ecological community assembly rules using foliar endophyte communities from a tropical rainforest, where leaves are considered as patches for both fungal and bacterial communities. We determined the diversity of fungal and bacterial endophytes using environmental DNA sequencing of 365 top‐canopy leaves, collected from 38 host trees belonging to 22 different species across a 4‐ha research plot. Three leaves were collected from three or more branches within each tree crown. We tested the effect of host tree species and their level of phylogenetic relatedness on community composition as well as the contribution of geographic distance between leaves to endophyte community diversity.

Endophyte diversity significantly differed across host tree species, as did community composition. Within certain endophytic orders (Xylariales, Rhizobiales) species assemblages significantly differed across host tree species, but this trend was weaker or non‐existent in other orders known to contain pathogens and saprotrophs (Polyporales, Solirubrobacterales). Phylogenetically related host tree species displayed more similar endophyte communities than expected by chance, but geographically close trees did not. Consistent with the finding of host‐specificity, nearby leaves tended to host more similar communities than distantly positioned ones.

These findings demonstrate that foliar endophytes are structured by dispersal across small spatial scales, but at the scale of the canopy they display patterns of neutral filtering, with only a small part of variation described by host tree differences. Endophyte communities thus act as a model system in evoking the rules predicted by theoretical community ecology.
Higher rates of liana regeneration after canopy fall drives species abundance patterns in central Amazonia
Authors: Rocha Elisangela X. , Schietti Juliana , Gerolamo Caian S. , Burnham Robyn J. , Nogueira Anselmo
Published: January 2020

In tropical rainforest, most vascular plants have some capacity to resprout, and lianas are often effective resprouters after canopy fall. However, the diversity of resprouting responses of liana species and the consequence for plant persistence are poorly understood. We hypothesized that variation in regeneration among liana species causes differences in liana species abundance in tropical rainforest through differential resprouting capacity, such that liana species with higher densities produce more resprouts after canopy falls.

We applied a manipulative field experiment investigating the effect of different levels of disturbance on the production of resprouts and adventitious roots in 10 liana species of the tribe Bignonieae (Bignoniaceae) with contrasting abundances in central Amazonia. We selected 15 individuals of each species and assigned the lianas to three distinct conditions: (a) total canopy fall with lianas severely damaged and detached from trees; (b) partial fall of lianas, without visible damage; and (c) intact lianas (control). We tested whether liana species regeneration patterns were related to species density. Liana species density was calculated using previous research on liana species distribution in 30 1‐ha plots systematically distributed in a 6 × 6 km2 grid at the Ducke Reserve.

The number of aerial resprouts produced by lianas under the total canopy fall treatment was twice that of plants under lower levels of disturbance, while the production of adventitious roots did not differ among treatments. Liana species showed different intensities of resprouting, and species with higher average densities on the forest landscape had more resprouts after the total canopy fall treatment.

Synthesis. Our results shed new light on the factors that influence liana species abundance, highlighting the role of resprouting after canopy fall and its variation among liana species. Resprouting mitigates the negative effects of canopy damage, suggesting that the impact of increased tree fall disturbances over time, which has been attributed to Amazonian forests in the literature, may increase already abundant liana species with effective resprouting capacity. We identify liana species that are more resilient to disturbance and may alter forest dynamics during climatic change.
The potential actions of angiotensin‐converting enzyme II (ACE2) activator diminazene aceturate (DIZE) in various diseases
Authors: Qaradakhi Tawar , Gadanec Laura Kate , McSweeney Kristen Renee , Tacey Alexander , Apostolopoulos Vasso , Levinger Itamar , Rimarova Kvetoslava , Egom Emmanuel E. , Rodrigo Luis , Kruzliak Peter , Kubatka Peter , Zulli Anthony
Published: January 2020

The renin angiotensin system (RAS) regulates fluid balance, blood pressure and maintains vascular tone. The potent vasoconstrictor angiotensin II (Ang II) produced by angiotensin‐converting enzyme (ACE) comprises the classical RAS. The non‐classical RAS involves the conversion of Ang II via ACE2 into the vasodilator Ang (1‐7) to counterbalance the effects of Ang II. Furthermore, ACE2 converts AngA into another vasodilator named alamandine. The over activation of the classical RAS (increased vasoconstriction) and depletion of the non‐classical RAS (decreased vasodilation) results in vascular dysfunction. Vascular dysfunction is the leading cause of atherosclerosis and cardiovascular disease (CVD). Additionally, local RAS is expressed in various tissues and regulates cellular functions. RAS dysregulation is involved in other several diseases such as inflammation, renal dysfunction and even cancer growth. An approach in restoring vascular dysfunction and other pathological diseases is to either increase the activity of ACE2 or reduce the effect of the classical RAS by counterbalancing Ang II effects. The antitrypanosomal agent, diminazene aceturate (DIZE), is one approach in activating ACE2. DIZE has been shown to exert beneficial effects in CVD experimental models of hypertension, myocardial infarction, type 1 diabetes and atherosclerosis. Thus, this review focuses on DIZE and its effect in several tissues such as blood vessels, cardiac, renal, immune and cancer cells.
Clinical significance of topoisomerase‐II expression in patients with advanced non‐small cell lung cancer treated with amrubicin
Authors: Sakurai Reiko , Kaira Kyoichi , Miura Yosuke , Sunaga Noriaki , Saito Ryusei , Oyama Tetsunari , Hisada Takeshi , Yamada Masanobu
Published: January 2020

Background

Amrubicin chemotherapy is a treatment option for patients with non‐small cell lung cancer (NSCLC) after third‐line treatment in Japan. Although topoisomerase‐II (Topo‐II), a target of amrubicin, has been reported to be a prognostic or predictive marker for chemosensitivity and clinical outcomes in various types of malignancies, its effects in the Japanese population remain unknown.

Methods

Data regarding 44 patients with advanced NSCLC treated with amrubicin between April 2004 and May 2014 were retrospectively analyzed. We evaluated the expression levels of Topo‐II by immunohistochemical staining of tumor specimens obtained via biopsy or surgical resection.

Results

The majority of enrolled patients were men (68%) with a median age of 67 (range, 43–78) years. The most common histological type was adenocarcinoma (70%). High Topo‐II expression was observed in 13 (30%) of the 44 patients. The median progression‐free survival and overall survival (OS) durations were 1.8 and 8.8 months, respectively. While there was no significant association between Topo‐II expression and progression‐free survival, patients with low Topo‐II expression had significantly longer OS than did those with high Topo‐II expression. Good performance status and low expression of Topo‐II were all significantly associated with a favorable OS.

Conclusion

Low expression of Topo‐II was identified as an independent prognostic factor for longer survival in patients with NSCLC receiving amrubicin, a Topo‐II inhibitor.

Key points

Significant findings of the study

The median progression‐free survival and overall survival (OS) durations were 1.8 and 8.8 months, respectively.

While there was no significant association between Topo‐II expression and progression‐free survival, patients with low Topo‐II expression had significantly longer OS than did those with high Topo‐II expression.

Good performance status and low expression of Topo‐II were all significantly associated with a favorable OS.

What this study adds

This study is the first to assess the effects of topoisomerase‐II (Topo‐II), a target of amrubicin, as a prognostic or predictive marker for chemosensitivity and clinical outcomes in the Japanese population.
Dermal denticle assemblages in coral reef sediments correlate with conventional shark surveys
Authors: Dillon Erin M. , Lafferty Kevin D. , McCauley Douglas J. , Bradley Darcy , Norris Richard D. , Caselle Jennifer E. , DiRenzo Graziella V. , Gardner Jonathan P. A. , O'Dea Aaron
Published: January 2020

It is challenging to assess long‐term trends in mobile, long‐lived and relatively rare species such as sharks. Despite ongoing declines in many coastal shark populations, conventional surveys might be too fleeting and too recent to describe population trends over decades to millennia. Placing recent shark declines into historical context should improve management efforts as well as our understanding of past ecosystem dynamics.

A new palaeoecological approach for surveying shark abundance on coral reefs is to quantify dermal denticle assemblages preserved in sediments. This approach assumes that denticle accumulation rates correlate with shark abundances. Here, we test this assumption by comparing the denticle record in surface sediments to three conventional shark survey methods at Palmyra Atoll, Line Islands, central Pacific Ocean, where shark density is high and spatially heterogeneous.

We generally found a significant positive correlation between denticle accumulation rates and shark abundances derived from underwater visual census, baited remote underwater video and hook and line surveys.

Denticle accumulation rates reflected shark abundances, suggesting that denticle assemblages can preserve a signal of time‐averaged shark abundance in low‐energy coral reef environments. We offer suggestions for applying this tool to measure shark abundance over long time‐scales in other contexts.
Does potassium iodide application following silver diamine fluoride reduce staining of tooth? A systematic review
Authors: Roberts A , Bradley J , Merkley S , Pachal T , Gopal JV , Sharma D
Published: January 2020

Objectives

To assess if using potassium iodide (KI) immediately after application of silver diamine fluoride (SDF) significantly reduces the staining of tooth structure.

Data source and selection

Four online databases (OVID, Scopus, PubMed and Google Scholar) were searched (June 2019). Additional studies were sought through grey literature search and hand searching the reference list of included articles. All studies that analysed the effect of KI on SDF staining of tooth structure with access to full text in English language were included.

Data synthesis

Of the six articles included in the review, five reported stain reduction in the teeth treated with application of KI to carious tooth structure following the application of SDF while one article reported no significant beneficial effect on reducing staining, when compared to SDF alone. Of the materials selected to restore SDF + KI treated teeth, resin‐modified glass ionomer was found to produce the lightest results, followed by glass ionomer cement and composite resin. An in vivo case report also revealed some staining after six months, even with SDF + KI treatment.

Conclusions

Although some studies reported a positive effect, insufficient evidence exists supporting a tangible clinical benefit of SDF + KI treatment on the tooth staining, mainly due to methodical variations within the current literature.
Effect of the double application of universal adhesives on the dentine bond strength after radiotherapy
Authors: Ugurlu M
Published: January 2020

Background

This study aimed to evaluate the effect of double application of universal adhesives on bond strength to dentine after ionizing radiation.

Methods

One hundred and forty caries‐free human third molars were used. Half of the teeth were irradiated (IR) (70.2 Gy). The IR and non‐IR teeth were assigned into seven groups (n = 10). Universal adhesives Single Bond Universal (3M Oral Care), Gluma Bond Universal (Heraeus Kulzer) and Prime&Bond Elect (Dentsply) were employed (following manufacturer’s instructions and double application). Two‐step self‐etch adhesive Clearfil SE Bond (Kuraray Noritake) was used as control. After composite build‐ups were bonded to mid‐coronal occlusal dentine surfaces, the specimens were stored in water (37°C/24 h) and sectioned into microspecimens. The specimens were subjected to μTBS testing (1.0 mm/min). Failure analysis was performed using stereomicroscope and scanning electron microscopy. Data were analysed with two‐way ANOVA and Tukey’s test (P = 0.05).

Results

The radiotherapy caused reduction in the bond strength of universal adhesives when the adhesives were used with single application after radiotherapy (P < 0.05). The double application resulted in increased bond strength of the universal adhesives to IR dentine (P < 0.05).

Conclusions

The double application was beneficial in improving the dentine bond strength of universal adhesives affected by radiotherapy after ionizing radiation.