bluuebunny/crossref_metadata_2025_split huggingface dataset:
Actin filament alignment causes mechanical hysteresis in cross-linked networks
Authors: Scheff Danielle R. , Redford Steven A. , Lorpaiboon Chatipat , Majumdar Sayantan , Dinner Aaron R. , Gardel Margaret L. 
Published: March 2021

AbstractCells dynamically control their material properties through remodeling of the actin cytoskeleton, an assembly of cross-linked networks and bundles formed from the biopolymer actin. We recently found that cross-linked networks of actin filaments reconstituted in vitro can exhibit adaptive behavior and thus serve as a model system to understand the underlying mechanisms of mechanical adaptation of the cytoskeleton. In these networks, training, in the form of applied shear stress, can induce asymmetry in the nonlinear elasticity. Here, we explore control over this mechanical hysteresis by tuning the concentration and mechanical properties of cross-linking proteins in both experimental and simulated networks. We find that this effect depends on two conditions: the initial network must exhibit nonlinear strain stiffening, and filaments in the network must be able to reorient during training. Hysteresis depends strongly and non-monotonically on cross-linker concentration, with a peak at moderate concentrations. In contrast, at low concentrations, where the network does not strain stiffen, or at high concentrations, where filaments are less able to rearrange, there is little response to training. Additionally, we investigate the effect of changing cross-linker properties and find that longer or more flexible cross-linkers enhance hysteresis. Remarkably plotting hysteresis against alignment after training yields a single curve regardless of the physical properties or concentration of the cross-linkers.
DNA Methylation Networks Underlying Mammalian Traits
Authors: Haghani A. , Lu A.T. , Li C.Z. , Robeck T.R. , Belov K. , Breeze C.E. , Brooke R.T. , Clarke S. , Faulkes C.G. , Fei Z. , Ferguson S.H. , Finno C.J. , Gladyshev V.N. , Gorbunova V. , Goya R.G. , Hogan A.N. , Hogg C.J. , Hore T.A. , Kiaris H. , Kordowitzki P. , Banks G. , Koski W.R. , Mozhui K. , Naderi A. , Ostrander E.A. , Parsons K.M. , Plassais J. , Robbins J. , Sears K.E. , Seluanov A. , Steinman K.J. , Szladovits B. , Thompson M.J. , Villar D. , Wang N. , Wilkinson G.S. , Young B.G. , Zhang J. , Zoller J.A. , Ernst J. , Yang X.W. , Raj K. , Horvath S. 
Published: March 2021

SummaryEpigenetics has hitherto been studied and understood largely at the level of individual organisms. Here, we report a multi-faceted investigation of DNA methylation across 11,117 samples from 176 different species. We performed an unbiased clustering of individual cytosines into 55 modules and identified 31 modules related to primary traits including age, species lifespan, sex, adult species weight, tissue type and phylogenetic order. Analysis of the correlation between DNA methylation and species allowed us to constructphyloepigenetictrees for different tissues that parallel the phylogenetic tree. In addition, while some stable cytosines reflect phylogenetic signatures, others relate to age and lifespan, and in many cases responding to anti-aging interventions in mice such as caloric restriction and ablation of growth hormone receptors. Insights uncovered by this investigation have important implications for our understanding of the role of epigenetics in mammalian evolution, aging and lifespan.
Short communication: Efficacy of two commercial disinfectants onPaenibacillus larvaespores
Authors: Kiriamburi Joseph , Muturi Jamleck , Mugweru Julius , Forsgren Eva , Nilsson Anna 
Published: March 2021

SHORT SUMMARYPaenibacillus larvaeis a spore-forming bacterium causing American foulbrood (AFB) in honey bee larvae. The remains of a diseased larva contains billions of extremely resilientP. larvaespores viable for decades. Burning clinically symptomatic colonies is widely considered the only workable strategy to prevent further spread of the disease, and the management practices used for decontamination requires high concentrations of chemicals or special equipment.The aim of this study was to test and compare the biocidal effect of two commercially available disinfectants, “ Disinfection for beekeeping” and Virkon S onP. larvae. The two products were applied toP. larvaespores in suspension as well as inoculated on two common beehive materials, wood and styrofoam.“ Disinfection for beekeeping” had a 100 % biocidal effect onP. larvaespores in suspension compared to 87.0-88.6 % for Virkon S which, however, had a significantly better effect onP. larvaeon styrofoam. The two disinfectants had similar effect on infected wood material.
Sex-specific interactions between procedural and deliberative decision-making systems in a mouse model of Alzheimer’s disease
Authors: Anderson Rachel , Hart Damyan W. , Sweis Brian , Sherman Mathew A. , Thomas Mark J. , Redish A. David , Lesné Sylvain E. 
Published: March 2021

AbstractA central question in aging and Alzheimer’s disease (AD) is when and how neural substrates underlying decision-making are altered. Here we show that while APP mice, a commonly used mouse model of AD, were able to learn Restaurant Row, a complex neuroeconomic decision-making task, they were significantly impaired in procedural, habit-forming, aspects of cognition and relied heavily on deliberation when making decisions. Surprisingly, these behavioral changes are associated with amyloid-beta (Aβ) pathology and network remodeling in the striatum, a key brain region involved in procedural cognition. Furthermore, APP mice and control mice relied on distinct sex-specific strategies in this neuroeconomic task. These findings provide foundational pillars to examine how aging and age-related neurodegenerative diseases impact decision-making across sexes. They also highlight the need for complex behavioral tasks that allow for the dissociation of competing neurally-distinct decision-making circuits to get an accurate picture of changes in neurodegenerative models of human disease.
Meiotic Cas9 expression mediates genotype conversion in the male and female mouse germline
Authors: Weitzel Alexander J. , Grunwald Hannah A. , Levina Rimma , Gantz Valentino M. , Hedrick Stephen M. , Bier Ethan , Cooper Kimberly L. 
Published: March 2021

AbstractHighly efficient genotype conversion systems have potential to facilitate the study of complex genetic traits using laboratory mice and to limit loss of biodiversity and disease transmission caused by wild rodent populations. We previously showed that such a system of genotype conversion from heterozygous to homozygous after a sequence targeted CRISPR/Cas9 double strand DNA break is feasible in the female mouse germline. In the male germline, however, all double strand breaks were instead repaired by end joining mechanisms to form an ‘insertion/deletion’ (indel) mutation. These observations suggested that timing Cas9 expression to coincide with meiosis I is critical to favor conditions when homologous chromosomes are aligned and interchromosomal homology directed repair (HDR) mechanisms predominate. Here, using a Cas9 knock-in allele at theSpo11locus, we show that meiotic expression of Cas9 does indeed mediate genotype conversion in the male as well as in the female germline. However, the low frequency of both HDR and indel mutation in both male and female germlines suggests that Cas9 may be expressed from theSpo11locus at levels too low for efficient double strand DNA break formation. We suggest that more robust Cas9 expression initiated during early meiosis I may improve the efficiency of genotype conversion and further increase the rate of ‘super-Mendelian’ inheritance from both male and female mice.
GdDO3NI allows imaging of hypoxia after brain injury
Authors: Moghadas Babak , Bharadwaj Vimala N. , Tobey John P. , Tian Yanqing , Stabenfeldt Sarah E. , Kodibagkar Vikram D. 
Published: March 2021

ABSTRACTPurposeIn this study, we use the hypoxia targeting agent (GdDO3NI, a nitroimidazole-based T1MRI contrast agent) for imaging hypoxia in the injured brain after experimental traumatic brain injury (TBI) using magnetic resonance imaging (MRI), and validate the results with immunohistochemistry (IHC) using pimonidazole.MethodsTBI induced mice (controlled cortical impact model) were imaged at 7T using a T2weighted fast spin-echo sequence to estimate the extent of the injury. The mice were then were intravenously injected with either conventional T1agent (gadoteridol) or GdDO3NI at 0.3 mmol/kg dose (n=5 for each cohort) along with pimonidazole (60 mg/kg). Mice were imaged pre- and post-contrast using a T1-weighted spin-echo sequence for three hours. Regions of interests were drawn on the brain injury region, the contralateral brain as well as on the cheek muscle region for comparison of contrast kinetics. Brains were harvested immediately post imaging for immunohistochemical analysis.ResultsGdDO3NI is retained in the injury region for up to 3 hours post-injection (p< 0.05 compared to gadoteridol) while it rapidly clears out of the muscle region. On the other hand, conventional MRI contrast agent gadoteridol clears out of both the injury region and muscle rapidly, although with a relatively more delayed wash out in the injury region. Minimal contrast enhancement was seen for both agents in the contralateral hemisphere. Pimonidazole staining confirms the presence of hypoxia in both gadoteridol and GdDO3NI cohorts, and the later cohort shows good agreement with MRI contrast enhancement.ConclusionGdDO3NI was successfully shown to visualize hypoxia in the brain post-TBI using T1-wt MRI.
Identification of anthracnose (Colletotrichum lentis) race 1 resistance loci in lentil by integrating linkage mapping and a genome-wide association study
Authors: Gela Tadesse S. , Ramsay Larissa , Haile Teketel A. , Vandenberg Albert , Bett Kirstin E. 
Published: March 2021

ABSTRACTAnthracnose, caused byColletotrichum lentis, is a devastating disease of lentil in Western Canada. Growing resistant lentil cultivars is the most cost-effective and environmentally friendly approach to prevent seed yield losses that can exceed 70%. To identify loci conferring resistance to anthracnose race 1 in lentil, biparental quantitative trait loci (QTL) mapping of two recombinant inbred line (RIL) populations was integrated with a genome-wide association study (GWAS) using 200 diverse lentil accessions from a lentil diversity panel (LDP). A major-effect QTL (qAnt1.Lc-3) conferring resistance to race 1 was mapped to lentil chromosome 3 and co-located on the lentil physical map for both RIL populations. Clusters of candidate nucleotide binding-leucine-rich repeats (NB-LRR) and other defense-related genes were uncovered within the QTL region. A GWAS detected 14 significant SNP markers associated with race 1 resistance on chromosomes 3, 4, 5, and 6. The most significant GWAS SNPs on chromosome 3 supportedqAnt1.Lc-3 and delineated a region of 1.6 Mb containing candidate resistance genes. The identified SNP markers can be directly applied in marker-assisted selection to accelerate the introgression of race 1 resistance in lentil breeding.
Characterization of anAgarophyton chilenseoleoresin containing PPARγ natural ligands with insulin-sensitizing effects in a C57BL/6J mouse model of diet-induced obesity and antioxidant activityin Caenorhabditis elegans
Authors: Pinto Claudio , Ibañez María Raquel , Loyola Gloria , León Luisa , Salvatore Yasmin , Gonzalez Carla , Barraza Victor , Castañeda Francisco , Aldunate Rebeca , Contreras-Porcia Loretto , Fuenzalida Karen , Bronfman Francisca C 
Published: March 2021

AbstractThe biomedical potential of the edible red seaweedAgarophyton chilense(formerGracilaria chilensis) has not been explored. Red seaweeds are enriched in polyunsaturated fatty acids and eicosanoids, which are known natural ligands of the PPARγ nuclear receptor. PPARγ is the molecular target of thiazolidinediones (TZDs), drugs used as insulin sensitizers to treat type 2 diabetes mellitus. TZDs medical use is limited due to undesired side effects, the fact that it has triggered the search for partial agonists without the TZDs side effects.We producedA.chilenseoleoresin (Gracilex®) that induces the activation of PPARγ without inducing adipocyte differentiation, similar to PPARγ partial agonists. In a model of high-fat diet-induced obesity in male mice, we showed that treatment withGracilex®improves insulin sensitivity, normalizing altered glucose and insulin parameters.Gracilex®was enriched in palmitic acid, arachidonic acid, oleic acid, and lipophilic antioxidants such as ß-carotene and tocopherols.Gracilex®possesses antioxidant activity in vitro (CUPRAC) and increased the antioxidant capacityin vivoinCaenorhabditis elegans.These findings support the idea thatGracilex®is an excellent source of healthy lipids targeting PPARγ with antioxidant activity and a high nutraceutical value.
Wheels within wheels, Nested Function-value Traits as a Tool for Modeling Ontogeny
Authors: Hodge John G. , Doust Andrew N. 
Published: March 2021

AbstractPlant morphologies exhibit a wide array of outcomes that have evolved as a consequence adapting to a wide array of ecological pressures. These disparate morphologies have provided a rich field for comparative morphologists, developmental biologists, and geneticists to explore. Ultimately the array of variation observed in nature across different plant species is built on the same functional unit, the phytomer, which is composed of a leaf, a node, and an internode. Sequentially produced phytomers exhibit heteroblasty, that is, a gradual or abrupt change in shape, either due to size changes or changes due to reproductive phase. The progression of shape change over time is often indirectly measured by sampling several stages of plant growth and comparing allometric relationships between shape variables. However, a more precise method is to use an absolute time scale and measure shape change of sequential organs directly. In this study we use such time-dependent measurements to build a general model of organ growth for several Setaria genotypes, for both leaves and internodes. We term this the second-order function-value trait (2FVT) model, because it generalizes individual function-value trait models generated for each organ. This model reduces phenotypic noise by averaging the general trend of ontogeny and provides a quantitative tool to describe where and when phenotypic shifts occur during the ontogenies of different genotypes. The ability to recognize how ontogenetic variation is distributed within equivalent positions of the body plan at the interspecific level can be used as a tool to explore various questions related to growth and form in plants both for comparative morphology and developmental genetics.
Case study of a rhizosphere microbiome assay on a bamboo rhizome with excessive shoots
Authors: Cui Fuqiang , Yang Yifan , Ye Mengyuan , Wei Wei , Huang Wenqian , Wu Ying , Jiao Xi , Ye Xiaoxue , Zhou Shutong , Hu Zhubing , Gui Renyi , Wu Wenwu , Yrjälä Kim , Overmyer Kirk , Liu Shenkui 
Published: March 2021

AbstractYoung Moso bamboo shoots are a very popular seasonal food. Bamboo is an important source of income for farmers and the value for cultivation has recently been estimated to $30,000 per hectare. A rare and valuable phenomenon has recently appeared where dozens of adjacent buds within a single Moso bamboo rhizome have grown into shoots. Due to its rarity, this phenomenon, which is of practical importance for the production of edible shoots, has not been scientifically studied. We report the occurrence of a rhizome with 18 shoots, of which the microbiome were analyzed, using rhizomes having one or no shoots as controls. The community of prokaryotes, but not fungi, correlated with the shoot numbers.Burkholderiawas the most abundant genus, which negatively correlated with rhizome shoot number, whileClostridiaandKtedonobacteriapositively correlated with many shoots. TwoBurkholderiastrains were isolated and their plant-growth promoting activity was tested. The isolatedBurkholderiastrains attenuated the growth of bamboo seedlings. Analysis of collected events of enhanced shoot production in China showed no evidence that enhanced shoot development was heritable. Overall, our data provides a firsthand study on excessive shoot development of bamboo.
fmr1mutation interacts with sensory experience to alter the early development of behavior and sensory coding in zebrafish
Authors: Zhu Shuyu , McCullough Michael , Pujic Zac , Sibberas Jordan , Sun Biao , Bucknall Bianca , Avitan Lilach , Goodhill Geoffrey J 
Published: March 2021

AbstractWhile Autism Spectrum Disorders (ASDs) are developmental in origin little is known about how they affect the early development of behavior and sensory coding, or how this is modulated by the sensory environment. The most common inherited form of autism is Fragile X syndrome, caused by a mutation inFMR1. Here we show that zebrafishfmr1-/-mutant larvae raised in a naturalistic visual environment display early deficits in hunting behavior, tectal map development, tectal network properties and decoding of spatial stimuli. However when given a choice they preferred an environment with reduced visual stimulation, and rearing them in this environment improved these metrics. Olderfmr1-/-fish showed differences in social behavior, spending more time observing a conspecific, but responding more slowly to social cues. Together these results help reveal howfmr1-/-changes the early development of vertebrate brain function, and how manipulating the environment could potentially help reduce these changes.
The Fragile X Mental Retardation Protein protects the lung from xenobiotic stress by facilitating the Integrated Stress Response
Authors: Basu Deblina Sain , Bhavsar Rital , Gulami Imtiyaz , Lingamallu Sai Manoz , Muddashetty Ravi , Veeranna Chandrakanth , Chattarji Sumantra , Thimmulappa Rajesh , Bhattacharya Aditi , Guha Arjun 
Published: March 2021

ABSTRACTStress response pathways protect the lung from the damaging effects of environmental toxicants. Here we investigate the role of the Fragile X Mental Retardation Protein (FMRP), a multifunctional protein implicated in stress responses, in the lung. We report that FMRP is expressed in murine and human lungs, in the airways and more broadly. Analysis of airway stress responses in mice and in a murine cell lineex vivo,using the well-established Naphthalene (Nap) injury model, reveals that FMRP-deficient cells exhibit increased expression of markers of oxidative and genotoxic stress and increased cell death. We find that FMRP-deficient cells fail to actuate the Integrated Stress Response Pathway (ISR) and upregulate the transcription factor ATF4. Knockdown of ATF4 expression phenocopies the loss of FMRP. We extend our analysis of the role of FMRP to human bronchial BEAS-2B cells, using a 9, 10-Phenanthrenequinone air pollutant model, to find that FMRP-deficient BEAS-2B also fail to actuate the ISR and exhibit greater susceptibility. Taken together, our data suggest that FMRP has a conserved role in protecting the airways by facilitating the ISR.
Function of theVibrioPomB plug region based on the stator rotation model for bacterial flagellar motor
Authors: Homma Michio , Terashima Hiroyuki , Koiwa Hiroaki , Kojima Seiji 
Published: March 2021

AbstractBacterial flagella are the only real rotational motor organs in the biological world. The spiral-shaped flagellar filaments that extend from the cell surface rotate like a screw to create a propulsive force. The base of the flagellar filament has a protein motor consisting of a stator and a rotor embedded in the membrane. The motor part has stators composed of two types of membrane subunits, PomA(MotA) and PomB(MotB), which are energy converters coupled to the ion flow that assemble around the rotor. Recently, structures of the stator, in which two molecules of MotB stuck in the center of the MotA ring made of five molecules, were reported and a model in which the MotA ring rotates with respect to MotB, which is coupled to the influx of ions, was proposed. We focused on theVibrioPomB plug region, which has been reported to control the activation of flagellar motors. We searched for the plug region, which is the interacting region, through site-directed photo-cross-linking and disulfide cross-linking experiments. Our results demonstrated that it interacts with the extracellular short loop region of PomA, which is between transmembrane 3 and 4. Although the motor halted following cross-linking, its function was recovered with a reducing reagent that disrupted the disulfide bond. Our results support the hypothesis, which has been inferred from the stator structure, that the plug region terminates the ion inflow by stopping the rotation of the rotor.ImportanceThe flagellar biological motor resembles a mechanical motor, which is composed of stator and rotor and where the rotational force is transmitted by gear-like movements. We hypothesized that the flagellar the rotation of stator that the pentamer of A subunits revolves around the axis of the B subunit dimer with ion flow. The plug region of the B subunit has been shown to regulate the ion flow. Herein, we demonstrated that the ion flow was terminated by the crosslinking between the plug region and the A subunit. These finding support the rotation hypothesis and explain the role of the plug region in terminating the rotation.
Estimating the elevated transmissibility of the B.1.1.7 strain over previously circulating strains in England using GISAID sequence frequencies
Authors: Piantham Chayada , Linton Natalie M. , Nishiura Hiroshi , Ito Kimihito 
Published: March 2021

AbstractThe B.1.1.7 strain, also referred to as Alpha variant, is a variant strain of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The Alpha variant is considered to possess higher transmissibility compared to the strains previously circulating in England. This paper proposes a new method to estimate the selective advantage of a mutant strain over another strain using the time course of strain frequencies and the distribution of the serial interval of infections. This method allows the instantaneous reproduction numbers of infections to vary over calendar time. The proposed method also assumes that the selective advantage of a mutant strain over previously circulating strains is constant. Applying the method to SARS-CoV-2 sequence data from England, the instantaneous reproduction number of the B.1.1.7 strain was estimated to be 26.6–45.9% higher than previously circulating strains in England. This result indicates that control measures should be strengthened by 26.6–45.9% when the B.1.1.7 strain is newly introduced to a country where viruses with similar transmissibility to the preexisting strain in England are predominant.