bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of fenbendazole resistance inAscaridia dissimilison the economics of production in turkeys
Authors: Collins James B. , Jordan Brian , Vidyashankar Anand N. , Castro Pablo Jimenez , Kaplan Ray M. 
Published: April 2021

ABSTRACTFeed conversion efficiency is among the most important factors affecting profitable production of poultry. Infections with parasitic nematodes can decrease efficiency of production, making parasite control through the use of anthelmintics an important component of health management. In ruminants and horses, anthelmintic resistance is highly prevalent in many of the most important nematode species, which greatly impacts their control. Recently, we identified resistance to fenbendazole in an isolate ofAscaridia dissimilis, the most common intestinal helminth of turkeys. Using this drug-resistant isolate, we investigated the impact that failure to control infections has on weight gain and feed conversion in growing turkeys. Birds were infected on Day 0 with either a fenbendazole-susceptible or -resistant isolate, and then half were treated with fenbendazole (SafeGuard®Aquasol) at 4- and 8-weeks post infection. Feed intake and bird weight were measured for each pen weekly throughout the study, and feed conversion rate was calculated. Necropsy was performed on birds from each treatment group to assess worm burdens at weeks 7 and 9 post infection. In the birds infected with the susceptible isolate, fenbendazole-treated groups had significantly better feed conversion as compared to untreated groups. In contrast, there were no significant differences in feed conversion between the fenbendazole-treated and untreated groups in the birds infected with the resistant isolate. At both weeks 7 and 9, worm burdens were significantly different between the treated and untreated birds infected with the drug-susceptible isolate, but not in the birds infected with the drug-resistant isolate. These significant effects on feed conversion were seen despite having a rather low worm establishment in the birds. Overall, these data indicate thatA. dissimiliscan produce significant reductions in feed conversion, and that failure of treatment due to the presence of fenbendazole-resistant worms can have a significant economic impact on turkey production. Furthermore, given the low worm burdens and an abbreviated grow out period of this study, the levels of production loss we measured may be an underestimate of the true impact that fenbendazole-resistant worms may have on a commercial operation.
An automated feeding system for the African killifish reveals effects of dietary restriction on lifespan and allows scalable assessment of associative learning
Authors: McKay Andrew , Costa Emma K. , Chen Jingxun , Hu Chi-Kuo , Chen Xiaoshan , Bedbrook Claire N. , Khondker Rishad C. , Thielvoldt Mike , Singh Param Priya , Wyss-Coray Tony , Brunet Anne 
Published: April 2021

AbstractThe African turquoise killifish is an exciting new vertebrate model for aging studies. A significant challenge for any model organism is the control over its diet in space and time. To address this challenge, we created an automated and networked fish feeding system. Our automated feeder is designed to be open-source, easily transferable, and built from widely available components. Compared to manual feeding, our automated system is highly precise and flexible. As a proof-of-concept for the feeding flexibility of these automated feeders, we define a favorable regimen for growth and fertility for the African killifish and a dietary restriction regimen where both feeding time and quantity are reduced. We show that this dietary restriction regimen extends lifespan in males (but not in females) and impacts the transcriptomes of killifish livers in a sex-specific manner. Moreover, combining our automated feeding system with a video camera, we establish a quantitative associative learning assay to provide an integrative measure of cognitive performance for the killifish. The ability to precisely control food delivery in the killifish opens new areas to assess lifespan and cognitive behavior dynamics and to screen for dietary interventions and drugs in a scalable manner previously impossible with traditional vertebrate model organisms.
Quantification of durable CRISPR-based gene silencing activity
Authors: Nakamura Muneaki , Ivec Alexis , Gao Yuchen , Qi Lei S. 
Published: April 2021

AbstractDevelopment of CRISPR-based technologies for regulating gene expression stands to provide novel methods for the study and engineering of biological behavior. New tools capable of inducing long-lasting changes in gene expression will increase the utility of these techniques, providing durable effects from one-time doses of reagents. We describe here a reporter system for quantifying the ability of CRISPR-based effectors to induce stable gene repression. We observe a continuous gradation of the ability of these effectors to silence gene expression, depending on the domain composition and configuration. We also report the creation of a single CRISPR protein capable of producing durable gene silencing. This assay should allow for the continued development of enhanced gene repression tools which will be useful in a wide array of biological research and engineering applications.
Effect of rapamycin on mitochondria and lysosomes in fibroblasts from patients with mtDNA mutations
Authors: Cheema Nashwa , Cameron Jessie M. , Hood David A. 
Published: April 2021

AbstractMaintaining mitochondrial function and dynamics is crucial for cellular health. In muscle, defects in mitochondria result in severe myopathies where accumulation of damaged mitochondria causes deterioration and dysfunction. Importantly, understanding the role of mitochondria in disease is a necessity to determine future therapeutics. One of the most common myopathies ismitochondrialencephalopathylacticacidosisstroke-like episodes (MELAS), which has no current treatment. Recently, MELAS patients treated with rapamycin exhibited improved clinical outcomes. However, the cellular mechanisms of rapamycin effects in MELAS patients are currently unknown. In this study, we used cultured skin fibroblasts as a window into the mitochondrial dysfunction evident in MELAS cells, as well as to study the mechanisms of rapamycin action, compared to control, healthy individuals. We observed that mitochondria from patients were fragmented, had a 3-fold decline in the average speed of motility, a 2-fold reduced mitochondrial membrane potential and a 1.5–2-fold decline in basal respiration. Despite the reduction in mitochondrial function, mitochondrial import protein Tim23 was elevated in patient cell lines. MELAS fibroblasts had increased MnSOD, p62 and lysosomal function when compared to healthy controls. Treatment of MELAS fibroblasts with rapamycin for 24 hrs resulted in increased mitochondrial respiration compared to control cells, a higher lysosome content, and a greater localization of mitochondria to lysosomes. Our studies suggest that rapamycin has the potential to improve cellular health even in the presence of mtDNA defects, primarily via an increase in lysosomal content.
Local Connectivity and Synaptic Dynamics in Mouse and Human Neocortex
Authors: Campagnola Luke , Seeman Stephanie C , Chartrand Thomas , Kim Lisa , Hoggarth Alex , Gamlin Clare , Ito Shinya , Trinh Jessica , Davoudian Pasha , Radaelli Cristina , Kim Mean-Hwan , Hage Travis , Braun Thomas , Alfiler Lauren , Andrade Juia , Bohn Phillip , Dalley Rachel , Henry Alex , Kebede Sara , Mukora Alice , Sandman David , Williams Grace , Larsen Rachael , Teeter Corinne , Daigle Tanya L. , Berry Kyla , Dotson Nadia , Enstrom Rachel , Gorham Melissa , Hupp Madie , Lee Samuel Dingman , Ngo Kiet , Nicovich Rusty , Potekhina Lydia , Ransford Shea , Gary Amanda , Goldy Jeff , McMillen Delissa , Pham Trangthanh , Tieu Michael , Siverts La’Akea , Walker Miranda , Farrell Colin , Schroedter Martin , Slaughterbeck Cliff , Cobb Charles , Ellenbogen Richard , Gwinn Ryder P , Keene C. Dirk , Ko Andrew L , Ojemann Jeffrey G , Silbergeld Daniel L , Carey Daniel , Casper Tamara , Crichton Kirsten , Clark Michael , Dee Nick , Ellingwood Lauren , Gloe Jessica , Kroll Matthew , Sulc Josef , Tung Herman , Wadhwani Katherine , Brouner Krissy , Egdorf Tom , Maxwell Michelle , McGraw Medea , Pom Christina Alice , Ruiz Augustin , Bomben Jasmine , Feng David , Hejazinia Nika , Shi Shu , Szafer Aaron , Wakeman Wayne , Phillips John , Bernard Amy , Esposito Luke , D’Orazi Florence D , Sunkin Susan , Smith Kimberly , Tasic Bosiljka , Arkhipov Anton , Sorensen Staci , Lein Ed , Koch Christof , Murphy Gabe , Zeng Hongkui , Jarsky Tim 
Published: April 2021

AbstractTo elucidate cortical microcircuit structure and synaptic properties we present a unique, extensive, and public synaptic physiology dataset and analysis platform. Through its application, we reveal principles that relate cell type to synapse properties and intralaminar circuit organization in the mouse and human cortex. The dynamics of excitatory synapses align with the postsynaptic cell subclass, whereas inhibitory synapse dynamics partly align with presynaptic cell subclass but with considerable overlap. Despite these associations, synaptic properties are heterogeneous in most subclass to subclass connections. The two main axes of heterogeneity are strength and variability. Cell subclasses divide along the variability axis, while the strength axis accounts for significant heterogeneity within the subclass. In human cortex, excitatory to excitatory synapse dynamics are distinct from those in mouse and short-term plasticity varies with depth across layers 2 and 3. With a novel connectivity analysis that enables fair comparisons between circuit elements, we find that intralaminar connection probability among cell subclasses exhibits a strong layer dependence.These and other findings combined with the analysis platform create new opportunities for the neuroscience community to advance our understanding of cortical microcircuits.
Towards a unified theory of the reference frame of the ventriloquism aftereffect
Authors: Lokša Peter , Kopčo Norbert 
Published: April 2021

ABSTRACTThe ventriloquism aftereffect (VAE), observed as a shift in the perceived locations of sounds after audio-visual stimulation, requires reference frame alignment since hearing and vision encode space in different reference frames (head-centered vs. eye-centered). Previous experimental studies reported inconsistent results, observing either a mixture of head-centered and eye-centered frames, or a predominantly head-centered frame. Here, a computational model is introduced to examine these inconsistencies. Based on experimental data, the model uses the measured size of the ventriloquism effect to predict the VAE adaptation in the auditory spatial map. Versions of the model examine whether the adaptation is induced by visual signals in head-centered frame, eye-centered frame, by eye-gaze direction-dependent signals, or their combination, and whether some biases are induced by the saccade-to-auditory-target response method used in the experiments. The model is first evaluated on three separate data sets. It can predict them well even without explicit need for an eye-centered signals influencing VAE, suggesting that the reference frame of VAE is mainly head-centered. The model predictions are qualitatively similar but less accurate when all three data sets are combined, suggesting that interactions between individual neural mechanisms are more complex than the simple linear combination assumed in the model.
A nascent polypeptide sequence modulates DnaA translation elongation in response to nutrient availability
Authors: Felletti Michele , Romilly Cedric , Wagner E. Gerhart H. , Jonas Kristina 
Published: April 2021

ABSTRACTThe ability to regulate DNA replication initiation in response to changing nutrient conditions is an important feature of most cell types. In bacteria, DNA replication is triggered by the initiator protein DnaA, which has long been suggested to respond to nutritional changes, nevertheless the underlying mechanisms remain poorly understood. Here, we report a novel mechanism that adjusts DnaA synthesis in response to nutrient availability inCaulobacter crescentus. By performing a detailed biochemical and genetic analysis of thednaAmRNA we identified a sequence downstream of thednaAstart codon that inhibits DnaA translation elongation upon carbon exhaustion. Our data show that the corresponding peptide sequence, but not the mRNA secondary structure or the codon choice, are critical for this response, suggesting that specific amino acids in the growing DnaA nascent chain tune translational efficiency. Our study provides new insights into DnaA regulation and highlights the importance of translation elongation as a regulatory target. We propose that nascent chain sequences, like the one described, might constitute a general strategy for modulating the synthesis rate of specific proteins under changing conditions.
Hydrogel-based slow release of a receptor-binding domain subunit vaccine elicits neutralizing antibody responses against SARS-CoV-2
Authors: Gale Emily C. , Powell Abigail E. , Roth Gillie A. , Meany Emily L. , Yan Jerry , Ou Ben S. , Grosskopf Abigail K. , Adamska Julia , Picece Vittoria C. T. M. , d’Aquino Andrea I. , Pulendran Bali , Kim Peter S. , Appel Eric A. 
Published: April 2021

AbstractThe development of effective vaccines that can be rapidly manufactured and distributed worldwide is necessary to mitigate the devastating health and economic impacts of pandemics like COVID-19. The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein, which mediates host cell entry of the virus, is an appealing antigen for subunit vaccines because it is efficient to manufacture, highly stable, and a target for neutralizing antibodies. Unfortunately, RBD is poorly immunogenic. While most subunit vaccines are commonly formulated with adjuvants to enhance their immunogenicity, we found that clinically-relevant adjuvants Alum, AddaVax, and CpG/Alum were unable to elicit neutralizing responses following a prime-boost immunization. Here we show that sustained delivery of an RBD subunit vaccine comprising CpG/Alum adjuvant in an injectable polymer-nanoparticle (PNP) hydrogel elicited potent anti-RBD and anti-spike antibody titers, providing broader protection against SARS-CoV-2 variants of concern compared to bolus administration of the same vaccine and vaccines comprising other clinically-relevant adjuvant systems. Notably, a SARS-CoV-2 spike-pseudotyped lentivirus neutralization assay revealed that hydrogel-based vaccines elicited potent neutralizing responses when bolus vaccines did not. Together, these results suggest that slow delivery of RBD subunit vaccines with PNP hydrogels can significantly enhance the immunogenicity of RBD and induce neutralizing humoral immunity.
IL-21 and IFN-alpha have both opposite and redundant role on human innate precursors and memory B-cell differentiation
Authors: Boudigou Marina , Michée-Cospolite Magalie , Hémon Patrice , Grasseau Alexis , Dantec Christelle Le , Porchet Emmanuelle , Jamin Christophe , Devauchelle Valérie , Mignen Olivier , Cornec Divi , Pers Jacques-Olivier , Pottier Laëtitia Le , Hillion Sophie 
Published: April 2021

ABSTRACTImmunological memory is essential for effective immune protection upon antigen rechallenge. Memory B cells encompass multiple subsets, heterogeneous in terms of phenotypes, origins and precursors, anatomical localization, and functional responses. B-cell responses are conditioned by micro-environmental signals, including cytokines. Here, we analyzedin vitrothe effects of two cytokines implicated in B-cell differentiation, interferon-alpha (IFN-α) and interleukin (IL)-21, on the early functional response of four different mature B-cell subsets (IgD-CD27-naive, IgD+CD27+unswitched, IgD-CD27+switched and double-negative B cells). The dual response of naive and memory B cells to IL-21 allowed us to uncover a unique IgD+CD27-CD10-B-cell population (referred to as NARB+) characterized by the expression of marginal zone B-cell markers CD45RB and CD1c. Similar to memory B cells, NARB+cells were in a pre-activated state, allowing them to rapidly differentiate into plasmablasts upon innate signals while maintaining their susceptibility to IL-21 activation-induced apoptosis as observed for the naive compartment. Both in-depth phenotypic analysis of circulating B cells, and identification of these cells in spleen, tonsil and gut-associated lymphoid tissues, supported that NARB+are uncommitted precursors of human marginal zone B cells.
Mechanistic basis for understanding the dual activities of the bifunctionalAzotobacter vinelandiimannuronan C-5 epimerase and alginate lyase AlgE7
Authors: Gaardløs Margrethe , Heggeset Tonje Marita Bjerkan , Tøndervik Anne , Tezé David , Svensson Birte , Ertesvåg Helga , Sletta Håvard , Aachmann Finn Lillelund 
Published: April 2021

AbstractThe functional properties of alginates are dictated by the monomer composition and molecular weight distribution. Mannuronan C-5 epimerases determine the former by epimerizing β-D-mannuronic acid residues (M) into α-L-guluronic acid residues (G). The molecular weight is affected by alginate lyases, which cleave alginate chains through β-elimination. The reaction mechanisms for the epimerization and cleavage are similar and some enzymes can perform both. These dualistic enzymes share high sequence identity with mannuronan C-5 epimerases without lyase activity, and the mechanism behind their activity as well as the amino acids responsible for it are still unknown. In this study, we investigate mechanistic determinants of the bifunctional epimerase and lyase activity of AlgE7 fromAzotobacter vinelandii. Based on sequence analyses, a range of AlgE7 variants were constructed and subjected to activity assays and product characterization by NMR. Our results show that the lyase activity of AlgE7 is regulated by the type of ion present: Calcium promotes it, whereas NaCl reduces it. By using defined poly-M and poly-MG substrates, the preferred cleavage sites of AlgE7 were found to be M↓XM and G↓XM, where X can be either M or G. By studying AlgE7 mutants, R148 was identified as an important residue for the lyase activity, and the point mutant R148G resulted in an enzyme with only epimerase activity. Based on the results obtained in the present study we suggest a unified catalytic reaction mechanism for both epimerase and lyase activities where H154 functions as the catalytic base and Y149 as the catalytic acid.ImportancePost-harvest valorisation and upgrading of algal constituents is a promising strategy in the development of a sustainable bioeconomy based on algal biomass. In this respect, alginate epimerases and lyases are valuable enzymes for tailoring of the functional properties of alginate, a polysaccharide extracted from brown seaweed with numerous applications in food, medicine and material industries. By providing a better understanding of the reaction mechanism and of how the two enzyme reactions can be altered by changes in reaction conditions, this study opens for further applications of bacterial epimerases and lyases in enzymatic tailoring of alginate polymers.
Photoswitchable epothilone-based microtubule stabilisers allow GFP-imaging-compatible, optical control over the microtubule cytoskeleton
Authors: Gao Li , Meiring Joyce C. M. , Heise Constanze , Rai Ankit , Müller-Deku Adrian , Akhmanova Anna , Thorn-Seshold Julia , Thorn-Seshold Oliver 
Published: April 2021

AbstractOptical methods to modulate microtubule stability and dynamics are promising approaches to reach the micron- and millisecond-scale resolution needed to decrypt the diverse roles of the microtubule cytoskeleton in biology. However, such optical methods have until now focussed nearly exclusively on microtubule destabilisation. Here, we introduce “STEpos” as light-responsive epothilone reagents, designed to photoswitchably bind to tubulin and stabilise lateral contacts in the microtubule lattice. Using a novel styrylthiazole photoswitch, designed to allow the hydrogen-bonding that is key to epothilone potency, we have created the first set of GFP-orthogonal photoswitchable microtubule stabilisers. The STEpos can photocontrol microtubule polymerisation, cell division, and cellular microtubule dynamics with micron- and second-scale spatiotemporal precision. STEpos offer substantial improvements of potency, solubility, and ease-of-use compared to the only previous photopharmaceuticals for microtubule stabilisation. The intriguing structure-photoswitching-activity relationship insights from this work will also assist future developments of improved STEpo reagents, and we anticipate that these will contribute greatly to high-precision cytoskeleton research across the fields of biophysics, cargo transport, cell motility, cell division, development, and neuroscience.
A Bioinspired Glycopolymer for Capturing Membrane Proteins in Native-Like Lipid-Bilayer Nanodiscs
Authors: Danielczak Bartholomäus , Rasche Marie , Lenz Julia , Pérez Patallo Eugenio , Weyrauch Sophie , Mahler Florian , Agbadaola Michael Tope , Meister Annette , Babalola Jonathan Oyebamiji , Vargas Carolyn , Kolar Cenek , Keller Sandro 
Published: April 2021

ABSTRACTAmphiphilic copolymers that directly extract membrane proteins and lipids from cellular membranes to form nanodiscs combine the advantages of harsher membrane mimics with those of a native-like membrane environment. Among the few commercial polymers that are capable of forming nanodiscs, alternating diisobutylene/maleic acid (DIBMA) copolymers have gained considerable popularity as gentle and UV-transparent alternatives to aromatic polymers. However, their moderate hydrophobicities and high electric charge densities render all existing aliphatic copolymers rather inefficient under near-physiological conditions. Here, we introduce Glyco-DIBMA, a bioinspired glycopolymer that possesses increased hydrophobicity and reduced charge density but nevertheless retains excellent solubility in aqueous solutions. Glyco-DIBMA outperforms established aliphatic copolymers in that it solubilizes lipid vesicles of various compositions much more efficiently, thereby furnishing smaller, more narrowly distributed nanodiscs that preserve a bilayer architecture and exhibit rapid lipid exchange. We demonstrate the superior performance of Glyco-DIBMA in preparative and analytical applications by extracting a broad range of integral membrane proteins from cellular membranes and further by purifying a membrane-embedded voltage-gated K+channel, which was fluorescently labeled and analyzed with the aid of microfluidic diffusional sizing (MDS) directly within native-like lipid-bilayer nano-discs.
Microfluidic delivery of cutting enzymes for fragmentation of surface-adsorbed DNA molecules
Authors: Budassi Julia , Cho NaHyun , Del Valle Anthony , Sokolov Jonathan 
Published: April 2021

AbstractWe describe a method for fragmenting, in-situ, surface-adsorbed and immobilized DNAs on polymethylmethacrylate(PMMA)-coated silicon substrates using microfluidic delivery of the cutting enzyme DNase I. Soft lithography is used to produce polydimethylsiloxane (PDMS) gratings which form microfluidic channels for delivery of the enzyme. Bovine serum albumin (BSA) is used to reduce DNase I adsorption to the walls of the microchannels and enable diffusion of the cutting enzyme to a distance of 10mm. Due to the DNAs being immobilized, the fragment order is maintained on the surface. Possible methods of preserving the order for application to sequencing are discussed.