bluuebunny/crossref_metadata_2025_split huggingface dataset:
A linear programming-based strategy to save pipette tips in automated DNA assembly
Authors: Sechkar Kirill , Tuza Zoltan A. , Stan Guy-Bart 
Published: October 2021

AbstractLaboratory automation and mathematical optimisation are key to improving the efficiency of synthetic biology research. While there are algorithms optimising the construct designs and synthesis strategies for DNA assembly, the optimisation of how DNA assembly reaction mixes are prepared remains largely unexplored. Here, we focus on reducing the pipette tip consumption of a liquid-handling robot as it delivers DNA parts across a multi-well plate where several constructs are being assembled in parallel. We propose a linear programming formulation of this problem based on the capacitated vehicle routing problem, along with an algorithm which applies a linear programming solver to our formulation, hence providing a strategy to prepare a given set of DNA assembly mixes using fewer pipette tips. The algorithm performed well in randomly generated and real-life scenarios concerning several modular DNA assembly standards, proving capable of reducing the pipette tip consumption by up to 61% in large-scale cases. Combining automatic process optimisation and robotic liquid-handling, our strategy promises to greatly improve the efficiency of DNA assembly, either used alone or in combination with other algorithmic methods.
Respiratory and diarrhoeal pathogens in Malawian children hospitalized with diarrhoea and association with short-term growth
Authors: Chisala Mphatso , Nyangulu Wongani , Nyirenda James , Tam Pui-Ying Iroh 
Published: October 2021

AbstractBackgroundPneumonia and diarrhoea are the leading causes of childhood mortality and morbidity worldwide. Recurrence of these common infections are one of the immediate causes of malnutrition, which puts children at risk of further infection. While studies have focused on how gut microbiota is broadly protective against respiratory infection, there has been less attention paid to the reverse relationship, of respiratory microbiota and pathogens influencing the gut, and subsequent association with growth.MethodsIn this sub-study of a prospective cohort study, 27 children (2-24 months) who tested positive forCryptosporidiumwere followed up over 8 weeks. Respiratory and stool pathogens were detected using quantitative molecular methods. Nutritional outcomes were assessed as length-for-age (LAZ), weight-for-length (WLZ) and weight-for-age (WAZ) z-scores. Changes over the study period were compared using repeated analysis of variance and mixed effects model analysis.ResultsIn this period,104 sputum and stool samples were collected. All stool samples had at least one pathogen detected, with an average of 5.1 (SD 2.1) stool pathogens, compared to 84% of the sputum samples with an average 3.5 (SD1.8). DiarrhoeagenicE. coliwere the most common stool pathogens (92%), followed byCryptosporidium(52%) andCampylobacterpan (39%). In sputum,S.pneumoniaewas most prevalent (84%), seconded by Rhinovirus (56%) andM. catarrhalis(50%). There was a significant change in WAZ over the follow-up period. Children who had ≥3 GI pathogens had significantly a lower LAZ mean score at enrollment (−1.8 (SD 1.4)) and across the follow-up period. No relationship between respiratory pathogens and short-term growth was observed. Out of 49 sputum samples that had ≥3 pathogens, 42 (85%) simultaneously had ≥3 GI pathogens.ConclusionAmong young children hospitalized with diarrhoea, multiple gut and respiratory pathogens were prevalent over an 8-week follow-up period. The presence of more GI, but not respiratory, pathogens was significantly associated with reduced short-term growth.Author summaryThe gut-lung axis interact in both health and illness, and we aimed to see whether presence of pathogens in the GI and/or respiratory tract is associated with short-term growth. In 104 sputum and stool samples, we observed lower mean short-term growth in participants with higher number of GI, but not respiratory, pathogens.
In vivoimaging of the GnRH pulse generator reveals a temporal order of neuronal activation and synchronization during each pulse
Authors: Moore Aleisha M. , Coolen Lique M. , Lehman Michael N. 
Published: October 2021

AbstractA hypothalamic pulse generator located in the arcuate nucleus controls episodic release of gonadotropin-releasing hormone (GnRH) and luteinizing hormone (LH) and is essential for reproduction. Recent evidence suggests this generator is comprised of arcuate “KNDy” cells, the abbreviation based on co-expression of kisspeptin, neurokinin B, and dynorphin. However, direct visual evidence of KNDy neuron activity at a single-cell level during a pulse is lacking. Here, we usein vivocalcium imaging in freely moving female mice to show that individual KNDy neurons are synchronously activated in an episodic manner, and these synchronized episodes always precede LH pulses. Furthermore, synchronization among KNDy cells occurs in a temporal order, with some subsets of KNDy cells serving as “leaders” and others as “followers” during each synchronized episode. These results reveal an unsuspected temporal organization of activation and synchronization within the GnRH pulse generator, suggesting that different subsets of KNDy neurons are activated at pulse onset than afterward during maintenance and eventual termination of each pulse. Further studies to distinguish KNDy “leader” from “follower” cells is likely to have important clinical significance, since regulation of pulsatile GnRH secretion is essential for normal reproduction and disrupted in pathological conditions such as polycystic ovary syndrome and hypothalamic amenorrhea.
Injury-induced inflammatory signaling and hematopoiesis in Drosophila
Authors: Evans Cory J. , Liu Ting , Girard Juliet R. , Banerjee Utpal 
Published: October 2021

AbstractInflammatory response in Drosophila to sterile (axenic) injury in embryos and adults has received some attention in recent years, and most concentrate on the events at the injury site. Here we focus on the effect sterile injury has on the hematopoietic organ, the lymph gland, and the circulating blood cells in the larva, the developmental stage at which major events of hematopoiesis are evident. In mammals, injury activates Toll-like receptor (TLR)/NFκB signaling in macrophages, which then express and secrete secondary, pro-inflammatory cytokines. In Drosophila larvae, distal puncture injury of the body wall epidermis causes a rapid activation of Toll and Jun kinase (JNK) signaling throughout the hematopoietic system and the differentiation of a unique blood cell type, the lamellocyte. Furthermore, we find that Toll and JNK signaling are coupled in their activation. Secondary to this Toll/JNK response, a cytokine, Upd3, is induced as a Toll pathway transcriptional target, which then promotes JAK/STAT signaling within the blood cells. Toll and JAK/STAT signaling are required for the emergence of the injury-induced lamellocytes. This is akin to the derivation of specialized macrophages in mammalian systems. Upstream, at the injury site, a Duox- and peroxide-dependent signal causes the activation of the proteases Grass and SPE needed for the activation of the Toll-ligand Spz, but microbial sensors or the proteases most closely associated with them during septic injury are not involved in the axenic inflammatory response.
Novelty and uncertainty interact to regulate the balance between exploration and exploitation in the human brain
Authors: Cockburn Jeffrey , Man Vincent , Cunningham William , O’Doherty John P. 
Published: October 2021

AbstractRecent evidence suggests that both novelty and uncertainty act as potent features guiding exploration. However, these variables are often conflated with each other experimentally, and an understanding of how these attributes interact to regulate the balance between exploration and exploitation has proved elusive. Using a novel task designed to decouple stimulus novelty and estimation uncertainty, we identify separable behavioral and neural mechanisms by which exploration is colored. We show that uncertainty was avoided except when the information gained through exploration could be reliably exploited in the future. In contrast, and contrary to existing theory, novel options grew increasingly attractive relative to familiar counterparts irrespective of the opportunity to leverage their consequences and despite the uncertainty inherent to novel options. These findings led us to develop a formal computational framework in which uncertainty directed choice adapts to the prospective utility of exploration, while novel stimuli persistently draw favor as a result of inflated reward expectations biasing an exploitative strategy. Crucially, novelty is proposed to actively modulate uncertainty processing, effectively blunting the influence of uncertainty in shaping the subjective utility ascribed to novel stimuli. Both behavioral data and fMRI activity sampled from the ventromedial prefrontal cortex, frontopolar cortex and ventral striatum validate this model, thereby establishing a computational account that can not only explain behavior but also shed light on the functional contribution of these key brain regions to the exploration/exploitation trade-off. Our results point to multiple strategies and neural substrates charged with balancing the explore/exploit dilemma, with each targeting distinct aspects of the decision problem to foster a manageable decomposition of an otherwise intractable task.
Respiratory syncytial virus matrix protein assembles as a lattice with local and extended order that coordinates the position of the fusion glycoprotein
Authors: Sibert Bryan S. , Kim Joseph Y. , Yang Jie E. , Ke Zunlong , Stobart Christopher C. , Moore Martin M. , Wright Elizabeth R. 
Published: October 2021

AbstractRespiratory syncytial virus (RSV) is a significant cause of respiratory illness in young children and adults worldwide. There is currently no vaccine or targeted antiviral for RSV. RSV is an enveloped, filamentous, negative-strand RNA virus. Individual virions vary in both diameter and length, with an average diameter of ∼130 nm and ranging from ∼500 nm to over 10 μm in length. The RSV matrix (M) protein is peripherally associated with the interior of the viral membrane. Though the general arrangement of structural proteins within the virion is known, the molecular organization of M and other structural proteins was previously unknown. Here, using whole-cell cryo-electron tomography and sub-tomogram averaging, we show that M is arranged in a packed helical-like lattice of M-dimers ordered at an angle of ∼47° to the viral long axis. Sub-tomogram averages including F and M indicate that the position of F on the viral surface is correlated with the underlying M lattice. Finally, we report that RSV F is frequently observed as pairs, with the F trimers oriented in an anti-parallel conformation to support potential interaction between trimers. These results provide insight into RSV assembly and virion organization and may aid in the identification and development of RSV vaccines and anti-viral targets.
The cyanotoxin 2,4-DAB enhances mortality and causes behavioral and molecular dysfunctions associated with neurodegeneration in larval zebrafish
Authors: Martin Rubia M. , Bereman Michael S. , Marsden Kurt C. 
Published: October 2021

AbstractExposure to cyanotoxins has been linked to neurodegenerative diseases, including amyotrophic lateral sclerosis, Alzheimer’s, and Parkinson’s disease. While the cyanotoxin β-methylamino-L-alanine (BMAA) has received much attention, cyanobacteria produce many cyanotoxic compounds, several of which have been detected in nature alongside BMAA including 2,4-diaminobutyric acid (2,4-DAB), and N-(2-aminoethyl)glycine (AEG). Thus, the question of whether DAB and AEG also cause neurotoxic effectsin vivois of great interest, as is the question of whether they interact to enhance toxicity. Here, we evaluate the toxic and neurotoxic effects of these cyanotoxins alone or in combination by measuring zebrafish larval viability and behavior after exposure. 2,4-DAB was the most potent cyanotoxin as it decreased larval viability by approximately 50% at 6 days post fertilization, while BMAA and AEG decreased viability by just 16% and 8%, respectively. Although we only observed minor neurotoxic effects on spontaneous locomotion, BMAA and AEG enhanced acoustic startle sensitivity, and they interacted in an additive manner to exert their effects. 2,4-DAB, however, only modulated the startle kinematics, an indication of motor dysfunction. To investigate the mechanisms of 2,4-DAB’s effects, we analyzed the protein profile of larval zebrafish exposed to 500μM 2,4-DAB at two time points and identified molecular signatures consistent with neurodegeneration, including disruption of metabolic pathways and downregulation of the ALS-associated genes SOD1 and UBQLN4. Together, our data demonstrate that BMAA and its isomers AEG and 2,4-DAB cause neurotoxic effectsin vivo, with 2,4-DAB as the most potent of the three in the zebrafish model.
Rilmenidine mimics caloric restriction via the nischarin I1-imidazoline receptor to extend lifespan inC. elegans
Authors: Bennett Dominic F. , Goyala Anita , Statzer Cyril , Beckett Charles W. , Tyshkovskiy Alexander , Gladyshev Vadim N. , Ewald Collin Y. , de Magalhães João Pedro 
Published: October 2021

AbstractCaloric restriction increases lifespan across species and has health benefits in humans. Because complying with a low-calorie diet is challenging, here we investigated pharmacological interventions mimicking the benefits of caloric restriction. Searching for compounds that elicit a similar gene expression signature to caloric restriction, we identified rilmenidine, an I1-imidazoline receptor agonist and prescription medication for the treatment of hypertension. We then show that treatingC. eleganswith rilmenidine at young and older ages increases lifespan. We also demonstrate that the stress-resilience, healthspan, and lifespan benefits upon rilmenidine treatment in worms are mediated by the I1-imidazoline receptornish-1, implicating this receptor as a potential longevity target. Furthermore, we show that rilmenidine treatment increased ERK phosphorylation via NISH-1. Consistent with the shared caloric-restriction-mimicking gene signature, supplementing rilmenidine to caloric restrictedC. elegans, genetic reduction of TORC1 function, or rapamycin treatment did not further increase lifespan. The rilmenidine-induced longevity required the transcription factors FOXO/DAF-16 and NRF1,2,3/SKN-1, both important for caloric restriction-mediated longevity. Furthermore, we find that autophagy, but not AMPK signaling, was needed for rilmenidine-induced longevity. Lastly, we find that treating mice with rilmenidine showed transcriptional changes in liver and kidney similar to caloric restriction. Overall, our findings reveal rilmenidine as a caloric restriction mimetic and as a novel geroprotective compound.
Conjugation-based genome engineering in Deinococcus radiodurans
Authors: Brumwell Stephanie L. , Van Belois Katherine D. , Giguere Daniel J. , Edgell David R. , Karas Bogumil J. 
Published: October 2021

ABSTRACTD. radiodurans has become an attractive microbial platform for the study of extremophile biology and industrial bioproduction. To improve the genomic manipulation and tractability of this species, the development of tools for whole genome engineering and design is necessary. Here, we report the development of a simple and robust conjugation-based transformation system from E. coli to D. radiodurans allowing for the introduction of stable, replicating plasmids expressing antibiotic resistance markers. Using this method with nonreplicating plasmids, we developed a protocol for creating sequential gene deletions in D. radiodurans by targeting re-striction-modification system genes. Importantly, we demonstrated a conjugation-based method for cloning the large (178 kb), high G+C content MP1 megaplasmid from D. radiodurans in E. coli. The conjugation-based tools described here will facilitate the development of D. radiodurans strains with synthetic genomes for biological studies and industrial applications.Abstract Figure
Gasotransmitter H2S accelerates seed germination via activating AOX mediated cyanide-resistant respiration pathway
Authors: Fang Huihui , Liu Ruihan , Yu Zhenyuan , Wu Gang , Pei Yanxi 
Published: October 2021

AbstractHydrogen sulfide (H2S) has been witnessed as a crucial gasotransmitter involving in various physiological processes in plants. H2S signaling has been reported to involve in regulating seed germination, but the underlying mechanism remains poorly understood. Here, we found that endogenous H2S production was activated in germinating Arabidopsis seeds, correlating with upregulated both the transcription and the activity of enzymes (LCD and DES1) responsible for H2S production. Moreover, NaHS (the H2S donor) fumigation significantly accelerated seed germination, while H2S-generation defective (lcd/des1) seeds exhibited decreased germination speed. Further results indicated that the alternative oxidase (AOX), a cyanide-insensitive terminal oxidase, can be stimulated by imbibition, and the expression of AOX genes was provoked lag behind H2S production during germination. Additionally, exogenous H2S fumigation significantly reinforced imbibition induced enhancement of AOX1A expression, and mediated post-translational modification to keep AOX in its reduced and active state, which mainly involved H2S induced increase of the GSH/GSSG ratio and the cell reducing power. Consequently, H2S signaling acts as a trigger to induce AOX mediated cyanide-resistant respiration to accelerate seed germination. Our study correlates H2S signaling to cyanide metabolism, which also participates in endogenous H2S generation, providing evidence for more extensive studies of H2S signaling.HighlightGasotransmitter H2S provokes AOX mediated cyanide-resistant respiration, mainly through both long-term (up-regulating AOX1A expression) and short-term (inducing post-translational activation of AOX) regulatory modes, to accelerate seed germination.
Inhibiting ACSL1 related ferroptosis restrains MHV-A59 infection
Authors: Xia Huawei , Zhang Zeming , You Fuping 
Published: October 2021

AbstractMurine hepatitis virus strain A59 (MHV-A59) belongs to the β -coronavirus and is considered as a representative model for studying coronavirus infection. MHV-A59 was shown to induce pyroptosis, apoptosis and necroptosis of infected cells, especially the murine macrophages. However, whether ferroptosis, a recently identified form of lytic cell death, was involved in the pathogenicity of MHV-A59, is unknown. Here, we demonstrate inhibiting ferroptosis suppresses MHV-A59 infection. MHV-A59 infection upregulates the expression of Acsl1, a novel ferroptosis inducer. MHV-A59 upregulates Acsl1 expression depending on the NF-kB activation, which is TLR4-independent. Ferroptosis inhibitor inhibits viral propagation, inflammatory cytokines release and MHV-A59 infection induced cell syncytia formation. ACSL1 inhibitor Triacsin C suppresses MHV-A59 infection induced syncytia formation and viral propagation. In vivo administration of liproxstatin-1 ameliorates lung inflammation and tissue injuries caused by MHV-A59 infection. Collectively, these results indicate that ferroptosis inhibition protects hosts from MHV-A59 infection. Targeting ferroptosis may serves as a potential treatment approach for dealing with hyper-inflammation induced by coronavirus infection.
Local and global crosstalk among heterochromatin marks drives epigenome patterning in Arabidopsis
Authors: To Taiko Kim , Yamasaki Chikae , Oda Shoko , Tominaga Sayaka , Kobayashi Akie , Tarutani Yoshiaki , Kakutani Tetsuji 
Published: October 2021

AbstractTransposable elements (TEs) are robustly silenced by targeting of multiple epigenetic marks, but dynamics of crosstalk among these marks remains enigmatic. In Arabidopsis, TEs are silenced by cytosine methylation in both CpG and non-CpG contexts (mCG and mCH) and histone H3 lysine 9 methylation (H3K9me). While mCH and H3K9me are mutually dependent for their maintenance, mCG and mCH/H3K9me are independently maintained. Here we show that establishment, rather than maintenance, of mCH depends on mCG, accounting for the synergistic colocalization of these silent marks in TEs. When mCG is lost, establishment of mCH is abolished in TEs. mCG also guides mCH in active genes, although genic mCH/H3K9me is removed there. Unexpectedly, the targeting efficiency of mCH depends on relative, rather than absolute, levels of mCG, suggesting underlying global negative controls. We propose that the local positive feedback in heterochromatin dynamics, together with global negative feedback, drive robust and balanced epigenome patterning.
A more complex basal complex: novel components mapped to theToxoplasma gondiicytokinesis machinery portray an expanded hierarchy of its assembly and function
Authors: Engelberg Klemens , Bechtel Tyler , Michaud Cynthia , Weerapana Eranthie , Gubbels Marc-Jan 
Published: October 2021

AbstractThe basal complex (BC) ofToxoplasma gondiihas an essential role in cell division but details on the mechanism are lacking. To promote insights in this process, reciprocal proximity based biotinylation was used to map the basal complex proteome. An assembled protein map was interrogated by spatiotemporal characterization of critical components as well as functionally by disrupting the expression of the components. Spatially, this revealed four proteins sub-complexes with distinct sub-structural BC localization. Temporally, several patterns were differentiated based on their first appearance and/or disappearance from the BC corresponding with different steps in BC development (initiation, expansion, constriction, maturation). We also identified a protein pre-ceding BC formation (BCC0) laid out in a 5-fold symmetry. This symmetry marks the apical annuli and site of alveolar suture formation. From here, it was determined that the apical cap is assembled in the apical direction, whereas the rest of the IMC expands in the basal direction, inspiring a new bi-directional daughter budding process. Furthermore, we discovered BCC4, an essential protein exclusively localizing to the BC during cell division. Although depletion of BCC4 did not prevent BC formation, it led to BC fragmentation at the mid-point of cell division. Based on these data, a model is presented wherein BCC4 and MORN1 stabilize each other and form a rubber band that implies an essential role for the BC in preventing the fraying of the basal end of the assembling daughter cytoskeleton scaffolds. Furthermore, one new component of the Myosin J and Centrin2 cluster was BCC1, a hypothetical protein whose depletion prevents the non-essential last step of BC constriction. Overall, the BC is a highly dynamic, multi-functional structure that is critical to the hierarchical assembly of the daughter parasites.