bluuebunny/crossref_metadata_2025 huggingface dataset:
A self-adjusting, progressive shock strength procedure to investigate resistance to punishment: characterization in male and female rats
Authors: Desmercieres Stevenson , Lardeux Virginie , Longueville Jean-Emmanuel , Hanna Myriam , Panlilio Leigh V. , Thiriet Nathalie , Solinas Marcello
Published: March 2022

Indifference to harmful consequences is one of the main characteristics of compulsive behaviors and addiction. Animal models that provide a rapid and effective measure of resistance to punishment could be critical for the investigation of mechanisms underlying these maladaptive behaviors. Here, analogous to the progressive ratio (PR) procedure widely used to evaluate appetitive motivation as the response requirement is increased, we developed a self-adjusting, progressive shock strength (PSS) procedure. The PSS provides, within a single session, a break point that quantifies the propensity to work for a reward in spite of receiving electric footshock that progressively increases in duration. In both male and female rats, the PSS break point was sensitive to 1) hunger; and 2) changes in the qualitative, but not quantitative, incentive value of the reward. In systematic comparisons between PSS and PR procedures in the same rats, we found that both measures are sensitive to manipulations of motivational states, but they are not intercorrelated, suggesting that they measure overlapping but partially distinct processes. Importantly, the PSS procedure represents a refinement in the 3Rs principles of animal research because animals can control the strength of shock that they are willing to tolerate. This self-adjusting PSS procedure may represent a useful tool to investigate mechanisms underlying maladaptive behavior that persists in certain individuals despite harmful consequences.
Revisiting Ancient Polyploidy in Leptosporangiate Ferns
Authors: Chen Hengchi , Fang Yuhan , Zwaenepoel Arthur , Huang Sanwen , Van de Peer Yves , Li Zhen
Published: March 2022

Ferns, and particularly homosporous ferns, have long been assumed to have experienced recurrent whole-genome duplication (WGD) events because of their substantially large genome sizes, surprisingly high chromosome numbers, and high degrees of polyploidy among many extant members. Although, consequently, the number of sequenced fern genomes is very limited, recent studies using transcriptome data to find evidence for WGDs in ferns reached conflicting results concerning the occurrence of ancient polyploidy, for instance, in the lineage of leptosporangiate ferns. Because identifying WGDs in a phylogenetic context is the foremost step in studying the contribution of ancient polyploidy to evolution, we revisited earlier identified WGDs in leptosporangiate ferns, mainly the core leptosporangiate ferns, by building age distributions and applying substitution rate corrections and by conducting statistical gene tree – species tree reconciliation analyses. Our integrative analyses confidently identified four ancient WGDs in the sampled core leptosporangiates and suggest both false positives and false negatives for the WGDs that recent studies have reported earlier. In conclusion, we underscore the significance of substitution rate corrections and uncertainties in gene tree – species tree reconciliations in calling WGD events, and that failing to do so likely leads to incorrect conclusions.
Organellar transcripts dominate the cellular mRNA pool across plants of varying ploidy levels
Authors: Forsythe Evan S. , Grover Corrinne E. , Miller Emma R. , Conover Justin L. , Arick Mark A. , Chavarro M. Carolina F. , Leal-Bertioli Soraya C. M. , Peterson Daniel G. , Sharbrough Joel , Wendel Jonathan F. , Sloan Daniel B.
Published: March 2022

Mitochondrial and plastid functions depend on coordinated expression of proteins encoded by genomic compartments that have radical differences in copy number of organellar and nuclear genomes. In polyploids, doubling of the nuclear genome may add challenges to maintaining balanced expression of proteins involved in cytonuclear interactions. Here, we use ribo-depleted RNA-seq to analyze transcript abundance for nuclear and organellar genomes in leaf tissue from four different polyploid angiosperms and their close diploid relatives. We find that, even though plastid genomes contain <1% of the number of genes in the nuclear genome, they generate the majority (69.9–82.3%) of mRNA transcripts in the cell. Mitochondrial genes are responsible for a much smaller percentage (1.3–3.7%) of the leaf mRNA pool but still produce much higher transcript abundances per gene compared to nuclear genome. Nuclear genes encoding proteins that functionally interact with mitochondrial or plastid gene products exhibit mRNA expression levels that are consistently more than ten-fold lower than their organellar counterparts, indicating an extreme cytonuclear imbalance at the RNA level despite the predominance of equimolar interactions at the protein level. Nevertheless, interacting nuclear and organellar genes show strongly correlated transcript abundances across functional categories, suggesting that the observed mRNA stoichiometric imbalance does not preclude coordination of cytonuclear expression. Finally, we show that nuclear genome doubling does not alter the cytonuclear expression ratios observed in diploid relatives in consistent or systematic ways, indicating that successful polyploid plants are able to compensate for cytonuclear perturbations associated with nuclear genome doubling.
Automated patch clamp screening of amiloride and 5-N,N-hexamethyleneamiloride (HMA) analogs identifies 6-iodoamiloride as a potent acid-sensing ion channel inhibitor
Authors: Finol-Urdaneta Rocio K. , McArthur Jeffrey R. , Aboelela Ashraf , Bujaroski Richard S. , Majed Hiwa , Rangel Alejandra , Adams David J. , Ranson Marie , Kelso Michael J. , Buckley Benjamin J.
Published: March 2022

Acid-sensing ion channels (ASICs) are transmembrane sensors of extracellular acidosis and potential drug targets in several disease indications, including neuropathic pain and cancer metastasis. The K+-sparing diuretic amiloride is a moderate non-specific inhibitor of ASICs and has been widely used as a probe for elucidating ASIC function. In this work, we screened a library of 6-substituted and 5,6-disubstituted amiloride analogs using a custom-developed automated patch-clamp protocol and identified 6-iodoamiloride as a more potent ASIC1 inhibitor. Follow-up IC50 determinations in tsA-201 cells confirmed higher ASIC1 inhibitory potency for 6-iodoamiloride 97 (hASIC1 97 IC50 88 nM cf. amiloride 11 IC50 1.7 μM). A similar improvement in activity was observed in ASIC3-mediated currents from rat small diameter dorsal root ganglion neurons (rDRG single-concentration 97 IC50 230 nM cf. 11 IC50 2.7 μM). 6-iodoamiloride represents the amiloride analogue of choice for studying the effects of ASIC inhibition on cell physiology.
Identification of the gene coding for seed cotyledon albumin SCA in the pea (Pisum L.) genome
Authors: Mglinets Anatoliy V. , Bogdanova Vera S. , Kosterin Oleg E.
Published: March 2022

Albumins SCA and SAA are short, highly hydrohylic proteins accumulated in large quantity in the cotyledons and seed axes, respectively, of a dry pea (Pisum sativum L.) seed. SCA was earlier shown to have two allelic variants differing in mobility in polyacrylamide gel electrophoresis in acid medium. Using them the corresponding gene SCA was mapped on Linkage Group V. This gene was used as a useful genetic and phylogeographical marker that still required electrophoretic analysis of the protein while the DNA sequence of the corresponding SCA gene remained unknown. Based the length, the positive charge in acid conditions and the number of lysine residues of SCA and SAA albumins, estimated earlier electrophoretically, the high throughput sequencing data available in public databases were searched for the respective candidates for the corresponding genes SCA and SAA genes among coding sequences residing in the region of the pea genome corresponding to the map position of SCA. Then we sequenced them in a number of pea accessions. Concordance of the earlier electrophoretic data and sequence variation indicated the sequence Psat0s797g0160 of the reference pea genome to be the SCA gene. The sequence Psat0s797g0240 could encode a minor related albumin SA-a2, while a candidate gene for albumin SAA is still missing (as well as electrophoretic variation of both latter albumins). DNA amplification using original primers SCA1_3f and SCA1_3r from genomic DNA and restriction by endonuclease Hind II made SCA a convenient CAPS marker in peas. Thus, the gene encoding the highly hydrophilic albumin SCA accumulated in pea seeds, with its alleles useful classification of pea wild relatives, is now identified in the pea genome and a convenient CAPS marker is worked out on its base.
Nementin is a Nematode-Selective Small Molecule Agonist of Neurotransmitter Release
Authors: Harrington Sean , Knox Jessica J. , Burns Andrew R. , Choo Ken-Loon , Au Aaron , Kitner Megan , Haeberli Cecile , Pyche Jacob , D’Amata Cassandra , Kim Yong-Hyun , Volpatti Jonathan R. , Guiliani Maximillano , Snider Jamie , Wong Victoria , Palmeira Bruna M. , Redman Elizabeth M. , Vaidya Aditya S. , Gilleard John S. , Stagljar Igor , Cutler Sean R. , Kulke Daniel , Dowling James J. , Yip Christopher M. , Keiser Jennifer , Zasada Inga , Lautens Mark , Roy Peter J.
Published: March 2022

Nematode parasites of humans, livestock and crops pose a significant burden on human health and welfare. Alarmingly, parasitic nematodes of animals have rapidly evolved resistance to anthelmintic drugs, and traditional nematicides that protect crops are facing increasing restrictions because of poor phylogenetic selectivity. Here, we present a pipeline that exploits multiple motor outputs of the model nematode C. elegans for nematicide discovery. This pipeline yielded multiple compounds that selectively kill and/or immobilize diverse nematode parasites. We focus on one compound that induces violent convulsions and paralysis that we call Nementin. We find that Nementin agonizes neuronal dense core vesicle release, which in turn agonizes cholinergic signaling. Consequently, Nementin synergistically enhances the potency of widely-used non-selective acetylcholinesterase inhibitors (AChEIs), but in a nematode-selective manner. Nementin therefore has the potential to reduce the environmental impact of toxic AChEI pesticides used to control nematode infections and infestations.

Significance Statement

Parasitic nematodes pose a considerable burden to human health and food security. Small molecules that have traditionally been used to control these parasites have either been banned because of toxicity concerns or are being rendered ineffective because of the evolution of resistance. Significant gaps in our nematicidal toolkit are therefore becoming an alarming problem. Here, we describe our discovery of Nementin, a small molecule that disrupts the nematode nervous system but is ineffective against non-targeted organisms. We find that Nementin also enhances the activity of non-selective pesticides but does so in a nematode-selective manner. Hence, Nementin is an innovative solution to combat parasitic nematodes in a safe and phylum-selective manner.

One-Sentence Summary

A C. elegans-based screening pipeline identifies a selective nematicide that also potentiates acetylcholinesterase inhibitors.
Phyllochron duration and changes through rice development shape the vertical leaf size profile
Authors: Pablo Janet P. , Clerget Benoit , Bueno Crisanta , Dionora Jacqueline , Domingo Abigail J. , De Guzman Constancio C. , Aguilar Edna A. , Cadiz Nina M. , Sta Cruz Pompe C.
Published: March 2022

Well-irrigated aerobic rice (Oryza sativa L.) plants are often shorter with smaller leaves, and the leaf appearance rate is slower in well-irrigated than in flooded environments. This observation questions the functional relationship between the leaf appearance rate, which is correlated with the apical cell production rate, and leaf length that is in turn correlated with the leaf division zone length.

Meristem size, blade size, and appearance were monitored for all leaves from leaf 6 on the main stem of rice plants in field experiments using two varieties, two watering systems, and three sowing dates.

Leaf blade and division zone lengths were correlated in all leaves of the main stem of rice plants. New stable linear relationships were found between the leaf division zone growth duration and internal cell production rate, which changed after leaf 11. These stable relationships imply a stable link between the rates of cell production in the stem apex and leaf meristem, explaining the vertical leaf size profile.

Overall, faster leaf appearance leads to shorter leaves and organs in rice because of a functional link, which is counterbalanced by additional acclimation in transplanted plants.
Sample size requirement for achieving multisite harmonization using structural brain MRI features
Authors: Parekh Pravesh , Bhalerao Gaurav Vivek ,   the ADBS consortium, John John P , Venkatasubramanian G
Published: March 2022

When data is pooled across multiple sites, the extracted features are confounded by site effects. Harmonization methods attempt to correct these site effects while preserving the biological variability within the features. However, little is known about the sample size requirement for effectively learning the harmonization parameters and their relationship with the increasing number of sites. In this study, we performed experiments to find the minimum sample size required to achieve multisite harmonization (using neuroHarmonize) using volumetric and surface features by leveraging the concept of learning curves. Our first two experiments show that site-effects are effectively removed in a univariate and multivariate manner; however, it is essential to regress the effect of covariates from the harmonized data additionally. Our following two experiments with actual and simulated data showed that the minimum sample size required for achieving harmonization grows with the increasing average Mahalanobis distances between the sites and their reference distribution. We conclude by positing a general framework to understand the site effects using the Mahalanobis distance. Further, we provide insights on the various factors in a cross-validation design to achieve optimal inter-site harmonization.
Effects of sub-chronic,in vivoadministration of sigma-1 receptor ligands on platelet and aortic arachidonate cascade in streptozotocin-induced diabetic rats
Authors: Váczi Sándor , Barna Lilla , Laczi Krisztián , Tömösi Ferenc , Rákhely Gábor , Penke Botond , Fülöp Lívia , Janáky Tamás , Deli Mária A. , Mezei Zsófia
Published: March 2022

Diabetes mellitus is a chronic metabolic disorder which induces endothelial dysfunction and platelet activation. Eicosanoids produced from arachidonic acid regulate cellular and vascular functions. Sigma-1 receptor expressed in platelets and endothelial cells can regulate intracellular signalization. Our aim was to examine the influence of sub-chronic,in vivoadministered sigma-1 receptor ligands (2-(4-morpholino)ethyl-1-phenylcyclohexane-1-carboxylate, PRE-084; S-N-Benzyl-6,7-dimethoxy-1,2,3,4-tetrahydro-1-isoquinolineethanamine, a new compound (S)-L1; and N,N-dipropyl-2-[4-methoxy-3-(2-phenylethoxy)-phenyl]-ethylamine monohydrochloride, NE-100) on theex vivoarachidonic acid metabolism of platelets and aorta in streptozotocin-induced diabetic rats. The serum level of sigma-1 receptor ligands was detected by liquid chromatography-mass spectrometry before theex vivoanalysis. Sigma-1 receptor and cyclooxygenase gene expression in platelets were determined by reverse transcription coupled quantitative polymerase chain reaction. The eicosanoid synthesis was examined by using of radiolabeled arachidonic acid substrate and enzyme-linked immunosorbent assay.

In diabetic rats, the sub-chronic,in vivoadministration of the sigma-1 receptor ligands modified the transcript levels of sigma-1 receptor and cyclooxygenase-1, the concentration of cyclooxygenase in platelets and the eicosanoid synthesis in both platelets and aorta. Sigma-1 receptor ligands, by changing platelet and blood vessel eicosanoid synthesis, may play a role in modulating diabetic complications.
Mechanistic and thermodynamic characterization of antivirals targeting druggable pocket of SARS-CoV-2 nucleocapsid
Authors: Dhaka Preeti , Singh Ankur , Choudhary Shweta , Peddinti Rama Krishna , Kumar Pravindra , Sharma Gaurav Kumar , Tomar Shailly
Published: March 2022

The N-terminal (NTD) and the C-terminal (CTD) domains comprises the structure of the SARS-CoV-2 Nucleocapsid (N) protein. Crystal structure of the SARS-CoV-2 N protein determined by Kang et al, 2020, reveals the N-terminal RNA binding domain as a unique drug binding site. The present study targets this unique pocket with identified antivirals using structure-based drug repurposing approach. The high-affinity binding of potential molecules was characterised thermodynamically using Isothermal titration calorimetry. The selected molecules showed an inhibitory RNA binding potential between 8.8 μM and 15.7 μM IC50when evaluated with a fluorescent-based assay. Furthermore, in an in vitro cell-based antiviral assay, these ten antiviral molecules demonstrated high effectiveness in halting SARS-CoV-2 replication. Telmisartan and BMS-189453, the two highly potent antivirals, have ∼0.98μM and 1.02 μM EC50values with the selective index of >102, and >98, respectively. For the first time, this study presents drug molecules specifically targeting the NTD of SARS-CoV-2, offering essential insights for the development of therapeutic interventions against this virus, which is still a potential global threat to public health.
Impairments in fear extinction memory and basolateral amygdala plasticity in the TgF344-AD rat model of Alzheimer’s disease are distinct from non-pathological aging
Authors: Hernandez Caesar M. , Jackson Nateka L. , Hernandez Abbi R. , McMahon Lori L.
Published: March 2022

Fear-based disorders such as posttraumatic stress disorder (PTSD) steepen age-related cognitive decline and doubles the risk for developing Alzheimer’s disease. Due to the seemingly hyperactive properties of fear memories, PTSD symptoms can worsen with age. Perturbations in the synaptic circuitry supporting fear memory extinction are key neural substrates of PTSD. The basolateral amygdala (BLA) is a medial temporal lobe structure critical in the encoding, consolidation, and retrieval of fear memories. As little is known about fear extinction memory and BLA synaptic dysfunction within the context of aging and AD, the goal of this study was to investigate how fear extinction memory deficits and basal amygdaloid nucleus (BA) synaptic dysfunction differentially associate in non-pathological aging and AD in the TgF344AD (TgAD) rat model of AD. Young, middle-aged, and older-aged WT and TgAD rats were trained on a delay fear conditioning and extinction procedure prior to ex vivo extracellular field potential recording experiments in the BA. Relative to young WT rats, long-term extinction memory was impaired, and in general, associated with a hyperexcitable BA and impaired LTP in TgAD rats at all ages. In contrast, long-term extinction memory was impaired in aged WT rats and associated with impaired LTP but not BA hyperexcitability. Interestingly, the middle-aged TgAD rats showed intact short-term extinction and BA LTP, suggestive of a compensatory mechanism, whereas differential neural recruitment in older-aged WT rats may have facilitated short-term extinction. As such, associations between fear extinction memory and amygdala deficits in non-pathological aging and AD are dissociable.

Significance

Adults with fear-based disorders like post-traumatic stress disorder are at an increased risk for developing age-related cognitive decline and Alzheimer’s disease (AD). Moreover, negative emotional affect is an early marker of AD. The link between fear-based disorders and AD creates a disadvantage for achieving positive outcomes later in life. Central to the circuitry underlying fear disorders are medial temporal lobe structures like the basal amygdaloid nucleus (BA). However, the role of the BA in fear-based disorders exacerbated by aging and AD is not well understood. Using the TgF344AD rat model of AD, we investigated how fear extinction memory impairments and BA synaptic function are impacted by aging and AD and whether these processes differentially associate in non-pathological aging and AD.
Generative and interpretable machine learning for aptamer design and analysis of in vitro sequence selection
Authors: Di Gioacchino Andrea , Procyk Jonah , Molari Marco , Schreck John S. , Zhou Yu , Liu Yan , Monasson Rémi , Cocco Simona , Šulc Petr
Published: March 2022

Selection protocols such as SELEX, where molecules are selected over multiple rounds for their ability to bind to a target molecule of interest, are popular methods for obtaining binders for diagnostic and therapeutic purposes. With the increasing amount of such high-throughput experimental data available, machine learning techniques have become increasingly popular for molecular datasets analysis. Here, we show that Restricted Boltzmann Machines (RBMs), a two-layer neural network architecture, can successfully be trained on sequence ensembles from SELEX experiments for thrombin aptamers, and used to estimate the fitness of the sequences obtained through the experimental protocol. As a direct consequence, we show that trained RBMs can be exploited to classify as well as generate novel molecules. To confirm our findings, we experimentally verify the generated sequences from RBM.
Landing manoeuvres predict roost-site preferences in bats
Authors: Chaverri Gloriana , Araya-Salas Marcelo , Barrantes Jose Pablo , Uribe-Etxebarria Tere , Peña-Acuña Marcela , Varela Angie Liz , Aihartza Joxerra
Published: March 2022

Roosts are vital for the survival of many species, and how individuals choose one site over another is affected by various ecological factors. Biomechanical constraints could also affect roost selection, particularly in volant taxa that require sites with easy access, thereby reducing costs (i.e., predation, accidents). To date, no studies have established an association between landing performance and roost-site selection, as predicted by biomechanical constraints associated with flight. We aim to determine roost-site selection in disc-winged bats (Thyroptera tricolor), a species known to roost within developing tubular leaves. This study is coupled with various experiments that measure how a conspicuous apex affects landing tactics and performance. We show that T. tricolor prefers leaves with a longer apex, the space typically used for landing. Bats also approach and enter these leaves more consistently, increasing task performance while reducing the risk of injuries.

Summary statement

Spix’s disc-winged bats prefer to roost in some types of leaves, which we show may be related to costly maneuvers during the approach and landing phases.
Invasiveness of Cancer Populations in a Two-dimensional Percolation cluster: a Stochastic Mathematical Approach
Authors: Yang Renlong , Shao Yuanzhi , Jiang Chongming
Published: March 2022

A framework for the software Unstructured Reaction-Diffusion Master Equation (URDME) was developed. A mitogenic paracrine signaling pathway was introduced phenomenologically to show how cells cooperate with one another. We modeled the emerging Allee effect using low seeding density culture (LSDC) assays to fit the model parameters. Finite time scaling (FTS) was found to be a useful tool for quantifying invasiveness in cancer populations. Through simulation, we analyzed the growth-migration dynamics of BT474 cancer cell populations in-vitro in a 2D percolation cluster and calculated the SPR (successful penetration rate). By analyzing the temporal trajectories of the SPR, we could determine the critical exponents of the critical SPR scaling relation. Moreover, the SPR transition point defined according to the FTS theory,Pc, is negatively correlated with the invasiveness of cancer cell populations. ThePcof the three virtual cancer populations distinctly designated by varying the parameter set of the same model are 0.3408, 0.3675, and 0.4454, respectively. Therefore, the FTS algorithm may be useful in determining invasiveness. Through the simplistic phenomenological paracrine model, inter-cell cooperation and mutual mitogenic boosting are enabled, causing the Allee effect to occur. Such a method could be applied to other circumstances as an example of the quantitatively falsifiable emerging theory.
Comprehensive phylogenomics of Methylobacterium reveals four evolutionary distinct groups and underappreciated phyllosphere diversity
Authors: Leducq Jean-Baptiste , Sneddon David , Santos Malia , Condrain-Morel Domitille , Bourret Geneviève , Martinez-Gomez N. Cecilia , Lee Jessica A. , Foster James A. , Stolyar Sergey , Shapiro B. Jesse , Kembel Steven W. , Sullivan Jack M , Marx Christopher J.
Published: March 2022

Methylobacterium is a group of methylotrophic microbes associated with soil, fresh water, and particularly the phyllosphere, the aerial part of plants that has been well-studied in terms of physiology but whose evolutionary history and taxonomy are unclear. Recent work has suggested that Methylobacterium is much more diverse than thought previously, questioning its status as an ecologically and phylogenetically coherent taxonomic genus. However, taxonomic and evolutionary studies of Methylobacterium have mostly been restricted to model species, often isolated from habitats other than the phyllosphere, and have yet to utilize comprehensive phylogenomic methods to examine gene trees, gene content, or synteny. By analyzing 189 Methylobacterium genomes from a wide range of habitats, including the phyllosphere, we inferred a robust phylogenetic tree while explicitly accounting for the impact of horizontal gene transfers. We showed that Methylobacterium contains four evolutionary distinct groups of bacteria (namely A, B, C, D), characterized by different genome size, GC content, gene content and genome architecture, revealing the dynamic nature of Methylobacterium genomes. In addition of recovering 59 described species, we identified 45 candidate species, mostly phyllosphere-associated, stressing the significance of plants as a reservoir of Methylobacterium diversity. We inferred an ancient transition from a free-living lifestyle to association with plant roots in Methylobacteriaceae ancestor, followed by phyllosphere association of three of the major groups (A, B, D), which early branching in Methylobacterium history was heavily obscured by HGT. Together, our work lays the foundations for a thorough redefinition of Methylobacterium taxonomy, beginning with the abandon of Methylorubrum.
Hyperuricemia triggers Renal Tubular Epithelial Pyroptosis by using ROS to activate the NLRP3 inflammasome
Authors: Wu Yansheng , Li Ruiling , Li Dongdong , Ou Jiaoying , Zhou Jiabao , Wang Chuanxu , Gao Jiandong
Published: March 2022

Renal injury resulting from hyperuricemia has gained a lot of interest. Pyroptosis refers to inflammatory cell death. The activated caspase-1 cleavage, and the pivotal protein - GSDMD could have an association with the hyperuricemic kidney lesion pathogenesis. ROS is a vital NLRP3 inflammasome antagonist in various cells. We investigated the mechanism through which ROS stimulates NLRP3 to modulate pyroptosis in renal tubular epithelial cells as well as hyperuricemic rat kidneys.

Methods

In vitrocultured renal tubular epithelial cells (NRK-52E cells) were incubated with a gradient concentration of uric acid for 24 hr to investigate the pyroptosis through flow cytometry. Next, we used the inhibitors of ROS, mitochondrial ROS, NLRP3 and Caspase-1 respectively to intervene in uric acid treated cells to analyse pyproptosis and activation of ROS- NLRP3 inflammasome signal pathway. Finally, we evaluated the mechanism of hyperuricemia triggering renal tubular epithelial pyroptosis in rat kidney tissues.

Results

The levels of ROS and mitochondrial ROS, the mRNA and protein expression of pyroptosis-associated factors Caspase-1 (p45, p20/10), NLRP3, and GSDMD were upregulated in uric acid, the induced NRK-52E cells as well as hyperuricemic model kidneys. The inhibition of ROS, mitochondrial ROS, NLRP3, or caspase-1 in the uric acid-induced NRK-52E cells may help in controlling pyroptosis. The expression of mRNA and protein by the cytokines IL-18 and IL-1β also increased.

Conclusions

Generally, hyperuricemia triggered renal tubular epithelial pyroptosis via excessive ROS to modulate NLRP3 inflammasome activation in uric acid stimulated renal tubular epithelial cells as well as the oxonic acid potassium induced hyperuricemia.
Asexual stage synchronicity in symptomatic and asymptomatic falciparum malaria
Authors: Watson James A , White Nicholas J
Published: March 2022

Andrade et al have reported that P. falciparum parasitised erythrocytes circulate for longer in persistent asymptomatic infections than in symptomatic malaria. This radical suggestion, attributed to in-vivo adaptation by the parasite population to reduced cytoadherence, is based largely on in-vivo transcriptomic data from 24 Malian children: 12 with acute falciparum malaria and 12 with asymptomatic parasitaemia. We show that the reported analysis generated erroneous results because of data formatting issues. We also show that the algorithm used to estimate the average asexual parasite developmental stage (hours post-invasion) from in-vivo transcriptomic data breaks down when applied to asynchronous infections. We argue that comparisons between asymptomatic and symptomatic malaria of asexual parasite developmental stage distributions are confounded by differences in synchronicity and gametocytaemia, and also by selection bias (because schizogony often precipitates clinical presentation). There is no convincing evidence of an adaptive delayed cytoadherence phenotype in chronic P. falciparum infections.
Experience of Adults with Upper-limb Difference and their Views on Sensory Feedback for Prostheses: A Mixed Methods Study
Authors: Jabban Leen , Metcalfe Benjamin W. , Raines Jonathan , Zhang Dingguo , Ainsworth Ben
Published: March 2022

Abstract

Background

Upper-limb prostheses are regularly abandoned, in part due to the mismatch between user needs and prostheses performance. Sensory feedback is among several technological advances that have been proposed to reduce device abandonment rates. While it has already been introduced in some high-end commercial prostheses, limited data is available about user expectations in relation to sensory feedback. The aim of this study is thus to use a mixed methods approach to provide a detailed insight of users’ perceptions and expectations of sensory feedback technology, to ensure the addition of sensory feedback is as acceptable, engaging and ultimately as useful as possible for users and, in turn, reduce the reliance on compensatory movements that lead to overuse syndrome.

Methods

The study involved an online survey (N=37) and video call interviews (N=15) where adults with upper-limb differences were asked about their experience with limb difference and prosthesis use (if applicable) and their expectations about sensory feedback to prostheses. The survey data were analysed quantitatively and descriptively to establish the range of sensory feedback needs and their variations across the different demographics. Reflexive thematic analysis was performed on the interview data, and data triangulation was used to understand key behavioural issues to generate actionable guiding principles for the development of sensory feedback systems.

Results

The survey provided a list of practical examples and suggestions that did not vary with the different causes of limb difference or prosthesis use. The interviews showed that although sensory feedback is a desired feature, it must prove to have more benefits than drawbacks. The key benefit mentioned by participants was increasing trust, which requires a highly reliable system that provides input from several areas of the hand rather than just the fingertips. The feedback system should also complement existing implicit feedback sources without causing confusion or discomfort. Further, the effect sensory feedback has on the users’ psychological wellbeing was highlighted as an important consideration that varies between individuals and should therefore be discussed. The results obtained were used to develop guiding principles for the design and implementation of sensory feedback systems.

Conclusions

This study provides a mixed-methods research on the sensory feedback needs of adults with upper-limb differences, enabling a deeper understanding of their expectations and worries. Guiding principles were developed based on the results of a survey and interviews to inform the development and assessment of sensory feedback for upper-limb prostheses.
Quantitative Trend Analysis of SARS-CoV-2 RNA in Municipal Wastewater Exemplified with Sewershed-Specific COVID-19 Clinical Case Counts
Authors: Pileggi Vince , Shurgold Jayson , Sun Jianxian , Yang Minqing Ivy , Edwards Elizabeth , Peng Hui , Tehrani Amir , Gilbride Kimberley , Oswald Claire , Wijayasri Shinthuja , Al-Bargash Dana , Stuart Rebecca , Khansari Zeinab , Raby Melanie , Thomas Janis , Fletcher Tim , Simhon Albert
Published: March 2022

We present and demonstrate a quantitative statistical linear trend analysis (QTA) approach to analyze and interpret SARS-CoV-2 RNA wastewater surveillance results concurrently with clinical case data. This demonstration is based on the work completed under the Ontario (Canada) Wastewater Surveillance Initiative (WSI) by two laboratories in four large sewersheds within the Toronto Public Health (TPH) jurisdiction. The sewersheds were sampled over a 9-month period and data were uploaded to the Ontario Wastewater Surveillance Data and Visualization Hub (Ontario Dashboard) along with clinical case counts, both on a sewershed-specific basis. The data from the last 5-months, representing a range of high and low cases, was used for this demonstration. The QTA was conducted on a sewershed specific approach using the recommendations for public health interpretation and use of wastewater surveillance data by the United States Centers for Disease Control and Prevention (US CDC). The interpretation of the QTA results was based on the integration of both clinical and wastewater virus signals using an integration matrix in an interim draft guide by the Public Health Agency of Canada (PHAC). The key steps in the QTA consisted of (i) the calculation of Pepper Mild Mottle Virus (PMMoV), flow and flow-PMMoV-normalized virus loads; (ii) computation of the linear trends including interval estimation to identify the key inflection points using a segmented linear regression method and (iii) integrated interpretations based on consideration of both the cases and wastewater signals, as well as end user actionability. This approach is considered a complementary tool to commonly used qualitative analyses of SARS-CoV-2 RNA in wastewater and is intended to directly support public health decisions using a systematic quantitative approach.
Duration of mRNA vaccine protection against SARS-CoV-2 Omicron BA.1 and BA.2 subvariants in Qatar
Authors: Chemaitelly Hiam , Ayoub Houssein H. , AlMukdad Sawsan , Coyle Peter , Tang Patrick , Yassine Hadi M. , Al-Khatib Hebah A. , Smatti Maria K. , Hasan Mohammad R. , Al-Kanaani Zaina , Kuwari Einas Al- , Jeremijenko Andrew , Kaleeckal Anvar Hassan , Latif Ali Nizar , Shaik Riyazuddin Mohammad , Abdul-Rahim Hanan F. , Nasrallah Gheyath K. , Al-Kuwari Mohamed Ghaith , Butt Adeel A. , Al-Romaihi Hamad Eid , Al-Thani Mohamed H. , Al-Khal Abdullatif , Bertollini Roberto , Abu-Raddad Laith J.
Published: March 2022

The SARS-CoV-2 Omicron (B.1.1.529) variant has two subvariants, BA.1 and BA.2, that are genetically quite divergent. We conducted a matched, test-negative, case-control study to estimate duration of protection of mRNA COVID-19 vaccines, after the second dose and after a third/booster dose, against BA.1 and BA.2 infections in Qatar’s population. BNT162b2 effectiveness against symptomatic BA.1 infection was highest at 46.6% (95% CI: 33.4-57.2%) in the first three months after the second dose, but then declined to ∼10% or below thereafter. Effectiveness rapidly rebounded to 59.9% (95% CI: 51.2-67.0%) in the first month after the booster dose, but then started to decline again. BNT162b2 effectiveness against symptomatic BA.2 infection was highest at 51.7% (95% CI: 43.2-58.9%) in the first three months after the second dose, but then declined to ∼10% or below thereafter. Effectiveness rapidly rebounded to 43.7% (95% CI: 36.5-50.0%) in the first month after the booster dose, but then declined again. Effectiveness against COVID-19 hospitalization and death was in the range of 70-80% any time after the second dose, and was greater than 90% after the booster dose. Similar patterns of protection were observed for the mRNA-1273 vaccine. mRNA vaccines provide only moderate and short-lived protection against symptomatic Omicron infections, with no discernable differences in protection against either the BA.1 or BA.2 subvariants. Vaccine protection against COVID-19 hospitalization and death is strong and durable after the second dose, but is more robust after a booster dose.
Diffusional variance-determined stochastic translation efficiency
Authors: Horvath Attila , Janapala Yoshika , Hannan Ross D. , Eyras Eduardo , Preiss Thomas , Shirokikh Nikolay E.
Published: March 2022

Full-transcriptome methods have brought versatile power to protein biosynthesis research, but remain difficult to apply for the quantification of absolute protein synthesis rates. Here we propose and, using modified translation complex profiling, confirm co-localisation of ribosomes on messenger(m)RNA resulting from their diffusional dynamics. We demonstrate that these stochastically co-localised ribosomes are linked with the translation initiation rate and provide a robust variable to model and quantify specific protein output from mRNA.
LANTSA: Landmark-based transferable subspace analysis for single-cell and spatial transcriptomics
Authors: Zhang Chuanchao , Wang Lequn , Li Xinxing , Guo Wei-Feng , Shi Qianqian , Chen Luonan
Published: March 2022

Single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) technologies provide new insights to understand tissue organization and biological function. Accurately capturing the relationships of samples (e.g., sequenced cells, spatial locations) will result in reliable and consistent outcomes in downstream analyses. However, this undertaking remains a challenge for large-volume or cross-platform datasets due to transcriptional heterogeneity and high computational demands. Here, we introduce landmark-based transferable subspace analysis (LANTSA) to solve such challenges for scRNA-seq and ST datasets. Specifically, LANTSA constructs a representation graph of samples for clustering and visualization based on a novel subspace model, which can learn a more accurate representation and is theoretically proven to be linearly proportional to data size in terms of the time consumption. Furthermore, LANTSA uses a dimensionality reduction technique as an integrative method to extract the discriminants underlying the representation structure, which enables label transfer from one (learning) dataset (i.e., scRNA-seq profiles) to the other (prediction) datasets (e.g., scRNA-seq or ST profiles), thus solving the massive-volume or cross-platform problem. We demonstrated the superiority of LANTSA to identify accurate data structures via clustering evaluation on benchmark datasets of various scRNA-seq protocols, 10x Visium, and Slide-seq ST platforms. Moreover, we confirmed the integration capability of LANTSA to transfer cell annotation on large-scale and cross-platform scRNA-seq datasets. Finally, we validated the effectiveness of LANTSA for the identification of multiple mouse brain areas as well as the spatial mapping of cell types within cortical layers by integrating scRNA-seq and ST data.
Immunization with recombinant accessory protein-deficient SARS-CoV-2 protects against lethal challenge and viral transmission
Authors: Ye Chengjin , Park Jun-Gyu , Chiem Kevin , Dravid Piyush , Allué-Guardia Anna , Garcia-Vilanova Andreu , Kapoor Amit , Walter Mark R. , Kobie James J. , Plemper Richard K. , Torrelles Jordi B. , Martinez-Sobrido Luis
Published: March 2022

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has led to a worldwide Coronavirus Disease 2019 (COVID-19) pandemic. Despite high efficacy of the authorized vaccines, protection against the surging variants of concern (VoC) was less robust. Live-attenuated vaccines (LAV) have been shown to elicit robust and long-term protection by induction of host innate and adaptive immune responses. We sought to develop a COVID-19 LAV by generating 3 double open reading frame (ORF)-deficient recombinant (r)SARS-CoV-2 simultaneously lacking two accessory open reading frame (ORF) proteins (ORF3a/ORF6, ORF3a/ORF7a, and ORF3a/ORF7b). Here, we report that these double ORF-deficient rSARS-CoV-2 have slower replication kinetics and reduced fitness in cultured cells as compared to their parental wild-type (WT) counterpart. Importantly, these double ORF-deficient rSARS-CoV-2 showed attenuation in both K18 hACE2 transgenic mice and golden Syrian hamsters. A single intranasal dose vaccination induced high levels of neutralizing antibodies against different SARS-CoV-2 VoC, and also activated viral component-specific T-cell responses. Notably, the double ORF-deficient rSARS-CoV-2 were able to protect, as determined by inhibition of viral replication, shedding, and transmission, against challenge with SARS-CoV-2. Collectively, our results demonstrate the feasibility to implement these double ORF-deficient rSARS-CoV-2 as safe, stable, immunogenic and protective LAV for the prevention of SARS-CoV-2 infection and associated COVID-19 disease.
Dbx1 controls the development of astrocytes of the intermediate spinal cord by modulating Notch signaling
Authors: Sartoretti M. Micaela , Campetella Carla A. , Lanuza Guillermo M.
Published: March 2022

Significant progress has been made in elucidating the basic principles that govern neuronal specification in the developing central nervous system. In contrast, much less is known about the origin of astrocytic diversity. Here we demonstrate that a restricted pool of progenitors in the mouse spinal cord, expressing the transcription factor Dbx1, produces a subset of astrocytes, in addition to interneurons. Ventral p0-derived astrocytes (vA0) exclusively populate intermediate regions of spinal cord with extraordinary precision. Postnatal vA0 population comprises gray matter protoplasmic and white matter fibrous astrocytes and a group of cells with strict radial morphology contacting the pia. We identified that vA0 cells in the lateral funiculus are distinguished by the expression of Reelin and Kcnmb4. We show that Dbx1 mutants have increased vA0 cells at the expense of p0-derived interneurons. Manipulation of the Notch pathway, together with the alteration in their ligands seen in Dbx1 knock-outs, suggest that Dbx1 controls neuron-glial balance by modulating Notch-dependent cell interactions. In summary, this study highlights that restricted progenitors in dorsal-ventral neural tube produce region-specific astrocytic subgroups and that progenitor transcriptional programs highly influence glial fate and are instrumental in creating astrocyte diversity.
In vivo CRISPR screens reveal Serpinb9 and Adam2 as regulators of immune therapy response in lung cancer
Authors: Dervovic Dzana , Chen Edward L.Y. , Malik Ahmad , Afiuni-Zadeh Somi , Boucher Jonathan , Berman Jacob M. , Teng Katie , Ayyaz Arshad , Lü YiQing , Narimatsu Masahiro , Mbamalu Geraldine , Loganathan Sampath , Martinez Sebastian , Tsai Ricky , Lee Jong Bock , Zhang Li , Wrana Jeffrey , Roux Philippe P. , Jackson Harland W. , Schramek Daniel
Published: March 2022

How the genetic landscape of a tumor governs the tumor’s response to immunotherapy remains largely elusive. Here, we established a direct in vivo CRISPR/Cas9 gene editing methodology to assess the immune-modulatory capabilities of 573 putative cancer genes associated with altered cytotoxic activity in human cancers. Using KrasG12D- and BrafV600E-driven mouse lung cancer models, we identify Serpinb9 and Adam2 as our top immune suppressive and immune enhancing genes, respectively. Mechanistically, we show that Serpinb9 ablation in KrasG12D- and BrafV600E-mutant lung tumor cells greatly enhances the efficacy of cytotoxic T-cells in vitro and in vivo. ADAM2 is a cancer testis antigen broadly expressed in human cancers such as lung adenocarcinoma (13.9%), renal (74.7%), prostate (72.4%), uterine (28.6%) and invasive breast (9.5%) cancer. In our mouse models, we show that Adam2 expression is induced in KrasG12D- but not BrafV600E-driven murine lung tumors and that its expression is further enhanced by immunotherapy. We show that loss of Adam2 significantly decreases KrasG12D-lung tumor burden but blocks the efficacy of cytotoxic T-cells. Consistently, Adam2 overexpression dramatically increases tumor growth and enhances immunotherapy efficacy. Mechanistically, we find that Adam2’s oncogenic function depends on modulating the tumor immune microenvironment by restraining productive type I and type II interferon responses as well as cytokine signaling, reducing the presentation of tumor-associated antigen, and modulating surface expression of several immunoregulatory receptors within Kras-driven lung tumors. Adam2 expression also leads to reduced levels of immune checkpoint inhibitors such as Pd-l1, Lag3, Tigit and Tim3. This reduced exhaustion within the tumor microenvironment may explain why ex vivo expanded and adoptively transferred cytotoxic T-cells show enhanced cytotoxic efficacy against Adam2 overexpressing lung tumors. Together, our study highlights the power of integrating cancer genomic with in vivo CRISPR/Cas9 screens to uncover how cancer-associated genetic alterations control responses to immunotherapies.
A minimal growth medium for Pseudomonas azotoformans associated with insect gut
Authors: Cavallin Ismaela , Chouaia Bessem
Published: March 2022

Pseudomonas spp. can be found associated with several insect hosts. Some of these strains play a crucial role in helping their hosts overcome biotic challenges such as plant defence effectors. Defined media and optimally minimal media are instrumental in studying the physiology and metabolic pathways of microorganisms. In the case of the insect-associated Pseudomonas azotoformans isolated from Galeruca laticollis’ gut, we tested six previously designed defined/minimal media. To determine the optimal medium, we compared the bacterium’s growth performances on the different defined/minimal media to its growth performance on a rich medium using the Dynamic Time Warping Algorithm. The growth results at both 25°C and 30°C indicated the SMM as the optimal medium, with bacterial growth performances being the closest to a rich medium. Therefore, this medium would be highly suitable to study the catabolic pathways for the degradation of some xenobiotics in P. azotoformans.