bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative investigation of the Diabetic foot ulcer microbiome
Authors: Saeb Amr T. M. , Tayeb Hamsa T. , Ouizi Samir , Nassar Majed S. , Alfadda Assim , Raja G. K Udaya , Mani Balavenkatesh , Youssef Amira , Alsuabeyl Mohammed S.
Published: January 2021

Background

Many factors may affect wound healing in Diabetic foot ulcer, namely, microbial density, microorganisms, microbial synergy, the host immune response, and infected tissue quality.

Methodology

This study used a cross-sectional design. We assessed 38 Subjects with DFUs, 23 neuroischaimic, and 15 neuropathic, for microbiota colonizing the DFU utilizing traditional cultures and 16S gene sequencing methods. All the relevant clinical factors were collected. Wound swabs were collected for both traditional microbiological analysis, direct swab (DSM), and cultured (CM) microbiome analysis. DNA isolation, and 16SrRNA hypervariable regions were amplified. Bioinformatics analysis was performed using IonReporter Software, statistical analysis, and diversity indices were computed with vegan R-package.

Results

The traditional microbiological method was able to detect a maximum of one or two pathogens, and, in some cases, no pathogen was detected. The total number of the observed species was 176. The number of identified species was higher in the cultured microbiome (155) than the direct swab microbiome (136). Diversity analysis indicated that biological diversity is higher in the cultured microbiome compared with the DSM. The Shannon H index was 2.75 for the cultured microbiome and 2.63 for DSM. We observed some differences in the major bacterial taxa amongst neuroischaimic and neuropathic DFU microbiomes.

Conclusions

Cultured microbiome is superior to both the traditional method and direct swab microbiome. The Neuroischaimic group showed higher values for the tested diversity indices than the Neuroischaimic group. Neither Cluster Analysis nor Principal Component Analysis showed apparent clustering amongst the two types of ulcers.
Computational ligands to VKORC1s and CYPs. Could they predict new anticoagulant rodenticides?
Authors: Bermejo-Nogales A , Navas J.M. , Coll J
Published: January 2021

Anticoagulant-resistance in rodents and anticoagulant off-target effects are some of the world-wide problems of increasing concern. To search for new anticoagulant rodenticide candidates we have computationally explored some of the rat genes previously implicated in resistance to actual anticoagulants. In particular, we searched among hundreds of anticoagulant-similar chemotypes those binding rat wild-type VKORC1 (the best-known anticoagulant target, a Vitamin K-recycling enzyme), VKORC1L1 (a VKORC1-related enzyme), Cytochrome P450 CYP enzymes (some of the most important enzymes implicated in detoxification) and anticoagulant-resistant VKORC1-mutants (to minimize propensity to resistance). Results predicted new VKORC1 leads with binding-scores in the low nM range (high binding-affinities) predicting hydroxycoumarin- and naphtoquinone-like chemotypes. We then selected top-leads with additional high binding-scores to more than three anticoagulant-related CYPs, suggesting minimal detoxification rates and therefore maximal anticoagulation expectatives. A downsized list of top top-leads maintaining VKORC1 low-binding scores to anticoagulant resistant mutants, was finally proposed for experimental validation. The combination of different rat targets for computational studies, could be used to search for unrelated chemotypes, for reduction of off-target environmental anticoagulant impacts, and/or as new tools to explore anticoagulant molecular mechanisms.
MYCN-induced nucleolar stress drives an early senescence-like transcriptional program in hTERT-immortalized RPE cells
Authors: Zanotti Sofia , Vanhauwaert Suzanne , Van Neste Christophe , Olexiouk Volodimir , Van Laere Jolien , Verschuuren Marlies , Mus Liselot M. , Durinck Kaat , Tilleman Laurentijn , Deforce Dieter , Van Nieuwerburgh Filip , Hogarty Michael D. , Decaesteker Bieke , De Vos Winnok H. , Speleman Frank
Published: January 2021

MYCNis an oncogenic driver in neural crest-derived neuroblastoma and medulloblastoma. To better understand the early effects of MYCN activation in a neural-crest lineage context, we profiled the transcriptome of immortalized human retina pigment epithelial cells with inducible MYCN activation. Gene signatures associated with elevated MYC/MYCN activity were induced after 24 h of MYCN activation, which attenuated but sustained at later time points. Unexpectedly, MYCN activation was accompanied by reduced cell growth. Gene set enrichment analysis revealed a senescence-like signature with strong induction of p53 and p21 but in the absence of canonical hallmarks of senescence such as beta-galactosidase positivity, suggesting incomplete cell fate commitment. When scrutinizing the putative drivers of this growth attenuation, differential gene expression analysis identified several regulators of nucleolar stress. This process was also reflected by phenotypic correlates such as cytoplasmic granule accrual and nucleolar coalescence. Hence, we propose that the induction of MYCN congests the translational machinery, causing nucleolar stress and driving cells into a transient pre-senescent state. Our findings shed new light on the early events induced by MYCN activation and may help unravelling which factors are required for cells to tolerate unscheduled MYCN overexpression during early malignant transformation.

Highlights

Activation of MYCN attenuates proliferation in RPE1 cells

Growth arrest is associated with an early senescence-like transcriptional signature

Transcriptional and phenotypic evidence of nucleolar stress

CDKN1Aupregulation in G2 phase primes cells for faltering in subsequent G1
TheArabidopsisimmune receptor EFR increases resistance to the bacterial pathogensXanthomonasandXylellain transgenic sweet orange
Authors: Mitre Letícia Kuster , Teixeira-Silva Natália Sousa , Rybak Katarzyna , Magalhães Diogo Maciel , de Souza-Neto Reinaldo Rodrigues , Robatzek Silke , Zipfel Cyril , de Souza Alessandra Alves
Published: January 2021

Plants employ cell surface receptors to recognize pathogen (or microbe)-associated molecular patterns (PAMPs/MAMPs), which are crucial for immune system activation. The well-studiedArabidopsis thalianaELONGATION FACTOR-TU RECEPTOR (EFR) recognizes the conserved bacterial PAMP EF-Tu, and the derived peptides elf18 and elf26. The interfamily transfer of EFR has been shown to increase disease resistance in several crops, such as tomato, rice, wheat, and potato. Here, we generated sweet orange (Citrus sinensis) transgenic lines expressingEFRto test if it would confer broad-spectrum resistance against two important citrus bacterial diseases: citrus canker and citrus variegated chlorosis (CVC). Independent EFR transgenic lines gained responsiveness to elf18 and elf26 peptides fromXanthomonas citriandXylella fastidiosa, as measured by reactive oxygen species (ROS) production, mitogen-activated protein kinase (MAPK) activation and defense gene expression. Consistently, infection assays showed thatCitrus-EFRtransgenic plants were more resistant to citrus canker and CVC. Our results show that the EFR immune receptor can improve plant immunity in a perennial crop against bacterial pathogens, opening perspectives to engineer durable broad-spectrum disease resistance under field conditions.
A parsimonious model for mass-univariate vertex-wise analysis
Authors: Couvy-Duchesne Baptiste , Zhang Futao , Kemper Kathryn E. , Sidorenko Julia , Wray Naomi R. , Visscher Peter M. , Colliot Olivier , Yang Jian
Published: January 2021

2.

Covariance between grey-matter measurements can reflect structural or functional brain networks though it has also been shown to be influenced by confounding factors (e.g. age, head size, scanner), which could lead to lower mapping precision (increased size of associated clusters) and create distal false positives associations in mass-univariate vertex-wise analyses. We evaluated this concern by performing state-of-the-art mass-univariate analyses (general linear model, GLM) on traits simulated from real vertex-wise grey matter data (including cortical and subcortical thickness and surface area). We contrasted the results with those from linear mixed models (LMMs), which have been shown to overcome similar issues in omics association studies. We showed that when performed on a large sample (N=8,662, UK Biobank), GLMs yielded large spatial clusters of significant vertices and greatly inflated false positive rate (Family Wise Error Rate: FWER=1, cluster false discovery rate: FDR>0.6). We showed that LMMs resulted in more parsimonious results: smaller clusters and reduced false positive rate (yet FWER>5% after Bonferroni correction) but at a cost of increased computation. In practice, the parsimony of LMMs results from controlling for the joint effect of all vertices, which prevents local and distal redundant associations from reaching significance. Next, we performed mass-univariate association analyses on five real UKB traits (age, sex, BMI, fluid intelligence and smoking status) and LMM yielded fewer and more localised associations. We identified 19 significant clusters displaying small associations with age, sex and BMI, which suggest a complex architecture of at least dozens of associated areas with those phenotypes.
Huygens synchronization of medial septal pacemaker neurons generates hippocampal theta oscillation
Authors: Kocsis Barnabás , Martínez-Bellver Sergio , Fiáth Richárd , Domonkos Andor , Sviatkó Katalin , Barthó Péter , Freund Tamás F. , Ulbert István , Káli Szabolcs , Varga Viktor , Hangya Balázs
Published: January 2021

Episodic learning and memory retrieval are critically dependent on a hippocampal 4-12 Hz oscillatory ‘clock’ signal, the theta oscillation. This clock is largely externally paced, by a network of GABAergic neurons in the medial septum (MS). Theoretical studies suggested a range of hypotheses how this network may achieve theta synchrony; however, experimental evidence is still lacking. By recording multiple single MS neurons and hippocampal local field potential oscillations simultaneously, with both acute and chronically implanted silicon probes, we show that MS pacemaker units oscillate at individual frequencies within the theta range in rodents. Synchronization of MS neuron frequencies, accompanied by an elevation of firing rates, was found to parallel hippocampal theta formation in multiple rodent model systems. This suggests a general mechanism for theta synchronization, akin to the synchronization of weakly coupled pendulum clocks observed by Huygens in the 17thcentury. We optogenetically identified the MS pacemaker units as parvalbumin-expressing GABAergic neurons, while the previously enigmatic MS glutamatergic neurons were mostly theta-activated non-rhythmic cells. Our data were consistent with a network model of partially connected single-compartment inhibitory pacemaker neurons, in which synchronization and de-synchronization in the frequency domain upon waxing and waning tonic excitatory drive was sufficient to toggle MS network output between theta and non-theta states. These results provide experimental and theoretical support to a frequency-synchronization mechanism for pacing hippocampal theta, which may serve as an inspirational prototype for the countless examples of synchronization processes in the central nervous system from Nematoda to Anthropoda to Chordate and Vertebrate phyla.
The limits of evolutionary convergence in sympatry: reproductive interference and historical constraints leading to local diversity in warning traits
Authors: Maisonneuve Ludovic , Elias Marianne , Smadi Charline , Llaurens Violaine
Published: January 2021

Mutualistic interactions between defended species represent a striking case of evolutionary convergence in sympatry, driven by the increased protection against predators brought by mimicry in warning traits. However, such convergence is often limited: sympatric defended species frequently display different or imperfectly similar warning traits. The phylogenetic distance between sympatric species may indeed prevent evolution towards the exact same signal. Moreover, warning traits are also involved in mate recognition, so that trait convergence might result in heterospecific courtship and mating. Here, we develop a mathematical model to investigate the strength and direction of evolution of warning trait in defended species with different ancestral traits. Specifically, we determine the effect of phenotypic distances between ancestral trait states of sympatric defended species and of costs of heterospecific sexual interactions on imperfect mimicry and trait divergence. Our analytical results confirm that reproductive interference and historical constraints limit the convergence of warning traits, leading to either complete divergence, or imperfect mimicry. Our model reveals that imperfect mimicry evolves only when ancestral trait values differ between species due to historical constraints and highlights the importance of female and predator discriminations in the evolution of such imperfect mimicry. Our study thus provides new predictions on how reproductive interference interacts with historical constraints and may promote the emergence of novel warning traits, enhancing mimetic diversity.
Emerging SARS-CoV-2 variants reduce neutralization sensitivity to convalescent sera and monoclonal antibodies
Authors: Hu Jie , Peng Pai , Wang Kai , Liu Bei-zhong , Fang Liang , Luo Fei-yang , Jin Ai-shun , Tang Ni , Huang Ai-long
Published: January 2021

SARS-CoV-2 Spike-specific antibodies contribute the majority of the neutralizing activity in most convalescent human sera. Two SARS-CoV-2 variants, N501Y.V1 (also known as B.1.1.7 lineage or VOC-202012/01) and N501Y.V2 (B.1.351 lineage), reported from the United Kingdom and South Africa, contain several mutations in the receptor binding domain of Spike and are of particular concern. To address the infectivity and neutralization escape phenotypes potentially caused by these mutations, we used SARS-CoV-2 pseudovirus system to compare the viral infectivity, as well as the neutralization activities of convalescent sera and monoclonal antibodies (mAbs) against SARS-CoV-2 variants. Our results showed that N501Y Variant 1 and Variant 2 increase viral infectivity compared to the reference strain (wild-type, WT)in vitro. At 8 months after symptom onset, 17 serum samples of 20 participants (85%) retaining titers of ID50>40 against WT pseudovirus, whereas the NAb titers of 8 samples (40%) and 18 samples (90%) decreased below the threshold against N501Y.V1 and N501Y.V2, respectively. In addition, both N501Y Variant 1 and Variant 2 reduced neutralization sensitivity to most (6/8) mAbs tested, while N501Y.V2 even abrogated neutralizing activity of two mAbs. Taken together the results suggest that N501Y.V1 and N501Y.V2 reduce neutralization sensitivity to some convalescent sera and mAbs.
Feline tooth resorption in a case-control study based on a subpopulation of 944 dentally examined cats from a Finnish questionnaire survey of over 8000 cats
Authors: Vapalahti Katariina , Neittaanmäki Henriikka , Lohi Hannes , Virtala Anna-Maija
Published: January 2021

Tooth resorption (TR) is one of cats’ most common dental diseases. It is a painful condition characterized by progressive dental destruction, which eventually results in loss of teeth. The aetiology of the TR remains unclear, but associations with old age, breed, other oral and dental diseases, and certain environmental factors have been suspected. In our study, we used part of the data from the extensive feline health and environmental survey of 8115 Finnish cats collected through an online survey targeted at cat owners. We aimed to investigate the characteristics of cats having TR and to study risk factors for TR. Because TR is difficult to detect and, in addition, the feline health survey was very comprehensive and included diagnoses defined by both veterinarians and owners themselves, we limited our study to a subpopulation of cats diagnosed with oral or dental disease by a veterinarian and undergone dental examination or surgery under sedation (n=944).

The frequency of veterinary-diagnosed TR was 3.9% in the entire health survey data (316/8115) and increased to 21% in the subpopulation of veterinarian-diagnosed and sedated cats (202/944). We utilized case-control multivariable logistic regression in this subpopulation to determine the risk factors and breed variation of feline TR. The 202 cats diagnosed with TR were defined as TR cases and the 742 cats without TR diagnoses served as controls. Results indicate that the risk of TR increases with age. Dental calculus, gingivitis, and periodontitis were associated with TR. These findings and the interaction of dental calculus with gingivitis and periodontitis might suggest that inflammatory changes caused by dental calculus increase the risk of TR. We found Cornish Rex, European, and Ragdoll at higher risk for TR. Exotic-Persians had lower risk, and Turkish van and Devon Rex had no TR. The observed differences between breeds highlight a genetic contribution. In addition, female cats that had food available constantly had significantly less TR than female cats that had feeding times. The underlying influential reasons for this result remain unexplained in our study.
Effect of hydroxyapatite microspheres, amoxicillin-hydroxyapatite and collagen-hydroxyapatite composites on human dental pulp-derived mesenchymal stem cells
Authors: Pupo Yasmine Mendes , Leite Lidiane Maria Boldrini , Senegaglia Alexandra Cristina , Antunes Lisiane , Nadal Jessica Mendes , de Lara Eliane Leal , Saito Rafael Eiji , Antunes Sandra Regina Masetto , Farago Paulo Vitor
Published: January 2021

The aim of this study was to evaluate the in vitro behavior of human dental pulp mesenchymal stem cells (hDPSCs) cultured on scaffolds of three hydroxyapatite-based materials: hydroxyapatite microspheres [HAp]; amoxicillin-hydroxyapatite composite [Amx-HAp]; and collagen-hydroxyapatite composite [Col-HAp]. These hydroxyapatites (HAps) were synthesized through three methods: microwave hydrothermal, hydrothermal reactor (teflon pouches), and precipitation, respectively. We performed an in vitro experimental study using dental pulp stem cells obtained from samples of third molars and characterized by immunophenotypic analysis. Cells were cultured on scaffolds with osteogenic differentiation medium and were maintained for 21 days. Cytotoxicity analysis and migration assay of hDPSCs were evaluated. Each experiment was performed in triplicate. Data analysis was performed using Kruskal-Wallis test and Dunn’s post-hoc test. After 21 days of induction, no differences in genes expression were observed. hDPSCs highly expressed the collagen IA and the osteonectin at the mRNA, which indicated these genes plays an important role in odontogenesis regardless of induction stimulus. Cytotoxicity assay using hDPSCs demonstrated that Col-HAp group presented a number of non-viable cells statistically lower than the control group (p=0.03). In the migration assay after 24h, biomaterials HAp, Amx-HAp, and Col-HAp revealed the same migration behavior for hDPSCs observed to the positive control. Col-HAp also provided a statistically significant higher migration of hDPSCs than HAp (p=0.02). The migration results in 48h for HAp, Amx-HAp, and Col-HAp was intermediate from those achieved by control groups. There was no statistical difference between positive control and Col-HAp (p>0.05). In general, Col-HAp scaffold showed better features for these dynamic parameters of cell viability and cell migration capacities for hDPSCs, leading to suitable adhesion, proliferation, and differentiation of this osteogenic lineage. These data present high clinical importance because Col-HAp can be used in a wide variety of therapeutic areas, including ridge preservation, minor bone augmentation, and periodontal regeneration.
Hosting sea anemones at the Perhentian reefs of Malaysia: population descriptives and associations with live coral cover
Authors: Versteeg Melissa , Campbell Alanah , Halid Hidayah
Published: January 2021

Around the Perhentian Islands, coral reefs have been undergoing degradation, as is reported by coral reef monitoring programmes. Current coral reef surveys around the Perhentian Islands do not specifically monitor hosting sea anemone populations, nor do they include investigation of how sea anemone abundance correlates to live coral cover on reef sites. As sea anemones can compete with corals for suitable substrate, nutrients, and light availability, the current study was designed to explore hosting sea anemone abundance and distribution patterns around the Perhentian Islands, as well as assess the presence of significant correlations between sea anemone abundance and live coral cover. Two sites with hosting sea anemone populations were assessed, and data was collected for sea anemone species, formation type, hosting status, and resident Amphiprion species. Additionally, live coral cover estimates were calculated and tested for associations between coral and sea anemone abundance. In total, 403 hosting sea anemone formations were analysed. Statistical analyses revealed that at the research site Village Reef, sea anemones that were actively hosting were larger, and more often encountered in clustered formations. In addition, sea anemone cover was significantly negatively correlated to live coral cover. At research site Teluk Keke, actively hosting sea anemones were also larger, but no other tests revealed significant results at this site. The current study offers a first population analysis of hosting sea anemone assemblages around the Perhentian Islands and provides a preliminary exploration of the associations between hosting sea anemone presence and live coral cover on these reefs.
Binaural (pre)processing for contralateral sound field attenuation and improved speech-in-noise recognition
Authors: Lopez-Poveda Enrique A. , Eustaquio-Martín Almudena , San Victoriano Fernando Martín
Published: January 2021

Understanding speech presented in competition with other sound sources can be challenging. Here, we reason that this task can be facilitated by improving the signal-to-noise ratio (SNR) in either of the two ears and that in free-field listening scenarios, this can be achieved by attenuating contralateral sounds. We present a binaural (pre)processing algorithm that improves the SNR in the ear ipsilateral to the target sound source by linear subtraction of the weighted contralateral stimulus. Although the weight is regarded as a free parameter, we justify setting it equal to the ratio of ipsilateral to contralateral head-related transfer functions averaged over an appropriate azimuth range. The algorithm is implemented in the frequency domain and evaluated technically and experimentally for normal-hearing listeners in simulated free-field conditions. Results show that (1) it can substantially improve the SNR (up to 20 dB) and the short-term intelligibility metric in the ear ipsilateral to the target source, particularly for speech-like maskers; (2) it can improve speech reception thresholds for sentences in competition with speech-shaped noise by up to 8.5 dB in bilateral listening and 10.0 dB in unilateral listening; (3) it hardly affects sound-source localization; and (4) the improvements, and the algorithm’s directivity pattern depend on the weights. The algorithm accounts qualitatively for binaural unmasking for speech in competition with multiple maskers and for multiple target-masker spatial arrangements, an unexpected property that can inspire binaural intelligibility models.
Effect of landscape heterogeneity on diurnal raptor community richness and diversity in JammuShiwaliks, Jammu and Kashmir
Authors: Kumar Sudesh , Sohil Asha , Ahmed Muzaffar , Sharma Neeraj
Published: January 2021

In this study, we examined the richness and diversity of diurnal raptors along with their foraging guilds across different land uses in a sub-tropical landscape during December 2016 to November 2018. A total of 80 vantage points, 19 line transects and 36 road transects were sampled in 33 sites in six different habitat types in the study area where we recorded 3409 individuals of 29 diurnal raptors in 2 orders and 3 families. Significant variation in bird abundance was observed among different habitat types, farmlands being more specious followed by pure forests, water bodies and forest-farmland interfaces. Among the seasons, summers recorded higher abundance followed by winter, monsoon and post-monsoon. A low diversity value (H′=2.22) however was observed for the whole study area with mean monthly highest recorded during February (H′=2.44) and least during June (H′=1.85). Most of the raptors observed for their food types and foraging were predators (n=22) and rest were carrion feeders (n=22). Fourteen among all observed diurnal raptors were winter visitors and 13 residents with 9 reported globally threatened. A moderately high richness of diurnal raptors substantiate high conservation value of these habitats especially the forest patches and farmlands and thus calls for effective management strategies for the conservation and proliferation of raptors in sub-tropical areas of Jammu region.
High variation in immune responses and parasite phenotypes in naturally acquiredTrypanosoma cruziinfection in a captive non-human primate breeding colony in Texas, USA
Authors: Padilla Angel M. , Yao Phil Y. , Landry Tre J. , Cooley Gretchen M. , Mahaney Susan M. , Ribeiro Isabela , VandeBerg John L. , Tarleton Rick L.
Published: January 2021

Trypanosoma cruzi, the causative agent of human Chagas disease, is endemic to the southern region of the United States where it routinely infects many host species. The indoor/outdoor housing configuration used in many non-human primate research and breeding facilities in the southern U.S. provides the opportunity for infection byT. cruziand thus provides source material for in-depth investigation of host and parasite dynamics in a natural host species under highly controlled and restricted conditions. For cynomolgus macaques housed at such a facility, we used a combination of serial blood quantitative PCR (qPCR) and hemoculture to confirm infection in >92% of seropositive animals, although each method alone failed to detect infection in >20% of cases. Parasite isolates obtained from 43 of the 64 seropositive macaques were of 2 broad genetic types (discrete typing units, (DTU’s) I and IV); both within and between these DTU groupings, isolates displayed a wide variation in growth characteristics and virulence, elicited host immune responses, and susceptibility to drug treatment in a mouse model. Likewise, the macaques displayed a diversity in T cell and antibody response profiles that rarely correlated with parasite DTU type, length of infection, or age of the primate. This study reveals the complexity of infection dynamics, parasite phenotypes, and immune response patterns that can occur in a primate group, despite being housed in a uniform environment at a single location, and the limited time period over which theT. cruziinfections were established.

Author Summary

We evaluated naturally occurring infections ofTrypanosoma cruzi, the causative agent of human Chagas disease, in an indoor/outdoor primate colony at a breeding facility in Texas, USA. Using serial quantitative PCR and hemoculture, we confirmed infection in 92% of the 64 seropositive animals, but neither of these two methods confirmed more than 80% of the cases. Parasites by hemoculture fell into two genetic groups (discrete typing units I and IV), and displayed large variation in growth characteristics, elicited cellular and humoral immune responses as well as virulence and drug susceptibility when tested in mice. EKG abnormalities were found in 13 out of 51 qPCR-positive macaques. Our results demonstrate the complexity of these infection parameters in this colony in spite of the uniform and geographically constrained housing conditions of the macaques.
Quantifying the impact of electric fields on single-cell motility
Authors: Prescott TP , Zhu K , Zhao M , Baker RE
Published: January 2021

Cell motility in response to environmental cues forms the basis of many developmental processes in multicellular organisms. One such environmental cue is an electric field (EF), which induces a form of motility known as electrotaxis. Electrotaxis has evolved in a number of cell types to guide wound healing, and has been associated with different cellular processes, suggesting that observed electrotactic behaviour is likely a combination of multiple distinct effects arising from the presence of an EF. In order to determine the different mechanisms by which observed electrotactic behaviour emerges, and thus to design EFs that can be applied to direct and control electrotaxis, researchers require accurate quantitative predictions of cellular responses to externally-applied fields. Here, we use mathematical modelling to formulate and parametrise a variety of hypothetical descriptions of how cell motility may change in response to an EF. We calibrate our model to observed data using synthetic likelihoods and Bayesian sequential learning techniques, and demonstrate that EFs bias cellular motility through only one of a selection of hypothetical mechanisms. We also demonstrate how the model allows us to make predictions about cellular motility under different EFs. The resulting model and calibration methodology will thus form the basis for future data-driven and model-based feedback control strategies based on electric actuation.

SIGNIFICANCE

Electrotaxis is attracting much interest and development as a technique to control cell migration due to the precision of electric fields as actuation signals. However, precise control of electrotactic migration relies on an accurate model of how cell motility changes in response to applied electric fields. We present and calibrate a parametrised stochastic model that accurately replicates experimental single-cell data and enables the prediction of input–output behaviour while quantifying uncertainty and stochasticity. The model allows us to elucidate and quantify how electric fields perturb the motile behaviour of the cell. This model and the associated simulation-based calibration methodology will be central to future developments in the control of electrotaxis.
Diversity of receptor expression in central and peripheral mouse neurons estimated from single cell RNA sequencing
Authors: Wangzhou Andi , Paige Candler , Ray Pradipta R. , Dussor Gregory , Price Theodore J.
Published: January 2021

Because somatosensory PNS neurons, in particular nociceptors, are specially tuned to be able to detect a wide variety of both exogenous and endogenous signals, it is widely assumed that these neurons express a greater variety of receptor genes. Because cells detect such signals via cell surface receptors, we sought to formally test the hypothesis that PNS neurons might express a broader array of cell surface receptors than CNS neurons using existing single cell RNA sequencing resources from mouse. We focused our analysis on ion channels, G-protein coupled receptors (GPCRS), receptor tyrosine kinase and cytokine family receptors. In partial support of our hypothesis, we found that mouse PNS somatosensory, sympathetic and enteric neurons and CNS neurons have similar receptor expression diversity in families of receptors examined, with the exception of GPCRs and cytokine receptors which showed greater diversity in the PNS. Surprisingly, these differences were mostly driven by enteric and sympathetic neurons, not by somatosensory neurons or nociceptors. Secondary analysis revealed many receptors that are very specifically expressed in subsets of PNS neurons, including some that are unique among neurons for nociceptors. Finally, we sought to examine specific ligand-receptor interactions between T cells and PNS and CNS neurons. Again, we noted that most interactions between these cells are shared by CNS and PNS neurons despite the fact that T cells only enter the CNS under rare circumstances. Our findings demonstrate that both PNS and CNS neurons express an astonishing array of cell surface receptors and suggest that most neurons are tuned to receive signals from other cells types, in particular immune cells.
Analysis ofDrosophilacardiac hypertrophy by micro-computerized tomography for genetic dissection of heart growth mechanisms
Authors: Petersen Courtney E , Tripoli Benjamin A , Schoborg Todd A , Smyth Jeremy T
Published: January 2021

Heart failure is often preceded by pathological cardiac hypertrophy, a thickening of the heart musculature driven by complex gene regulatory and signaling processes. TheDrosophilaheart has great potential as a genetic model for deciphering the underlying mechanisms of cardiac hypertrophy. However, current methods for evaluating hypertrophy of theDrosophilaheart are laborious and difficult to carry out reproducibly. Here we demonstrate that micro-computerized tomography (microCT) is an accessible, highly reproducible method for non-destructive, quantitative analysis ofDrosophilaheart morphology and size. To validate our microCT approach for analyzingDrosophilacardiac hypertrophy, we show that expression of constitutively active Ras (Ras85DV12), previously shown to cause hypertrophy of the fly heart, results in significant thickening of both adult and larval heart walls when measured from microCT images. We then show using microCT analysis that genetic upregulation of store-operated Ca2+entry (SOCE) driven by expression of constitutively active Stim (StimCA) or Orai (OraiCA) proteins also results in significant hypertrophy of theDrosophilaheart, through a process that specifically depends on Orai Ca2+influx channels. Intravital imaging of heart contractility revealed significantly reduced end diastolic dimensions in StimCAand OraiCAexpressing hearts, consistent with the hypertrophic phenotype. These results demonstrate that increased SOCE activity is an important driver of hypertrophic cardiomyocyte growth, and demonstrate how microCT analysis combined with tractable genetic tools inDrosophilacan be used to delineate molecular signaling processes that underlie cardiac hypertrophy and heart failure.

NEW AND NOTEWORTHY

Genetic analysis of cardiac hypertrophy inDrosophilaholds immense potential for the discovery of new therapeutic targets to prevent and treat heart failure. However, this potential has been hindered by a lack of rapid and effective methods for analysis of heart size in flies. Here we demonstrate that analysis of theDrosophilaheart with micro-computerized tomography yields accurate and highly reproducible heart size measurements that can be used to efficiently analyze heart growth and cardiac hypertrophy inDrosophila.
Fast but not furious: a streamlined selection method for genome edited cells
Authors: Ramachandran Haribaskar , Martins Soraia , Kontarakis Zacharias , Krutmann Jean , Rossi Andrea
Published: January 2021

In the last decade, Transcription Activator-Like Effector Nucleases (TALEN) and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) based genome engineering have revolutionized our approach to biology. Due to their high efficiency and ease of use, the development of custom knock-out and knock-in animal or cell models is now within reach for almost every laboratory. Nonetheless, the generation of genetically modified cells often requires a selection step, usually achieved by antibiotics or fluorescent markers. The choice of the selection marker is based on the available laboratory resources, such as cell types, and parameters like time and cost should also be taken into consideration. Here, we present a new and fast strategy calledMAGECS(magnetic-activated genome edited cell sorting), to select genetically modified cells based on the ability to magnetically sort surface antigens (i.e. tCD19) present in Cas9 positive cells. By using MAGECS, we successfully generated and isolated genetically modified human induced pluripotent stem cells (hiPSCs), primary human fibroblasts, SH-SY5Y neuroblast-like cells, HaCaT and HEK293T cells.

Our strategy expands the genome editing toolbox by offering a fast, cheap, and an easy to use alternative to the available selection methods.
Identification of genes associated with productivity traits and salinity tolerance from activation tagged lines of rice
Authors: Raja Kota Vamsee , Madhanasekhar Kalva , Reddy Vudem Dashavantha , Reddy Attipalli Ramachandra , Rao Khareedu Venkateswara
Published: January 2021

World-wide crop productivity is hugely impacted by diverse eco-environmental conditions. In the present investigation, activation tagged (AT) lines of rice endowed with improved agronomic attributes have been analyzed for tolerance to salinity stress besides identification of genes associated with these attributes. Under salinity stress conditions, AT lines exhibited increased seed germination rates, improved plant growth and development at vegetative and reproductive stages as compared to wild-type (WT) plants. Furthermore, AT lines disclosed enhanced plant water content, photosynthetic efficiency, stomatal conductance, water use efficiency and maximum quantum yield when compared to WT plants, leading to improved yields and delayed onset of stress symptoms. Moreover, AT lines revealed effective antioxidant systems causing decreased accumulation of reactive oxygen species and delayed salinity stress symptoms compared to WT plants. Reduced accumulation of malondialdehyde with concomitant increases in proline and soluble sugars of AT lines further endorsing their improved stress tolerance levels. TAIL and qRT-PCR analyses of AT lines revealed Ds element integrations at different loci and respective overexpression of identified candidate genes involved in various aspects of plant development and stress tolerance. Accordingly, the AT lines plausibly serve as a rare genetic resource for fortifying stress tolerance and productivity traits of elite rice cultivars.

Highlight

Activation tagged lines of rice endowed with improved agronomic attributes have been analyzed for tolerance to salinity stress besides identification and expression analysis of genes associated with these attributes.
Human airway cells prevent SARS-CoV-2 multibasic cleavage site cell culture adaptation
Authors: Lamers Mart M. , Mykytyn Anna Z. , Breugem Tim I. , Wang Yiquan , Wu Douglas C. , Riesebosch Samra , van den Doel Petra B. , Schipper Debby , Bestebroer Theo , Wu Nicholas C. , Haagmans Bart L.
Published: January 2021

Virus propagation methods generally use transformed cell lines to grow viruses from clinical specimens, which may force viruses to rapidly adapt to cell culture conditions, a process facilitated by high viral mutation rates. Upon propagation in VeroE6 cells, SARS-CoV-2 may mutate or delete the multibasic cleavage site (MBCS) in the spike protein that facilitates serine protease-mediated entry into human airway cells. We report that propagating SARS-CoV-2 on the human airway cell line Calu-3 - that expresses serine proteases - prevents MBCS mutations. Similar results were obtained using a human airway organoid-based culture system for SARS-CoV-2 propagation. Thus, in-depth knowledge on the biology of a virus can be used to establish methods to prevent cell culture adaptation.
Social prediction modulates activity of macaque superior temporal cortex
Authors: Roumazeilles Lea , Schurz Matthias , Lojkiewiez Mathilde , Verhagen Lennart , Schüffelgen Urs , Marche Kevin , Mahmoodi Ali , Emberton Andrew , Simpson Kelly , Joly Olivier , Khamassi Mehdi , Rushworth Matthew FS. , Mars Rogier B. , Sallet Jérôme
Published: January 2021

The ability to attribute thoughts to others, also called theory of mind (TOM), has been extensively studied. Computationally, the basis of TOM in humans has been interpreted within the predictive coding framework and associated with activity in the temporo-parietal junction (TPJ). However, the evolutionary origins of these human mindreading abilities have been challenged since the concept was coined. Here we identify a brain region in the Rhesus macaque that shares computational properties with the human TPJ. We revealed, using a non-linguistic task and functional magnetic resonance imaging, that activity in a region of the macaque middle superior temporal cortex was specifically modulated by the predictability of social interactions. As in human TPJ, this region could be distinguished from other temporal regions involved in face processing. Our result suggests the existence of a precursor for the theory of mind ability in the last common ancestor of human and old-world monkeys.
Dopamine transporter is a master regulator of dopaminergic neural network connectivity
Authors: Miller Douglas , Guenther Dylan T. , Maurer Andrew P. , Hansen Carissa A. , Zalesky Andrew , Khoshbouei Habibeh
Published: January 2021

Dopaminergic neurons of the substantia nigra (SNC) and ventral tegmental area (VTA) exhibit spontaneous firing activity. The dopaminergic neurons in these regions have been shown to exhibit differential sensitivity to neuronal loss and psychostimulants targeting dopamine transporter. However, it remains unclear whether these regional differences scale beyond individual neuronal activity to regional neuronal networks. Here we utilized live-cell calcium imaging to show that network connectivity greatly differs between SNC and VTA regions with higher incidence of hub-like neurons in the VTA. Specifically, the frequency of hub-like neurons was significantly lower in SNC dopamine neurons than in the adjacent VTA, consistent with the interpretation of a lower network resilience to SNC neuronal loss. We tested this hypothesis when activity of an individual dopaminergic neuron is suppressed, through whole-cell patch clamp electrophysiology, in either SNC, or VTA networks. Neuronal loss in the SNC decreased network clustering, whereas the larger number of hub-neurons in the VTA overcompensated by increasing network clustering in the VTA. We further show that network properties are regulatable via a dopamine transporter but not a D2 receptor dependent mechanism. Our results demonstrate novel regulatory mechanisms of functional network topology in dopaminergic brain regions.
Identification of a filamentous form of kunitz protease inhibitor inAsteraceae
Authors: Bratsch Sara , Olszewski Neil , Lockhart Benham
Published: January 2021

Filamentous structures were observed in purified extracts from chrysanthemum, gerbera, sunflower and zinnia. When purified filament proteins were subjected to SDS-PAGE, the major protein associated with filaments from all three species has an apparent molecular mass of ≈25 kDa. Protein bands from chrysanthemum, gerbera, and zinnia were subjected to N-terminal protein sequencing while proteins from sunflower were sequenced by CID MS/MS. All of the sequences shared highest similarity to the kunitz trypsin inhibitor family. The sequencing results indicated that the proteins lacked the signal sequences. We tested the gerbera filament protein for glycosylation and found that it was a glycoprotein. Together these results indicate that the filaments are composed of mature KTI protein. This is the first report of a KTI assembling into filaments and the first report of a filament formingAsteraceaeenzyme.
Severe COVID-19 associated variants linked to chemokine receptor gene control in monocytes and macrophages
Authors: Stikker Bernard , Stik Grégoire , Hendriks Rudi W. , Stadhouders Ralph
Published: January 2021

Genome-wide association studies have identified 3p21.31 as the main risk locus for severe disease in COVID-19 patients, although underlying biological mechanisms remain elusive. We performed a comprehensive epigenomic dissection of the 3p21.31 locus, identifying a CTCF-dependent tissue-specific 3D regulatory chromatin hub that controls the activity of several tissue-homing chemokine receptor (CCR) genes in monocytes and macrophages. Risk SNPs colocalized with regulatory elements and were linked to increased expression ofCCR1,CCR2andCCR5in monocytes and macrophages. As excessive organ infiltration of inflammatory monocytes and macrophages is a hallmark of severe COVID-19, our findings provide a rationale for the genetic association of 3p21.31 variants with elevated risk of hospitalization upon SARS-CoV-2 infection.
Temporal Self-Compression: Behavioral and neural evidence that past and future selves are compressed as they move away from the present
Authors: Brietzke Sasha , Meyer Meghan L.
Published: January 2021

Although it is well-known that people feel disconnected from their past and future selves, the underlying mechanism supporting this phenomenon is unknown. To help fill this gap, we considered a basic principle of perception. As objects increase in distance from an observer, they also become logarithmically compressed in perception (i.e., not differentiated from one another), making them hard to distinguish. Here, we report four studies that suggest we may feel disconnected from distant selves, in part, because they are increasingly indiscriminable with temporal distance from the present self. In Studies 1-3, participants made trait ratings across various time points in the past and future. We found that participants compressed their past and future selves, relative to their present self. This effect was preferential to the self and could not be explained by the alternative possibility that individuals simply perceive arbitrary self-change with time irrespective of temporal distance. In Study 4, we tested for neural evidence of temporal self-compression by having participants complete trait ratings across time points while undergoing functional magnetic resonance imaging (fMRI). Representational similarity analysis (RSA) was used to determine if neural self-representations are compressed with temporal distance, as well. We found evidence of temporal self-compression in areas of the default network, including medial prefrontal cortex (MPFC) and posterior cingulate cortex (PCC). Specifically, neural pattern similarity between self-representations was logarithmically compressed with temporal distance. Taken together, these findings reveal a “temporal self-compression” effect, with temporal selves becoming increasingly indiscriminable with distance from the present.

Significance Statement

For centuries, great thinkers have struggled to understand why we feel disconnected from our past and future selves. Insight may come from a basic principle of perception: as objects become distant, they also become less discriminable, or ‘compressed.’ In Studies 1-3, we demonstrate that people’s ratings of their own personality become increasingly less differentiated as they consider more distant past and future selves. In Study 4, we found neural evidence that the brain compresses self-representations with time, as well. When we peer out a window, objects close to us are in clear view whereas distant objects are hard to tell apart. We provide novel evidence that self-perception may operate similarly, with the nuance of distant selves increasingly harder to perceive.