bluuebunny/crossref_metadata_2025 huggingface dataset:
The archives are half-empty: a field-wide assessment of the availability of microbial community sequencing data
Authors: Jurburg Stephanie D. , Konzack Maximilian , Eisenhauer Nico , Heintz-Buschart Anna
Published: April 2020

The sequencing revolution has resulted in the explosive growth of public genetic repositories. These repositories now hold invaluable collections of 16S rRNA gene amplicon sequences, but the extent to which the currently archived data is findable, accessible, and reusable has not been evaluated. We conducted a field-wide assessment of the availability and state of publicly archived 16S rRNA gene amplicon sequencing data. Using custom-built pattern-based text extraction algorithms, we searched 26,927 publications in 17 microbiology or microbial ecology journals, and identified 2,015 studies which performed 16S rRNA gene amplicon sequencing. We found, for example, that 7.2% of these had not been made public at the time of analysis, a trend which increased over time. Of the 635 studies targeting the V3-V4 region of the 16S rRNA gene, 40.3% contained data which was not available or not reusable, and for 25.5% of the studies, faults in data formatting or data labelling were likely to create obstacles in data reuse. Taken together, only 34% of these datasets had potentially reusable data. Our study reveals significant gaps in the availability of currently deposited community sequencing data, identifies major contributors to data loss, and offers suggestions for improving data archiving practices in the future.
[18F]DCP, First Generation PET Radiotracer for Diagnosis of Radiation Resistant Head and Neck Cancer
Authors: Chen Xiaofei , Sai Kiran Kumar Solingapuram , Li Zhe , Zhu Caigang , Shukla Kirtikar , Forshaw Tom E. , Wu Hanzhi , Vance Stephen A. , Madonna Megan , Dewhirst Mark W. , Tsang Allen W. , Poole Leslie B. , Ramanujam Nimmi , King S. Bruce , Furdui Cristina M.
Published: April 2020

Redox metabolism plays essential functions in the pathology of cancer. As tumor redox profiles uniquely reflect cancer stage and in select cases, therapeutic sensitivity, the capability to image redox molecular features is essential to improve diagnosis, treatment, and overall quality-of-life (QOL) of cancer patients. While a number of radiotracers for imaging redox metabolism have been developed, there are no reports of radiotracers for in vivo imaging of protein oxidation. Here we take the first step towards this goal and describe the synthesis and kinetic properties of a new positron emission tomography (PET) [18F]DCP radiotracer for in vivo imaging of protein sulfenylation. Time course biodistribution and PET/CT studies using xenograft animal models of Head and Neck Squamous Cell Cancer (HNSCC) demonstrate feasibility of diagnosing radiation resistant tumors, which display lower [18F]DCP signal. These findings are consistent with our previous reports of decreased protein sulfenylation in clinical specimens of radiation resistant HNSCC. We anticipate further development and implementation of this concept in clinical practice to improve the diagnosis of patients with radiation resistant tumors and the accuracy of prognosis for patients undergoing radiation treatment.

Single Sentence Summary

The study introduces a new PET radiotracer for profiling tumor protein oxidation as a prognostic indicator of resistance to radiation therapy.
Associations Between Resting State Functional Connectivity and a Hierarchical Dimensional Structure of Psychopathology in Middle Childhood
Authors: Karcher Nicole R. , Michelini Giorgia , Kotov Roman , Barch Deanna M.
Published: April 2020

Background

Previous research from the Adolescent Brain Cognitive Development (ABCD) study delineated and validated a hierarchical 5-factor structure with a general psychopathology (‘p’) factor at the apex and five specific factors (internalizing, somatoform, detachment, neurodevelopmental, externalizing) using parent-reported child symptoms. The current study is the first examining associations between dimensions from a hierarchical structure and resting state functional connectivity (RSFC) networks.

Methods

Using 9-11-year-old children from the ABCD baseline sample, we compared the variance explained by each hierarchy level (p-factor, 2-factor, 3-factor, 4-factor, and 5-factor models) in RSFC. Analyses were first conducted in a discovery dataset (n=3790) with significant associations examined in a replication dataset (n=3791).

Results

The current study found associations between p-factor and lower connectivity within default mode network (DMN), although stronger effects emerged for the neurodevelopmental factor. Neurodevelopmental impairments were related to variation in RSFC networks associated with attention to internal states and external stimuli. These networks included within DMN, DMN with cingulo-opercular (CON) and ‘Other’ (Unassigned) networks, CON with ventral attention and ‘Other’ network, and dorsal attention with ‘Other’ network. Results held when accounting for parental psychopathology.

Conclusion

The hierarchical structure of psychopathology showed replicable links to RSFC alterations in middle childhood. The p-factor had minimal association with altered connectivity, while the specific neurodevelopmental dimension showed robust associations with multiple RSFC impairments. Results show the utility of examining associations between intrinsic brain architecture and specific dimensions of psychopathology, revealing associations specifically with neurodevelopmental impairments.
Serotonergic control in initiating defensive responses to unexpected tactile stimuli in the trap-jaw antOdontomachus kuroiwae
Authors: Aonuma Hitoshi
Published: April 2020

A decision to express a defensive response or an escape response to a potential threat is crucial for insects to survive. This study investigated an aminergic mechanism underlying defensive responses to unexpected touch in an ant that has powerful mandibles, the so-called trap-jaw. The mandibles close extremely quickly and are used as a weapon during hunting. Tactile stimulation to the abdomen elicited quick forward movements in a “dart escape” in 90% of the ants in a colony. Less than 10% of the ants responded with a quick “defensive turn” towards the source of stimulation. To reveal the neuronal control mechanisms underlying this defensive behavior, the effects of brain biogenic amines on the responses to tactile stimulus were investigated. The levels of octopamine (OA), dopamine (DA) and serotonin (5HT) in the brain were significantly elevated in ants that responded with a defensive turn to the unexpected stimulus compared to ants that responded with a dart escape. Oral administration of DA and 5HT demonstrated that both amines contributed to the initiation of a defensive response to the stimulus. Oral administration of L-DOPA weakly affected the initiation of the defensive turn, while 5HTP strongly affected the initiation of defensive behavior. Oral administration of an antagonist of 5HT, ketanserin, abolished the effect of 5HTP. These results indicate that endogenous 5HT in the brain has a key role to play in modulating the initiation of defensive behavior in the trap-jaw ant.
A Bayesian neural network for toxicity prediction
Authors: Semenova Elizaveta , Williams Dominic P. , Afzal Avid M. , Lazic Stanley E.
Published: April 2020

Predicting the toxicity of a compound preclinically enables better decision making, thereby reducing development costs and increasing patient safety. It is a complex issue, butin vitroassays and physico-chemical properties of compounds can be used to predict clinical toxicity. Neural networks (NNs) are a popular predictive tool due to their flexibility and ability to model non-linearities, but they are prone to overfitting and therefore are not recommended for small data sets. Furthermore, they don’t quantify uncertainty in the predictions. Bayesian neural networks (BNNs) are able to avoid these pitfalls by using prior distributions on the parameters of a NN model and representing uncertainty about the predictions in the form of a distribution. We model the severity of drug-induced liver injury (DILI) to provide an example of a BNN performing better than a traditional but less flexible proportional odds logistic regression (POLR) model. We use appropriate metrics to evaluate predictions of the ordinal data type. To demonstrate the effect of a hierarchical prior for BNNs as an alternative to hyperparameter optimisation for NNs, we compare the performance of a BNN against NNs with dropout or penalty regularisation. We reduce the task to multiclass classification in order to be able to perform this comparison. A BNN trained for the multiclass classification produces poorer results than a BNN that captures the order. The current work lays a foundation for more complex models built on larger datasets, but can already be adopted by safety pharmacologists for risk quantification.
Gene duplication drives genome expansion in Thaumarchaeota
Authors: Sheridan Paul O. , Raguideau Sebastien , Quince Christopher ,   Thames Consortium, Williams Tom A. , Gubry-Rangin Cécile
Published: April 2020

Ammonia-oxidising archaea of the phylum Thaumarchaeota are keystone species in global nitrogen cycling. However, only three of the six known families of the terrestrially ubiquitous order Nitrososphaerales possess representative genomes. Here we provide genomes for the three remaining families and examine the impact of gene duplication, loss and transfer events across the entire phylum. Much of the genomic divergence in this phylum is driven by gene duplication and loss, but we also detected early lateral gene transfer that introduced considerable proteome novelty. In particular, we identified two large gene transfer events into Nitrososphaerales. The fate of gene families originating on these branches was highly lineage-specific, being lost in some descendant lineages, but undergoing extensive duplication in others, suggesting niche-specific roles within soil and sediment environments. Overall, our results suggest that lateral gene transfer followed by gene duplication drives Nitrososphaerales evolution, highlighting a previously under-appreciated mechanism of genome expansion in archaea.
ST6GAL1-mediated heterogeneity in sialic acid levels potentiates invasion of breast cancer epithelia
Authors: Pally Dharma , Pramanik Durjay , Hussain Shahid , Verma Shreya , Srinivas Anagha , Kumar Rekha V , Bhat Ramray
Published: April 2020

Heterogeneity in phenotypes of malignantly transformed cells and aberrant glycan expression on their surface are two prominent hallmarks of cancers that have hitherto not been linked to each other. In this paper, we identify heterogeneity in a specific glycan linkage: α2,6-linked sialic acids within breast cancer cellsin vivoand in culture. Upon sorting out two populations with moderate and relatively higher cell surface α2,6-linked sialic acid levels from the triple negative breast cancer cell line MDA-MB-231, both populations (denoted as medium and high-2,6-Sial cells respectively) stably retained their levels in early passages. Upon continuous culturing, medium 2,6-Sial cells recapitulated the heterogeneity of the unsorted line whereas high 2,6-Sial cells showed no such tendency. Compared with the high 2,6-Sial, the medium 2,6-Sial cells showed greater adhesion to reconstituted extracellular matrices (ECM) as well as invaded faster as single cells. The level of α2,6-linked sialic acids in the two sublines was found to be consistent with the expression of a specific glycosyl transferase,ST6GAL1. Stably knocking downST6GAL1in the high 2,6-Sial cells, enhanced their invasiveness. When cultured together, medium 2,6-Sial cells differentially migrated to the edge of growing tumoroid-like cultures, whereas high 2,6-Sial cells formed the central bulk. Simulations in a Cellular Potts model-based computational environment that is calibrated to our experimental findings suggest that the heterogeneity of cell-ECM adhesion, likely regulated by α2,6-linked sialic acids facilitates niches of highly invasive cells to efficiently migrate centrifugally as the invasive front of a malignant tumor.

Significance Statement

Cell-surface sugars are aberrantly expressed in cancer but their contributions to tumor heterogeneity are not known. In this study, we uncover and separate breast cancer populations with distinct α2,6-linked sialic acid levels. The moderately expressing population shows stronger adhesion to extracellular matrix than the high expressing population. It also invades faster through the matrix as single cells. Combining experiments with computational modelling, we show that the heterogeneity in matrix adhesion is vital to accentuating cell invasion. In some conditions, invasion of heterogeneous populations may compare with, or exceed that of, homogeneous moderately expressing populations. Our findings are vital to furthering our understanding of how cancers spread and potentially qualify efforts to manage the disease through glycan-editing or immunotherapeutic approaches.
Collateral sensitivity interactions between antibiotics depend on local abiotic conditions
Authors: Allen Richard C. , Pfrunder-Cardozo Katia R. , Hall Alex R.
Published: April 2020

Mutations conferring resistance to one antibiotic can increase (cross resistance) or decrease (collateral sensitivity) resistance to others. Drug combinations displaying collateral sensitivity could be used in treatments that slow resistance evolution. However, lab-to-clinic translation requires understanding whether collateral effects are robust across different environmental conditions. Here, we isolated and characterized resistant mutants ofEscherichia coliusing five antibiotics, before measuring collateral effects on resistance to other antibiotics. During both isolation and phenotyping, we varied conditions in ways relevant in nature (pH, temperature, bile). This revealed local abiotic conditions modified expression of resistance against both the antibiotic used during isolation and other antibiotics. Consequently, local conditions influenced collateral sensitivity in two ways: by favouring different sets of mutants (with different collateral sensitivities), and by modifying expression of collateral effects for individual mutants. These results place collateral sensitivity in the context of environmental variation, with important implications for translation to real-world applications.
Functional and diffusion MRI reveal the functional and structural basis of infants’ noxious-evoked brain activity
Authors: Baxter Luke , Moultrie Fiona , Fitzgibbon Sean , Aspbury Marianne , Mansfield Roshni , Bastiani Matteo , Rogers Richard , Jbabdi Saad , Duff Eugene , Slater Rebeccah
Published: April 2020

Understanding the neurophysiology underlying pain perception in infants is central to improving early life pain management. In this multimodal MRI study, we use resting-state functional and white matter diffusion MRI to investigate individual variability in infants’ noxious-evoked brain activity. In an 18-infant nociception-paradigm dataset, we show it is possible to predict infants’ cerebral haemodynamic responses to experimental noxious stimulation using their resting-state activity across nine networks from a separate stimulus-free scan. In an independent 215-infant Developing Human Connectome Project dataset, we use this resting-state-based prediction model to generate noxious responses. We identify a significant correlation between these predicted noxious responses and infants’ white matter mean diffusivity, and this relationship is subsequently confirmed within our nociception-paradigm dataset. These findings reveal that a newborn infant’s pain-related brain activity is tightly coupled to both their spontaneous resting-state activity and underlying white matter microstructure. This work provides proof-of-concept that knowledge of an infant’s functional and structural brain architecture could be used to predict pain responses, informing infant pain management strategies and facilitating evidence-based personalisation of care.
Effect of MIND Diet Intervention on Cognitive Performance and Brain Structure in Healthy Obese Women: A Randomized Controlled Trial
Authors: Arjmand Golnaz , Abbas-Zadeh Mojtaba , Eftekhari Mohammad Hassan
Published: April 2020

Background and Aim

Previous studies suggested adherence to recently developed Mediterranean-DASH Intervention for Neurodegenerative Delay (MIND) associated with cognitive performance. There was no prior Randomized controlled Trial (RCT) to investigate this association. This study aimed to examine the effect of MIND dietary pattern on features of cognitive performance and also changes in brain structure in healthy obese women.

Methods

As a total of 50 obese women assessed for eligibility, we randomly allocated 40 participants with mean BMI 32 ± 4.31 and mean age 48 ± 5.38 years to either calorie-restricted modified MIND diet or a calorie-restricted standard control diet. Change in cognitive performance was the primary outcome measured with a comprehensive neuropsychological test battery. We also performed voxel-based morphometry as a secondary outcome to quantify the differences in brain structure. All of the measurements administered at baseline and three months follow up.

Results

Thirty-seven participants (MIND group=22 and control group=15) completed the study. The results found in the MIND diet group working memory +1.37 (95% CI: 0.79,1.95), verbal recognition memory +4.85 (95% CI: 3.30,6.40), and attention +3.75 (95% CI: 2.43,5.07) improved more compared with the control group (ps< 0.05). Results of brain MRI consists of an increase in surface area of inferior frontal gyrus in the MIND diet group. Furthermore, the results showed a decrease in the cerebellum-white matter and cerebellum-cortex in two groups of study. Still, the effect in the MIND group was greater than the control group.

Conclusions

The study findings declare for the first time that the MIND diet intervention can reverse the destructive effects of obesity on cognition and brain structure, which could be strengthened by a modest calorie restriction.
The E3 ubiquitin-protein ligase MDM2 is a novel interactor of the von Hippel-Lindau tumor suppressor
Authors: Falconieri Antonella , Minervini Giovanni , Bortolotto Raissa , Piovesan Damiano , Lopreiato Raffaele , Sartori Geppo , Pennuto Maria , Tosatto Silvio C.E.
Published: April 2020

Mutations of the von Hippel-Lindau (pVHL) tumor suppressor are causative of a familiar predisposition to develop different types of cancer. pVHL is mainly known for its role in regulating hypoxia-inducible factor 1-α (HIF-1α) degradation, thus modulating the hypoxia response. There are different pVHL isoforms, including pVHL30 and pVHL19. However, little is known about isoform-specific functions and protein-protein interactions. Integratingin silicopredictions within vitroand invivoassays, we describe a novel interaction between pVHL and mouse double minute 2 homolog (MDM2). Importantly, we found that pVHL30, and not pVHL19, forms a complex with MDM2, and that the N-terminal acidic tail of pVHL30 is required for its association with MDM2. Further, we demonstrate that an intrinsically disordered region upstream of the tetramerization domain of MDM2 is responsible for its isoform-specific association with pVHL30. This region is highly conserved in higher mammals, including primates, similarly to what has been already proposed for the N-terminal tail of pVHL30. Finally, we show that overexpression of pVHL30 and MDM2 together reduces cell proliferation, suggesting a synergistic effect of these E3 ubiquitin ligases. Collectively, our data support the idea that pVHL30 plays a role in MDM2 regulation, suggesting a wider interplay among hypoxia sensing and cell cycle regulation.
Inhibition of HIV-1 gene transcription by KAP1 in myeloid lineage
Authors: Ait Ammar Amina , Bellefroid Maxime , Daouad Fadoua , Martinelli Valérie , Van Assche Jeanne , Wallet Clémentine , De Rovere Marco , Fahrenkrog Birthe , Schwartz Christian , Van Lint Carine , Gautier Virginie , Rohr Olivier
Published: April 2020

HIV-1 latency generates reservoirs that prevent viral eradication by the current therapies. To find strategies toward an HIV cure, detailed understandings of the molecular mechanisms underlying establishment and persistence of the reservoirs are needed. The cellular transcription factor KAP1 is known as a potent repressor of gene transcription. Here we report that KAP1 represses HIV-1 gene expression in myeloid cells including microglial cells, the major reservoir of the central nervous system. Mechanistically, KAP1 interacts and colocalizes with the viral transactivator Tat to promote its degradation via the proteasome pathway and repress HIV-1 gene expression. In myeloid models of latent HIV-1 infection, the depletion of KAP1 increased viral gene elongation and reactivated HIV-1 expression. Bound to the latent HIV-1 promoter, KAP1 associates and cooperates with CTIP2, a key epigenetic silencer of HIV-1 expression in microglial cells. In addition, Tat and CTIP2 compete for KAP1 binding suggesting a dynamic modulation of the KAP1 cellular partners upon HIV-1 infection. Altogether, our results suggest that KAP1 contributes to the establishment and the persistence of HIV-1 latency in myeloid cells.
Infection with CagA+Helicobacter pyloriinduces epithelial to mesenchymal transition in human cholangiocytes
Authors: Thanaphongdecha Prissadee , Karinshak Shannon E. , Ittiprasert Wannaporn , Mann Victoria H. , Chamgramol Yaovalux , Pairojkul Chawalit , Fox James G. , Suttiprapa Sutas , Sripa Banchob , Brindley Paul J.
Published: April 2020

Recent reports suggest that the East Asian liver fluke,Opisthorchis viverrini, infection with which is implicated in opisthorchiasis-associated cholangiocarcinoma, serves as a reservoir ofHelicobacter pylori. The opisthorchiasis-affected cholangiocytes that line the intrahepatic biliary tract are considered to be the cell of origin of this malignancy. Here, we investigated interactionsin vitroamong human cholangiocytes, a CagA-positive strain ofHelicobacter pylori, and the related bacillus,Helicobacter bilis. Exposure to increasing numbers ofH. pyloriat 0, 1, 10, 100 bacilli per cholangiocyte induced phenotypic changes including the profusion of thread-like filopodia and a loss of cell-cell contact, in a dose-dependent fashion. In parallel, following exposure toH. pylori, changes were evident in levels of mRNA expression of epithelial to mesenchymal transition (EMT)-encoding factors including snail, slug, vimentin, matrix metalloprotease, zinc finger E-box-binding homeobox, and the cancer stem cell marker CD44. Transcription levels encoding the cell adhesion marker CD24 decreased. Analysis to quantify cellular proliferation, migration and invasion in real time using the xCELLigence approach revealed that exposure to ≥10H. pyloristimulated migration and invasion by the cholangiocytes through an extracellular matrix. In addition, 10 bacilli of CagA-positiveH. pyloristimulated contact-independent colony establishment in soft agar. These findings support the hypothesis that infection withH. pyloricontributes to the malignant transformation of the biliary epithelium.
The impact of purifying and background selection on the inference of population history: problems and prospects
Authors: Johri Parul , Riall Kellen , Becher Hannes , Excoffier Laurent , Charlesworth Brian , Jensen Jeffrey D.
Published: April 2020

Current procedures for inferring population history generally assume complete neutrality - that is, they neglect both direct selection and the effects of selection on linked sites. We here examine how the presence of direct purifying selection and background selection may bias demographic inference by evaluating two commonly-used methods (MSMC andfastsimcoal2), specifically studying how the underlying shape of the distribution of fitness effects (DFE) and the fraction of directly selected sites interact with demographic parameter estimation. The results show that, even after masking functional genomic regions, background selection may cause the mis-inference of population growth under models of both constant population size and decline. This effect is amplified as the strength of purifying selection and the density of directly selected sites increases, as indicated by the distortion of the site frequency spectrum and levels of nucleotide diversity at linked neutral sites. We also show how simulated changes in background selection effects caused by population size changes can be predicted analytically. We propose a potential method for correcting for the mis-inference of population growth caused by selection. By treating the DFE as a nuisance parameter and averaging across all potential realizations, we demonstrate that even directly selected sites can be used to infer demographic histories with reasonable accuracy.
Adolescent intermittent ethanol exposure induces sex-dependent divergent changes in ethanol drinking and motor activity in adulthood in C57BL/6J mice
Authors: Maldonado-Devincci Antoniette M. , Makdisi Joseph G. , Hill Andrea M. , Waters Renee C. , Hall Nzia I. , Shobande Mariah , Kumari Anjali
Published: April 2020

With alcohol readily accessible to adolescents, its consumption leads to many adverse effects, including impaired learning, attention, and behavior. Adolescents report higher rates of binge drinking compared to adults. Adolescents are also more prone to substance use disorder during adulthood due to physiological changes during the adolescent developmental period. We used C57BL/6J male and female mice to investigate the long-lasting impact of binge ethanol exposure during adolescence on voluntary ethanol intake and open field behavior during later adolescence and in young adulthood. The present set of experiments were divided into four stages: (1) chronic intermittent vapor inhalation exposure, (2) abstinence, (3) voluntary ethanol intake, and (4) open field behavioral testing. During adolescence, male and female mice were exposed to air or ethanol using an intermittent vapor inhalation with repeated binge pattern ethanol exposure from postnatal day (PND) 28–42. Following this, mice underwent abstinence during late adolescence from PND 43–49 (Experiment 1) or PND 43–69 (Experiment 2). Beginning on PND 49–76 (Experiment 1) or PND 70–97 (Experiment 2), mice were assessed for intermittent voluntary ethanol consumption using a two-bottle drinking procedure over 28 days. Male mice that were exposed to ethanol during adolescence showed increased ethanol consumption during later adolescence (Experiment 1) and in emerging adulthood (Experiment 2), while the female mice showed decreased ethanol consumption. These data demonstrate a sexually divergent shift in ethanol consumption following binge ethanol exposure during adolescence and differences in open field behavior. These data highlight sex-dependent vulnerability to developing substance use disorders in adulthood.

Significance Statement

Currently, it is vital to determine the sex-dependent impact of binge alcohol exposure during adolescence, given that until recently females have largely been ignored. Here we show that adolescent male mice that are exposed to binge ethanol during adolescence show long-term changes in behavior in adulthood. In contrast, female mice show a transient decrease in ethanol consumption in adulthood and decreased motor activity spent in the center zone of the open field test. Male mice appear to be more susceptible to the long-term changes in ethanol consumption following binge ethanol exposure during adolescence.
The Past, Present and Future of Elephant Landscapes in Asia
Authors: de Silva Shermin , Wu Tiffany , Nyhus Philip , Thieme Alison , Weaver Ashley , Johnson Josiah , Wadey Jamie , Mossbrucker Alexander , Vu Thinh , Neang Thy , Chen Becky Shu , Songer Melissa , Leimgruber Peter
Published: April 2020

Habitat loss drives species’ declines worldwide, but is seldom quantified over centennial timescales. We constructed ecological niche models for Asian elephants based on land-use change between 850-2015, and predictions under six different climate/socioeconomic scenarios from 2015-2099. We find that over 64% of suitable natural habitat across diverse ecosystems was lost over the past three centuries. Average patch size dropped 83% from approximately 99,000 km2to 16,000 km2and the area occupied by the largest patch decreased 83% from ~ 4 million km2(45% of area) to 54,000 km2(~7.5% of area). Over half of current elephant range appears unsuitable. Habitat availability is predicted to decline further this century across all scenarios. The most severe losses occur under RCP3.4-SSP4, representing mid-range emissions but high regional inequities. We conclude that climate change mitigation measures must include policies to ensure inter-regional socioeconomic equity to safeguard landscapes for elephants, humans, and other species.
Baseline Resting-State Functional Connectivity Determines Subsequent Pain Ratings to a Tonic Ecologically Valid Experimental Model of Orofacial Pain
Authors: Ayoub Lizbeth J. , McAndrews Mary Pat , Barnett Alexander J. , Jeremy Ho Ka Chun , Cioffi Iacopo , Moayedi Massieh
Published: April 2020

Pain is a subjective experience with significant individual differences. Laboratory studies investigating pain thresholds and experimental acute pain have identified structural and functional neural correlates. However, these types of pain stimuli have limited ecological validity to real-life pain experiences. Here, we use an orthodontic procedure—the insertion of an elastomeric separator between teeth—which typically induces mild to moderate pain that peaks within 2 days and lasts several days. We aimed to determine whether the baseline structure and resting-state functional connectivity (rsFC) of key regions along the trigeminal nociceptive and pain modulatory pathways correlate with subsequent peak pain ratings. Twenty-six healthy individuals underwent structural and resting-state functional (rs-fMRI) scanning prior to the placement of a separator between the first and second molars, which was kept in place for five days. Participants recorded pain ratings three times daily on a 100-mm visual analogue scale. Peak pain was not significantly correlated with diffusion metrics of the trigeminal nerve, or grey matter volume of any brain region. Peak pain did, however, positively correlate with baseline rsFC between the thalamus contralateral to the separator and bilateral insula, and negatively correlated with connectivity between the periaqueductal gray (PAG) and core nodes of the default mode network (medial prefrontal and posterior cingulate cortices). The ascending (thalamic) nociceptive and the descending (PAG) pain modulatory pathways at baseline each explained unique variation in peak pain intensity ratings. In sum, pre-interventional functional neural architecture of both systems determined the individual pain experience to a subsequent ecologically valid pain stimulus.
Dopamine D2R upregulation in nucleus accumbens indirect pathway does not affect Pavlovian or Go/No-Go Learning
Authors: Martyniuk Kelly , Dandeneau Michelle , Balsam Peter , Kellendonk Christoph
Published: April 2020

Ventral striatal dopamine is thought to be important for associative learning. Dopamine exerts its role via activation of dopamine D1 and D2 receptors in the ventral striatum. Upregulation of dopamine D2R in the indirect pathway of the nucleus accumbens (NAc) impairs incentive motivation via inhibiting synaptic transmission to the ventral pallidum. Here, we determined whether upregulation of D2Rs and the resulting impairment in indirect pathway function modulates associative learning in an auditory Pavlovian reward learning task as well as Go/No-Go learning in an operant based reward driven Go/No-Go task. We found that upregulation of D2Rs in indirect pathway neurons of the NAc did not affect Pavlovian learning or the extinction of Pavlovian responses, and neither did it alter No-Go learning. A delay in the Go component of the task however could indicate a deficit in learning though it may be attributed to locomotor hyperactivity of the mice. In combination with previously published findings our data suggest that D2Rs in the NAc core play a specific role in regulating motivation by balancing cost/benefit computations but do not necessarily affect associative learning.
Social isolation stress in adolescence, but not adulthood, produces hypersocial behavior in adult male and female C57BL/6J mice
Authors: Rivera-Irizarry Jean K. , Skelly Mary Jane , Pleil Kristen E.
Published: April 2020

Chronic stress during the developmental period of adolescence increases susceptibility to many neuropsychiatric diseases in adulthood, including anxiety, affective, and alcohol/substance use disorders. Preclinical rodent models of adolescent stress have produced varying results that are species, strain, sex, and laboratory-dependent. However, adolescent social isolation is a potent stressor in humans that has been reliably modeled in male rats, increasing adult anxiety-like and alcohol drinking behaviors, among others. In this study, we examined the generalizability and sex-dependence of this model in C57BL/6J mice, the most commonly used rodent strain in neuroscience research. We also performed a parallel study using social isolation in adulthood to understand the impact of adult social isolation on basal behavioral phenotypes. We found that six weeks of social isolation in adolescence beginning at postnatal day (PD) 28 produced a hypersocial phenotype in both male and female adults in multiple assays and a female-specific anxiolytic phenotype in the elevated plus maze, but it had no effects in other assays for avoidance behavior, fear conditioning, alcohol drinking, reward or aversion sensitivity, novel object exploration, or forced swim behavior in either sex. In contrast, social isolation in adulthood beginning at PD77 produced an anxiogenic phenotype in the light/dark box but had no effects on any other assays. Altogether, our results suggest that 1) adolescence is a critical period for social stress in C57BL/6J mice, producing aberrant social behavior in a sex-independent manner and 2) chronic individual housing in adulthood does not alter basal behavioral phenotypes that may confound interpretation of behavior following other laboratory manipulations.
Glycocalyx-Mediated Vascular Dissemination of Circulating Tumor Cells
Authors: Offeddu Giovanni S. , Hajal Cynthia , Foley Colleen , Wan Zhengpeng , Ibrahim Lina , Coughlin Mark F. , Kamm Roger D.
Published: April 2020

The glycocalyx on tumor cells has been recently identified as an important driver for cancer progression, possibly providing critical opportunities for treatment. Metastasis, in particular, is often the limiting step in the survival to cancer, yet our understanding of how tumor cells escape the vascular system to initiate metastatic sites remains limited. Using anin vitromodel of the human microvasculature, we assess here the importance of the tumor and vascular glycocalyces during tumor cell extravasation. Through selective manipulation of individual components of the glycocalyx, we reveal a novel mechanism whereby tumor cells prepare an adhesive vascular niche by depositing components of the glycocalyx along the endothelium. Accumulated hyaluronic acid shed by tumor cells subsequently mediates adhesion to the endothelium via the glycoprotein CD44. Trans-endothelial migration and invasion into the stroma occurs through binding of the isoform CD44v to components of the sub-endothelial extra-cellular matrix. Targeting of the hyaluronic acid-CD44 glycocalyx complex results in significant reduction in the extravasation of tumor cells. These studies provide evidence of tumor cells repurposing the glycocalyx to promote adhesive interactions leading to cancer progression. Such glycocalyx-mediated mechanisms may be therapeutically targeted to hinder metastasis and improve patient survival.
Relative salience signaling within a thalamo-orbitofrontal circuit governs learning rate
Authors: Namboodiri Vijay Mohan K , Hobbs Taylor , Pisanty Ivan Trujillo , Simon Rhiana C , Gray Madelyn M , Stuber Garret D
Published: April 2020

Learning to predict rewards is essential for the sustained fitness of animals. Contemporary views suggest that such learning is driven by a reward prediction error (RPE) — the difference between received and predicted rewards. The magnitude of learning induced by an RPE is proportional to the product of the RPE and a learning rate. Here we demonstrate using two- photon calcium imaging and optogenetics in mice that certain functionally distinct subpopulations of ventral/medial orbitofrontal cortex (vmOFC) neurons signal learning rate control. Consistent with learning rate control, trial-by-trial fluctuations in vmOFC activity positively correlates with behavioral updating when RPE is positive, and negatively correlates with behavioral updating when RPE is negative. Learning rate is affected by many variables including the salience of a reward. We found that the average reward response of these neurons signals the relative salience of a reward, as it decreases after reward prediction learning or the introduction of another highly salient aversive stimulus. The relative salience signaling in vmOFC is sculpted by medial thalamic inputs. These results support emerging theoretical views that the prefrontal cortex encodes and controls learning parameters.
The TAT Protein Transduction Domain as an Intra-articular Drug-Delivery Technology
Authors: Mailhiot Sarah E. , Thompson Matthew A. , Eguchi Akiko E. , Dinkel Sabrina E. , Lotz Martin K. , Dowdy Steven F. , June Ronald K.
Published: April 2020

Objective

Intra-articular drug delivery holds great promise for the treatment of joint diseases such as osteoarthritis. The objective of this study was to evaluate the TAT peptide transduction domain (TAT-PTD) as a potential intra-articular drug delivery technology for synovial joints.

Design

Experiments examined the ability of TAT conjugates to associate with primary chondrocytes and alter cellular function bothin vitroandin vivo. Further experiments examined the ability of the TAT-PTD to bind to human osteoarthritic cartilage.

Results

The results show that the TAT-PTD associates with chondrocytes, is capable of delivering siRNA for chondrocyte gene knockdown, and that the recombinant enzyme TAT-Cre is capable of inducingin vivogenetic recombination within the knee joint in a reporter mouse model. Lastly, binding studies show that osteoarthritic cartilage preferentially uptakes the TAT-PTD from solution.

Conclusions

The results suggest that the TAT-PTD is a promising delivery strategy for intra-articular therapeutics.
Analyses of spike protein from first deposited sequences of SARS-CoV2 from West Bengal, India
Authors: Begum Feroza , Mukherjee Debica , Thagriki Dluya , Das Sandeepan , Tripathi Prem Prakash , Banerjee Arup Kumar , Ray Upasana
Published: April 2020

India has recently started sequencing SARS-CoV2 genome from clinical isolates. Currently only few sequences are available from three states in India. Kerala was the first state to deposit complete sequence from two isolates followed by one from Gujarat. On April 27, 2020, the first five sequences from the state of West Bengal (Eastern India) were deposited on ‘a global initiative on sharing avian flu data’ (GISAID) platform. In this paper we have analysed the spike protein sequences from all these five isolates and also compared for their similarities or differences with other sequences reported in India and with isolates of Wuhan origin. We report one unique mutation at position 723 and the other at 1124 in the S2 domain of spike protein of the isolates from West Bengal only and one mutation downstream of the receptor binding domain at position 614 in S1 domain which was common with the sequence from Gujarat (a state of western part of India). Mutation in the S2 domain showed changes in the secondary structure of the spike protein at region of mutation. We also studied molecular dynamics using normal mode analyses and found that this mutation decreases the flexibility of S2 domain. Since both S1 and S2 are important in receptor binding followed by entry in the host cells, such mutations may define the affinity or avidity of receptor binding.
Passenger-surface microbiome interactions in the subway of Mexico City
Authors: Vargas-Robles Daniela , Gonzalez-Cedillo Carolina , Hernandez Apolinar M. , Alcaraz Luis D. , Peimbert Mariana
Published: April 2020

Interaction between hands and the environment permits the interchange of microorganisms. The Mexico City subway is used daily by millions of passengers that get in contact with its surfaces. In this study, we used 16S rRNA gene sequencing to characterize the microbiomes of frequently touched surfaces, also comparing regular and women-only wagons. We also explored the effect of surface cleaning on microbial resettling. Finally, we studied passenger behavior and characterized microbial changes after traveling.

Most passengers (99%), showed some type of surface interaction during a wagon trip, mostly with the hands (92%). We found microbiome differences associated with surfaces, probably reflecting diverse surface materials and usage frequency. The platform floor was the most bacterial diverse surface, while the stair handrail and pole were the least diverse ones. After pole cleaning, the resettling of microbial diversity was fast (5-30 minutes); however, it did not resemble the initial composition.

After traveling, passengers significantly increased their hand microbial diversity and converged to a similar microbial composition among passengers. Additionally, passenger hand microbiomes resembled subway surfaces in diversity and also in the frequency of potentially pathogenic taxa. However, microbial fingerprints were preserved within passengers after traveling.
The phylogenetic functional conservation ofDrosophilaSeven-In-Absentia (SINA) E3 ligase and its two human paralogs, SIAH1 and SIAH2, inDrosophilaeye development
Authors: Van Sciver Robert E. , Cao Yajun , Tang Amy H.
Published: April 2020

Seven-IN-Absentia (SINA) is the most downstream signaling gatekeeper identified thus far in the RAS/EGFR pathway that controls photoreceptor cell fate determination inDrosophila. Underscoring the central importance of SINA is its phylogenetic conservation in metazoans, with over 83% amino acid identities shared betweenDrosophilaSINA and human SINA homologs (SIAHs). SIAH is a major tumor vulnerability in multidrug-resistant and incurable cancer. SIAH inhibition is an effective strategy to shut down the tumor-driving K-RAS/EGFR/HER2 pathway activation that promotes malignant tumor growth and metastatic dissemination. To further delineate the SINA function in the RAS/EGFR pathway, a genetic modifier screen was conducted, and 28 newsinamutant alleles were isolated via ethyl methanesulfonate (EMS) and X-ray mutagenesis. Among them, 26 of the newsinamutants are embryonic, larval, or pupal lethal, and stronger than the five publishedsinamutants (sina1,sina2,sina3,sina4, andsina5) which are early adult lethal. By sequencing the SINA-coding region ofsinaES10,sinaES26,sinaES79, andsinaES473homozygous mutant animals, we identified three invariable amino acid residues in SINA’s RING-domain whose single point mutation ablates SINA function. To demonstrate the functional conservation of this medically important family of RING domain E3 ligases inDrosophila, we established a collection of transgenic lines, expressing either wild type (WT) or proteolysis-deficient (PD) SINA/SIAH inhibitors ofDrosophilaSINAWT/PDand human SIAH1WT/PD/2WT/PDunder tissue-specific GAL4-drivers inDrosophilaeye, wing, and salary gland. Our results showed thatDrosophilaSINA and human SIAH1/2 are functionally conserved. Our bioengineered SINAPD/SIAHPDinhibitors are effective in blocking the RAS-dependent neuronal cell fate determination inDrosophila.
The SecA motor generates mechanical force during protein translocation
Authors: Gupta Riti , Toptygin Dmitri , Kaiser Christian M.
Published: April 2020

The Sec translocon moves proteins across lipid bilayers in all cells. The Sec channel enables passage of unfolded proteins through the bacterial plasma membrane, driven by the cytosolic ATPase SecA. Whether SecA generates mechanical force to overcome barriers to translocation posed by structured substrate proteins is unknown. Monitoring translocation of a folded substrate protein with tunable stability at high time resolution allowed us to kinetically dissect Secdependent translocation. We find that substrate unfolding constitutes the rate-limiting step during translocation. Using single-molecule force spectroscopy, we have also defined the response of the protein to mechanical force. Relating the kinetic and force measurements revealed that SecA generates at least 10 piconewtons of mechanical force to actively unfold translocating proteins, comparable to cellular unfoldases. Combining biochemical and single-molecule measurements has thus allowed us to define how the SecA motor ensures efficient and robust export of proteins that contain stable structure.
Downy Mildew effector HaRxL21 interacts with the transcriptional repressor TOPLESS to promote pathogen susceptibility
Authors: Harvey Sarah , Kumari Priyanka , Lapin Dmitry , Griebel Thomas , Hickman Richard , Guo Wenbin , Zhang Runxuan , Parker Jane , Beynon Jim , Denby Katherine , Steinbrenner Jens
Published: April 2020

Hyaloperonospora arabidopsidis (Hpa) is an oomycete pathogen causing Arabidopsis downy mildew. Effector proteins secreted from the pathogen into the plant play key roles in promoting infection by suppressing plant immunity and manipulating the host to the pathogen’s advantage. One class of oomycete effectors share a conserved ‘RxLR’ motif critical for their translocation into the host cell. Here we characterize the interaction between an RxLR effector, HaRxL21 (RxL21), and the Arabidopsis transcriptional co-repressor Topless (TPL). We establish that RxL21 and TPL interact via an EAR motif at the C-terminus of the effector, mimicking the host plant mechanism for recruiting TPL to sites of transcriptional repression. We show that this motif, and hence interaction with TPL, is necessary for the virulence function of the effector. Furthermore, we provide evidence that RxL21 uses the interaction with TPL, and its close relative TPL-related 1, to repress plant immunity and enhance host susceptibility to both biotrophic and necrotrophic pathogens.
Evaluation of 19 antiviral drugs against SARS-CoV-2 Infection
Authors: Liu Shufeng , Lien Christopher Z. , Selvaraj Prabhuanand , Wang Tony T.
Published: April 2020

The global pandemic of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 or 2019-nCoV) has prompted multiple clinical trials to jumpstart search for anti-SARS-CoV-2 therapies from existing drugs, including those with reportedin vitroefficacies as well as those ones that are not known to inhibit SARS-CoV-2, such as ritonavir/lopinavir and favilavir. Here we report that after screening 19 antiviral drugs that are either in clinical trials or with proposed activity against SARS-CoV-2, remdesivir was the most effective. Chloroquine only effectively protected virus-induced cytopathic effect at around 30 µM with a therapeutic index of 1.5. Our findings also suggest that velpatasvir, ledipasvir, ritonavir, litonavir, lopinavir, favilavir, sofosbuvir, danoprevir, and pocapavir do not have direct antiviral effect.