bluuebunny/crossref_metadata_2025 huggingface dataset:
Overcoming racism in the twin spheres of conservation science and practice
Authors: Rudd Lauren F. , Allred Shorna , Bright Ross Julius G. , Hare Darragh , Nkomo Merlyn Nomusa , Shanker Kartik , Allen Tanesha , Biggs Duan , Dickman Amy , Dunaway Michael , Ghosh Ritwick , González Nicole Thompson , Kepe Thembela , Mbizah Moreangels M. , Middleton Sara L. , Oommen Meera Anna , Paudel Kumar , Sillero-Zubiri Claudio , Dávalos Andrea
Published: November 2021

It is time to acknowledge and overcome conservation's deep-seated systemic racism, which has historically marginalized Black, Indigenous and people of colour (BIPOC) communities and continues to do so. We describe how the mutually reinforcing ‘twin spheres’ of conservation science and conservation practice perpetuate this systemic racism. We trace how institutional structures in conservation science (e.g. degree programmes, support and advancement opportunities, course syllabuses) can systematically produce conservation graduates with partial and problematic conceptions of conservation's history and contemporary purposes. Many of these graduates go on to work in conservation practice, reproducing conservation's colonial history by contributing to programmes based on outmoded conservation models that disproportionately harm rural BIPOC communities and further restrict access and inclusion for BIPOC conservationists. We provide practical, actionable proposals for breaking vicious cycles of racism in the system of conservation we have with virtuous cycles of inclusion, equality, equity and participation in the system of conservation we want.
Late Ediacaran life on land: desiccated microbial mats and large biofilm streamers
Authors: McMahon S. , Matthews J. J. , Brasier A. , Still J.
Published: November 2021

The Ediacaran period witnessed transformational change across the Earth–life system, but life on land during this interval is poorly understood. Non-marine/transitional Ediacaran sediments preserve a variety of probable microbially induced sedimentary structures and fossil matgrounds, and the ecology, biogeochemistry and sedimentological impacts of the organisms responsible are now ripe for investigation. Here, we report well-preserved fossils from emergent siliciclastic depositional environments in the Ediacaran of Newfoundland, Canada. These include exquisite, mouldically preserved microbial mats with desiccation cracks and flip-overs, abundantArumberia-type fossils and, most notably, assemblages of centimetre-to-metre-scale, subparallel, branching, overlapping, gently curving ribbon-like features preserved by aluminosilicate and phosphate minerals, with associated filamentous microfossils. We present morphological, petrographic and taphonomic evidence that the ribbons are best interpreted as fossilized current-induced biofilm streamers, the earliest record of an important mode of life (macroscopic streamer formation) for terrestrial microbial ecosystems today. Their presence shows that late Ediacaran terrestrial environments could produce substantial biomass, and supports recent interpretations ofArumberiaas a current-influenced microbial mat fossil, which we here suggest existed on a ‘streamer–arumberiamorph spectrum’. Finally, the absence of classic Ediacaran macrobiota from these rocks despite evidently favourable conditions for soft tissue preservation upholds the consensus that those organisms were exclusively marine.
Variimorphobacter saccharofermentans gen. nov., sp. nov., a new member of the family Lachnospiraceae, isolated from a maize-fed biogas fermenter
Authors: Rettenmaier Regina , Thieme Nils , Streubel Johanna , Di Bello Luca , Kowollik Marie-Louise , Huang Liren , Maus Irena , Klingl Andreas , Liebl Wolfgang , Zverlov Vladimir V.
Published: November 2021

Strain MD1T is an anaerobic, Gram-stain-negative bacterium isolated from a lab-scale biogas fermenter fed with maize silage. It has a rod-shaped morphology with peritrichously arranged appendages and forms long chains of cells and coccoid structures. The colonies of MD1T were white, circular, slightly convex and had a smooth rim. The isolate is mesophilic, displaying growth between 25 and 45 °C with an optimum at 40 °C. It grew at pH values of pH 6.7–8.2 (optimum, pH 7.1) and tolerated the addition of up to 1.5% (w/v) NaCl to the medium. The main cellular fatty acids of MD1T are C14:0 DMA and C16:0. Strain MD1T fermented xylose, arabinose, glucose, galactose, cellobiose, maltose, maltodextrin10, lactose starch, and xylan, producing mainly 2-propanol and acetic acid. The genome of the organism has a total length of 4163427 bp with a G+C content of 38.5 mol%. The two closest relatives to MD1T are

Mobilitalea sibirica

P3M-3T and

Anaerotaenia torta

FH052T with 96.44 or 95.8 % 16S rRNA gene sequence similarity and POCP values of 46.58 and 50.58%, respectively. As MD1T showed saccharolytic and xylanolytic properties, it may play an important role in the biogas fermentation process. Closely related variants of MD1T were also abundant in microbial communities involved in methanogenic fermentation. Based on morphological, phylogenetic and genomic data, the isolated strain can be considered as representing a novel genus in the family

Lachnospiraceae

, for which the name Variimorphobacter saccharofermentans gen. nov., sp. nov. (type strain MD1T=DSM 110715T=JCM 39125T) is proposed.
A Retrospective Cohort Study of COVID-19 among Children in Fulton County, Georgia, March 2020 - June 2021
Authors: Barrera Chloe M. , Hazell Mallory , Chamberlain Allison T. , Gandhi Neel R. , Onwubiko Udodirim , Liu Carol Y. , Prieto Juliana , Khan Fazle , Shah Sarita
Published: November 2021

Objective

To describe case rates, testing rates, and percent positivity of coronavirus disease 2019 (COVID-19) among children aged 0-18 years by school-age grouping.

Design

We abstracted data from Georgia’s State Electronic Notifiable Disease Surveillance System on all 10,437 laboratory-confirmed COVID-19 cases among children aged 0-18 years during March 30, 2020 to June 6, 2021. We examined case rates, testing rates, and percent positivity by school-aged groupings, namely: preschool (0-4 years), elementary school (5-10 years), middle school (11-13 years), and high school (14-18 years) and compared these data among school aged children to those in the adult population (19 years and older).

Setting

Fulton County, Georgia.

Main outcome measures

COVID-19 case rates, testing rates, and percent positivity.

Results

Over time, the proportion of pediatric cases rose substantially from 1.1% (April 2020) to 21.6% (April 2021) of all cases in the county. Age-specific case rates and test rates were consistently highest among high-school aged children. Test positivity was similar across school-age groups, with periods of higher positivity among high-school aged children.

Conclusions

Low COVID-19 testing rates among children, especially early in the pandemic, likely underestimate the true burden of disease in this age group. Despite children having lower measured incidence of COVID-19, we found when broader community incidence increased, incidence also increased among all pediatric age groups. As the COVID-19 pandemic continues to evolve, it remains critical to continue learning about the incidence and transmissibility of COVID-19 in children.
A new tripartite landmark in posterior cingulate cortex
Authors: Willbrand Ethan H. , Parker Benjamin J. , Voorhies Willa I. , Miller Jacob A. , Lyu Ilwoo , Hallock Tyler , Aponik-Gremillion Lyndsey ,   Alzheimer’s Disease Neuroimaging Initiative, Bunge Silvia A. , Foster Brett L. , Weiner Kevin S.
Published: November 2021

Understanding brain structure-function relationships, and their development and evolution, is central to neuroscience research. Here, we show that morphological differences in posterior cingulate cortex (PCC), a hub of functional brain networks, predict individual differences in macroanatomical, microstructural, and functional features of PCC. Manually labeling 4,319 sulci in 552 hemispheres, we discovered a consistently localized shallow cortical indentation (termed the inframarginal sulcus; ifrms) within PCC that is absent from neuroanatomical atlases, yet co-localized with a region within the cognitive control, but not default mode, network. Morphological analyses in humans and chimpanzees showed that unique properties of the ifrms differ across the lifespan and between hominoid species. Intriguingly, the consistency of the ifrms also debunks the uniqueness of the morphology of Einstein’s PCC. These findings support a classic theory that shallow, tertiary sulci serve as landmarks in association cortices. They also beg the question: how many other cortical indentations have we missed?
Configuring a federated network of real-world patient health data for multimodal deep learning prediction of health outcomes
Authors: Haudenschild Christian , Vaickus Louis , Levy Joshua
Published: November 2021

Vast quantities of electronic patient medical data are currently being collated and processed in large federated data repositories. For instance, TriNetX, Inc., a global health research network, has access to more than 300 million patients, sourced from healthcare organizations, biopharmaceutical companies, and contract research organizations. As such, pipelines that are able to algorithmically extract huge quantities of patient data from multiple modalities present opportunities to leverage machine learning and deep learning approaches with the possibility of generating actionable insight. In this work, we present a modular, semi-automated end-to-end machine and deep learning pipeline designed to interface with a federated network of structured patient data. This proof-of-concept pipeline is disease-agnostic, scalable, and requires little domain expertise and manual feature engineering in order to quickly produce results for the case of a user-defined binary outcome event. We demonstrate the pipeline’s efficacy with three different disease workflows, with high discriminatory power achieved in all cases.
Wildlife is imperiled in peri-urban landscapes: threats to arboreal mammals
Authors: Chaves Oscar M. M , Júnior Júlio Souza , Buss Gerson , Hirano Zelinda MB , Jardim Marcia , Amaral Erica , Godoy João , Peruchi Amanda , Michel Thais , Bicca-Marques Júlio César
Published: November 2021

Urbanization and deforestation impose severe challenges to wildlife, particularly for forest-living vertebrates. Understanding how the peri-urban matrix impacts their survival is critical for designing strategies to promote their conservation. We investigated the threats faced by brown howler monkeys (Alouatta guariba clamitans) in peri-urban regions of Rio Grande do Sul (RS) and Santa Catarina (SC) states, southern Brazil, by compiling negative interaction events (hereafter NIE) reported over more than two decades. We assessed the major NIEs, their distribution among age-sex classes, and the predictors of NIE-related mortality. After 20+ years of monitoring, we compiled 540 NIEs (RS = 248 and SC = 292). Electrocution by power lines was the most frequent cause of death or injury (37%), followed by dog attack (34%), vehicle collision (17%), and human mistreatment (12%). The occurrence of lethal injuries ranged from 5% to 69% depending on the type of NIE and on which state it occurred in. The overall post-NIE mortality was 56%. Adults of both sexes were the most affected individuals in both study regions. The minimal adequate GLM model explained 83% of the variation in NIE-related mortality. State, NIE type, and age-sex class were the main predictors of mortality. Overall, mortality was lower in SC and higher among adult females than in the other classes. We found that the survival of brown howler monkeys in the forest-urban interface is constrained by both the urban infrastructure and the growing interactions with humans and domestic and stray dogs (Canis familiaris). We propose the placement of aerial bridges, road signs and speed bumps in areas of frequent animal crossing, the sterilization of stray dogs, and the sensitization of local inhabitants on the importance of respecting and protecting wildlife to reduce their NIEs with humans and domestic animals in the forest-urban interface.
Chronic Cochlear Implantation with and without Electric Stimulation in a Mouse Model Induces Robust Cochlear Influx of CX3CR1+/GFP Macrophages
Authors: Claussen Alexander D. , Quevedo René Vielman , Higgins Timon , Mostaert Brian , Rahman Muhammad Taifur , Kirk Jonathon , Hirose Keiko , Hansen Marlan R.
Published: November 2021

Background

Cochlear implantation is an effective auditory rehabilitation strategy for those with profound hearing loss, including those with residual low frequency hearing through use of hybrid cochlear implantation techniques. Post-mortem studies demonstrate the nearly ubiquitous presence of intracochlear fibrosis and neo-ossification following cochlear implantation. Current evidence suggests post-implantation intracochlear fibrosis is associated with delayed loss of residual acoustic hearing in hybrid cochlear implant (CI) recipients and may also negatively influence outcomes in traditional CI recipients. This study examined the contributions of surgical trauma, foreign body response and electric stimulation to intracochlear fibrosis and the innate immune response to cochlear implantation and the hierarchy of these contributions.

Methods

Normal hearing CX3CR1+/GFP mice underwent either round window opening (sham), acute CI insertion or chronic CI insertion with no, low- or high-level electric stimulation. Electric stimulation levels were based on neural response telemetry (NRT), beginning post-operative day 7 for 4 hours per day. Subjects (n=3 per timepoint) were sacrificed at 4 hours, 1,4,7,8,11,14 and 21 days. An unimplanted group (n=3) served as controls. Cochleae were harvested at each time-point and prepared for immunohistochemistry with confocal imaging. The images were analyzed to obtain CX3CR1+ macrophage cell number and density in the lateral wall (LW), scala tympani (ST) and Rosenthal’s canal (RC).

Results

A ST peri-implant cellular infiltrate and fibrosis occurred exclusively in the chronically implanted groups starting on day 7 with a concurrent infiltration of CX3CR1+ macrophages not seen in the other groups. CX3CR1+ macrophage infiltration was seen in the LW and RC in all experimental groups within the first week, being most prominent in the 3 chronically implanted groups during the second and third week. There were no significant differences in macrophage infiltration related to levels of electric stimulation.

Conclusions

The cochlear immune response was most prominent in the presence of chronic cochlear implantation, regardless of electric stimulation level. Further, the development of intracochlear ST fibrosis was dependent on the presence of the indwelling CI foreign body. An innate immune response was evoked by surgical trauma alone (sham and acute CI groups) to a lesser degree. These data suggest that cochlear inflammation and intrascalar fibrosis after cochlear implantation are largely dependent on the presence of a chronic indwelling foreign body and are not critically dependent on electrical stimulation. Also, these data support a role for surgical trauma in inciting the initial innate immune response.
Identifying metabolic adaptations during cardiotoxicity using paired transcriptomics and metabolomics data integrated with a model of heart metabolism
Authors: Dougherty Bonnie V. , Rawls Kristopher D. , Jenior Matthew L. , Chun Bryan , Nagdas Sarbajeet , Saucerman Jeffrey J. , Kolling Glynis L. , Wallqvist Anders , Papin Jason A.
Published: November 2021

Improvements in the diagnosis and treatment of cancer has revealed the long-term side effects of chemotherapeutics, particularly cardiotoxicity. Here, we present paired transcriptomics and metabolomics data characterizing in vitro cardiotoxicity to three compounds: 5-fluorouracil, acetaminophen, and doxorubicin. Standard gene enrichment and metabolomics approaches identify some commonly affected pathways and metabolites but are not able to readily identify metabolic adaptations in response to cardiotoxicity. The paired data was integrated with a genome-scale metabolic network reconstruction (GENRE) of the heart to identify shifted metabolic functions, unique metabolic reactions, and changes in flux in metabolic reactions in response to these compounds. Using this approach, we confirm known mechanisms of doxorubicin-induced cardiotoxicity and provide hypotheses for metabolic adaptations in cardiotoxicity for 5-fluorouracil, doxorubicin, and acetaminophen.
Postmitotic accumulation of histone variant H3.3 in new cortical neurons establishes neuronal chromatin, transcriptome, and identity
Authors: Funk Owen H. , Qalieh Yaman , Doyle Daniel Z. , Lam Mandy M. , Kwan Kenneth Y.
Published: November 2021

Histone variants, which can be expressed outside of S-phase and deposited DNA synthesis-independently, provide long-term histone replacement in postmitotic cells, including neurons. Beyond replenishment, histone variants also play active roles in gene regulation by modulating chromatin states or enabling nucleosome turnover. Here, we uncover crucial roles for the histone H3 variant H3.3 in neuronal development. We find that newborn cortical excitatory neurons, which have only just completed replication-coupled deposition of canonical H3.1 and H3.2, substantially accumulate H3.3 immediately post mitosis. Co-deletion of H3.3-encoding genes H3f3a and H3f3b from newly postmitotic neurons abrogates H3.3 accumulation, markedly alters the histone posttranslational modification (PTM) landscape, and causes widespread disruptions to the establishment of the neuronal transcriptome. These changes coincide with developmental phenotypes in neuronal identities and axon projections. Thus, preexisting, replication-dependent histones are insufficient for establishing neuronal chromatin and transcriptome; de novo H3.3 is required. Stage-dependent deletion of H3f3a and H3f3b from (1) cycling neural progenitor cells, (2) neurons immediately post mitosis, or (3) several days later, reveals the first postmitotic days to be a critical window for de novo H3.3. After H3.3 accumulation within this developmental window, co-deletion of H3f3a and H3f3b does not lead to immediate H3.3 loss, but causes progressive H3.3 depletion over several months without widespread transcriptional disruptions or cellular phenotypes. Our study thus uncovers key developmental roles for de novo H3.3 in establishing neuronal chromatin, transcriptome, identity, and connectivity immediately post mitosis that are distinct from its role in maintaining total histone H3 levels over the neuronal lifespan.

Significance

DNA is packaged around histones into chromatin, which compacts the genome, but also restricts access to DNA. Gene transcription thus requires chromatin reorganization that is precisely regulated, including via variant forms of histones. Here, we find that during a critical developmental window for establishing postmitotic neuronal identity, newly generated cortical excitatory neurons substantially accumulate the histone H3 variant H3.3. Conditional deletion of H3.3-encoding genes from new neurons abrogates de novo H3.3 accumulation, and broadly disrupts neuronal histone modifications, gene expression, subtype identity, and axon projections. Thus, preexisting H3 histones are insufficient for establishing neuronal chromatin and transcriptome; de novo H3.3 is essential. This developmental requirement for H3.3 is distinct from H3.3 contribution to long-term maintenance of histones in mature neurons.
More than a feeling: scalp EEG and eye correlates of conscious tactile perception
Authors: Gusso Mariana M. , Christison-Lagay Kate L. , Zuckerman David , Chandrasekaran Ganesh , Kronemer Sharif I. , Ding Julia Z. , Freedman Noah C. , Nohama Percy , Blumenfeld Hal
Published: November 2021

Understanding the neural basis of consciousness is a fundamental goal of neuroscience. Many of the studies tackling this question have focused on conscious perception, but these studies have been largely vision-centric, with very few involving tactile perception. Therefore, we developed a novel tactile threshold perception task, which we used in conjunction with high-density scalp electroencephalography and eye-metric recordings. Participants were delivered threshold-level vibrations to one of the four non-thumb fingers, and were asked to report their perception using a response box. With false discovery rate (FDR) mass univariate analysis procedures, we found significant event-related potentials (ERP) including bilateral N140 and P300 for perceived vibrations; significant bilateral P100 and P300 were found following vibrations that were not perceived. Significant differences between perceived and not perceived trials were found bilaterally in the N140 and P300. Additionally, we found that pupil diameter and blink rate increased and that microsaccade rate decreased following vibrations that were perceived relative to those that were not perceived. While many of the signals are consistent with similar ERP-findings across sensory modalities, our results indicating a significant P300 in not perceived trials raise more questions regarding P300’s perceptual meaning. Additionally, our findings support the use of eye metrics as a measure of physiological arousal as pertains to conscious perception, and may represent a novel path toward the creation of tactile no-report tasks in the future.

Abstract Figure

Highlights

A novel tactile perceptual threshold task yields robust behavioral results

Event-related potentials differ according to perception status

P300 is observed in both perceived and not perceived trials

Blink rate, pupil diameter, and microsaccades differ across trial conditions
Evolution of warfare by resource raiding favors polymorphism in belligerence and bravery
Authors: Mullon Charles , Lehmann Laurent
Published: November 2021

From protists to primates, intergroup aggression and warfare over resources has been observed in several taxa whose populations typically consist of groups connected by limited genetic mixing. Here, we model the co-evolution between four traits relevant to this setting: (i) investment into common-pool resource production within groups (“helping”); (ii) proclivity to raid other groups to appropriate their resources (“bel-ligerence”); and investments into (iii) defense and (iv) offense of group contests (“defensive and offensive bravery”). We show that when traits co-evolve, the population often experiences disruptive selection favouring two morphs: “Hawks”, who express high levels of both belligerence and offensive bravery; and “Doves”, who express neither. This social polymorphism involves further among-traits associations when the fitness costs of helping and bravery interact. In particular if helping is antagonistic with both forms of bravery, co-evolution leads to the coexistence of individuals that either: (i) do not participate into common-pool resource production but only in its defense and appropriation (“Scrounger Hawks”); or (ii) only invest into common pool resource production (“Producer Doves”). Provided groups are not randomly mixed, these findings are robust to several modelling assumptions. This suggests that inter-group aggression is a potent mechanism in favoring within-group social diversity and behavioural syndromes.
Interfering with contextual fear memories by post-reactivation administration of propranolol in mice: a series of null findings
Authors: Cox Wouter R. , Faliagkas Leonidas , Besseling Amber , van der Loo Rolinka J. , Spijker Sabine , Kindt Merel , Rao-Ruiz Priyanka
Published: November 2021

Post-reactivation amnesia of contextual fear memories by blockade of noradrenergic signaling has been shown to have limited replicability in rodents. This is usually attributed to several boundary conditions that gate the destabilization of memory during its retrieval. How these boundary conditions can be overcome, and what neural mechanisms underlie post-reactivation changes in contextual fear memories remain largely unknown. Here, we report a series of experiments in a contextual fear-conditioning paradigm in mice, that were aimed at solving these issues. We first attempted to obtain a training paradigm that would consistently result in contextual fear memory that could be destabilized upon reactivation, enabling post-retrieval amnesia by administration of propranolol. Unexpectedly, our attempts were unsuccessful to this end. Specifically, over a series of experiments in which we varied different parameters of the fear acquisition procedure, at best small and inconsistent effects were observed. Additionally, we found that propranolol did not alter retrieval-induced neural activity, as measured by the number of c-Fos+ cells in the hippocampal dentate gyrus. To determine whether propranolol was perhaps ineffective in interfering with reactivated contextual fear memories, we also included anisomycin (i.e., a potent and well-known amnesic drug) in several experiments, and measures of synaptic glutamate receptor subunit GluA2 (i.e., a marker of memory destabilization). No post-retrieval amnesia by anisomycin and no altered GluA2 expression by reactivation was observed, suggesting that the memories did not undergo destabilization. The null findings are surprising, given that the training paradigms we implemented were previously shown to result in memories that could be modified upon reactivation. Together, our observations illustrate the elusive nature of reactivation-dependent changes of non-human fear memory.
Platelet generation from circulating megakaryocytes is triggered in the lung vasculature
Authors: Zhao Xiaojuan , Alibhai Dominic , Walsh Tony G. , Tarassova Nathalie , Birol Semra Z. , Williams Christopher M. , Neil Chris R. , Aitken Elizabeth W. , Waller Amie K. , Ballester-Beltran Jose , Gunning Peter W. , Hardeman Edna C. , Agbani Ejaife O. , Hers Ingeborg , Ghevaert Cedric , Poole Alastair W.
Published: November 2021

Platelets, small hemostatic blood cells, are derived from megakaryocytes, although the generation process is not clear. Only small numbers of platelets have been produced in systems outside the body, where bone marrow and lung are proposed as sites of platelet generation. Here we show that perfusion of megakaryocytes ex vivo through the mouse lung vasculature generates very large numbers of platelets, up to 3,000 per megakaryocyte. Despite their large size, megakaryocytes were able repeatedly to passage through the lung vasculature, leading to enucleation and fragmentation to generate platelets intravascularly. Using the ex vivo lung and a novel in vitro microfluidic chamber we determined the contributions of oxygenation, ventilation and endothelial cell health to platelet generation, and showed a critical role for the actin regulator TPM4.

One-Sentence Summary

Megakaryocytes form platelets intravascularly in the lung, dependent upon oxygenation, endothelium and megakaryocyte TPM4
Task-independent acute effects of delta-9-tetrahydrocannabinol on human brain function and its relationship with cannabinoid receptor gene expression: a neuroimaging meta-regression analysis
Authors: Gunasekera Brandon , Davies Cathy , Blest-Hopley Grace , Veronese Mattia , Ramsey Nick F. , Bossong Matthijs G. , Radua Joaquim , Bhattacharyya Sagnik ,   CBE Consortium
Published: November 2021

Background

The neurobiological mechanisms underlying the effects of delta-9-tetrahydrocannabinol (THC) remain unclear. Here, we examined the spatial acute effect of THC on human on regional brain activation or blood flow (hereafter called ‘activation signal’) in a ‘core’ network of brain regions that subserve a multitude of processes. We also investigated whether the neuromodulatory effects of THC are related to the local expression of its key molecular target, cannabinoid-type-1 (CB1R) but not type-2 (CB2R) receptor.

Methods

A systematic search was conducted of acute THC-challenge studies using fMRI, PET, and arterial spin labelling in accordance with established guidelines. Using pooled summary data from 372 participants, tested using a within-subject repeated measures design under experimental conditions, we investigated the effects of a single dose (6-42mg) of THC, compared to placebo, on brain signal.

Findings

As predicted, THC augmented the activation signal, relative to placebo, in the anterior cingulate, superior frontal cortices, middle temporal and middle and inferior occipital gyri, striatum, amygdala, thalamus, and cerebellum crus II and attenuated it in the middle temporal gyrus (spatially distinct from the cluster with THC-induced increase in activation signal), superior temporal gyrus, angular gyrus, precuneus, cuneus, inferior parietal lobule, and the cerebellum lobule IV/V. Using post-mortem gene expression data from an independent cohort from the Allen Human Brain atlas, we found a direct relationship between the magnitude of THC-induced brain signal change, indexed using pooled effect-size estimates, and CB1R gene expression, a proxy measure of CB1R protein distribution, but not CB2R expression. A dose-response relationship was observed with THC dose in certain brain regions.

Interpretation

These meta-analytic findings shed new light on the localisation of the effects of THC in the human brain, suggesting that THC has neuromodulatory effects in regions central to many cognitive tasks and processes, with greater effects in regions with higher levels of CB1R expression.
Initial efficacy determination and resistance profile of anti-Acinetobacter antibiotics, turnercyclamycins
Authors: Miller Bailey W. , Lim Albebson L. , Haygood Margo G. , Schmidt Eric W.
Published: November 2021

Drug-resistant Acinetobacter is a challenging, deadly pathogen of increasing prevalence in the US healthcare system. Recently, we described a series of lipopeptides, the turnercyclamycins, which retain potency against Acinetobacter strains that are resistant to the last-line antibiotic, colistin. To further evaluate the potential of turnercyclamycins, we completed mouse efficacy, pharmacokinetics, and toxicity studies. These demonstrate that turnercyclamycin A has a pharmacological profile with similarity to other lipopeptides that are in clinical use. Turnercyclamycin A was well tolerated in mice up to 25 mg/kg, and exhibited >99% and >98% reduction in bacterial load compared to vehicle control in a thigh infection model at 25 and 12.5 mg/kg, respectively. This result closely reflected the anticipated effectiveness based upon in vitro activity and was similar to the colistin control. Acinetobacter strains resistant to colistin often harbor the mcr-1 resistance gene. Here, we show that the effectiveness of turnercyclamycins against Escherichia coli is not greatly altered by mcr-1 (0- to 2-fold) whereas there is a 16-fold increase in the colistin minimal inhibitory concentration when mcr-1 is present. These data suggest that turnercyclamycins are suitable for further investigation and optimization as anti-Acinetobacter lead compounds.
A powerful and versatile new fixation protocol for immunohistology and in situ hybridization that preserves delicate tissues in planaria
Authors: Guerrero-Hernández Carlos , Doddihal Viraj , Mann Frederick G. , Alvarado Alejandro Sánchez
Published: November 2021

Whole-mount in situ hybridization (WISH) is a powerful and widely used technique to visualize the expression pattern of genes in different biological systems. Here we describe a new protocol for ISH and immunostaining in the planarian Schmidtea mediterranea. The new Nitric Acid/Formic Acid (NAFA) protocol is compatible with both assays and prevents degradation of the epidermis or blastema. Instead of proteinase K digestion, formic acid treatment is used to permeabilize tissues and preserve antigen epitopes. We show that the NAFA protocol successfully permits development of chromogenic and fluorescent signals in situ, while preserving the anatomy of the animal. Further, the immunostaining of different proteins was compatible with the NAFA protocol following fluorescent in situ hybridization. Finally, we demonstrate with high resolution confocal imaging that the regeneration blastema is preserved when using the new method. This new NAFA protocol will be a valuable technique to study the process of wounding response and regeneration.
Glycan-masking spike antigen in NTD and RBD elicits broadly neutralizing antibodies against SARS-CoV-2 variants
Authors: Lin Wei-Shuo , Chen I-Chen , Chen Hui-Chen , Lee Yi-Chien , Wu Suh-Chin
Published: November 2021

Glycan-masking the vaccine antigen by mutating the undesired antigenic sites with an additional N-linked glycosylation motif can refocus B-cell responses to desired/undesired epitopes, without affecting the antigen’s overall-folded structure. This study examine the impact of glycan-masking mutants of the N-terminal domain (NTD) and receptor-binding domain (RBD) of SARS-CoV-2, and found that the antigenic design of the S protein increases the neutralizing antibody titers against the Wuhan-Hu-1 ancestral strain and the recently emerged SARS-CoV-2 variants Alpha (B.1.1.7), Beta (B.1.351), and Delta (B.1.617.2). Our results demonstrated that the use of glycan-masking Ad-S-R158N/Y160T in the NTD elicited a 2.8-fold, 6.5-fold, and 4.6-fold increase in the IC-50 NT titer against the Alpha (B.1.1.7), Beta (B.1.351) and Delta (B.1.617.2) variants, respectively. Glycan-masking of Ad-S-D428N in the RBD resulted in a 3.0-fold and 2.0-fold increase in the IC50 neutralization titer against the Alpha (B.1.1.7) and Beta (B.1.351) variants, respectively. The use of glycan-masking in Ad-S-R158N/Y160T and Ad-S-D428N antigen design may help develop universal COVID-19 vaccines against current and future emerging SARS-CoV-2 variants.
A critical role for E2-p53 interaction during the HPV16 life cycle
Authors: Fontan Christian T. , James Claire D. , Bristol Molly L. , Prabhakar Apurva T. , Otoa Raymonde , Wang Xu , Karimi Elmira , Rajagopalan Pavithra , Basu Devraj , Morgan Iain M.
Published: November 2021

Human papillomaviruses (HPV) are causative agents in ano-genital and oral cancers; HPV16 is the most prevalent type detected in human cancers. The HPV16 E6 protein targets p53 for proteasomal degradation to facilitate proliferation of the HPV16 infected cell. However, in HPV16 immortalized cells E6 is predominantly spliced (E6*) and unable to degrade p53. Here we demonstrate that human foreskin keratinocytes immortalized by HPV16 (HFK+HPV16), and HPV16 positive oropharyngeal cancers, retain significant expression of p53. In addition, p53 levels can be increased in HPV16+ head and neck cancer cell lines following treatment with cisplatin. Introduction of full-length E6 into HFK+HPV16 resulted in attenuation of cellular growth (in hTERT immortalized HFK, E6 expression promoted enhanced proliferation). An understudied interaction is that between E2 and p53 and we investigated whether this was important for the viral life cycle. We generated mutant genomes with E2 unable to interact with p53 resulting in profound phenotypes in primary HFK. The mutant induced hyper-proliferation, but an ultimate arrest of cell growth; β-galactosidase staining demonstrated increased senescence, and COMET assays showed increased DNA damage compared with HFK+HPV16 wild type cells. There was failure of the viral life cycle in organotypic rafts with the mutant HFK resulting in premature differentiation and reduced proliferation. The results indicate that the E2-p53 interaction is critical during the HPV16 life cycle, and that disruption of this interaction has anti-viral potential. We discuss potential mechanisms to explain these phenotypes.

Importance

Human papillomaviruses are causative agents in around 5% of all cancers. There are currently no antivirals available to combat these infections and cancers, therefore it remains a priority to enhance our understanding of the HPV life cycle. Here we demonstrate that an interaction between the viral replication/transcription/segregation factor E2 and the tumor suppressor p53 is critical for the HPV16 life cycle. HPV16 immortalized cells retain significant expression of p53, and the critical role for the E2-p53 interaction demonstrates why this is the case. If the E2-p53 interaction is disrupted then HPV16 immortalized cells fail to proliferate, have enhanced DNA damage and senescence, and there is premature differentiation during the viral life cycle. Results suggest that targeting the E2-p53 interaction would have therapeutic benefits, potentially attenuating the spread of HPV16.
Powerful synergistic effects of a STING agonist and an IL-2 superkine in cancer immunotherapy against MHC I-deficient and MHC I+ tumors
Authors: Wolf Natalie , Blaj Cristina , Picton Lora , Snyder Gail , Zhang Li , Nicolai Christopher J. , Ndubaku Chudi O. , McWhirter Sarah M. , Garcia K. Christopher , Raulet David H.
Published: November 2021

Cyclic dinucleotides (CDNs) and TLR ligands mobilize antitumor responses by NK cells and T cells, potentially serving as complementary therapies to immune checkpoint therapy. In the clinic thus far, however, CDN therapy has yielded mixed results, perhaps because it initiates responses potently, but does not provide signals to sustain activation and proliferation of activated cytotoxic lymphocytes. To improve efficacy, we combined CDNs with a half-life extended IL-2 superkine, H9-MSA. CDN/H9-MSA therapy induced dramatic long-term remissions of the most difficult-to-treat MHC I-deficient and MHC I+ tumor transplant models. H9-MSA combined with CpG oligonucleotide also induced potent responses. Mechanistically, tumor elimination required CD8 T cells and not NK cells in the case of MHC I+ tumors and NK cells but not CD8 T cells in the case of MHC-deficient tumors. Furthermore, combination therapy resulted in more prolonged and more intense NK cell activation, cytotoxicity and expression of cytotoxic effector molecules in comparison to monotherapy. Remarkably, in a primary autochthonous sarcoma model that is refractory to PD-1 checkpoint therapy, the combination of CDN/H9-MSA combined with checkpoint therapy yielded long-term remissions in the majority of animals, mediated by T cells and NK cells. This novel combination therapy has potential to activate responses in tumors resistant to current therapies and prevent MHC I-loss accompanying acquired resistance of tumors to checkpoint therapy.

One sentence summary

Powerful immunotherapy effects mediated by the combination of innate agonists and superkine.
A deep exon cryptic splice site promotes aberrant intron retention in a von Willebrand disease patient
Authors: Conboy John G.
Published: November 2021

A translationally silent single nucleotide mutation, in exon 44 of the von Willebrand factor (VWF) gene, is associated with inefficient removal of intron 44 in a von Willebrand disease (VWD) patient. This intron retention (IR) event was previously attributed to altered secondary structure that sequesters the normal splice donor site. We propose an alternative mechanism: that the mutation introduces a cryptic splice donor site that interferes with function of the annotated site to favor IR. We evaluated both models using minigene splicing reporters engineered to vary in secondary structure and/or cryptic splice site content. Analysis of reporter splicing efficiency in transfected K562 cells suggested that the mutation-generated internal splice site was sufficient to induce substantial IR. Mutations predicted to vary secondary structure at the annotated site had modest effects on IR, and also shifted the balance of residual splicing between the cryptic site and annotated site, supporting competition between the sites. Further studies demonstrated that introduction of cryptic splice donor motifs at other positions in E44 did not promote IR, indicating that interference with the annotated site is context-dependent. We conclude that mutant deep exon splice sites can interfere with proper splicing by inducing IR.
A gradient of electrophysiological novelty responses along the human hippocampal long axis
Authors: Yebra Mar , Jensen Ole , Kunz Lukas , Moratti Stephan , Axmacher Nikolai , Strange Bryan A
Published: November 2021

The hippocampus is implicated in novelty detection, thought to be important for regulating entry of information into long-term memory. Whether electrophysiological responses to novelty differ along the human hippocampal long axis is currently unknown. By recording from electrodes implanted longitudinally in the hippocampus of epilepsy patients, here we show a gradual increase of theta frequency oscillatory power from anterior to posterior in response to unexpected stimuli, superimposed on novelty responses common to all long axis portions. Intracranial event-related potentials (iERPs) were larger for unexpected vs. expected stimuli and demonstrated a polarity inversion between the hippocampal head (HH) and body (HB). We observed stronger theta coherence between HH and hippocampal tail (HT) than between HB and HT, similarly for expected and unexpected stimuli. This was accompanied by theta and alpha traveling waves with surprisingly variable direction of travel characterized by a ∼180° phase lag between hippocampal poles. Interestingly, this phase lag showed a pronounced phase offset between anterior and middle (HH-HB) hippocampal portions coinciding anatomically with a drop in theta coherence and the novelty iERP polarity inversion. Our findings indicate common response properties along the hippocampal long axis to unexpected stimuli, as well as a multifaceted, non-uniform engagement along the long axis for novelty processing.
Comprehensive identification of fetal cis-regulatory elements in the human genome by single-cell multi-omics analysis
Authors: Yu Hao , Ai Na , Peng Ping , Ke Yuwen , Chen Xuepeng , Li Yun , Zhao Ting , Jiang Shan , Liu Jiang , Jiang Lan
Published: November 2021

The regulatory programs driving early organogenesis in human is complex and still poorly understood. We performed parallel profiling of gene expression and chromatin accessibility to 28 human fetal tissue samples representing 14 organs in the first trimester. Collectively, we have generated 415,793 single-cell profiles. By integration analysis of transcriptome and chromatin accessibility, we detected 225 distinct cell types and 848,475 candidate accessible cis-regulatory elements (aCREs). By linking regulatory elements to their putative target genes, we identified not only 108,699 enhancers, but also 23,392 silencers elements. We uncovered thousands of genes regulated by both enhancers and silencers in an organ or cell-type-specific manner. Furthermore, our unique approach revealed a substantial proportion of distal DNA elements are transcribed CREs (tCREs), which show both open chromatin signal and transcription initiation activity of non-coding transcript. The landscape of fetal cis-regulatory elements facilitates the interpretation of the genetic variant of complex disease and infer the cell type of origin for cancer. Overall, our data provide a comprehensive map of the fetal cis-regulatory elements at single-cell resolution and a valuable resource for future study of human development and disease.
ASC proneural transcription factors mediate the timely initiation of the neural program during neuroectodermal to neuroblast transition ensuring progeny fidelity
Authors: Theodorou Vasiliki , Stefanaki Aikaterini , Drakos Minas , Triantafyllou Dafne , Delidakis Christos
Published: November 2021

Background

ASC/ASCL proneural transcription factors are oncogenic and exhibit impressive reprogramming and pioneer activities. In both Drosophila and mammals, these factors are central in the early specification of the neural fate, where they act in opposition to Notch signalling. However, the role of ASC on the chromatin during CNS neural stem cells birth remains elusive.

Results

We investigated the chromatin changes accompanying neural commitment using an integrative genetics and genomics methodology. We found that ASC factors bind equally strongly to two distinct classes of cis-regulatory elements: open regions remodeled earlier during maternal to zygotic transition by Zelda and Zelda-independent, less accessible regions. Both classes cis-elements exhibit enhanced chromatin accessibility during neural specification and correlate with transcriptional regulation of genes involved in many biological processes necessary for neuroblast function. We identified an ASC-Notch regulated TF network that most likely act as the prime regulators of neuroblast function. Using a cohort of ASC target genes, we report that ASC null neuroblasts are defectively specified, remaining initially stalled, lacking expression of many proneural targets and unable to divide. When they eventually start proliferating, they produce compromised progeny. Generation of lacZ reporter lines driven by proneural-bound elements display enhancer activity within neuroblasts and proneural dependency. Therefore, the partial neuroblast identity seen in the absence of ASC genes is driven by other, proneural-independent, cis-elements. Neuroblast impairment and the late differentiation defects of ASC mutants are corrected by ectodermal induction of individual ASC genes but not by individual members of the TF network downstream of ASC. However, in wild type embryos induction of individual members of this network induces CNS hyperplasia, suggesting that they synergize with the activating function of ASC to establish the chromatin dynamics that promote neural specification.

Conclusion

ASC factors bind a large number of enhancers to orchestrate the timely activation of the neural chromatin program during neuroectodermal to neuroblast transition. This early chromatin remodeling is crucial for both neuroblast homeostasis as well as future progeny fidelity.
Targeting the Annexin A1-FPR2/ALX pathway for host-directed therapy in dengue disease
Authors: Costa Vivian V , Sugimoto Michelle A , Hubner Josy , Bonilha Caio S , Queiroz-Junior Celso M , Gonçalves Pereira Marcela Helena , Chen Jianmin , Gobbetti Thomas , Libanio Rodrigues Gisele Olinto , Bambirra Jordana L. , Passos Ingredy , Machado Lopes Carla Elizabeth , Moreira Thaiane P. , Bonjour Kennedy , Melo Rossana C. N. , Oliveira Milton A. P. , Andrade Marcus Vinicius M. , Sousa Lirlândia Pires , Souza Danielle Gloria , Costa Santiago Helton da , Perretti Mauro , Teixeira Mauro Martins
Published: November 2021

Host immune responses contribute to dengue’s pathogenesis and severity, yet the possibility that failure in endogenous inflammation resolution pathways could characterise the disease has not been contemplated. The pro-resolving protein Annexin A1 (AnxA1) is known to counterbalance overexuberant inflammation and mast cell (MC) activation. We hypothesised that inadequate AnxA1 engagement underlies the cytokine storm and vascular pathologies associated with dengue disease. Levels of AnxA1 were examined in the plasma of dengue patients and infected mice. Immunocompetent, IFNα/βR-/-, AnxA1-/-and FPR2/ALX-/-mice were infected withDengue virus(DENV) and treated with the AnxA1 mimetic peptide Ac2-26for analysis. Additionally, the effect of Ac2-26on DENV-induced MC degranulation was assessedin vitroandin vivo. We observed that circulating levels of AnxA1 were reduced in dengue patients and DENV-infected mice. While the absence of AnxA1 or its receptor FPR2/ALX aggravated illness in infected mice, treatment with AnxA1 agonistic peptide attenuated disease manifestations. Both clinical outcomes were attributed to modulation of DENV-mediated viral load-independent MC degranulation. We have thereby identified that altered levels of the pro-resolving mediator AnxA1 are of pathological relevance in DENV infection, suggesting FPR2/ALX agonists as a therapeutic target for dengue disease.