bluuebunny/crossref_metadata_2025 huggingface dataset:
Prefrontal cortex neural compensation during an operant devaluation task
Authors: Fisher Hayley , Lin Hongyu , May Jensen , McLean Caitlin , Pickens Charles L.
Published: August 2021

Deficits in goal-directed action are reported in multiple neuropsychiatric conditions, including schizophrenia. However, dysfunction is not always apparent in early stages of schizophrenia, possibly due to neural compensation. We designed a novel devaluation task in which goal-directed action could be guided by stimulus-outcome (S-O) [presumably orbitofrontal cortex (OFC)-mediated] or response-outcome (R-O) associations [presumably prelimbic cortex (PL)-mediated]. We previously found suggestive evidence that OFC and PL could compensate for each other in this task, and we more directly assessed this potential compensation here. In Experiment 1, rats received OFC, PL, combined OFC+PL, or sham lesions and then completed our devaluation task. The OFC+PL lesion group exhibited impaired devaluation. In Experiment 2, rats received cholera-toxin-b (CTb) into OFC and either neurotoxic or sham PL lesions. Rats were then sacrificed on the last training day to double-label for Arc and CTb. We found increased Arc+CTb in mediodorsal thalamus (MD) and increased Arc+ neurons in OFC when PL was lesioned, suggesting that PL lesions lead to a compensatory increased activation of the MD→OFC circuit. Our results suggest that our devaluation task can model neural compensation between OFC and PL and this compensation may be regulated by MD.

Significance Statement

To detect compensatory responses, behavioral models that use different strategies must be developed to determine if the strategies shift when a brain area or circuit is incapacitated. Neural compensation is commonly observed in human research but only a few models of neural compensation exist, and few identify compensation within the prefrontal cortex. This research is among the first to show neural compensation between prefrontal cortex regions and implicate a thalamocortical circuit in modulating this compensation. Not only will this model provide a way to behaviorally identify subtle neurological shifts, it can also elucidate basic neurological mechanisms that mediate how circuits interact with each other and how dysfunction in one circuit can affect connectivity in other brain areas.
Thought Extramission: The Eyes Project Conceptual Maps at Close Distance
Authors: Dumitru Magda L. , Joergensen Gitte H.
Published: August 2021

Light extramission is a popular yet erroneous model of human vision positing that light projects through the eyes over surrounding objects, allowing them to become visible. However, light extramission research has failed to distinguish between light and other types of emissions coming from the eyes, thereby discounting the possibility that extramission mechanisms might hold true for phenomena other than light. Here, we explored the thought extramission model, which is the notion that thoughts emanate from the eyes in the form of visualized representations. We show that the eyes project thoughts a short distance away in the form of high-resolution conceptual maps whose structure collapses at great distances. We also demonstrate that sensory filtering of thought projection by reducing light contrast lowers the resolution of conceptual maps. Our results highlight the supporting role of the visual system for thought processes relying on contrast, luminance, and perspective formation.
Environment dependent benefits of inter-individual variation in honey bee recruitment
Authors: Rajagopal Supraja , Brockmann Axel , George Ebi Antony
Published: August 2021

Inter-individual differences in behaviour within the members of a social group can affect the group’s productivity. In eusocial insects, individual differences amongst workers in a colony play a central role division of labour and task allocation. Extensive empirical and theoretical work has highlighted variation in response thresholds as a proximate mechanism underlying individual behavioural differences and hence division of labour. However, other response parameters, like response probability and intensity, can affect these differences. In this study, we first extended a previously published agent-based model on honey bee foraging to understand the relative importance of response (dance) probability and response (dance) intensity in the task of recruitment. Comparing variation obtained from the simulations with previously published empirical data, we found that response intensity plays a more important role than probability in producing consistent inter-individual differences in recruitment behaviour. We then explored the benefits provided by this individual variation in recruitment behaviour to the colony’s collective foraging effort under different environmental conditions. Our results revealed that individual variation leads to a greater energetic yield per forager, but only when food is abundant. Our study highlights the need to consider all response parameters while studying division of labour and adds to the growing body of evidence linking individual variation in behavioural responses to the success of social groups.
Rhythmic clock gene expression in Atlantic salmon parr brain
Authors: Bolton Charlotte M , Bekaert Michaël , Eilertsen Mariann , Helvik Jon Vidar , Migaud Herve
Published: August 2021

To better understand the complexity of clock genes in salmonids, a taxon with an additional whole genome duplication, an analysis was performed to identify and classify gene family members (clock, arntl, period, cryptochrome, nr1d, ror, and csnk1). The majority of clock genes, in zebrafish and Northern pike, appeared to be duplicated. In comparison to the 29 clock genes described in zebrafish, 48 clock genes were discovered in salmonid species. There was also evidence of species-specific reciprocal gene losses conserved to the Oncorhynchus sister clade. From the six period genes identified three were highly significantly rhythmic, and circadian in their expression patterns (per1a.1, per1a.2, per1b) and two was significantly rhythmically expressed (per2a, per2b). The transcriptomic study of juvenile Atlantic salmon (parr) brain tissues confirmed gene identification and revealed that there were 2,864 rhythmically expressed genes (p < 0.001), including 1,215 genes with a circadian expression pattern, of which 11 were clock genes. The majority of circadian expressed genes peaked two hours before and after daylight. These findings provide a foundation for further research into the function of clock genes circadian rhythmicity and the role of an enriched number of clock genes relating to seasonal driven life history in salmonids.
Divergent transcriptional and transforming properties of PAX3-FOXO1 and PAX7-FOXO1 paralogs
Authors: Manceau Line , Richard Albert Julien , Lollini Pier-Luigi , Greenberg Maxim V. C. , Gilardi-Hebenstreit Pascale , Ribes Vanessa
Published: August 2021

The hallmarks of the alveolar subclass of rhabdomyosarcoma are chromosomal translocations that generate chimeric PAX3-FOXO1 or PAX7-FOXO1 transcription factors. Both PAX-FOXO1s result in related cell transformation in animal models, but both mutations are associated with distinct pathological manifestations in patients. To assess the mechanisms underlying these differences, we generated isogenic fibroblast lines expressing either PAX-FOXO1 paralog. Mapping of their genomic recruitment using CUT&Tag revealed that the two chimeric proteins have distinct DNA binding preferences. In addition, PAX7-FOXO1 causes stronger de novo transactivation of its bound regions than PAX3-FOXO1, resulting in greater transcriptomic dynamics involving genes regulating cell shape and cycle. Consistently, PAX3-FOXO1 accentuates fibroblast cellular traits associated with contractility and surface adhesion and limits entry into M phase. In contrast, PAX7-FOXO1 drives cells to adopt an amoeboid shape, reduces entry into S phase, and causes more genomic instabilities. Altogether, our results argue that the diversity of rhabdomyosarcoma manifestation arises, in part, from the divergence between the transcriptional activities of PAX3-FOXO1 and PAX7-FOXO1. Furthermore, the identified pronounced deleterious effects of PAX7-FOXO1 provide an explanation for the low frequency of the translocation generating this factor in patients with rhabdomyosarcoma.
Sarcoptic mange outbreak decimates South American camelid populations in San Guillermo National Park, Argentina
Authors: Ferreyra Hebe , Rudd Jaime , Foley Janet , Vanstreels Ralph E. T. , Martín Ana M. , Donadio Emiliano , Uhart Marcela M.
Published: August 2021

Sarcoptic mange epidemics can devastate wildlife populations. In 2014, mange was first detected in vicuña (Vicugna vicugna) and guanaco (Lama guanicoe) in San Guillermo National Park (SGNP), Argentina. This study characterized the potential source and the impacts of the outbreak in 2017–2019. Transect surveys indicated a sharp decrease in the density of live vicuña and guanaco by 68% and 77%, respectively, from May 2017 to June 2018. By April 2019 no vicuña or guanaco were recorded on transect surveys, suggesting a near-extinction at the local level. Clinical signs consistent with mange (e.g. intense pruritus, hyperkeratosis, alopecia) were observed in 24% of live vicuña (n = 478) and 33% of live guanaco (n = 12) during surveys, as well as in 94% of vicuña carcasses (n = 124) and 85% of guanaco carcasses (n = 20) opportunistically examined during the study period. Histological examination (n = 15) confirmed sarcoptic mange as the cause of the cutaneous lesions. Genetic characterization revealed thatSarcoptes scabieirecovered from seven vicuña (n = 13) and three guanaco (n = 11) shared the same genotype, which is consistent with a single source and recent origin of the epidemic. A governmental livestock incentive program introduced llama (Lama glama) in areas adjacent to SGNP in 2009, some of which reportedly had alopecic scaling consistent with sarcoptic mange. We hypothesize that the introduction of mange-infected llama may have triggered the outbreak in wild camelids which has now put them at a high risk of local extinction. This unprecedented event highlights that the accidental introduction of disease may be underestimated at the onset yet can have devastating effects on native ungulate populations with potentially profound effects at the community and ecosystem levels.
Flexible pri-miRNA structures enable tunable production of 5’ isomiRs
Authors: Bofill-De Ros Xavier , Hong Zhenyi , Birkenfeld Ben , Alamo-Ortiz Sarangelica , Yang Acong , Dai Lisheng , Gu Shuo
Published: August 2021

Drosha cleavage of a pri-miRNA defines mature microRNA sequence. Drosha cleavage at alternative positions generates 5’ isoforms (isomiRs) which have distinctive functions. To understand how pri-miRNA structures influence Drosha cleavage, we performed a systematic analysis of the maturation of endogenous pri-miRNAs and their variants both in vitro and in vivo. We show that, in addition to previously known features, the overall structural flexibility of pri-miRNA impacts Drosha cleavage fidelity. Internal loops and nearby G·U wobble pairs on the pri-miRNA stem induce the use of non-canonical cleavage sites by Drosha, resulting in 5’ isomiR production. By analyzing patient data deposited in The Cancer Genome Atlas, we provide evidence that alternative Drosha cleavage of pri-miRNAs is a tunable process that responds to the level of pri-miRNA-associated RNA-binding proteins. Together, our findings reveal that Drosha cleavage fidelity can be modulated by altering pri-miRNA structure, a potential mechanism underlying 5’ isomiR biogenesis in tumors.

HIGHLIGHTS

Flexible pri-miRNA structures lead to 5’ isomiR production

Internal loops and G·U pairs of pri-miRNA contribute to alternative Drosha cleavages

Alternative Drosha cleavage results in 5’ isomiRs from both strands of pre-miRNAs

5’ isomiR production is upregulated by pri-miRNA-associated RBPs in cancers

GRAPHICAL ABSTRACT
Benchmarking of SpCas9 variants enables deeper base editor screens of BRCA1 and BCL2
Authors: Sangree Annabel K , Griffith Audrey L , Szegletes Zsofia M , Roy Priyanka , DeWeirdt Peter C , Hegde Mudra , McGee Abby V , Hanna Ruth E , Doench John G
Published: August 2021

Numerous rationally-designed and directed-evolution variants of SpCas9 have been reported to expand the utility of CRISPR technology. Here, we benchmark PAM preferences, on-target activity, and off-target susceptibility of 11 variants of SpCas9 in cell culture assays with thousands of guides targeting endogenous genes. To enhance the coverage and thus utility of base editing screens, we demonstrate that the SpCas9-NG and SpG variants are compatible with both A>G and C>T base editors, more than tripling the number of guides and assayable residues. We demonstrate the performance of these technologies by screening for loss-of-function mutations in BRCA1 and Venetoclax-resistant mutations in BCL2, identifying both known and new insights into these clinically-relevant genes. We anticipate that the tools and methodologies described here will facilitate the investigation of genetic variants at a finer and deeper resolution for any locus of interest.
Abnormal Neurite Density and Orientation Dispersion in Frontal Lobe Link to Elevated Hyperactive/Impulsive Behaviors in Young Adults with Traumatic Brain Injury
Authors: Cao Meng , Luo Yuyang , Wu Ziyan , Wu Kai , Li Xiaobo
Published: August 2021

Traumatic brain injury is a major public health concern. A significant proportion of individuals experience post-traumatic brain injury behavioral impairments, especially in attention and inhibitory control domains. Traditional diffusion-weighted MRI techniques, such as diffusion tensor imaging, have provided tools to assess white matter structural disruptions reflecting the long-term brain tissue alterations associated with traumatic brain injury. The recently developed neurite orientation dispersion and density imaging is a more advanced diffusion-weighted MRI modality, which provides more refined characterization of brain tissue microstructures by assessing the neurite orientation dispersion and neurite density properties. In this study, we investigated the morphometrical and microstructural alterations at chronic brain injury stage and their relationships with the functional outcomes. Neurite orientation dispersion and density imaging data from 44 young adults with chronic traumatic brain injury (ranging from 18 27 years of age; 23 males/21 females) who had no prior-traumatic brain injury history of attention deficits and/or hyperactivity and 45 group-matched normal controls (23 males /22 females) were collected. Maps of fractional anisotropy, neurite orientation dispersion index, and neurite density index were calculated. Vertex-wise and voxel-wise analyses were conducted for gray matter and white matter, respectively. Post-hoc region of interest-based analyses were also performed. Compared to the controls, the group of traumatic brain injury showed significantly increased orientation dispersion index in various gray matter regions and significantly decreased orientation dispersion index in several white matter regions. Brain-behavioral association analyses indicated that the reduced neurite density index of left precentral gyrus and the reduced orientation dispersion index of left superior longitudinal fasciculus were significantly associated with elevated hyperactive/impulsive symptoms in the patients with traumatic brain injury. These findings suggest that traumatic brain injury-induced chronic neurite orientation dispersion alterations of left superior longitudinal fasciculus and left precentral may significantly contribute to post-traumatic brain injury hyperactive/impulsive behaviors in young adults with traumatic brain injury.
Nuclear Translocation of Vitellogenin in the Honey Bee (Apis mellifera)
Authors: Salmela Heli , Harwood Gyan , Münch Daniel , Elsik Christine , Herrero-Galán Elías , Vartiainen Maria K. , Amdam Gro
Published: August 2021

Vitellogenin (Vg) is a conserved protein used by nearly all oviparous animals to produce eggs. It is also pleiotropic and performs functions in oxidative stress resistance, immunity, and, in honey bees, behavioral development of the worker caste. It has remained enigmatic how Vg affects multiple traits. Here, we asked whether Vg enters the nucleus and acts via DNA-binding. We used immunohistology, cell fractionation and cell culturation to show that a structural subunit of honey bee Vg translocates into cell nuclei. We then demonstrated Vg-DNA binding theoretically and empirically with prediction software and chromatin immunoprecipitation with sequencing (ChIP-seq), finding binding sites at genes influencing immunity and behavior. Finally, we investigated the immunological and enzymatic conditions affecting Vg cleavage and nuclear translocation, and constructed a 3D structural model. Our data are the first to show Vg in the nucleus and suggests a new fundamental regulatory role for this ubiquitous protein.
Microbiota induces aging-related leaky gut and inflammation by dampening mucin barriers and butyrate-FFAR2/3 signaling
Authors: Mishra Sidharth P , Wang Bo , Wang Shaohua , Nagpal Ravinder , Miller Brandi , Jain Shalini , Lee Jea Young , Borlongan Cesar , Taraphdar Subhash , Rane Sushil G. , Yadav Hariom
Published: August 2021

Increased chronic inflammation is one of the key risk factors of aging-related disorders although its precise etiology remains elusive. Here, we demonstrate that aged, but not young, microbiota triggers inflammation by promoting gut permeability (leaky gut) via disruption of mucus barriers. Levels of the beneficial short-chain fatty acid, butyrate, are suppressed in the aged gut. Consistent with feedback regulation, the expression of butyrate-sensing receptors, free fatty acid receptor 2/3 (FFAR2/3), are also reduced in aged gut. Butyrate treatment of aged mice revereses the reduced mucin production, increased gut permeability and inflammation associated with low butyrate levels. In agreement, intestine-specific FFAR2/3 knockout mice manifest a compromised gut phenotype typically seen in aged mice,, such as increased gut permeability and inflammation with reduced mucin production. Taken together, our results demonstrate that an aged gut microbiota causally instigates inflammation by increasing gut permeability due to reduced butyrate levels, FFAR2/3 expression, and mucin barriers. Thus, butyrate-FFAR2/3 agonism could ameliorate the deleterious effects seen in aged gut and their implications on metabolic health.
Effects of the exercise-inducible myokine irisin on proliferation and malignant properties of ovarian cancer cells through the HIF-1 α signaling pathway
Authors: Zarei Marziyeh Alizadeh , Hosseini Elahe Seyed , Kashani Hamed Haddad , Ahmad Ejaz , Nikzad Hossein
Published: August 2021

Background

Exercise has been shown to be associated with reduced risk and improving outcomes of several types of cancers. Irisin −a novel exercise-related myokine- has been proposed to exert beneficial effects in metabolic disorders including cancer. No previous studies have investigated whether irisin may regulate malignant characteristics of ovarian cell lines.

Methods

In the present study, we aimed to explore the effect of irisin on viability and proliferation of ovarian cancer cells which was examined by MTT assay. Then, we evaluated migratory and invasive ability of the cells via transwell assays. Moreover, the percentage of apoptosis induction was determined by flowcytometery. Furthermore, the mRNA expression level of genes related to the aerobic respiration (HIF-1α, c-Myc, LDHA, PDK1 and VEGF) were detected by real-time PCR.

Results

Our data revealed that irisin treatment significantly attenuated the proliferation, migration and invasion of ovarian cancer cells. Besides, irisin induced apoptosis in ovarian cancer cells. We also observed that irisin regulated the expression of genes involved in aerobic respiration of ovarian cancer cells.

Conclusion

Our results indicate that irisin may play a crucial role in inhibition of cell growth and malignant characteristics of ovarian cancer. This findings may open up avenues for future studies to identify the further therapeutic use of irisin in ovarian cancer management.
Mapping Vegetation Species Succession in a Mountainous Grassland ecosystem using Landsat and Sentinel-2 data
Authors: Adagbasa G.E , Mukwada G
Published: August 2021

Vegetation species succession and composition are significant factors determining the rate of ecosystem biodiversity recovery after being disturbed and subsequently vital for sustainable and effective natural resource management and biodiversity. The succession and composition of grasslands ecosystems worldwide have significantly been affected by the accelerated changes in the environment due to natural and anthropogenic activities. Therefore, understanding spatial data on the succession of grassland vegetation species and communities through mapping and monitoring is essential to gain knowledge on the ecosystem and other ecosystem services. This study used a random forest machine learning classifier on the Google Earth Engine platform to classify grass vegetation species with Landsat 7 ETM+ and ASTER multispectral imager (MI) data resampled with the current Sentinel-2 MSI data to map and estimate the changes in vegetation species succession. The results indicate that ASTER IM has the least accuracy of 72%, Landsat 7 ETM+ 84%, and Sentinel-2 had the highest of 87%. The result also show that other species had replaced four dominant grass species totaling an area of about 49 km2 throughout the study.
Poly-gamma-glutamic acid secretion protects Bacillus subtilis from zinc and copper intoxication
Authors: Deol Reina , Louis Ashweetha , Glazer Harper Lee , Hosseinion Warren , Chandrangsu Pete
Published: August 2021

Zinc and copper are essential micronutrients that serve as a cofactors for numerous enzymes. However, when present at elevated concentrations, zinc and copper are highly toxic to bacteria. To combat the effects of zinc and copper excess, bacteria have evolved a wide array of defense mechanisms. Here, we show that the Gram positive soil bacterium, Bacillus subtilis, produces the extracellular polymeric substance, poly-gamma-glutamate (γ-PGA) as a protective mechanism in response to zinc and copper excess. Furthermore, we provide evidence that zinc and copper dependent γ-PGA production is independent of the DegS-DegQ two component regulatory system and likely occurs at a post-transcriptional level. These data provide new insight into bacterial metal resistance mechanisms and contribute to our understanding of the regulation of bacterial γ-PGA biosynthesis.

Importance

Zinc and copper are potent antimicrobial compounds. As such, bacteria have evolved a diverse range of tools to prevent metal intoxication. Here, we show that the Gram-positive model organism, Bacillus subtilis, produces poly-gamma-glutamic acid (γ-PGA) as a protective mechanism against zinc and copper intoxication and that zinc and copper dependent γ-PGA production occurs by a yet undefined mechanism independent of known γ-PGA regulation pathways.
Identifying Therapeutic Strategies in IgA Nephropathy through Comprehensive Transcriptomic Characterization
Authors: Ofori Kenneth , Yakubu Amin , Rai Alex J.
Published: August 2021

IgA nephropathy (IgAN) is an autoimmune disease and the most common primary glomerulonephritis. The four-hit hypothesis describes mechanism of the disease, from synthesis of galactose deficient IgA (GD-IgA), to recognition of GD-IgA by anti-glycan antibodies and deposition of the formed immune complex in the mesangium. Complement and coagulation cascade activation ensues, resulting in mesangial activation and cytokine release, podocyte injury, mesangial sclerosis and tubulointerstitial damage. Currently, there is no disease cure, and 30-40% of patients progress to end stage renal disease.

Using complementary bioinformatic approaches, we demonstrate different levels of deviation of the transcriptome of the glomerulus in IgAN from normal, with the aim of identifying therapeutic targets. Approaches used herein include, deconvolution of the transcriptome to estimate immune constitution, co-regulation-based functional analysis of differentially expressed genes, modular co-expression analysis, network analysis of metabolic pathways and differential gene correlation analysis.

We describe the immune composition in IgAN and the relatively low fold changes of the abundance of different immune cells and strength of immune signatures compared with control. Additionally, we identify enrichment of the intestinal network for IgA synthesis, repression of expression and dysregulation of networks of amino acid metabolism and PPAR signaling pathways in IgAN glomeruli. We also find loss of correlation between expression of matrix synthesizing and matrix degrading genes in IgAN.

We conclude by discussing how therapies based on some nodes in these altered pathways described have been shown to be efficacious in IgAN and/or other inflammatory diseases and the potential of others in effective treatment.
Goal-centered representations in the human hippocampus
Authors: Crivelli-Decker Jordan , Clarke Alex , Park Seongmin A. , Huffman Derek J. , Boorman Erie , Ranganath Charan
Published: August 2021

Recent work in cognitive and systems neuroscience has suggested that the hippocampus might support planning, imagination, and navigation by forming “cognitive maps” that capture the structure of physical spaces, tasks, and situations. Critically, navigation involves planning within a context and disambiguating similar contexts to reach a goal. We examined hippocampal activity patterns in humans during a goal-directed navigation task to examine how contextual and goal information are incorporated in the construction and execution of navigational plans. Results demonstrate that, during planning, the hippocampus carries a context-specific representation of a future goal. Importantly, this effect could not be explained by stimulus or spatial information alone. During navigation, we observed reinstatement of activity patterns in the hippocampus ahead of participants’ required actions, which was strongest for behaviorally relevant points in the sequence. These results suggest that, rather than simply representing overlapping associations, hippocampal activity patterns are powerfully shaped by context and goals.
In vivo hemostatic capability of a novel Tetra-PEG hydrogel
Authors: Okata Shinya , Hoshina Katsuyuki , Hanada Kazumasa , Kamata Hiroyuki , Fujisawa Ayano , Yoshikawa Yuki , Sakai Takamasa
Published: August 2021

TetraStat is a novel synthetic sealant created with a tetra-armed polyethylene glycol (PEG) hydrogel. It has no risk of infection from biological pathogens and has a hemostatic mechanism independent of the blood coagulation pathway and controllable gelation. We evaluated the hemostatic effect of TetraStat in ex vivo and in vivo experiments for future clinical application. In ex vivo experiments using a circulatory system filled with phosphate-buffered saline under high pressure, needle punctures were astricted with TetraStat and two commercially available hemostatic agents (SURGICEL and TachoSil). For in vivo experiments, rat vena cavae were punctured with 14, 18, and 20 gauge needles, and hemorrhage occurred for several seconds. A porous PEG sponge soaked with TetraStat was applied as a hemostatic system for the massive hemorrhage. In the ex vivo experiment, punctures were sealed completely after 1 min astriction with TetraStat gel; in contrast, SURGICEL and TachoSil failed to seal the hole. In vivo experiments demonstrated that TetraStat successfully caused hemostasis in the punctured vena cava within 1 min of application in a dose-dependent manner. For SURGICEL and TachoSil, successful hemostasis occurred after 5 min astriction but was less frequent after 1 min astriction. Ex vivo and in vivo experiments revealed TetraStat’s high hemostatic ability under high pressure and in rat vena cava injuries under massive hemorrhage. A porous PEG sponge soaked with TetraStat is a promising advancement in hemostatic systems.
The IgE production is initially induced in subcutaneous fat and depends on extrafollicular B cells
Authors: Chudakov Dmitrii Borisovich , Fattakhova Gulnar Vaisovna , Konovalova Mariya Vladimirovna , Tsaregorotseva Daria Sergeevna , Shevchenko Marina Alexandrovna , Kotsareva Olga Dmitrievna , Sergeev Anton Andreevich , Svrshcehvskaya Elena Victorovna
Published: August 2021

Background

Growing body of evidence indicates that IgE production can be developed by mechanisms that differ from those responsible for IgG and IgA production. One potential possibility is generation of IgE producing cells from tissue-associated B-cells and/or through extrafollicular pathway. But the role of subcutaneous fat-associated B-cells in this process is poorly investigated. The aim of the present study was to investigate the role of different B- and T- cell subpopulations after long-term antigen administration in IgE response.

Methods

BALB/c mice were immunized 3 times a eeks for 4 weeks in withers region enriched with subcutaneous fat with high and low antigen doses as well as by intraperitoneal route in region enriched with visceral fat for comparison.

Results

After long-term antigen administration that promotes the type of immune response which is more similar to one observed in young allergic children, subcutaneous fat tissue B-cells generates more rapid and active IgE class switched and IgE-produced cells. Although IgE production at later time points was initiated also in regional lymph nodes, the early IgE production was exclusively linked with subcutaneous fat. We observed that low-dose induced strong IgE production accompanied by minimal IgG1 production was linked with extrafollicular B-2 derived plasmablasts as well as extrafollicular T- helpers accumulation. Delayed IgE class switching in regional lymph nodes and visceral fat tissue was characterized by the absence of both stable plasmablasts and T-extrafollicular helpers accumulation.

Conclusion

Extrafollicular B- and T-cell responses in subcutaneous fat are necessary for early IgE class switching and sensitization process in the case of allergen penetration through skin.
Neutralising antibodies against the SARS-CoV-2 Delta variant induced by Alhydroxyquim-II-adjuvanted trimeric spike antigens
Authors: Counoupas Claudio , Pino Paco , Stella Alberto O. , Ashley Caroline , Lukeman Hannah , Bhattacharyya Nayan D. , Tada Takuya , Anchisi Stephanie , Metayer Charles , Martinis Jacopo , Aggarwal Anupriya , Dcosta Belinda M. , Kint Joeri , Wurm Maria J , Landau Nathaniel R. , Steain Megan , Turville Stuart G , Wurm Florian M , David Sunil A. , Triccas James A.
Published: August 2021

Global control of COVID-19 will require the deployment of vaccines capable of inducing long-term protective immunity against SARS-CoV-2 variants. In this report, we describe an adjuvanted subunit candidate vaccine that affords elevated, sustained and cross-variant SARS-CoV-2 neutralising antibodies (NAbs) in multiple animal models. Alhydroxiquim-II is a TLR7/8 small-molecule agonist chemisorbed on aluminium hydroxide. Vaccination with Alhydroxiquim-II combined with a stabilized, trimeric form of the SARS-CoV-2 spike protein (termed CoVac-II) resulted in high-titre NAbs in mice, with no decay in responses over an 8-month period. NAbs from sera of CoVac-II-immunized mice, horses and rabbits were broadly neutralising against SARS-CoV-2 variants. Boosting long-term CoVac-II-immunized mice with adjuvanted spike protein from the Beta variant markedly increased levels of NAb titres against multiple SARS-CoV-2 variants; notably high titres against the Delta variant were observed. These data strongly support the clinical assessment of Alhydroxiquim-II-adjuvanted spike proteins to protect against SARS-CoV-2 variants of concern.
Single amino-acid mutation in a Drosophila melanogaster ribosomal protein: an insight in uL11 transcriptional activity
Authors: Grunchec Héloïse , Deraze Jérôme , Dardalhon-Cuménal Delphine , Ribeiro Valérie , Coléno-Costes Anne , Dias Karine , Bloyer Sébastien , Mouchel-Vielh Emmanuèle , Peronnet Frédérique , Thomassin Hélène
Published: August 2021

The ribosomal protein uL11 is located at the basis of the ribosome P-stalk and plays a paramount role in translational efficiency. In addition, no mutant for uL11 is available suggesting that this gene is haplo-insufficient as many other Ribosomal Protein Genes (RPGs). We have previously shown that overexpression of Drosophila melanogaster uL11 enhances the transcription of many RPGs and Ribosomal Biogenesis genes (RiBis) suggesting that uL11 might globally regulate the level of translation through its transcriptional activity. Moreover, uL11 trimethylated on lysine 3 (uL11K3me3) interacts with the chromodomain of the Enhancer of Polycomb and Trithorax Corto, and both proteins co- localize with RNA Polymerase II at many sites on polytene chromosomes. These data have led to the hypothesis that the N-terminal end of uL11, and more particularly the trimethylation of lysine 3, supports the extra-ribosomal activity of uL11 in transcription. To address this question, we mutated the lysine 3 codon using a CRISPR/Cas9 strategy and obtained several lysine 3 mutants. We describe here the first mutants of D. melanogaster uL11. Unexpectedly, the uL11K3A mutant, in which the lysine 3 codon is replaced by an alanine, displays a genuine Minute phenotype known to be characteristic of RPG deletions (longer development, low fertility, high lethality, thin and short bristles) whereas the uL11K3Y mutant, in which the lysine 3 codon is replaced by a tyrosine, is unaffected. In agreement, the rate of translation decreases in uL11K3A but not in uL11K3Y. Co-immunoprecipitation experiments show that the interaction between uL11 and the Corto chromodomain is impaired by both mutations. RNA- seq analysis from wing imaginal discs shows enrichment in the GO categories “glutathione metabolism” for up-regulated genes in both uL11K3A and uL11K3Y mutants and “regulation of transcription” for down-regulated genes in uL11K3A only. Analysis of the cis-regulatory sequences of these genes suggests that uL11 might regulate transcription of target genes in concert with the couple of transcription factors Mad/Med that mediate response to the Bone Morphogenetic Protein (BMP) signaling pathway.
Data Matrix Normalization and Merging Strategies Minimize Batch-specific Systemic Variation in scRNA-Seq Data
Authors: Babcock Benjamin R. , Kosters Astrid , Yang Junkai , White Mackenzie L. , Ghosn Eliver E. B.
Published: August 2021

Single-cell RNA sequencing (scRNA-seq) can reveal accurate and sensitive RNA abundance in a single sample, but robust integration of multiple samples remains challenging. Large-scale scRNA-seq data generated by different workflows or laboratories can contain batch-specific systemic variation. Such variation challenges data integration by confounding sample-specific biology with undesirable batch-specific systemic effects. Therefore, there is a need for guidance in selecting computational and experimental approaches to minimize batch-specific impacts on data interpretation and a need to empirically evaluate the sources of systemic variation in a given dataset. To uncover the contributions of experimental variables to systemic variation, we intentionally perturb four potential sources of batch-effect in five human peripheral blood samples. We investigate sequencing replicate, sequencing depth, sample replicate, and the effects of pooling libraries for concurrent sequencing. To quantify the downstream effects of these variables on data interpretation, we introduced a new scoring metric, the Cell Misclassification Statistic (CMS), which identifies losses to cell type fidelity that occur when merging datasets of different batches. CMS reveals an undesirable overcorrection by popular batch-effect correction and data integration methods. We show that optimizing gene expression matrix normalization and merging can reduce the need for batch-effect correction and minimize the risk of overcorrecting true biological differences between samples.
Src acts with WNT/FGFRL signaling to pattern the planarian anteroposterior axis
Authors: Bonar Nicolle A. , Gittin David I. , Petersen Christian P.
Published: August 2021

Tissue identity determination is critical for regeneration, and the planarian anteroposterior (AP) axis uses positional control genes expressed from bodywall muscle to determine body regionalization. Canonical Wnt signaling establishes anterior versus posterior pole identities through notum and wnt1 signaling, and two Wnt/FGFRL signaling pathways control head and trunk domains, but their downstream signaling mechanisms are not fully understood. Here we identify a planarian Src homolog that restricts head and trunk identities to anterior positions. src-1(RNAi) animals formed enlarged brains and ectopic eyes and also duplicated trunk tissue, similar to a combination of Wnt/FGFRL RNAi phenotypes. src-1 was required for establishing territories of positional control gene expression, indicating it acts at an upstream step in patterning the AP axis. Double RNAi experiments and eye regeneration assays suggest src-1 can act in parallel to at least some Wnt and FGFRL factors. Co-inhibition of src-1 with other posterior-promoting factors led to dramatic patterning changes and a reprogramming of Wnt/FGFRLs into controlling new positional outputs. These results identify src-1 as a factor that promotes robustness of the AP positional system that instructs appropriate regeneration.

Highlights

Src-1 suppresses head and trunk identity

Src-1 can regulate positional control gene domains

Src-1 likely acts independently of notum/Wnt and FGFRL signals

Src-1 inhibition broadly sensitizes animals to AP pattern disruption
A method for high throughput image based antifungal screening
Authors: Sabburg Rosalie , Gregson Aphrika , Urquhart Andrew S. , Aitken Elizabeth A. B. , Smith Linda , Thatcher Louise F. , Gardiner Donald M.
Published: August 2021

Robust antifungal screening is technically challenging particularly for filamentous fungi. We present a method for undertaking antifungal screening assays that builds upon existing broth dilution protocols and incorporates time resolved image-based assessment of fungal growth. We show that the method performs with different fungi, particularly those for which spores can be used as inoculum, and with different compound classes, can accurately assess susceptibility or otherwise in only few hours, performs well even without replication and can even account for differences in inherent growth properties of strains.
Deploying anin vitrogut model to assay the impact of a mannan-oligosaccharide prebiotic, Bio-Mos® on the Atlantic salmon (Salmo salar) gut microbiome
Authors: Kazlauskaite R. , Cheaib B. , Humble J. , Heys C. , Ijaz U. Z. , Connelly S. , Sloan W.T. , Russell J. , Martinez-Rubio L. , Sweetman J. , Kitts A. , McGinnity P. , Lyons P. , Llewellyn M.S.
Published: August 2021

Mannose-oligosaccharide (MOS) pre-biotics are widely deployed in animal agriculture as immunomodulators as well as to enhance growth and gut health. Their mode of action is thought to be mediated through their impact on host microbial communities and the associated metabolism. Bio-Mos is a commercially available pre-biotic currently used in the agri-feed industry. To assess Bio-Mos for potential use as a prebiotic growth promotor in salmonid aquaculture, we have modified an established Atlantic salmonin vitrogut model, SalmoSim, to evaluate its impact on the host microbial communities. Inoculated from biological triplicates of adult farmed salmon pyloric caeca compartments, the microbial communities were stabilised in SalmoSim followed by a twenty-day exposure to the prebiotic and in turn followed by an eight day ‘wash out’ period. Dietary inclusion of MOS resulted in a significant increase in formate (p=0.001), propionate (p=0.037) and isovalerate (p=0.024) levels, correlated with increased abundances of several, principally, anaerobic microbial genera (Fusobacterium,Agarivorans,Pseudoalteromonas). DNA metabarcoding with the 16S rDNA marker confirmed a significant shift in microbial community composition in response to MOS supplementation with observed increase in lactic acid producingCarnobacterium. In conjunction with previousin vivostudies linking enhanced volatile fatty acid production alongside MOS supplementation to host growth and performance, our data suggests that Bio-Mos may be of value in salmonid production. Furthermore, our data highlights the potential role ofin vitrogut models to augmentin vivotrials of microbiome modulators.

Importance

In this paper we report the results of the impact of prebiotic (MOS supplementation) on microbial communities within recently developed Atlantic salmon gut microbiomein vitrosimulator. Our data suggest that Bio-Mos may be of value in salmonid production as it enhances volatile fatty acid production in the Atlantic salmon gut and correlates with a significant shift in microbial community composition with observed increase in lactic acid producingCarnobacterium. In conjunction with previousin vivostudies linking enhanced volatile fatty acid production alongside MOS supplementation to host growth and performance, our data suggest that Bio-Mos may be of value in salmonid production. Furthermore, our data highlights the potential role ofin vitrogut models to augmentin vivotrials of microbiome modulators.
Semantic scene-object consistency modulates N300/400 EEG components, but does not automatically facilitate object representations
Authors: Chen Lixiang , Cichy Radoslaw Martin , Kaiser Daniel
Published: August 2021

During natural vision, objects rarely appear in isolation, but often within a semantically related scene context. Previous studies reported that semantic consistency between objects and scenes facilitates object perception, and that scene-object consistency is reflected in changes in the N300 and N400 components in EEG recordings. Here, we investigate whether these N300/400 differences are indicative of changes in the cortical representation of objects. In two experiments, we recorded EEG signals while participants viewed semantically consistent or inconsistent objects within a scene; in Experiment 1, these objects were task-irrelevant, while in Experiment 2, they were directly relevant for behavior. In both experiments, we found reliable and comparable N300/400 differences between consistent and inconsistent scene-object combinations. To probe the quality of object representations, we performed multivariate classification analyses, in which we decoded the category of the objects contained in the scene. In Experiment 1, in which the objects were not task-relevant, object category could be decoded from around 100 ms after the object presentation, but no difference in decoding performance was found between consistent and inconsistent objects. By contrast, when the objects were task-relevant in Experiment 2, we found enhanced decoding of semantically consistent, compared to semantically inconsistent, objects. These results show that differences in N300/400 components related to scene-object consistency do not index changes in cortical object representations, but rather reflect a generic marker of semantic violations. Further, our findings suggest that facilitatory effects between objects and scenes are task-dependent rather than automatic.
Axonal T2 estimation using the spherical variance of the strongly diffusion-weighted MRI signal
Authors: Pizzolato Marco , Andersson Mariam , Canales-Rodríguez Erick Jorge , Thiran Jean-Philippe , Dyrby Tim B.
Published: August 2021

In magnetic resonance imaging, the application of a strong diffusion weighting suppresses the signal contributions from the less diffusion-restricted constituents of the brain’s white matter, thus enabling the estimation of the transverse relaxation time T2 that arises from the more diffusion-restricted constituents such as the axons. However, the presence of cell nuclei and vacuoles can confound the estimation of the axonal T2, as diffusion within those structures is also restricted, causing the corresponding signal to survive the strong diffusion weighting. We devise an estimator of the axonal T2 based on the directional spherical variance of the strongly diffusion-weighted signal. The spherical variance T2 estimates are insensitive to the presence of isotropic contributions to the signal like those provided by cell nuclei and vacuoles. We show that with a strong diffusion weighting these estimates differ from those obtained using the directional spherical mean of the signal which contains both axonal and isotropically-restricted contributions. Our findings hint at the presence of an MRI-visible isotropically-restricted contribution to the signal in the white matter ex vivo fixed tissue (monkey) at 7T, and do not allow us to discard such a possibility also for in vivo human data collected with a clinical 3T system.
Heterozygous loss of ZBTB38 leads to early embryonic lethality in mice via suppressing Nanog and Sox2
Authors: Nishio Miki , Matsuura Takuya , Hibi Shunya , Ohta Shiomi , Oka Chio , Sasai Noriaki , Ishida Yasumasa , Matsuda Eishou
Published: August 2021

Mammalian DNA methylation is an epigenetic modification which is involved in various biological processes, including gene expression regulation. In mice, methyltransferases are responsible for DNA methylation, which are critical for early embryogenesis. However, the significance of methyl-CpG binding proteins (MBPs) that bind methylated CpG remains largely unknown. We previously demonstrated that ZBTB38/CIBZ-a zinc finger type of MBP-is required for ES cell proliferation by positively regulating Nanog expression. However, the physiological function of ZBTB38 remains unclear. In this study, we generated conditional ZBTB38 knockout mice using Cre-loxP technology. Unexpectedly, our results showed that germline loss of the ZBTB38 single allele resulted in decreased epiblast cell proliferation and increased apoptosis shortly after implantation, leading to early embryonic lethality. We found that heterozygous loss of ZBTB38 reduced the expression of Nanog, Sox2, and the genes responsible for epiblast proliferation, differentiation, and cell viability. Despite this lethal phenotype, ZBTB38 is dispensable for ES cell establishment and identity. Together, these findings indicate that ZBTB38 is essential for early embryonic development, providing new insights into the roles of MBP in implantation.
Identification of HCN1 as a 14-3-3 client
Authors: Lankford Colten , Houtman Jon , Baker Sheila
Published: August 2021

Hyperpolarization activated cyclic nucleotide-gated channel 1 (HCN1) is expressed throughout the nervous system and is critical for regulating neuronal excitability, with mutations being associated with multiple forms of epilepsy. Adaptive modulation of HCN1 has been observed as has pathogenic dysregulation. While the mechanisms underlying this modulation remain incompletely understood, regulation of HCN1 has been shown to include phosphorylation. A candidate phosphorylation-dependent regulator of HCN1 channels is 14-3-3. We used bioinformatics to identify three potential 14-3-3 binding sites in HCN1. Isothermal titration calorimetry demonstrated that recombinant 14-3-3 binds all three phospho-peptides with low micromolar affinity. We confirmed that 14-3-3 could pull down HCN1 from multiple tissue sources and used HEK293 cells to detail the interaction. Two binding sites in the intrinsically disordered C-terminus of HCN1 were necessary and sufficient for a phosphorylation-dependent interaction with 14-3-3. The same region of HCN1 containing the 14-3-3 binding sites is required for phosphorylation-independent protein degradation. We propose a model in which phosphorylation of S810 and S867 (human S789 and S846) recruits 14-3-3 to inhibit a yet unidentified factor signaling for protein degradation, thus increasing the half-life of HCN1.