bluuebunny/crossref_metadata_2025 huggingface dataset:
Dynamic characteristics and Functional Analysis Provide new insights into the role of GauERF105 in resistance against Verticillium wilt in Cotton
Authors: Wang Yanqing , Umer Muhammad Jawad , Hou Yuqing , Xu Yanchao , Mehari Teame Gereziher , Zheng Jie , Wang Yuhong ,   CAI, Zhou Zhongli , Li Zhikun , Liu Fang
Published: January 2022

Verticillium wilt is the most devastating disease of cotton and it results in huge yield losses every year in the fields. The underlying mechanisms of VW in cotton are not well explored yet. In the current approach we used the transcriptome data from G. australe in response to Verticillium wilt attack to mine the ERF TFs and prove their potential role in resistance against VW attack in cotton. We identified 23 ERFs in total, and on the basis of expression at different time points i.e., 24h, 48h and 72h post inoculation and selected GauERF105 for further validation. We performed VIGS in cotton and over expression in Arabidopsis respectively. Moreover, DAB and trypan staining also suggests that the impact of disease was more in the wildtype as compared to transgene lines. On the basis of our results, we confirmed that GauERF105 is the key candidate and playing a key role for defending cotton against VW attack. Current finding might be helpful for generating resistance germplasm in cotton and it will be beneficial to recover the yield losses in field.
Predicting COVID-19 severity using major risk factors and received vaccines
Authors: Israel Ariel , Schäffer Alejandro A. , Merzon Eugene , Green Ilan , Magen Eli , Golan-Cohen Avivit , Vinker Shlomo , Ruppin Eytan
Published: January 2022

Background

Vaccines are highly effective in preventing severe disease and death from COVID-19, and new medications that can reduce severity of disease have been approved. However, many countries are facing limited supply of vaccine doses and medications. A model estimating the probabilities for hospitalization and mortality according to individual risk factors and vaccine doses received could help prioritize vaccination and yet scarce medications to maximize lives saved and reduce the burden on hospitalization facilities.

Methods

Electronic health records from 101,039 individuals infected with SARS-CoV-2, since the beginning of the pandemic and until November 30, 2021 were extracted from a national healthcare organization in Israel. Logistic regression models were built to estimate the risk for subsequent hospitalization and death based on the number of BNT162b2 mRNA vaccine doses received and few major risk factors (age, sex, body mass index, hemoglobin A1C, kidney function, and presence of hypertension, pulmonary disease and malignancy).

Results

The models built predict the outcome of newly infected individuals with remarkable accuracy: area under the curve was 0.889 for predicting hospitalization, and 0.967 for predicting mortality. Even when a breakthrough infection occurs, having received three vaccination doses significantly reduces the risk of hospitalization by 66% (OR=0.339) and of death by 78% (OR=0.223).

Conclusions

The models enable rapid identification of individuals at high risk for hospitalization and death when infected. These patients can be prioritized to receive booster vaccination and the yet scarce medications. A calculator based on these models is made publicly available on http://covidest.web.app
Inferring effects of mutations on SARS-CoV-2 transmission from genomic surveillance data
Authors: Lee Brian , Quadeer Ahmed Abdul , Sohail Muhammad Saqib , Finney Elizabeth , Ahmed Syed Faraz , McKay Matthew R , Barton John P
Published: January 2022

New and more transmissible variants of SARS-CoV-2 have arisen multiple times over the course of the pandemic. Rapidly identifying mutations that affect transmission could improve our understanding of viral biology and highlight new variants that warrant further study. Here we develop a generic, analytical epidemiological model to infer the transmission effects of mutations from genomic surveillance data. Applying our model to SARS-CoV-2 data across many regions, we find multiple mutations that substantially affect the transmission rate, both within and outside the Spike protein. The mutations that we infer to have the largest effects on transmission are strongly supported by experimental evidence. Importantly, our model detects lineages with increased transmission even at low frequencies. As an example, we infer significant transmission advantages for the Alpha, Delta, and Omicron variants shortly after their appearances in regional data, when their local frequencies were only around 1-2%. Our model thus facilitates the rapid identification of variants and mutations that affect transmission from genomic surveillance data.
Anin vivopig model for testing novel PET radioligands targeting cerebral protein aggregates
Authors: Raval Nakul Ravi , Nasser Arafat , Madsen Clara Aabye , Beschorner Natalie , Beaman Emily Eufaula , Juhl Morten , Lehel Szabolcs , Palner Mikael , Svarer Claus , Plavén-Sigray Pontus , Jørgensen Louise Møller , Knudsen Gitte Moos
Published: January 2022

Positron emission tomography (PET) has become an essential clinical tool for diagnosing neurodegenerative diseases with abnormal accumulation of proteins like amyloid-β or tau. Despite many attempts, it has not been possible to develop an appropriate radioligand for imaging aggregated α-synuclein in the brain for diagnosing, e.g., Parkinson’s Disease. Access to a large animal model with α-synuclein pathology would critically enable a more translationally appropriate evaluation of novel radioligands.

We here establish a pig model with cerebral injections of α-synuclein preformed fibrils or brain homogenate from postmortem human brain tissue from individuals with Alzheimer’s disease (AD) or dementia with Lewy body (DLB) into the pig’s brain, using minimally invasive surgery and validated against saline injections. In the absence of a suitable α-synuclein radioligand, we validated the model with the unselective amyloid-β tracer [11C]PIB, which has a high affinity for β-sheet structures in aggregates. Gadolinium-enhanced MRI confirmed that the blood-brain barrier was intact. A few hours post-injection, pigs were PET scanned with [11C]PIB. Quantification was done with Logan invasive graphical analysis and simplified reference tissue model 2 using the occipital cortex as a reference region. After the scan, we retrieved the brains to confirm successful injection using autoradiography and immunohistochemistry.

We found four times higher [11C]PIB uptake in AD-homogenate-injected regions and two times higher uptake in regions injected with α-synuclein-preformed-fibrils compared to saline. The [11C]PIB uptake was the same in non-injected (occipital cortex, cerebellum) and injected (DLB-homogenate, saline) regions. With its large brains and ability to undergo repeated PET scans as well as neurosurgical procedures, the pig provides a robust, cost-effective, and good translational model for assessment of novel radioligands including, but not limited to, proteinopathies.
AVATAR: AI Vision Analysis for Three-dimensional Action in Real-time
Authors: Kim Dae-Gun , Shin Anna , Jeong Yong-Cheol , Park Seahyung , Kim Daesoo
Published: January 2022

Artificial intelligence (AI) is an emerging tool for high-resolution behavioural analysis and conduction of human-free behavioural experiments. Here, we applied an AI-based system, AVATAR, which automatically virtualises 3D motions from the detection of 9 body parts. This allows quantification, classification and detection of specific action sequences in real-time and facilitates closed-loop manipulation, triggered by the onset of specific behaviours, in freely moving mice.
Release of HIV-1 particles from the viral compartment in macrophages requires an associated cytoskeleton and is driven by mechanical constraints
Authors: Rodrigues Vasco , Taheraly Sarah , Maurin Mathieu , San-Roman Mabel , Granier Emma , Hanouna Anael , BENAROCH Philippe
Published: January 2022

A defining feature of HIV-1 replication in macrophages is that viral assembly occurs at the limiting membrane of a compartment often named VCC (virus-containing compartments) that is connected to the extracellular medium. The newly formed viral progeny pinches of the membrane and accumulates in the lumen of the VCC. While HIV budding has been extensively studied, very little is known about how viral particles present in the lumen of VCC are released in the extracellular medium. Here we show that the actin dynamics are critical for this process by combining ultrastructural analyses, time-lapse microscopy and perturbations of the actin cytoskeleton. We found that jasplakinolide, which stabilizes actin fibres, inhibited viral release from HIV-1-infected macrophages. Furthermore, in jasplakinolide-treated macrophages, VCC became scattered and no longer co-localized with the integrin CD18, nor the phosphorylated form of the focal adhesion kinase PYK2. Inhibition of PYK2 activity in infected macrophages promoted intracellular retention of viral particles in VCC that were no longer connected to the plasma membrane. Finally, we stimulated the rapid release of viral particles from the VCC by subjecting infected macrophages to frustrated phagocytosis. As macrophages spread on IgG-coated glass surfaces, VCC rapidly migrated to the basal membrane and released their viral content in the extracellular medium, which required their association with CD18 and the actin cytoskeleton. These results highlight that VCC trafficking and virus release are intimately linked to the reorganization of the macrophage actin cytoskeleton in response to external physical cues, suggesting that it might be regulated in tissues by the mechanical stress to which these cells are exposed.
Importance of small diameter woody plants and treelet species in tropical wet evergreen forest of southern western ghats, india
Authors: Sreejith K. A. , Sanil M.S. , Prasad T.S. , Prejith M. P. , Sreekumar V.B. , Murali Akhil
Published: January 2022

Tropical forests have long been accepted for their productivity and ecosystem services on account of their high diversity and stand structural attributes. In spite of their significance, tropical forests, and especially those of Asia, remain understudied. Until recently, most forest inventories in Asia have concentrated on trees 10 cm in diameter. Floristic composition, plant species diversity, above ground biomass, basal area and diversity were investigated across different life form and two-diameter classes in a large scale 10-ha plot, in the undisturbed tropical seasonal rain forest of Southern Western Ghats, Kerala, India. Regeneration pattern of the study area was examined by evaluating fisher’s alpha and IVI (Important Value Index) across three layer of vegetation (seedling, sapling, and tree). Within the plot, we recorded 25,390 woody plant species ≥1 cm dbh from 45 families, 91 genera, and 106 species. Plant density was 2539 woody individuals per hectare, with a basal area of 47.72 m2/ha and an above-ground biomass of 421.77 Mg/ha. By basal area, density, and frequency, the Rubiaceae, Sapotaceae, and Malvaceae families were the most important. Small-diameter trees (1 cm ≤ dbh ≤10 cm) found to be 78 percent of the total tree population, 20.2 percent of the basal area, and 1.4 percent of the aboveground biomass. They also possessed 6 percent more diversity at the family level, 10% more diversity at the genus level, and 12% more diversity at the species level than woody individuals under 10 cm dbh.. Woody individuals of treelets life form and small-diameter classes were much more diverse and dense than the other groups, indicating that results based only on larger canopy trees and larger diameter class may be not an appropriate representation of the diversity status of a particular tropical forest type. Lower density of individuals in initial girth class indicates the vulnerability of the forest system to anthropogenic, natural disturbance and a changing climate. Reduce the minimum diameter limit down to 1 cm, in contrast to 10 cm limit used in most of the evergreen forest inventories, revealed a high density and diversity in thelower stories.
Expectation violations produce error signals in mouse V1
Authors: Price Byron H. , Jensen Cambria M. , Khoudary Anthony A. , Gavornik Jeffrey P.
Published: January 2022

Repeated exposure to visual sequences changes the form of evoked activity in the primary visual cortex (V1). Predictive coding theory provides a potential explanation for this, namely that plasticity shapes cortical circuits to encode spatiotemporal predictions and that subsequent responses are modulated by the degree to which actual inputs match these expectations. Here we use a recently developed statistical modeling technique called Model-Based Targeted Dimensionality Reduction (MbTDR) to study visually-evoked dynamics in mouse V1 in context of a previously described experimental paradigm called “sequence learning”. We report that evoked spiking activity changed significantly with training, in a manner generally consistent with the predictive coding framework. Neural responses to expected stimuli were suppressed in a late window (100-150ms) after stimulus onset following training, while responses to novel stimuli were not. Omitting predictable stimuli led to increased firing at the expected time of stimulus onset, but only in trained mice. Substituting a novel stimulus for a familiar one led to changes in firing that persisted for at least 300ms. In addition, we show that spiking data can be used to accurately decode time within the sequence. Our findings are consistent with the idea that plasticity in early visual circuits is involved in coding spatiotemporal information.
Reduced synaptic activity and dysregulated extracellular matrix pathways are common phenotypes in midbrain neurons derived from sporadic and mutation-associated Parkinson’s disease patients
Authors: Stern Shani , Lau Shong , Manole Andreea , Rosh Idan , Percia Menahem , Ezer Ran Ben , Shokhirev Maxim N. , Qiu Fan , Schafer Simon , Mansour Abed , Stern Tchelet , Ofer Pola , Stern Yam , Diniz Ana Mendes , Moore Lynne Randolph , Nayak Ritu , Aicher Aidan , Rhee Amanda , Wong Thomas L. , Nguyen Thao , Linker Sara B. , Winner Beate , Freitas Beatriz C. , Jones Eugenia , Bardy Cedric , Brice Alexis , Winkler Juergen , Marchetto Maria C. , Gage Fred H.
Published: January 2022

Several mutations that cause Parkinson’s disease (PD) have been identified over the past decade. These account for 15-25% of PD cases; the rest of the cases are considered sporadic. Currently, it is accepted that PD is not a single monolithic disease but rather a constellation of diseases with some common phenotypes. While rodent models exist for some of the PD-causing mutations, research on the sporadic forms of PD is lagging due to a lack of cellular models. In our study, we differentiated PD patient-derived dopaminergic (DA) neurons from induced pluripotent stem cells (iPSCs) of several PD-causing mutations as well as from sporadic PD patients. Strikingly, we observed a common neurophysiological phenotype: Neurons derived from PD patients had a severe reduction in the rate of synaptic currents compared to those derived from healthy controls. While the relationship between mutations in genes such as the SNCA and LRRK2 and a reduction in synaptic transmission has been investigated before, here we show evidence that the pathogenesis of the synapses in neurons is a general phenotype in PD. Analysis of RNA sequencing results displayed changes in gene expression in different synaptic mechanisms as well as other affected pathways such as extracellular matrix-related pathways. Some of these dysregulated pathways are common to all PD patients (monogenic or idiopathic). Our data, therefore, shows changes that are central and convergent to PD and suggests a strong involvement of the tetra-partite synapse in PD pathophysiology.
Low-cost arabinose induced genetic circuit for protein production: Modeling
Authors: Gómez Christian J. Flores , García Barrera Jorge L. , de la Cruz Edgar Valeria
Published: January 2022

A low-cost reagent-producing genetic circuit was designed during this work. Its functioning is based on a positive feedback loop induced by a small amount of arabinose, allowing users to obtain reactants in a safe, constant, and controlled manner. The “design only” approach to the project allows us to work in different kinds of computational models, thus, an ODE-based model was thoroughly developed and a cellular automata-based one was experimented with.

Working on the ODE model, equilibrium states and system stability were studied. Circuit properties were also focused on one of which was a high concentration of interest protein produced by low inductor inputs. As a result, a mathematical expression capable of describing the quantity of produced reagent was obtained. In addition, the cellular automata model offers a new perspective, given its differences from the ODE model e.g. this type of model is a stochastic analysis and describes each cell individually instead of describing the whole cellular population.
STReTCh: a strategy for facile detection of mechanical forces across proteins in cells
Authors: Zhong Brian L. , Vachharajani Vipul T. , Dunn Alexander R.
Published: January 2022

Numerous proteins experience and respond to mechanical forces as an integral part of their cellular functions, but measuring these forces remains a practical challenge. Here, we present a compact, 11 kDa molecular tension sensor termed STReTCh (Sensing Tension by Reactive Tag Characterization). Unlike existing genetically encoded tension sensors, STReTCh does not rely on experimentally demanding Förster resonance energy transfer (FRET)-based measurements and is compatible with typical fix-and-stain protocols. Using a magnetic tweezers assay, we calibrate the STReTCh module and show that it responds to physiologically relevant, piconewton forces. As proof-of-concept, we use an extracellular STReTCh-based sensor to visualize cell-generated forces at integrin-based adhesion complexes. In addition, we incorporate STReTCh into vinculin, a cytoskeletal adaptor protein, and show that STReTCh reports on forces transmitted between the cytoskeleton and cellular adhesion complexes. These data illustrate the utility of STReTCh as a broadly applicable tool for the measurement molecular-scale forces in biological systems.
Viscoelastic RNA entanglement and advective flow underlie nucleolar form and function
Authors: Riback Joshua A. , Eeftens Jorine M. , Lee Daniel S. W. , Quinodoz Sofia A. , Beckers Lien , Becker Lindsay A. , Brangwynne Clifford P.
Published: January 2022

The nucleolus facilitates transcription, processing, and assembly of ribosomal RNA (rRNA), the most abundant RNA in cells. Nucleolar function is facilitated by its multiphase liquid properties, but nucleolar fluidity and its connection to ribosome biogenesis remain unclear. Here, we used quantitative imaging, mathematical modeling, and pulse-chase nucleotide labelling to map nucleolar rRNA dynamics. Inconsistent with a purely diffusive process, rRNA steadily expands away from the transcriptional sites, moving in a slow (~1Å/s), radially-directed fashion. This motion reflects the viscoelastic properties of a highly concentrated gel of entangled rRNA, whose constant polymerization drives steady outward flow. We propose a new viscoelastic rRNA release model, where nucleolar rRNA cleavage and processing reduce entanglement, fluidizing the nucleolar periphery to facilitate release of mature pre-ribosomal particles.
Neuronal cell-type and circuit basis for visual predictive processing
Authors: Zou Jinmao , Huang Lawrence , Wang Lizhao , Xu Yuanyuan , Li Chenchang , Peng Qilin , Zeng Hongkui , Zhang Siyu , Li Lu
Published: January 2022

Bayesian Brain theory suggests brain utilises predictive processing framework to interpret the noisy world1-11. Predictive processing is essential to perception, action, cognition and psychiatric disease12, but underlying neural circuit mechanisms remain undelineated. Here we show the neuronal cell-type and circuit basis for visual predictive processing in awake, head-fixed mice during self-initiated running. Preceding running, vasoactive intestinal peptide (VIP)-expressing inhibitory interneurons (INs) in primary visual cortex (V1) are robustly activated in absence of structured visual stimuli. This pre-running activation is mediated via distal top-down projections from frontal, parietal and retrosplenial areas known for motion planning, but not local excitatory inputs associated with the bottom-up pathway. Somatostatin (SST) INs show pre-running suppression and post-running activation, indicating a VIP-SST motif. Differential VIP-SST peri-running dynamics anisotropically suppress neighbouring pyramidal (Pyr) neurons, preadapting Pyr neurons to the incoming running. Our data delineate key neuron types and circuit elements of predictive processing brain employs in action and perception.

One Sentence Summary

VIP-SST-Pyr microcircuit in visual predictive processing during voluntary running
Cyanopeptides Restriction and Degradation Co-mediate Microbiota Assembly During a Freshwater Cyanobacterial Harmful Algal Bloom (CyanoHAB)
Authors: Gao Han , Zhao Ze , Zhang Lu , Ju Feng
Published: January 2022

Cyanobacterial harmful algal blooms (CyanoHABs) are globally intensifying and exacerbated by climate change and eutrophication. However, microbiota assembly mechanisms underlying CyanoHABs remain scenario specific and elusive. Especially, cyanopeptides, as a group of bioactive secondary metabolites of cyanobacteria, could affect microbiota assembly and ecosystem function. Here, the trajectory of cyanopeptides were followed and linked to microbiota duringMicrocystis-dominated CyanoHABs in lake Taihu, China. The most abundant cyanopeptide classes detected included microginin, spumigin, microcystin, nodularin and cyanopeptolin with total MC-LR-equivalent concentrations between 0.23 and 2051.54 ppb, of which cyanotoxins beyond microcystins (e.g., cyanostatin B and nodularin_R etc.) far exceeded reported organismal IC50and negatively correlated with microbiota diversity, exerting potential collective eco-toxicities stronger than microcystins alone. The microbial communities were differentiated by size fraction and sampling date throughout CyanoHABs, and surprisingly, their variances were better explained by cyanopeptides (19-38%) than nutrients (0-16%). Cyanopeptides restriction (e.g., inhibition) and degradation are first quantitatively verified as the deterministic drivers governing community assembly, with stochastic processes being mediated by interplay between cyanopeptide dynamics and lake microbiota. This study presents an emerging paradigm in which cyanopeptides restriction and degradation co-mediate lake water microbiota assembly, unveiling new insights about the ecotoxicological significance of CyanoHABs to freshwater ecosystems.
Whole genome sequencing of hematologically stained cells catapulted from Cell smears
Authors: Bae Sangwook , Jung Yushin , Kim Sungsik , Kim Jinhyun , Lee Amos Chungwon , Lee Dongsoon , Kwon Sunghoon
Published: January 2022

Analyzing archived peripheral blood smears is a potential route towards gaining cell morphology and genome information of blood cell types from various diseases. Yet, acquiring whole genome information from morphologically targeted cells was difficult, especially for rare cell types. The main causes for such difficulty were the inevitable usage of cell stains leading to whole genome amplification inhibition, and insufficient cell isolation performance of previously introduced laser microdissection (LMD) techniques. Here, we introduce a new laser-based cell isolation technique and a whole genome amplification (WGA) protocol optimized for whole genome analysis from minute input of hematologically stained cells. We were able to perform whole genome copy number profiling and SNP analysis from as little as 5 cells.
Applying biostimulants boosts forage productivity without affecting soil biotic and abiotic parameters on a Central Coast California rangeland
Authors: Carey Chelsea J. , Strohm Hayley , Smith Ford , Biaggi Mark
Published: January 2022

There is increasing interest in using biostimulant products, such as microbial inoculants and humic substances, to help manage rangelands regeneratively. Understanding how plant and soil communities on rangelands respond to these products is therefore important. In this study, we examined the combined effects of a commercial inoculant and humic product that are currently on the market, and asked whether they influenced rangeland forage productivity and quality, soil microbial biomass and community composition, and abiotic soil parameters in Central Coastal California. We found that forage productivity and some metrics of forage quality responded positively to the foliar application of a commercial microbial inoculant and humic product, but that these benefits were not mirrored by changes belowground in the microbial community or abiotic parameters. Depending on the goals of using the products, this could be seen as a winning scenario and suggests microbial inoculants and humic products could warrant attention as a potential tool for regenerative stewardship of rangelands. While our study derives from one ranch and therefore requires confirmation of its ubiquity prior to broadscale adoption, our results provide new insights into the usefulness of this approach for managing rangeland productivity in California’s Central Coast.
Robust hydrogel-integrated microsystems enabled by enhanced interfacial bonding strength
Authors: Bae Sang Wook , Kim Yong-Woo , Sun Jeong-Yun , Kwon Sunghoon
Published: January 2022

Noncovalent hydrogels, compared to covalent hydrogels, have distinctive advantages including biocompatibility and self-healing property but tend to have poor mechanical robustness, thus restricting their application spectrum. A clue to increase utility of such soft hydrogels without chemical bulk modification can be witnessed in biological organ walls where soft mucous epithelial layers are juxtaposed with tough connective tissues. Perhaps, similarly, bonding noncovalent hydrogels to stronger materials, such as tough hydrogels, might be a viable approach for increasing stability and scalability as well as creating novel functions for hydrogel-based systems. However when attempting to bond these two materials, each of the four existing hydrogel-hydrogel bonding method has practical shortcomings. In this work, we introduce a mucosa-inspired bonding method that realizes interfacial bonding of noncovalent hydrogels to tough, hybrid hydrogels without external glue or bulk modification of the noncovalent gel while preserving interfacial micropatterns. The procedure is simple and we confirmed broad applicability with various noncovalent hydrogels and tough hydrogels. We demonstrated the utility of our bonding method with novel applications regarding in vitro assay, soft robotics and biologically inspired systems.
Transcriptomic changes in the pituitary of female mice with androgen excess through dihydrotestosterone (DHT) treatment
Authors: Joseph Serene , Divall Sara , Wu Sheng
Published: January 2022

Androgen excess in women is associated with the development of PCOS and its abnormalities. The Hypothalamus Pituitary Ovarian axis signaling is altered with excessed androgens, leading to anovulation and infertility. Previous studies in the lab have shown that AR signaling in the pituitary alters gonadotrophin release. Hence, the present pioneering study was an approach to determine the transcriptomic changes responsible to the phenotype seen with DHT excess. RNA seq data showed that 583 genes were differentially regulated by DHT in pituitary, of which 344 were upregulated and 239 downregulated. Pathways involved for these genes included endoplasmic reticulum, Golgi apparatus, calcium signaling and vesicles. Meanwhile, Transcriptional factor analysis showed that majority of the genes changed had Androgen responsive elements.
Intestinal epithelial MHC class II regulation by HDAC3 instructs microbiota-specific CD4+ T cells
Authors: Eshleman Emily M. , Shao Tzu-Yu , Woo Vivienne , Rice Taylor , Whitt Jordan , Engleman Laura , Way Sing Sing , Alenghat Theresa
Published: January 2022

Aberrant immune responses to resident microbes promote inflammatory bowel disease and other chronic inflammatory conditions. However, how microbiota-specific immunity is controlled in mucosal tissues remains poorly understood. Here, we find that mice lacking epithelial expression of microbiota-sensitive histone deacetylase 3 (HDAC3) exhibit increased accumulation of commensal-specific CD4+ T cells in the intestine, provoking the hypothesis that epithelial HDAC3 may instruct local microbiota-specific immunity. Consistent with this, microbiota-specific CD4+ T cells and epithelial HDAC3 expression were concurrently induced following early-life microbiota colonization. Further, epithelial-intrinsic ablation of HDAC3 promoted T cell driven-colitis and primed development of pathogenic commensal-specific Th17 cells. Mechanistically, HDAC3 was essential for MHC class II (MHCII) expression by the intestinal epithelium, and epithelial-intrinsic MHCII actively limited commensal-specific Th17 cells and prevented microbiota-triggered inflammation. Remarkably, HDAC3 enabled the microbiota to induce MHCII on epithelial cells and limit the number of commensal-specific T cells in the intestine. Collectively, these data reveal a central role for an epithelial histone deacetylase in controlling development of tissue-intrinsic T cells that recognize commensal microbes and drive pathologic inflammation.
Cooperative phagocytosis underlies macrophage immunotherapy of solid tumours and initiates a broad anti-tumour IgG response
Authors: Andrechak Jason C. , Dooling Lawrence J. , Hayes Brandon H. , Kadu Siddhant , Zhang William , Pan Ruby , Vashisth Manasvita , Irianto Jerome , Alvey Cory M. , Discher Dennis E.
Published: January 2022

Macrophages are abundant in solid tumours and typically associate with poor prognosis, but macrophage clusters in tumour nests have also been reported as beneficial even though dispersed macrophages would have more contacts with cancer cells. Here, by maximizing both phagocytic activity and macrophage numbers, we discover cooperative phagocytosis by low entropy clusters in rapidly growing engineered immuno-tumouroids. The results fit the calculus of proliferation-versus-engulfment, and rheological measurements and molecular perturbations provide a basis for understanding phagocytic disruption of a tumour’s cohesive forces in soft cellular phases. The perturbations underscore the utility of suppressing a macrophage checkpoint in combination with an otherwise ineffective tumour-opsonizing monoclonal antibody, and the approach translates in vivo to tumour elimination that durably protects mice from re-challenge and metastasis. Adoptive transfer of engineered macrophages increases the fraction of mice that eliminate tumours and potentially overcomes checkpoint blockade challenges in solid tumours like insufficient permeation of blocking antibodies and on-target, off-tumour binding. Finally, anti-cancer IgG induced in vivo are tumour-specific but multi-epitope and contribute to a phagocytic feedback that drives macrophage clustering in vitro. Given that solid tumours remain challenging for immunotherapies, durable anti-tumour responses here illustrate unexpected advantages in maximizing net phagocytic activity.
Novel Methods for Elucidating Modality Importance in Multimodal Electrophysiology Classifiers
Authors: Ellis Charles A. , Sendi Mohammad S.E. , Zhang Rongen , Carbajal Darwin A. , Wang May D. , Miller Robyn L. , Calhoun Vince D.
Published: January 2022

Multimodal classification is increasingly common in biomedical informatics studies. Many such studies use deep learning classifiers with raw data, which makes explainability difficult. As such, only a few studies have applied explainability methods, and new methods are needed. In this study, we propose sleep stage classification as a testbed for method development and train a convolutional neural network with electroencephalogram (EEG), electrooculogram, and electromyogram data. We then present a global approach that is uniquely adapted for electrophysiology analysis. We further present two local approaches that can identify subject-level differences in explanations that would be obscured by global methods and that can provide insight into the effects of clinical and demographic variables upon the patterns learned by the classifier. We find that EEG is globally the most important modality for all sleep stages, except non-rapid eye movement stage 1 and that local subject-level differences in importance arise. We further show that sex, followed by medication and age had significant effects upon the patterns learned by the classifier. Our novel methods enhance explainability for the growing field of multimodal classification, provide avenues for the advancement of personalized medicine, and yield novel insights into the effects of demographic and clinical variables upon classifiers.
Maturation of prefrontal input to dorsal raphe nucleus increases behavioral persistence in mice
Authors: Gutierrez-Castellanos Nicolas , Sarra Dario , Godinho Beatriz S. , Mainen Zachary F.
Published: January 2022

The ability to persist towards a desired objective is a fundamental aspect of behavioral control whose impairment is implicated in several behavioral disorders. One of the prominent features of behavioral persistence is that its maturation occurs relatively late in development. This is presumed to echo the developmental time course of a corresponding circuit within late-maturing parts of the brain, such as the prefrontal cortex, but the specific identity of the responsible circuits is unknown. Here, we describe the maturation of the projection from layer 5 neurons of the prefrontal cortex to the dorsal raphe nucleus in mice. We show using pathway-specific optogenetic stimulation that this connection undergoes a dramatic increase in synaptic potency between postnatal weeks 3 and 8, corresponding to the transition from juvenile to adult. We then show that this period corresponds to an increase in the behavioral persistence that mice exhibit in a foraging task. Finally, we use genetic targeting to selectively ablate this pathway in adulthood and show that mice revert to a behavioral phenotype similar to juveniles. These results suggest that the prefrontal to dorsal raphe pathway is a critical anatomical and functional substrate of the development and manifestation of behavioral control.
GNNQQNY: Methodology for biophysical and structural understanding of aggregation
Authors: Burra Gunasekhar , Maina Mahmoud B. , Serpell Louise C. , Thakur Ashwani K.
Published: January 2022

GNNQQNY sequence offers crucial information about the formation and structure of an amyloid fibril. In this study, we demonstrate a reproducible solubilisation protocol where the reduction of pH to 2.0 resulted in the generation of GNNQQNY monomers. The subsequent ultracentrifugation step removes the residual insoluble peptide from the homogeneous solution. This procedure ensures and allows the peptides to remain monomers till their aggregation is triggered by adjusting the pH to 7.2. The aggregation kinetics analysis showed a distinct lag-phase that is concentration-dependent, indicating nucleation-dependent aggregation kinetics. Nucleation kinetics analysis suggested a critical nucleus of size ∼7 monomers at physiological conditions. The formed nucleus acts as a template for further self-assembly leading to the formation of highly ordered amyloid fibrils. These findings suggest that the proposed solubilisation protocol provides the basis for understanding the kinetics and thermodynamics of amyloid nucleation and elongation in GNNQQNY sequences. This procedure can also be used for solubilising such small amyloidogenic sequences for their biophysical studies.
Efficient learning in children with rapid GABA boosting after training
Authors: Frank Sebastian M. , Becker Markus , Qi Andrea , Geiger Patricia , Frank Ulrike I. , Malloni Wilhelm M. , Sasaki Yuka , Greenlee Mark W. , Watanabe Takeo
Published: January 2022

It is unclear why and how children learn more efficiently than adults, although inhibitory systems, which play an important role in stabilizing learning, are immature in children. Here, we found that despite a lower baseline concentration of γ-aminobutyric acid (GABA) in early visual cortical areas in children (8 to 11 years old) than adults (18 to 35 years old), children exhibited a rapid boost of GABA immediately after visual training, whereas the concentration of GABA in adults remained unchanged after training. Moreover, behavioral experiments showed that children stabilized visual learning much faster than adults, showing rapid development of resilience to retrograde interference. These results together suggest that inhibitory systems in children’s brains are more dynamic and adapt more quickly to stabilize learning than in adults.

One Sentence Summary

Children learn more efficiently than adults due to faster stabilization of learning with rapid GABA boosting after training.
Local climate and vernalization requirements explain the latitudinal patterns of flowering initiation in the crop wild relativeLinum bienne
Authors: Landoni Beatrice , Suárez-Montes Pilar , Habeahan Rico H. F. , Brennan Adrian C. , Pérez-Barrales Rocío
Published: January 2022

Background and Aims

Days to flowering initiation in species with large geographic distribution often correlate with latitude. Latitude reflects climatic gradients, but it is unclear if large-scale differentiation in flowering results from adaptation to local climate, and whether adaptation to local climate could constrain shifts in distribution and colonization of new environments.

Methods

In its Western range in Europe,L. biennepopulations were surveyed to describe latitudinal patterns of flowering initiation and determine its correlation with the local climate of populations. This was measured under standardized greenhouse conditions, with a vernalization experiment to learn if chilling advances flowering, and with a reciprocal transplant experiment at three sites along the latitudinal gradient, recording flowering at the central site and plant survival in all sites. Also, genetic differentiation of populations along the latitudinal range was studied using microsatellite markers.

Key Results

Flowering initiation varied with latitude, with southern populations flowering earlier than northern populations. Latitude also predicted population response to vernalization, with chilling inducing a greater advance of flowering initiation in northern than southern populations. In general, plant survival in the reciprocal transplant experiment decreased with the geographic distance of populations to the experimental site and, at the central site, flowering initiation varied with latitude of origin. However, across experiments, the local climate of populations better predicted the differentiation in flowering initiation and vernalization response than latitude of origin. Finally, the microsatellite data revealed genetic differentiation of populations forming two groups that agree with a Mediterranean and Atlantic lineage.

Conclusions

The consistent result across experiments of a latitudinal cline in flowering initiation and in the vernalization response suggests that flowering is under genetic regulation and yet dependent on particular environmental and climatic cues at local scale. However, the genetic differentiation suggests that past population history might influenced the flowering initiation patterns detected.
Multiplex labeling and manipulation of endogenous neuronal proteins using sequential CRISPR/Cas9 gene editing
Authors: Droogers Wouter J , Willems Jelmer , MacGillavry Harold D , de Jong Arthur PH
Published: January 2022

Recent advances in CRISPR/Cas9-mediated knock-in methods enable labeling of individual endogenous proteins with fluorophores, to determine their spatiotemporal expression in intact biological preparations. However, multiplex knock-in methods remain limited, particularly in postmitotic cells, due to a high degree of crosstalk between genome editing events. We present Conditional Activation of Knock-in Expression (CAKE), which delivers efficient, flexible and accurate multiplex genome editing in neurons. CAKE is based on sequential gRNA expression operated by a Cre- or Flp-recombinase to control the time window for genomic integration of each donor sequence, which diminishes crosstalk between genome editing events. Importantly, CAKE is compatible with multiple CRISPR/Cas9 strategies, and we show the utilization of CAKE for co-localization of various endogenous proteins, including synaptic scaffolds, ion channels and neurotransmitter receptor subunits. Knock-in efficacy was highly sensitive to DNA vector amount, while knock-in crosstalk was dependent on the rate of donor DNA integration and timing of Cre activation. We applied CAKE to study the co-distribution of endogenous synaptic proteins using dual-color single-molecule localization microscopy, and we introduced dimerization modules to acutely control synaptic receptor dynamics in living neurons. Taken together, CAKE is a versatile method for multiplex protein labeling, enabling accurate detection, precise localization and acute manipulation of endogenous proteins in single cells.
Contribution of behavioural variability to representational drift
Authors: Sadeh Sadra , Clopath Claudia
Published: January 2022

Neuronal responses to similar stimuli change dynamically over time, raising the question of how internal representations can provide a stable substrate for neural coding. Recent work has suggested a large degree of drift in neural representations even in sensory cortices, which are believed to store stable representations of the external world. While the drift of these representations is mostly characterized in relation to external stimuli, the behavioural state of the animal (for instance, the level of arousal) is also known to strongly modulate the neural activity. We therefore asked how the variability of such modulatory mechanisms can contribute to representational changes. We analysed large-scale recording of neural activity from the Allen Brain Observatory, which was used before to document representational drift in the mouse visual cortex. We found that, within these datasets, behavioural variability significantly contributes to representational changes. This effect was broadcasted across various cortical areas in the mouse, including the primary visual cortex, higher order visual areas, and even regions not primarily linked to vision like hippocampus. Our computational modelling suggests that these results are consistent with independent modulation of neural activity by behaviour over slower time scales. Importantly, our analysis suggests that reliable but variable modulation of neural representations by behaviour can be misinterpreted as representational drift, if neuronal representations are only characterized in the stimulus space and marginalised over behavioural parameters.
Counting fluorescently labeled proteins in tissues in the spinning disk microscope using single-molecule calibrations
Authors: Liao Maijia , Kuo Yin-Wei , Howard Jonathon
Published: January 2022

Quantification of molecular numbers and concentrations in living cells is critical for testing models of complex biological phenomena. Counting molecules in cells requires estimation of the fluorescence intensity of single molecules, which is generally limited to imaging near cell surfaces, in isolated cells, or where motions are diffusive. To circumvent this difficulty, we have devised a calibration technique for spinning-disk confocal (SDC) microscopy, commonly used for imaging in tissues, that uses single-step bleaching kinetics to estimate the single-fluorophore intensity. To cross-check our calibrations, we compared the brightness of fluorophores in the SDC microscope to those in the total-internal-reflection (TIRF) and epifluorescence microscopes. We applied this calibration method to quantify the number of EB1-eGFP proteins in the comets of growing microtubule ends and to measure the cytoplasmic concentration of EB1-eGFP in sensory neurons in fly larvae. These measurements allowed us to estimate the dissociation constant of EB1-eGFP from the microtubules as wells as the GTP-tubulin cap size. Our results show the unexplored potential of single-molecule imaging using spinning disk confocal microscopy and provide a straight-forward method to count the absolute number of fluorophores in tissues which can be applied to a wide range of biological systems and imaging techniques.
Parent‐delivered contingency management for a treatment‐refusing young adult with gaming disorder: Case report
Authors: Riley Ben J. , Baigent Michael , Battersby Malcolm W. , King Daniel L.
Published: January 2022

Online video gaming is a popular activity among people of all ages. For some, however, gaming can become problematic. While evidence exists for the effectiveness of cognitive behavioural therapy for gaming disorder (GD), a major challenge is that adolescents and young adults, particularly males, are often reluctant to seek help and engage long term with a mental health practitioner. This report presents a case involving brief parent‐delivered contingency management for a 19‐year‐old male with GD who refused to engage with treatment services following a significant decline in functioning and a high‐lethality suicide attempt. This approach led to a substantial reduction in gaming time, as well as related gains in self‐care and independence. This case highlights the value and feasibility of developing a therapeutic alliance with a parent to manage excessive gaming behaviours among treatment‐refusing individuals with GD. Practical challenges and associated lessons from managing this case are discussed.

Practitioner points

Brief parent‐delivered contingency management was implemented for a 19‐year‐old treatment‐refusing male with GD.

This approach led to a substantial reduction in the young man's gaming time as well as related gains in areas of self‐care and independence at 6‐month follow‐up.

This case highlights the value and feasibility of developing a therapeutic alliance with a parent to manage excessive gaming behaviours among treatment‐refusing individuals with GD.
Soluble PD‐L1 and B7‐H4 serum levels during the course of physiological pregnancy
Authors: Mach Pawel , Köninger Angela , Reisch Beatrix , Kimmig Rainer , Gellhaus Alexandra
Published: January 2022

Problem

The aim of this study was to evaluate the soluble programmed death‐ligand (sPD‐L1) and soluble B7‐H4 (sB7‐H4) serum concentration levels longitudinal throughout the three trimesters of uncomplicated pregnancies.

Method of the study

sPD‐L1 and sB7‐H4 levels were determined with enzyme‐linked immunosorbent assay (ELISA). The patients (n = 26) were divided into three groups according to the pregnancy trimester. Among 26 women involved in the study 14 had longitudinal sB7‐H4 and sPD‐L1 measurements in each trimester of pregnancy.

Results

During the course of pregnancy, the sB7‐H4 blood serum levels were significant higher in second trimester than in first and third trimester, whereas sPD‐L1 levels increased significantly over the course of pregnancy.

Conclusion

The highest serum levels of sPD‐L1 in the third trimester suggest increasing suppression of maternal immunity throughout pregnancy, whereas elevated sB7‐H4 concentration levels in second trimester suggests different profile of T‐cell regulation in physiological pregnancy.