bluuebunny/crossref_metadata_2025 huggingface dataset:
miR-223 Plays A Critical Role in Obesogen-Enhanced Adipogenesis in Mesenchymal Stem Cells and in Transgenerational Obesity
Authors: Chang Richard C. , Joloya Erika M. , Li Zhuorui , Shoucri Bassem M. , Shioda Toshi , Blumberg Bruce
Published: October 2022

Exposure of pregnant F0 mouse dams to the obesogen tributyltin (TBT) predisposes unexposed male descendants to obesity and diverts mesenchymal stem cells (MSCs) toward the adipocytic lineage. TBT also promotes adipogenic commitment and differentiation of MSCs, in vitro. We sought to identify TBT-induced factors predisposing MSCs toward the adipocytic fate. We exposed mouse MSCs to TBT, the PPARγ-selective agonist rosiglitazone or the RXR-selective agonist LG-100268 and determined their transcriptomal profiles to determine candidate microRNAs (miR) regulating adipogenic commitment and differentiation. Of the top 10 candidate microRNAs predicted by Ingenuity Pathway Analysis, miR-21, miR-33 and miR-223 were expressed in a manner consistent with an ability to differentially regulate target genes during adipogenesis. After 24 hours exposure to 50 nM TBT, miR-223 levels in MSCs were increased and expression of its target genes ZEB1, NFIB, and FOXP1 was decreased. Both ROSI and TBT increased miR-223 levels, and this induction was inhibited by the PPARγ antagonist T0070907 but not by the RXR antagonists HX531 or UVI3003, placing miR-223 downstream of PPARγ. Chromatin immunoprecipitation confirmed TBT-induced binding of PPARγ to regulatory elements in the miR-223 promoter. miR-223 levels were elevated in white adipose tissue of F2 and F3 male descendants of pregnant F0 mouse dams exposed to 50 nM TBT throughout gestation. miR-223 levels were further induced in males fed with an increased fat diet. We infer that TBT induced miR-223 expression and increased adipogenesis in MSCs through the PPARγ pathway and that transgenerationally increased expression of miR-223 plays an important role in the development of obesity caused by TBT exposure.
Limited codiversification of the gut microbiota with humans
Authors: Good Benjamin H.
Published: October 2022

A recent study by Suzuki & Fitzstevenset al(1) argued that dozens of species of gut bacteria have codiversified with modern human populations. Reanalysis of their data reveals that the correlations between human and microbial phylogenies are substantially weaker than unlinked human chromosomes, and that similar correlations can arise through geographic structure alone. This suggests that codiversification has been limited within humans.
Heritable changes in chromatin contacts linked to transgenerational obesity
Authors: Chang Richard C. , Egusquiza Riann J. , Huang Yikai , Amato Angélica Amorim , Joloya Erika M. , Wheeler Hailey B. , Nguyen Angela , Shioda Keiko , Odajima Junko , Shioda Toshi , Blumberg Bruce
Published: October 2022

Burgeoning evidence demonstrates that responses to environmental exposures can be transmitted to subsequent generations through the germline without DNA mutations1,2. This is controversial because underlying mechanisms remain to be identified. Therefore, understanding how effects of environmental exposures are transmitted to unexposed generations without DNA mutations is a fundamental unanswered question in biology. Here, we used an established murine model of transgenerational obesity to show that direct or ancestral exposure to the obesogen tributyltin (TBT) elicited persistent changes in topologically associating domains (TADs) in primordial germ cells (PGCs) isolated from embryos of exposed and subsequent unexposed generations. New TAD boundaries were formed within theIdegene encoding insulin degrading enzyme in the exposed PGCs, then stably maintained in PGCs of the subsequent (unexposed) two generations. Concomitantly,IdemRNA expression was decreased in livers of male descendants from the exposed dams. These animals were hyperinsulinemic and hyperglycemic, phenocopyingIde-deficient mice that are predisposed to adult-onset obesity. Creation of new TAD boundaries in PGCs, suppression of hepaticIdemRNA, increased fat mass, hyperinsulinemia and hyperglycemia were male-specific. Our results provide a plausible molecular mechanism underlying transmission of the transgenerational predisposition to obesity caused by gestational exposure to an environmental obesogen. They also provide an entry point for future studies aimed at understanding how environmental exposures alter chromatin structure to influence physiology across multiple generations in mammals.
Using the AKAR3-EV biosensor to assess Sch9- & PKA-signalling in budding yeast
Authors: Botman Dennis , Kanagasabapathi Sineka , Teusink Bas
Published: October 2022

Budding yeast uses the well-conserved TORC1-Sch9 and cAMP-PKA signalling pathways to regulate adaptations to changing nutrient environments. Dynamic and single-cell measurements of the activity of these two cascades will improve our understanding of cellular adaptation of yeast. Here, we employed the AKAR3-EV biosensor developed for mammalian cells to measure the cellular phosphorylation status determined by Sch9 and PKA activity in budding yeast. Using various mutant strains and inhibitors, we show that AKAR3-EV robustly measures the Sch9- and PKA-dependent phosphorylation status in intact yeast cells. At the single-cell level, we found that the phosphorylation responses are homogenous for glucose, sucrose and fructose, but highly heterogeneous for mannose. The Sch9 and PKA pathways have a relatively high affinity for glucose (K0.5of 0.24 mM) under glucose derepressed conditions. Lastly, steady-state FRET levels of AKAR3-EV seem to be independent of growth rates, suggesting that the Sch9- and PKA-dependent phosphorylation activity are transient responses to nutrient transitions. We believe that the AKAR3-EV sensor is an excellent addition to the biosensor arsenal for illuminating cellular adaptation in single yeast cells.
A whole blood intracellular cytokine assay optimised for field site studies demonstrates polyfunctionality of CD4+ T cells in acute scrub typhus
Authors: Inthawong Manutsanun , Pinthong Nattapon , Thaiprakhong Areerat , Wangrangsimakul Tri , Sunyakumthorn Piyanate , Hill Jennifer , Sonthayanon Piengchan , Paris Daniel H. , Dunachie Susanna , Kronsteiner Barbara
Published: October 2022

Background

Assessment of cellular immune responses by combining intracellular cytokine staining and immunophenotyping using flow cytometry enables the simultaneous measurement of T cell phenotype and effector function in response to pathogens and vaccines. The use of whole blood samples rather than peripheral blood mononuclear cells avoids both the need for immediate processing and loss of functional antigen presenting cells due to processing and cryopreservation. Using whole blood provides the possibility to stimulate peripheral T cellsin situ, and is more suitable for studies where sample volume is limited, such as those involving children, the elderly and critically ill patients. The aim of this study was to provide a robust tool for the assessment of antigen-specific T cell responses in a field site setting with limited resources.

Methodology/Principle Findings

We optimised a flow cytometry-based whole blood intracellular cytokine assay (WBA) with respect to duration of antigen stimulation and intracellular protein retention time. We demonstrate the ability of the WBA to capture polyfunctional T cell responses in the context of acute scrub typhus infection, by measuring IFN-γ, TNF and IL-2 in CD4+ and CD8+ T cells in response to the causative agentO. tsutsugamushi(OT). Using an optimised OT antigen preparation, we demonstrate the presence of polyfunctional antigen-specific memory CD4+ T cells in the blood of scrub typhus patients.

Conclusions/Significance

In conclusion, this flow cytometry-based WBA is well-suited for use at field study sites, and enables the assessment of polyfunctional T cell responses to infectious agents and vaccines through delineation of antigen-specific cytokine secretion at the single cell level.

Author summary

Scrub typhus is an acute febrile illness caused by the bite of infected chigger mites transmittingO. tsutsugamushi, agramnegative obligate intracellular bacteria in the familyRickettsiaceae. The disease progression and clinical manifestations are closely associated with host immune responses. T cell responses are in strong relation with immune protection against scrub typhus. As there is limited knowledge on specific T cell roles against scrub typhus, we optimized a flow-cytometer based protocol to assessO. tsutsugumushi-specific T cell responses in whole blood samples, which is suitable for studies in limited resource settings. This method requires low blood volumes, but enables multiparametric immunophenotyping assessments. The optimized WBA protocol could be a useful tool for comprehensive immunopathological studies in scrub typhus, and other infectious diseases as well as vaccine studies in areas with limited availability of specialized equipment, while reliably capturing the complexity of the immune response.
The Rapid-Tome, a 3D-Printed Microtome, and an Updated Hand-Sectioning Method for High-Quality Plant Sectioning
Authors: Thomas David J. , Rainbow Jordan , Bartley Laura E.
Published: October 2022

Background

Microscopic analysis of plant anatomy is a common procedure in biology to study structure and function that requires high-quality sections for accurate measurements. Hand sectioning of specimens is typically limited to moderately soft tissue while harder samples prohibit sectioning by hand and/or result in inconsistent thicknesses.

Results

Here we present both a clearly described hand-sectioning method and a novel microtome design that together provide the means to section a variety of plant sample types. The described hand-sectioning method for herbaceous stems works well for softer subjects but is less suitable for samples with secondary growth (e.g., wood production). Instead, the “Rapid-Tome” is a novel tool for sectioning both soft and tougher high-aspect-ratio samples, such as stems and roots, with excellent sample control. The Rapid-Tome can be 3D-printed in approximately 13 hours on a mid-quality printer common at university maker spaces. After printing and trimming, Rapid-Tome assembly takes a few minutes with five metal parts common at hardware stores. Users sectioned a variety of plant samples including the hollow internodes of switchgrass (Panicum virgatum), fibrous switchgrass roots containing aerenchyma, and woody branches of eastern red cedar (Juniper virginiana) and American sycamore (Platanus occidentalis). A comparative analyses with Rapid-Tome-produced sections readily revealed a significant difference in seasonal growth of sycamore xylem vessel area in spring (49%) vs. summer (23%). Additionally, high school students with no prior experience produced sections with the Rapid-Tome adequate for comparative analyses of various plant samples in less than an hour.

Conclusions

The described hand-sectioning method is suitable for softer tissues, including hollow-stemmed grasses and similar samples. In addition, the Rapid-Tome provides capacity to safely produce high-quality sections of tougher plant materials at a fraction of the cost of traditional microtomes combined with excellent sample control. The Rapid-Tome features rapid sectioning, sample advancement, blade changes, and sample changes; is highly portable and can be used easily with minimal training making production of thin sections accessible for classroom and outreach use, in addition to research.
BrainPy: a flexible, integrative, efficient, and extensible framework towards general-purpose brain dynamics programming
Authors: Wang Chaoming , Chen Xiaoyu , Zhang Tianqiu , Wu Si
Published: October 2022

The neural mechanisms underlying brain functions are extremely complicated. Brain dynamics modeling is an indispensable tool for elucidating these mechanisms by modeling the dynamics of the neural circuits that execute brain functions. To ease and facilitate brain dynamics modeling, a general-purpose programming framework is needed to enable users to freely define neural models across multiple scales; efficiently simulate, train, and analyze model dynamics; and conveniently extend new modeling approaches. By utilizing the advanced just-in-time (JIT) compilation, we developed BrainPy. BrainPy provides a rich infrastructure tailored for brain dynamics programming, which supports an integrated platform for brain dynamics model building, simulation, training, and analysis. Models in BrainPy can be JIT compiled into binary instructions for multiple devices (including CPU, GPU, and TPU) to achieve a high running performance comparable to native C or CUDA. Moreover, BrainPy features an extensible architecture allowing easy expansion of new infrastructure, utilities, and machine learning approaches.
SMbiot: A Shared Latent Model for Microbiomes and their Hosts
Authors: Krishnamurthy Madan , Herron Lukas , Susanti Dwi , Volland-Munson Alyssa , Plata Germán , Dixit Purushottam
Published: October 2022

The collective nature of the variation in host associated microbial communities suggest that they exhibit low dimensional characteristics. To identify these lower dimensional descriptors, we propose SMbiot (pronounced SIM BY OT): aShared LatentModel for Microbiomes and their hosts. In SMbiot, latent variables embed host-specific microbial communities in a lower dimensional space and the corresponding features reflect controlling axes that dictate community compositions. Using data from different animal hosts, organ sites, and microbial kingdoms of life, we show that SMbiot identifies a small number of host-specific latent variables that accurately capture the compositional variation in host associated microbial communities. By using the same latents to describe hosts’ phenotypic states and the host-associated microbiomes, we show that the latent space embedding is informed by host physiology as well as the associated microbiomes. Importantly, SMbiot enables the quantification of host phenotypic differences associated with altered microbial community compositions in a host-specific manner, underscoring the context specificity of host-microbiome associations. SMbiot can also predict missing host metadata or microbial community compositions. This way, SMbiot is a concise quantitative method to understand the low dimensional collective behavior of host-associated microbiomes.
Highlighter: an optogenetic actuator for light-mediated, high resolution gene expression control in plants
Authors: Larsen Bo , Hofmann Roberto , Camacho Ines S , Clarke Richard W , Lagarias J Clark , Jones Alex R , Jones Alexander M
Published: October 2022

Optogenetic actuators have revolutionized the resolution at which we can assert control over biological processes in living systems. In plants, deployment of optogenetics is challenging due to the need for these light-responsive systems to maintain a single activation state in conventional horticultural environments with light-dark cycling. Furthermore, many available optogenetic actuators are based on plant photoreceptors that might crosstalk with endogenous signaling processes, while others depend on exogenously supplied cofactors. To overcome such challenges, we have developed Highlighter; a synthetic, light-gated gene expression system tailored forin plantafunction. Highlighter is based on the photoswitchable CcaS-CcaR system from cyanobacteria and is repurposed for plants as a fully genetically encoded system, engineered to photoswitch with the endogenous plant chromophore, phytochromobilin. We deployed Highlighter in transiently transformedNicotiana benthamianafor optogenetic control of fluorescent protein expression and innate immune responses. Using light to guide differential fluorescent protein expression in nuclei of neighboring cells, we demonstrate unprecedented spatiotemporal control of target gene expression. We furthermore regulate activation of plant immunity by modulating the spectral composition of white light, demonstrating optogenetic control of a biological process in horticultural light environments. Highlighter is a step forward for optogenetics in plants and a technology for high-resolution gene induction that will advance fundamental plant biology and provide new opportunities for crop improvement.
Intercellular crosstalk in adult dental pulp is mediated by heparin-binding growth factors Pleiotrophin and Midkine
Authors: Jiravejchakul Natnicha , Abe Gabriela L. , Loza Martin , Park Soyoung , Matangkasombut Ponpan , Sasaki Jun-Ichi , Imazato Satoshi , Diez Diego , Standley Daron M.
Published: October 2022

In-depth knowledge of the cellular and molecular composition of dental pulp (DP) and the crosstalk between DP cells that drive tissue homeostasis or regeneration are not well understood. To address these questions, we performed data analysis of publicly available single-cell transcriptomes of DP. This analysis revealed that DP resident fibroblasts have a unique gene expression profile when compared with fibroblasts from 5 other reference tissues: blood, bone marrow, adipose tissue, lung, and skin. Genes coded for heparin-binding growth-factors, pleiotrophin (PTN) and midkine (MDK), possessed the highest differential expression levels in DP fibroblasts. In addition, we identified extensive crosstalk between DP fibroblasts and several other DP cells, including Schwann cells, MSCs and odontoblasts. These findings suggest that fibroblast-derived growth factors regulate DP niches, and thus have a potential role as dental therapeutic targets.
Light-regulated pro-angiogenic engineered living materials
Authors: Dhakane Priyanka , Tadimarri Varun Sai , Sankaran Shrikrishnan
Published: October 2022

I.

Despite their promise, the application of growth factors in regenerative medicine is limited by their poor stability in the body, high costs of production/storage and need for localized and tightly controlled delivery to minimize adverse side effects. In this study, a unique strategy to overcome these limitations is explored based on engineered living materials (ELMs). These are an emerging class of composite materials, which contain live microorganisms that can be engineered to produce and secrete proteins in response to external stimuli. Herein, the development of an ELM that light-responsively releases a pro-angiogenic protein is described. This is achieved by optogenetically engineering bacteria to synthesize and secrete a fusion protein containing a vascular endothelial growth factor peptidomimetic linked to a collagen-binding domain. The bacteria are securely encapsulated in bilayer hydrogel constructs that support bacterial functionality but prevent their escape from the ELM. The possibility to switch protein release ON and OFF with light and to tune the amount released with different light intensities is demonstrated. Finally, it is shown that the released protein is active through its ability to bind to collagen and promote angiogenic network formation in human vascular endothelial cell cultures, indicating the regenerative potential of these ELMs.
A Common Resequencing-Based Genetic Marker Dataset for Global Maize Diversity
Authors: Grzybowski Marcin W. , Mural Ravi V. , Xu Gen , Turkus Jonathan , Yang Jinliang , Schnable James C.
Published: October 2022

Maize (Zea mays ssp. mays) populations exhibit vast amounts of genetic and phenotypic diversity. As sequencing costs have declined, an increasing number of projects have sought to measure genetic differences between and within maize populations using whole genome resequencing strategies, identifying millions of segregating single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels). Unlike older genotyping strategies like microarrays and genotyping by sequencing, resequencing should, in principle, frequently identify and score common genetic variants. However, in practice, different projects frequently employ different analytical pipelines, often employ different reference genome assemblies, and consistently filter for minor allele frequency within the study population. This constrains the potential to reuse and remix data on genetic diversity generated from different projects to address new biological questions in new ways. Here we employ resequencing data from 1,276 previously published maize samples and 239 newly resequenced maize samples to generate a single unified marker set of ∼366 million segregating variants and ∼46 million high confidence variants scored across crop wild relatives, landraces as well as tropical and temperate lines from different breeding eras. We demonstrate that the new variant set provides increased power to identify known causal flowering time genes using previously published trait datasets, as well as the potential to track changes in the frequency of functionally distinct alleles across the global distribution of modern maize.
LTP-like noninvasive striatal brain stimulation enhances striatal activity and motor skill learning in humans
Authors: Wessel Maximilian J. , Beanato Elena , Popa Traian , Windel Fabienne , Vassiliadis Pierre , Menoud Pauline , Beliaeva Valeriia , Violante Ines R. , Abderrahmane Hedjoudje , Dzialecka Patrycja , Park Chang-Hyun , Maceira-Elvira Pablo , Morishita Takuya , Cassara Antonino , Steiner Melanie , Grossman Nir , Neufeld Esra , Hummel Friedhelm C.
Published: October 2022

The stimulation of deep brain structures has thus far been possible only with invasive methods. Transcranial electrical temporal interference stimulation (tTIS) is a novel, noninvasive technology that might overcome this limitation. The initial proof-of-concept was obtained through modeling, physics experiments and rodent models. Here, we show for the first time successful noninvasive neuromodulation of the striatum via tTIS in humans using computational modeling, fMRI studies and behavioral evaluations. Theta-burst patterned, LTP-like striatal tTIS increased activity in the striatum and associated motor network. Furthermore, striatal tTIS enhanced motor learning capacity, especially in healthy older participants, who have lower natural learning capacity than younger subjects. These findings suggest exciting methods for noninvasively targeting deep brain structures in humans, thus enhancing our understanding of their functional roles. Moreover, our results lay the groundwork for innovative, noninvasive treatment strategies for brain disorders, in which deep brain structures play key pathophysiological roles.
Cytotoxicity, Mutagenicity and Genotoxicity of Electronic Cigarettes Emission Aerosols Compared to Cigarette Smoke: the REPLICA project
Authors: Emma Rosalia , Fuochi Virginia , Distefano Alfio , Rust Sonja , Zadjali Fahad , Tobi Mohammed Al , Zadjali Razan , Alharthi Zaina , Pulvirenti Roberta , Furneri Pio Maria , Polosa Riccardo , Caruso Massimo , Volti Giovanni Li
Published: October 2022

During the last decade electronic cigarettes (e-cigarettes) have been studied as an alternative devices to the tobacco cigarette, but with better safety for the health of smokers, so as to create a new approach to smoking addiction, such as the “smoking harm reduction”. This new approach, suggested by a part of the scientific world, aroused interest and debates in the regulatory field, involving all the major regulatory bodies and often creating divergences from nation to nation on the rules driving the production, distribution and consumption of these alternative products. Many studies have been conducted both in vitro and in vivo, to clarify the effects of the e-cigarette compared to the classic one. In this context, the Center of Excellence for the Acceleration of HArm Reduction (CoEHAR) was established within the University of Catania (Italy) and the multi-center project, created under its leadership, the REPLICA project, which aims to replicate in vitro studies originally conducted by tobacco and e-cigarette manufacturers, in order to verify the robustness and replicability of the data. In this work the REPLICA Team replicated part of the work published by Rudd and colleagues in 2020, which aims to establish the aerosol-induced cytotoxicity, mutagenesis and genotoxicity of a pod system e-cigarette aerosol compared to tobacco cigarette smoke. As in the original paper, we performed Neutral Red Test (NRU) for the evaluation of cytotoxicity, AMES test for the evaluation of mutagenesis and In Vitro Micronuclei (IVM) assay for the evaluation of genotoxicity on cells treated with cigarette smoke or e-cigarette aerosol. The results obtained showed high cytotoxicity, mutagenicity and genotoxicity induced by cigarette smoke, but slight or no cytotoxic, mutagenic and genotoxic effects induced by the e-cigarette aerosol. The data obtained support those previously presented by Rudd and colleagues, although we have highlighted some methodological flaws of their work. Overall, we can affirm that the results obtained by Rudd and colleagues have been established and our data also confirm the idea that e-cigarette aerosol is much safer and less harmful than cigarette smoking, making it a useful device in smoking harm reduction.
Mutations inNAKED-ENDOSPERMIDD genes reveal functional interactions withSCARECROWand a maternal influence on leaf patterning in C4grasses
Authors: Hughes Thomas E. , Sedelnikova Olga , Thomas Mimi , Langdale Jane A.
Published: October 2022

Leaves comprise a number of different cell-types that are patterned in the context of either the epidermal or inner cell layers. In grass leaves, two distinct anatomies develop in the inner leaf tissues depending on whether the leaf carries out C3or C4photosynthesis. In both cases a series of parallel veins develops that extends from the leaf base to the tip but in ancestral C3species veins are separated by a greater number of intervening mesophyll cells than in derived C4species. We have previously demonstrated that the GRAS transcription factor SCARECROW (SCR) regulates the number of photosynthetic mesophyll cells that form between veins in the leaves of the C4species maize, whereas it regulates the formation of stomata in the epidermal leaf layer in the C3species rice. Here we show that SCR is required for inner leaf patterning in the C4speciesSetaria viridisbut in this species the presumed ancestral stomatal patterning role is also retained. Through a comparative mutant analysis between maize, setaria and rice we further demonstrate that loss of NAKED-ENDOSPERM (NKD) INDETERMINATE DOMAIN (IDD) protein function exacerbates loss of functionscrphenotypes in the inner leaf tissues of maize and setaria but not rice. Specifically, in both setaria and maize,scr;nkdmutants exhibit an increased proportion of fused veins with no intervening mesophyll cells, whereas inner leaf tissues are patterned normally inscr;nkdmutants of rice. Thus, combined action of SCR and NKD may control how many mesophyll cells are specified between veins in the leaves of C4but not C3grasses. Finally, we identified a maternal effect in maize in which maternally derived NKD can affect patterning of cells in leaf primordia that are initiated during embryogenesis. Together our results provide insight into the evolution of cell patterning in grass leaves, demonstrate a novel patterning role for IDD genes in C4leaves and suggest that NKD can influence embryonic leaf development non-cell autonomously from the surrounding maternal tissue.

Summary statement

Mutations inNKDIDD genes enhance loss of functionscrphenotypes in the leaves of C4grasses maize andSetaria viridisbut not in the C3grass rice, and reveal a maternal effect on cell-type patterning in leaves that are initiated during embryogenesis.
Concurrent maintenance of both veridical and transformed working memory representations within unique coding schemes
Authors: Kandemir Güven , Wolff Michael J. , Karabay Aytaç , Stokes Mark G. , Axmacher Nikolai , Akyürek Elkan G.
Published: October 2022

In the dynamic environment we live in, the already limited information that human working memory can maintain needs to be constantly updated to optimally guide behaviour. Indeed, previous studies showed that leading up to a response, representations maintained in working memory representations are transformed continuously. This goes hand-in-hand with the removal of task-irrelevant items. However, does such removal also include the representations of stimuli as they were originally, prior to transformation? Here we assessed the neural representation of task-relevant transformed representations, and the no-longer-relevant veridical representations they originated from. We applied multivariate pattern analysis to electroencephalographic data during maintenance of orientation gratings with and without mental rotation. During maintenance, we perturbed the representational network by means of a visual impulse stimulus, and were thus able to successfully decode veridical as well as imaginary, transformed orientation gratings from impulse-driven activity. The impulse response reflected only task-relevant (cued), but not task-irrelevant (uncued) items, suggesting that the latter were quickly discarded from working memory. By contrast, even though the original cued orientation gratings were also no longer task-relevant after mental rotation, these items continued to be represented next to the rotated ones, in different representational formats. This seemingly inefficient use of scarce working memory capacity was associated with reduced probe response times and may thus serve to increase precision and flexibility in guiding behaviour in dynamic environments.
Co-option of the transcription factorSALL1in mole ovotestis formation
Authors: Schindler Magdalena , Osterwalder Marco , Harabula Izabela , Wittler Lars , Tzika Athanasia C. , Dechmann Dina , Vingron Martin , Visel Axel , Haas Stefan , Real Francisca M.
Published: October 2022

Changes in gene expression represent an important source for phenotypical innovation. Yet, how such changes emerge and impact the evolution of traits remains elusive. Here, we explore the molecular mechanisms associated with the development of masculinizing ovotestes in female moles. By performing comparative analyses of epigenetic and transcriptional data in mole and mouse, we identifiedSALL1as a co-opted gene for the formation of testicular tissue in mole ovotestes. Chromosome conformation capture analyses highlight a striking conservation of the 3D organization at theSALL1locus, but a prominent evolutionary turnover of enhancer elements. Interspecies reporter assays support the capability of mole-specific enhancers to activate transcription in urogenital tissues. Through overexpression experiments in transgenic mice, we further demonstrate the capability ofSALL1to induce the ectopic gene expression programs that are a signature of mole ovotestes. Our results highlight the co-option of gene expression, through changes in enhancer activity, as a prominent mechanism for the evolution of traits.
Assistive loading promotes goal-directed tuning of stretch reflex gains
Authors: Torell Frida , Franklin Sae , Franklin David W. , Dimitriou Michael
Published: October 2022

Voluntary movements are prepared before they are executed. Preparatory activity has been observed across the CNS and recently documented in first order neurons of the human PNS i.e., in muscle spindles. The changes seen in these sensory organs suggest that the independent modulation of stretch reflex gains may represent an important component of movement preparation. The aim of the current study was to further investigate the preparatory modulation of short- and long-latency stretch reflex responses (‘SLR’ and ‘LLR’) of the dominant upper limb. Specifically, we investigated how different target parameters (target distance and direction) affect the preparatory tuning of stretch reflex gains in the context of goal-directed reaching, and whether any such tuning depends on preparation duration and the direction of background loads. We found that target distance produced only small variations in reflex gains. In contrast, both SLR and LLR gains were strongly modulated as a function of target direction, in a manner that facilitated the upcoming voluntary movement. This goal-directed tuning of SLR and LLR gains was present or enhanced when the preparatory delay was sufficiently long (>250 ms) and the homonymous muscle was unloaded i.e., when a background load was first applied in the direction of homonymous muscle action (assistive loading). The results extend further support for a relatively slow-evolving process in reach preparation that functions to modulate reflexive muscle stiffness, likely via the independent control of fusimotor neurons. Such control can augment voluntary goal-directed movement and is triggered or enhanced when the homonymous muscle is unloaded.

Significance Statement

It is well-known that movement preparation improves motor performance. That is, briefly delaying the onset of a goal-directed movement can significantly benefit the overall quality of movement. However, the mechanisms underlying movement preparation remain unclear. In this study we examined the preparatory modulation of short- and long-latency stretch reflex responses in the dominant upper limb. We found that goal-directed tuning of stretch reflex gains is consistently triggered or enhanced in cases where preparation is sufficiently long (>250 ms) and a background -‘assistive’- load is first applied in the direction of homonymous muscle action. A better understanding of movement preparation will likely also benefit the development of rehabilitation regimes and movement augmentation devices.
Temporary knockdown of p53 during focal limb irradiation increases the development of sarcomas
Authors: Daniel Andrea R. , Lee Chang-Lung , Su Chang , Williams Nerissa T. , Li Zhiguo , Huang Jianguo , Lopez Omar , Luo Lixia , Ma Yan , De Silva Campos Lorraine , Selitsky Sara R. , Modliszewski Jennifer L. , Liu Siyao , Mowery Yvonne M. , Cardona Diana M. , Kirsch David G.
Published: October 2022

Background

Approximately half of all cancer patients receive radiotherapy and, as cancer survivorship rates increase with more effective therapies, the very low rate of radiation-associated sarcomas is rising. Radiation-associated sarcomas are life-threatening cancers, and radiation exposure is a primary risk factor for sarcoma development. During radiotherapy or other genotoxic cancer therapy forp53mutant cancers, pharmacological inhibition of p53 has been proposed to ameliorate acute injury of normal tissues. However, enhancing the survival of normal cells that sustain DNA damage by temporarily inhibiting p53 has the potential to increase the risk of cancer development. Here, we usein vivoshRNA technology to examine the consequences of temporarily reducing p53 expression on radiation-induced sarcoma development.

Methods

We utilized a mouse model of radiation-induced sarcoma where mice express a doxycycline (dox)-inducible p53 shRNA to temporarily and reversibly reduce p53 expression. Mice were placed on a dox diet 10 days prior to receiving 30 or 40 Gy hind limb irradiation in a single fraction and then returned to normal chow. Mice were examined weekly for sarcoma development and scored for radiation-induced normal tissue injuries. Radiation-induced sarcomas were harvested and subjected to RNA sequencing.

Results

Following single high-dose irradiation, 21% of temporary p53 knockdown animals developed a sarcoma in the radiation field compared to 2% of control animals. Mice with more severe acute injuries in the first 3 months after irradiation had a significantly increased risk of developing late persistent wounds in the soft tissue and bone. Chronic radiation-induced wounds were associated with sarcomagenesis. Examination of muscle stem cells by flow cytometry following hind limb irradiation indicated p53 knockdown preserves muscle stem cells in the irradiated limb, supporting the notion that temporary p53 knockdown at the time of irradiation reduces death of cells with DNA damage which may then persist to develop into a sarcoma. We performed RNA sequencing on 16 radiation-induced sarcomas compared to normal muscle controls. Gene set enrichment analysis revealed upregulation in the sarcomas of genes related to translation, epithelial mesenchymal transition (EMT), inflammation, and the cell cycle versus downregulation of genes related to myogenesis and tumor metabolism. Furthermore, genes with increased copy number such asMetandCdk4were overexpressed in tumors.

Conclusions

Temporary reduction of p53 during high-dose irradiation increases late effects including tissue injuries and sarcoma development.
Biological Sex Influences the Contribution of Sign-Tracking and Anxiety-Like Behaviour toward Remifentanil Self-Administration
Authors: Zumbusch Alicia , Samson Ana , Chernoff Chloe , Coslovich Brandi , Hynes Tristan
Published: October 2022

Most people sample addictive drugs, but use becomes disordered in only a small minority. Two important factors that influence susceptibility to addiction are individual differences in personality traits and biological sex. The influence of traits on addiction-like behaviour is well characterized in preclinical models of cocaine self-administration, but less is understood in regards to opioids. How biological sex influences trait susceptibility to opioid self-administration is likewise less studied than psychostimulants. Thus, we sought to elucidate how biological sex and several addiction-relevant traits interact with the propensity to self-administer the opioid remifentanil. We first screened female (n=19) and male (n=19) rats for four addiction-relevant traits: impulsivity, novelty place-preference, anxiety-like behaviour, and attribution of incentive value to reward cues. Rats were then trained to self-administer remifentanil in a “conflict model” of drug self-administration. Rats had to endure a mild electric shock to access the response manipulandum that triggered an intravenous infusion of remifentanil. In male rats, high anxiety-like behaviour was positively correlated with the number of drug infusions if the shock level was low or completely absent. In females, sign-tracking was predictive of greater resistance to punishment during drug seeking; an effect that was mediated by anxiety-like behaviour. Females consumed more remifentanil under all conditions, and their drug seeking persisted in the face of significantly greater current than males. These findings demonstrate that the influence of behavioural traits over the propensity to self-administer opioids is dependent upon biological sex.
Comprehensive multi-omics characterization of gut microbiome extracellular vesicles reveals a connection to gut-brain axis signaling
Authors: Sultan Salma , Yousuf Basit , Yeo JuDong , Ahmed Tamer , Bouhlel Nour Elhouda , Hassan Heba , Minic Zoran , Mottawea Walid , Hammami Riadh
Published: October 2022

Microbiota-gut-brain axis is an evident pathway of host-microbiota crosstalk that is linked to multiple brain disorders. Microbiota released extracellular vesicles (MEVs) has emerged as a key player in intercellular signaling in host microbiome communications. However, their role in gutbrain axis signaling is poorly investigated. Here, we performed a deep multi-omics profiling of MEVs content generated ex vivo and from stool samples in order to get some insights on their role in gut-brain-axis signaling. Metabolomics profiling identified a wide array of metabolites embedded in MEVs, including lipids, carbohydrates, amino acids, vitamins, and organic acids. Interestingly, many neurotransmitter-related compounds were detected inside MEVs, including arachidonyl-dopamine (NADA), gabapentin, glutamate and N-acylethanolamines. Next, we aimed to identify commensal microbes with psychobiotic activity. We isolated 58Bacteroidesstrains assigned to four genera, 11 species, and 4 new species based on 16S rDNA sequencing. We performed whole genome sequencing of 18 representative isolates, followed by a comparative analysis of the structure of polysaccharide utilization loci (PUL) and glutamate decarboxylase (GAD), a genetic system involved in GABA production. Quantifying GABA was done using competitive ELISA, wherein three isolates (B. finegoldii, B. faecis, andB. caccae) showed high GABA production (4.5-7 mM range) in supernatant whereas 2.2 to 4 uM GABA concentration was detected inside microvesicles extracted using ultracentrifugation. To test the biodistribution of MEVs from the gut to other parts of the body, CACO-2, RIN-14 B, and hCMEC/D3 cells showed a capacity to internalize labeled MEVs through an endocytic mechanism. Additionally, MEVs exhibited a dose dependent paracellular transport through CACO-2 intestinal cells and hCMEC/D3 brain endothelial cells. In vivo results showed biodistribution of MEVs to liver, stomach and spleen. Overall, our results reveal the capabilities of MEVs to cross the intestinal and blood brain barriers to deliver their cargoes of neuroactive molecules to the brain as a new signaling mechanism in microbiota-gut-brain axis communications.
What is an urban bird? Trait-based predictions of urban tolerance for the world’s birds are modulated by latitude and human population density
Authors: Neate-Clegg Montague H. C. , Tonelli Benjamin A. , Youngflesh Casey , Wu Joanna X. , Montgomery Graham A. , Şekercioğlu Çağan H. , Tingley Morgan W.
Published: October 2022

As human density increases, biodiversity must increasingly co-exist with urbanization or face local extinction. Tolerance of urban areas has been linked to numerous functional traits, yet few globally-consistent patterns have emerged to explain variation in urban tolerance, which stymies attempts at a generalizable predictive framework. Here, we calculate an Urban Association Index (UAI) for 3768 bird species in 137 cities across all permanently inhabited continents. We then assess how UAI varies as a function of ten species-specific traits and further test whether the strength of trait relationships vary as a function of three city-specific variables. Of the ten species traits, nine were significantly associated with urban tolerance. Urban-associated species tend to be smaller, less territorial, have greater dispersal ability, broader dietary and habitat niches, larger clutch sizes, greater longevity, and have lower elevational limits. Only bill shape showed no global association with urban tolerance. Additionally, the strength of several trait relationships varied across cities as a function of latitude and/or human population density. For example, the effects of body mass and diet breadth are more pronounced at higher latitudes, while the effects of territoriality and longevity were reduced in cities with higher population density. Thus, the importance of trait filters in birds varies predictably across cities, indicating biogeographic variation in selection for urban tolerance that could explain prior challenges in the search for global patterns. A globally-informed framework that predicts urban tolerance will be integral to conservation as increasing proportions of the world’s biodiversity are impacted by urbanization.
T Residues Preceded by Runs of G are Hotspots of T→G Mutation in Bacteria
Authors: Cherry Joshua L.
Published: October 2022

The rate of mutation varies among positions in a genome. Local sequence context can affect the rate, and has different effects on different types of mutation. Here I report an effect of local context that operates to some extent in all bacteria examined: the rate of T→G mutation is greatly increased by preceding runs of three or more G residues. The strength of the effect increases with the length of the run. InSalmonella, in which the effect is strongest, a G run of length three increases the rate by a factor of ~26, a run of length four increases it by almost a factor of 100, and runs of length five or more increase it by a factor of more than 400 on average. The effect is much stronger when the T is on the leading rather than the lagging strand of DNA replication. Several observations eliminate the possibility that this effect is an artifact of sequencing error.
The potential impact of novel tuberculosis vaccines on health equity and financial protection in low- and middle-income countries
Authors: Portnoy Allison , Clark Rebecca A. , Weerasuriya Chathika K. , Mukandavire Christinah , Quaife Matthew , Bakker Roel , Garcia Baena Ines , Gebreselassie Nebiat , Zignol Matteo , Jit Mark , White Richard G. , Menzies Nicolas A.
Published: October 2022

Background: One in two patients developing tuberculosis (TB) in low- and middle-income countries (LMICs) faces catastrophic household costs. We assessed the potential financial risk protection from introducing novel TB vaccines, and how health and economic benefits would be distributed across income quintiles. Methods: We modelled the impact of introducing TB vaccines meeting the WHO preferred product characteristics in 105 LMICs. For each country, we assessed the distribution of health gains, patient costs, and household financial vulnerability following introduction of an infant vaccine, and separately for an adolescent/adult vaccine, compared to a 'no-new-vaccine' counterfactual. Patient-incurred direct and indirect costs of TB disease exceeding 20% of annual household income were defined as catastrophic. Findings: Over 2028-2050, the health gains resulting from vaccine introduction were greatest in lower income quintiles, with the poorest two quintiles in each country accounting for 56% of total LMIC TB cases averted. Over this period, the infant vaccine was estimated to avert $5.9 (95% uncertainty interval: $5.3-6.5) billion in patient-incurred total costs, and the adolescent/adult vaccine was estimated to avert $38.9 ($36.6-41.5) billion. Over this period, 3.7 (3.3-4.1) million fewer households were projected to face catastrophic costs with the infant vaccine, and 22.9 (21.4-24.5) million with the adolescent/adult vaccine, with 66% of these gains accruing in the poorest two income quintiles. Interpretation: Under a range of assumptions, introducing novel TB vaccines would reduce income-based inequalities in the health and household economic outcomes of TB in LMICs.