bluuebunny/crossref_metadata_2025 huggingface dataset:
Simultaneous 3D Cellular Positioning and Apical Dendritic Morphology of Transgenic Fluorescent Mouse CA3 Hippocampal Pyramidal Neurons
Authors: Handwerk Christopher J. , Bland Katherine M. , Denzler Collin J. , Kalinowski Anna R. , Brett Cooper A. , Swinehart Brian D. , Rodriguez Hilda V. , Cook Hollyn N. , Vinson Elizabeth C. , Florenz Madison E. , Vidal George S.
Published: August 2022

Background

Pyramidal neurons throughout hippocampal CA3 are diverse in their dendritic morphology, and CA3 is not homogenous in its structure or function. Nonetheless, few structural studies have captured the precise 3D somatic position and the 3D dendritic morphology of CA3 pyramidal neurons simultaneously.

New method

Here, we present a simple approach to reconstruct the apical dendritic morphology of CA3 pyramidal neurons using the transgenic fluorescentThy1-GFP-M line. The approach simultaneously tracks the dorsoventral, tangential, and radial positions of reconstructed neurons within the hippocampus. It is especially designed for use with transgenic fluorescent mouse lines, which are commonly used in genetic studies of neuronal morphology and development.

Results

We demonstrate how topographic and morphological data are captured from transgenic fluorescent mouse CA3 pyramidal neurons.

Comparison with existing methods

There is no need to select and label CA3 pyramidal neurons with the transgenic fluorescentThy1-GFP-M line. By taking transverse (not coronal) serial sections, we preserve fine dorsoventral, tangential, and radial somatic positioning of 3D-reconstructed neurons. Because CA2 is well defined by PCP4 immunohistochemistry, we use that technique here to to increase precision in defining tangential position along CA3.

Conclusions

We developed a method for simultaneously collecting precise somatic positioning as well as 3D morphological data among transgenic fluorescent mouse hippocampal pyramidal neurons. This fluorescent method should be compatible with many other transgenic fluorescent reporter lines and immunohistochemical methods, facilitating the capture of topographic and morphological data from a wide variety of genetic experiments in mouse hippocampus.

Highlights

Simultaneous capture of 3D location and pyramidal dendritic morphology in CA3

Method utilizes replicable techniques and reagents available to most laboratories

Method is adaptable to other transgenic mouse lines and immunohistochemical studies
Scaling pattern of the carnivoran hind limb: Main deviations from a conservative pattern
Authors: Gálvez-López Eloy , Casinos Adrià
Published: August 2022

The scaling pattern of the hind limb in Carnivora was determined using a sample of 13 variables measured on the femur, tibia, and calcaneus, of 429 specimens belonging to 141 species. Standardized major axis regressions on body mass were calculated for all variables, using both traditional regression methods and phylogenetically independent contrasts (PIC). Significant differences were found between the allometric slopes obtained with traditional and PIC regression methods, emphasizing the need to take into account phylogenetic relatedness in scaling studies. Overall, the scaling of the carnivoran hind limb conformed to geometric similarity, although some deviations from its predictions (including differential scaling) were detected, especially in relation with swimming adaptations. The scaling pattern of several phyletic lines and locomotor habits within Carnivora was also determined. Significant deviations from the scaling pattern of the order were found in some phyletic lines, but not in the locomotor habit subsamples. This suggests that the scaling of the carnivoran hind limb is both more heavily influenced by phylogenetic relatedness than by locomotor specializations, and more conservative than that of the forelimb. Finally, together with our previous work on the carnivoran forelimb, the results of the present study suggest that, in large non-aquatic carnivorans, size-related increases in bone stresses are compensated primarily by limb posture changes instead of by modifying limb bone scaling. However, increasing bone robusticity might also occur in the forelimb in response to the heavier stresses acting on the forelimbs due to asymmetrical body weight distribution.
Resolving marine–freshwater transitions by diatoms through a fog of discordant gene trees
Authors: Roberts Wade R. , Ruck Elizabeth C. , Downey Kala M. , Pinseel Eveline , Alverson Andrew J.
Published: August 2022

Despite the obstacles facing marine colonists, most lineages of aquatic organisms have colonized and diversified in freshwaters repeatedly. These transitions can trigger rapid morphological or physiological change and, on longer timescales, lead to increased rates of speciation and extinction. Diatoms are a lineage of ancestrally marine microalgae that have diversified throughout freshwater habitats worldwide. We generated a phylogenomic dataset of genomes and transcriptomes for 59 diatom taxa to resolve freshwater transitions in one lineage, the Thalassiosirales. Although most parts of the species tree were consistently resolved with strong support, we had difficulties resolving a Paleocene radiation, which affected the placement of one freshwater lineage. This and other parts of the tree were characterized by high levels of gene tree discordance caused by incomplete lineage sorting and low phylogenetic signal. Despite differences in species trees inferred from concatenation versus summary methods and codons versus amino acids, traditional methods of ancestral state reconstruction supported six transitions into freshwaters, two of which led to subsequent species diversification. Evidence from gene trees, protein alignments, and diatom life history together suggest that habitat transitions were largely the product of homoplasy rather than hemiplasy, a condition where transitions occur on branches in gene trees not shared with the species tree. Nevertheless, we identified a small set of putatively hemiplasious genes, many of which have been associated with shifts to low salinity, indicating that hemiplasy played a small but potentially important role in freshwater adaptation. Accounting for differences in evolutionary outcomes, in which some taxa became locked into freshwaters while others were able to return to the ocean or become salinity generalists, might help further distinguish different sources of adaptive mutation in freshwater diatoms.
A two-process model ofDrosophilasleep reveals an inter-dependence between circadian clock speed and the rate of sleep pressure decay
Authors: Abhilash Lakshman , Shafer Orie Thomas
Published: August 2022

Sleep is controlled by two processes – a circadian clock that regulates its timing and a homeostat that regulates the drive to sleep.Drosophilahas been an insightful model for understanding both processes. For four decades, Borbély and Daan’s two-process model has provided a powerful framework for understanding how circadian and homeostatic processes regulate sleep. However, the field of fly sleep has not employed such a model as a framework for the investigation of sleep. To this end, we have adapted the two-process model to the fly and establish its utility by showing that it can provide empirically testable predictions regarding the circadian and homeostatic control of fly sleep. We show that the ultradian rhythms previously reported for loss-of-function clock mutants are a predictable consequence of a functional sleep homeostat in the absence of a functioning circadian system. We find that a model in which the circadian clock speed and homeostatic rates act without influencing each other provides imprecise predictions regarding how clock speed influences the strength of sleep rhythms and the amount of daily sleep. We also find that quantitatively good fits between empirical values and model predictions were achieved only when clock speeds were positively correlated with rates of decay of sleep pressure. Our results indicate that longer sleep bouts better reflect the homeostatic process than the current definition of sleep as any inactivity lasting five minutes or more. This two-process model represents a powerful framework for future work on the molecular and physiological regulation of fly sleep.
Learning representations for image-based profiling of perturbations
Authors: Moshkov Nikita , Bornholdt Michael , Benoit Santiago , Smith Matthew , McQuin Claire , Goodman Allen , Senft Rebecca A. , Han Yu , Babadi Mehrtash , Horvath Peter , Cimini Beth A. , Carpenter Anne E. , Singh Shantanu , Caicedo Juan C.
Published: August 2022

Measuring the phenotypic effect of treatments on cells through imaging assays is an efficient and powerful way of studying cell biology, and requires computational methods for transforming images into quantitative data that highlight phenotypic outcomes. Here, we present an optimized strategy for learning representations of treatment effects from high-throughput imaging data, which follows a causal framework for interpreting results and guiding performance improvements. We use weakly supervised learning (WSL) for modeling associations between images and treatments, and show that it encodes both confounding factors and phenotypic features in the learned representation. To facilitate their separation, we constructed a large training dataset with Cell Painting images from five different studies to maximize experimental diversity, following insights from our causal analysis. Training a WSL model with this dataset successfully improves downstream performance, and produces a reusable convolutional network for image-based profiling, which we call Cell Painting CNN-1. We conducted a comprehensive evaluation of our strategy on three publicly available Cell Painting datasets, discovering that representations obtained by the Cell Painting CNN-1 can improve performance in downstream analysis for biological matching up to 30% with respect to classical features, while also being more computationally efficient.
Antiproliferative Effects of Novel Copper (II) Complexes on Lung Cancer Cell Line
Authors: Abdullah Muhammed Fawaz , Cinkilic Nilufer , Vatan Ozgur , Inci Duygu , Aydin Rahmiye
Published: August 2022

Copper is an essential metalloelement that plays key fundamental roles in both health and pathology, and is increasingly been implicated in molecular pathogenesis of many cancer types. It has shown promise as a replacement to cisplatin in coordination complexes presently in mainstream chemotherapeutic practices.

In this study, two newly synthesized water-soluble ternary copper (II) mixed ligand complexes; complex 1 - (Cu(4-mphen)(tyr)(H2O)]NO3·2H2O)(C.1) and complex 2 - (Cu(5-mphen)(tyr)(H2O)]NO3·2H2O (C.2) where (4-m= 4-methyl; 5-m = 5-methyl; phen-1, 10 = phenanthroline; tyr = tyrosine)), were investigated on adenocarcinomic human alveolar basal epithelial cell, A549 and non-cancerous human bronchial epithelial cell, BEAS-2B for their antiproliferative effects using the XTT assay (cytotoxicity), Comet assay (genotoxicity) and DCFH-DA assay (intracellular ROS) tests.

C.1 was significantly more cytotoxic in A549 than C.2. Data from the Comet and ROS assay tests support each other. C.2 caused more copper-induced DNA damage, possibly through significant induction of ROS-mediated oxidative damage in the cancer cell, but a minimal insignificant ROS rise in normal cells. These results can only be preliminary and further studies are required to better understand the cellular effects and functional interactions of these agents, for an efficient therapeutic design and application.
Apolipoprotein E genotype modulates longitudinal atrophy at the temporal lobe after mild traumatic brain injury
Authors: Gan Shuoqiu , Wang Shan , Liu Yuling , Sun Yingxiang , Liu Kejia , Jia Xiaoyan , Li Xuan , Zhang Ming , Bai Lijun
Published: August 2022

Backgrounds

Moderate or severe traumatic brain injury (TBI) is one of the strongest environmental risks for late-life dementia, especially Alzheimer’s disease (AD). However, the interaction between genetic factors and environmental exposure to mild TBI triggering neurodegenerative processes is still unclear. We used longitudinal imaging to differentiate spatial patterns of progressive brain volume loss in individual patients with and without carrying apolipoprotein E (APOE) ε4 carriers.

Methods

For 59 patients with acute mild TBI (mTBI, age: 36.92 ± 11.91 years; 14 APOE ε4 carriers) and 48 matched healthy controls (HCs, age: 37.92 ± 11.72 years; 10 APOE ε4 carriers), longitudinal (6-12 months follow-up) brain structure was assessed using voxel-based morphometry on T1-weighted scans. Longitudinal volume changes in the temporal lobe were characterized by the Jacobian determinant (JD) metric, reflecting spatial warping between the baseline and follow-up scans. JD values were regionally calculated and correlated with neuropsychological measures.

Results

MTBI patients lost a mean of 0.27% (SD = 0.43) of GM and 0.27% (SD = 0.50) of WM volume in the temporal lobe over the 6-12 month follow-up. Patients with a high genetic risk for AD (APOE ε4 allele carries) were associated with severer atrophy in the left superior temporal gyrus and middle temporal gyrus regions than the controls (P < 0.05). Furthermore, atrophy in these regions of gray matter could predict the performance change ratio of the language fluency in mTBI APOE ε4 carriers (β = 0.570, P < 0.05). While, compared with HC APOE ε4 non-carriers, mTBI non-carriers exhibited volume loss in the medial temporal lobe.

Conclusions

This prospective study provided evidence that the APOE ε4 allele interacting with mTBI increased the risk of AD phenotype development with language dysfunction.

Graphic Abstract
Species-specific CD4+ T cells Enable Prediction of Mucosal Immune Phenotypes from Microbiota Composition
Authors: Spindler Matthew P. , Mogno Ilaria , Suri Prerna , Britton Graham J. , Faith Jeremiah J.
Published: August 2022

How bacterial strains within a complex human microbiota collectively shape intestinal T cell homeostasis is not well-understood. Methods that quickly identify effector strains or species that drive specific mucosal T cell phenotypes are needed to define general principles for how the microbiota modulates host immunity. We colonize germ-free mice with defined communities of cultured strains and profile antigen-specific responses directed towards individual strains ex vivo. We find that lamina propria T cells are specific to bacterial strains at the species level and can discriminate between strains of the same species. Ex vivo restimulations consistently identify the strains within complex communities that induce Th17 responses in vivo providing the potential to shape baseline immune tone via community composition. Using an adoptive transfer model of colitis, we find that lamina propria T cells respond to different bacterial strains in conditions of inflammation versus homeostasis. Collectively, our approach represents a novel method for efficiently predicting the relative impact of individual bacterial strains within a complex community and for parsing microbiota-dependent phenotypes into component fractions.

SIGNIFICANCE

Determining the mechanisms by which the gut microbiome modulates the host immune system has translational potential for treating or preventing immune mediated disease. A key challenge is identifying the immunogenic bacterial strains in the setting of a complex microbiota. We use a combination of anaerobic culturing, in vitro T cell assays, gnotobiotic mouse models, and ex vivo T cell restimulations to explore the influence of species and strain diversity on the specificity of mucosal T cells. Our approach efficiently predicts the relative impact of individual bacterial strains within a complex community and can be used to parse microbiota-dependent phenotypes into component fractions.
Sweat and sebum preferences of the human skin microbiota
Authors: Swaney Mary Hannah , Nelsen Amanda , Sandstrom Shelby , Kalan Lindsay R
Published: August 2022

The microorganisms that inhabit human skin, collectively termed the skin microbiome, must overcome numerous challenges that typically impede microbial growth, including low pH, osmotic pressure, and low nutrient availability. Yet, the skin microbiota thrive on the skin and have adapted to these stressful conditions. Limited skin nutrients are available for microbial use in this unique niche, including those from host-derived sweat, sebum, and corneocytes. Here, we have developed physiologically-relevant, skin-like growth media that is composed of compounds present in human sweat and sebum. We find that skin-associated bacterial species exhibit unique growth profiles in different concentrations of sweat and sebum. The majority of strains evaluated demonstrate a preference for high sweat concentrations, while sebum preference is highly variable, suggesting that the capacity for sebum utilization may be an important driver of skin microbial community structure. Furthermore, these findings provide experimental rationale for why different skin microenvironments harbor distinct microbiome communities. In all, our study further emphasizes the importance of studying microorganisms in an ecologically-relevant context, which is critical for our understanding of their physiology, ecology, and function on the skin.
An off-the-shelf multi-well scaffold-supported platform for tumour organoid-based tissues
Authors: Li Nancy T , Wu Nila C , Cao Ruonan , Cadavid Jose L , Latour Simon , Lu Xiaoya , Zhu Yutong , Mijalkovic Mirjana , Roozitalab Reza , McGuigan Alison P
Published: August 2022

Complex 3D bioengineered tumour models provide the opportunity to better capture the heterogeneity of patient tumours. Patient-derived organoids are emerging as a useful tool to study tumour heterogeneity and variation in patient responses. Organoid cultures typically require a 3D microenvironment that can be manufactured easily to facilitate screening. Here we set out to create a high-throughput, “off-the-shelf” platform which permits the generation of organoid-containing microtissues for standard phenotypic bioassays and image-based readings. To achieve this, we developed the Scaffold-supported Platform for Organoid-based Tissues (SPOT) platform. SPOT is a 3D gel-embedded in vitro platform that can be produced in a 96- or 384-well plate format and enables the generation of flat, thin and dimensionally-defined microgels. SPOT has high potential for adoption due to its reproducible manufacturing methodology, compatibility with existing instrumentation, and reduced within-sample and between-sample variation, which can pose challenges to both data analysis and interpretation. Using SPOT we generate cultures from patient derived pancreatic ductal adenocarcinoma organoids and assess the cellular response to standard-of-care chemotherapeutic compounds, demonstrating our platform’s usability for drug screening. We envision 96/384-SPOT will provide a useful tool to assess drug sensitivity of patient-derived organoids and easily integrate into the drug discovery pipeline.
A desert green alga that thrives at extreme high-light intensities using a unique photoin-hibition protection mechanism
Authors: Levin Guy , Yasmin Michael , Simanowitz Marc C. , Meir Ayala , Tadmor Yaakov , Hirschberg Joseph , Adir Noam , Schuster Gadi
Published: August 2022

While light is the driving force of photosynthesis, excessive light can be harmful. Photoinhibition, or light-induced photo-damage, is one of the key processes limiting photosynthesis. When the absorbed light exceeds the amount that can be dissipated by photosynthetic electron flow and other processes, damaging radicals are formed that mostly inactivate photosystem II (PSII). A well-defined mechanism that protects the photosynthetic apparatus from photoinhibition has been described in the model green alga Chlamydomonas reinhardtii and plants. Chlorella oha-dii is a green micro-alga, isolated from biological desert soil crusts, that thrives under extreme high light (HL) in which other organisms do not survive. Here, we show that this alga evolved unique protection mechanisms distinct from those of C. reinhardtii and plants. When grown under extreme HL, significant structural changes were noted in the C. ohadii thylakoids, including a drastic reduction in the antennae and the formation of stripped core PSII, lacking its outer and inner antennae. This is accompanied by a massive accumulation of protective carotenoids and proteins that scavenge harmful radicals. At the same time, several elements central to photoinhibition protection in C. reinhardtii, such as psbS, the stress-related light harvesting complex, PSII protein phosphorylation and state-transitions are entirely absent or were barely detected in C. ohadii. Taken together, a unique photoinhibition protection mechanism evolved in C. ohadii, enabling the species to thrive under extreme-light intensities where other photo-synthetic organisms fail to survive.
Asparagine starvation suppresses histone demethylation through iron depletion
Authors: Jiang Jie , Srivastava Sankalp , Liu Sheng , Seim Gretchen , Zhong Minghua , Cao Sha , Davé Utpal , Kapur Reuben , Mosley Amber L. , Zhang Chi , Wan Jun , Fan Jing , Zhang Ji
Published: August 2022

Nutrient availability can impact epigenome to modify gene expression and dictate cell fate decision (Etchegaray and Mostoslavsky, 2016; Kinnaird et al., 2016). α-ketoglutarate is an indispensable substrate for the Jumonji family of histone demethylases (JHDMs) mediating most of the cellular demethylation reactions on histone subunits (Schvartzman et al., 2018). Since α-ketoglutarate is an intermediate of the tricarboxylic acid (TCA) cycle and a product of transamination, its intracellular levels are regulated by the metabolism of several amino acids (Baksh et al., 2020; Carey et al., 2015; Raffel et al., 2017; Vardhana et al., 2019). Here we show that asparagine starvation suppresses global histone demethylation. This process is neither due to the change of expression of histone modifying enzymes, nor due to the change of intracellular level of α-ketoglutarate. Rather, asparagine starvation reduces intracellular pool of labile iron (Fe2+), which is a key cofactor for the JHDMs to function. Mechanistically, asparagine starvation post-transcriptionally suppresses the expression of iron responsive element binding protein 2 (IREB2), an iron sensing protein, which then reduces the mRNA expression of the transferrin receptor (TFRC), a major carrier for iron uptake (Hentze et al., 2010). Furthermore, iron supplementation to the culture medium restores histone demethylation and alters global gene expression to accelerate cell death under conditions of asparagine starvation. Collectively, our results uncover that suppression of iron-dependent histone demethylation is part of the cellular adaptive response to asparagine starvation.
Delaying quantitative resistance to pesticides and antibiotics
Authors: Hardy Nate B.
Published: August 2022

How can we best vary the application of pesticides and antibiotics to delay resistance evolution? Previous theoretical studies have focused on qualitative resistance traits, and have mostly assumed that resistance alleles are already present in a population. But many real resistance traits are quantitative, and the evolution of resistant genotypes in the field may depend onde novomutation and recombination. Here, I use an individual-based, forward-time, quantitative-genetic simulation model to investigate the evolution of quantitative resistance. I evaluate the performance of four application strategies for delaying resistance evolution, to wit, the (1) sequential, (2) mosaic, (3) periodic, and (4) combined strategies. I find that which strategy is best depends on initial efficacy. When at the onset, xenobiotics completely prevent reproduction in treated demes, a combined strategy is best. On the other hand, when populations are partially resistant, the combined strategy is inferior to mosaic and periodic strategies, especially when resistance alleles are antagonistically pleiotropic. Thus, the optimal application strategy for managing against the rise of quantitative resistance depends on pleiotropy and whether or not partial resistance is already present in a population. This result appears robust to variation in pest reproductive mode and migration rate, direct fitness costs for resistant phenotypes, and the extend of refugial habitats.
IRIS: Integrated Retinal Functionality in Image Sensors
Authors: Yin Zihan , Kaiser Md Abdullah-Al , Camara Lamine Ousmane , Camarena Mark , Parsa Maryam , Jacob Ajey , Schwartz Gregory , Jaiswal Akhilesh
Published: August 2022

Neuromorphic image sensors draw inspiration from the biological retina to implement visual computations in electronic hardware. Gain control in phototransduction and temporal differentiation at the first retinal synapse inspired the first generation of neuromorphic sensors, but processing in downstream retinal circuits, much of which has been discovered in the past decade, has not been implemented in image sensor technology. We present a technology-circuit co-design solution that implements two motion computations occurring at the output of the retina that could have wide applications for vision based decision making in dynamic environments. Our simulations on Globalfoundries 22nm technology node show that, by taking advantage of the recent advances in semiconductor chip stacking technology, the proposed retina-inspired circuits can be fabricated on image sensing platforms in existing semiconductor foundries. Integrated Retinal Functionality in Image Sensors (IRIS) technology could drive advances in machine vision applications that demand robust, high-speed, energy-efficient and low-bandwidth real-time decision making.
Dietary choline intake is necessary to prevent systems-wide organ pathology and reduce Alzheimer’s disease hallmarks
Authors: Dave Nikhil , Judd Jessica M. , Decker Annika , Winslow Wendy , Sarette Patrick , Espinosa Oscar V. , Sandler Jessica , Bilal Alina , Tallino Savannah , McDonough Ian , Winstone Joanna K , Blackwood Erik A. , Glembotski Christopher , Karr Timothy , Velazquez Ramon
Published: August 2022

Evidence suggests that environmental factors may contribute to Alzheimer’s disease (AD). The B-like vitamin choline plays key roles in body- and brain-related functions. Choline produced endogenously by the phosphatidylethanolamine N-methyltransferase (PEMT) enzyme in the liver is not sufficient for adequate physiological functions, necessitating daily dietary intake. ∼90% of Americans don’t reach the recommended daily choline intake. Thus, it’s imperative to determine whether dietary deficiency increases disease outcomes. Here, we placed 3xTg-AD, a model of AD, and non-transgenic (NonTg) control mice on either a sufficient choline (ChN) or choline deficient (Ch-; choline deficiency) diet from 3 to 12 (early to late adulthood) months of age. Ch- reduced plasma choline and acetylcholine levels, increased weight, and impaired both glucose metabolism and motor function in NonTg, with 3xTg-AD mice showing greater deficits. Tissue analyses showed cardiac and liver pathology, and elevated Amyloid-β and phosphorylated tau in the hippocampus and cortex of 3xTg-AD Ch- mice. Unbiased proteomic analyses revealed Ch- altered hippocampal networks associated with microtubule function and postsynaptic membrane regulation. In plasma, Ch- altered protein networks associated with insulin metabolism, mitochondrial function, and inflammation. Collectively, our data highlight that dietary choline intake is necessary to prevent systems-wide organ pathology and reduce AD hallmark pathologies.
Inline SAXS-coupled chromatography under extreme hydrostatic pressure
Authors: Miller Robert , Cummings Cody , Huang Qingqiu , Ando Nozomi , Gillilan Richard E.
Published: August 2022

As continuing discoveries highlight the surprising abundance and resilience of deep ocean and subsurface microbial life, the effects of extreme hydrostatic pressure on biological structure and function have attracted renewed interest. Biological small angle X-ray scattering (BioSAXS) is a widely used method of obtaining structural information from biomolecules in solution under a wide range of solution conditions. Due to its ability to reduce radiation damage, remove aggregates, and separate monodisperse components from complex mixtures, size-exclusion chromatography coupled SAXS (SEC-SAXS) is now the dominant form of BioSAXS at many synchrotron beamlines. While BioSAXS can currently be performed with some difficulty under pressure with non-flowing samples, it has not been clear how, or even if, continuously flowing SEC-SAXS, with its fragile media-packed columns, might work in an extreme high-pressure environment. Here we show, for the first time, that reproducible chromatographic separations coupled directly to high-pressure BioSAXS can be achieved at pressures up to at least 100 MPa and that pressure-induced changes in folding and oligomeric state and other properties can be observed. The apparatus described here functions at a range of temperatures (0° C - 50° C), expanding opportunities for understanding biomolecular rules of life in deep ocean and subsurface environments.
Insplico: Effective computational tool for studying intron splicing order genome-wide with short and long RNA-seq reads
Authors: Gohr Andre , Torres-Méndez Antonio , Bonnal Sophie , Irimia Manuel
Published: August 2022

Although splicing occurs largely co-transcriptionally, the order by which introns are removed does not necessarily follow the order in which they are transcribed. Whereas several genomic features are known to influence whether or not an intron is spliced before its downstream neighbour, multiple questions related to intron splicing order (ISO) remain unanswered. Here, we present Insplico, the first standalone tool to quantify ISO that works with both short and long read sequencing technologies. We first demonstrate its applicability and effectiveness recapitulating previously reported patterns, while unveiling overlooked biases associated with long read sequencing. We next show that ISO around individual exons is remarkably constant across cell and tissue types and even upon major spliceosomal disruption, and it is evolutionarily conserved between human and mouse brains. We also establish a set of universal features associated with ISO patterns across various animal and plant species. Finally, we used Insplico to investigate ISO in the context of tissue-specific exons, particularly focusing on SRRM4-dependent microexons. We found that the majority of such microexons have non-canonical ISO, in which the downstream intron is spliced first, and we revealed two potential modes of SRRM4 regulation of microexons related to their ISO and various splicing-related features. Insplico is available on gitlab.com/aghr/insplico.
Extending Janus lectins architecture: characterization and application to protocells
Authors: Notova Simona , Siukstaite Lina , Rosato Francesca , Vena Federica , Audfray Aymeric , Bovin Nicolai , Landemarre Ludovic , Römer Winfried , Imberty Anne
Published: August 2022

Synthetic biology is a rapidly growing field with applications in biotechnology and biomedicine. Through various approaches, remarkable achievements, such as cell and tissue engineering, have been already accomplished. In synthetic glycobiology, the engineering of glycan binding proteins is being developed for producing tools with precise topology and specificity. We developed the concept of chimeric lectins, i.e., Janus lectin, with increased valency, and additional specificity. The novel engineered lectin, assembled as a fusion protein between the β-propeller domain from Ralstonia solanacearum and the β-trefoil domain from fungus Marasmius oreades, is specific for fucose and α-galactose and its unique protein architecture allows to bind these ligands simultaneously. The protein activity was tested with glycosylated giant unilamellar vesicles, resulting in the formation of proto-tissue-like structures through cross-linking of such protocells. The synthetic protein binds to H1299 lung epithelial cancer cells by its two domains. The biophysical properties of this new construct were compared with the two already existing Janus lectins, RSL-CBM40 and RSL-CBM77Rf. Denaturation profiles of the proteins indicate that the fold of each has a significant role in protein stability and should be considered during protein engineering.
Microsporidian obligate intracellular parasites subvert autophagy of infected mammalian host cells to promote their own growth
Authors: Panek Johan , Sendra Kacper , Glenwright Helen , Kosta Gregor , Korolchuk Viktor I. , Hirt Robert P.
Published: August 2022

Intracellular pathogens such as Microsporidia can interact with host proteostasis pathways such as autophagy. Previous work done inCaenorhabditis elegansdemonstrated involvement of autophagy in controlling Microsporidian proliferation through ubiquitin labelling of the parasite and subsequent degradation by autolysomes. However, it remains unknown if such mechanisms also play the role in mammalian models. Here we used immunochemistry assays, super-resolution fluorescence microscopy, and modulation of the host’s autophagy flux through siRNA silencing and chemical agents to elucidate how Microsporidia interact with host mammalian cell autophagy flux. We show that despite targeting by early autophagy markers (ubiquitin and p62); the host cell was not able to complete autophagy-mediated removal ofEncephalitozoon cuniculi. Furthermore, instead of helping to control Microsporidia proliferation, the induction of autophagy dramatically increased proliferation of two Microsporidian species in two different mammalian cell models. Finally, we showed that the reduction of the autophagy flux using siRNA treatment or gut microbiota-derived metabolites known to be important for the intestinal epithelium homeostasis was able to reduce the parasite proliferation. Taken together, our results indicate that Microsporidia infecting mammalian cells not only developed strategies to evade the host autophagy but also evolved way to divert the autophagy flux to promote their own growth.
Environmentalism as an independent dimension of political preferences
Authors: KENNY JOHN , LANGSÆTHER PETER EGGE
Published: August 2022

Environmental issues are an important aspect of party competition and voters’ political preferences. Yet political behaviour research often considers environmental attitudes as a component of a broader ‘second‐dimension’ and either subsumes it into this or omits it. Using data from the fifth wave of the European Values Study, we demonstrate through factor analysis that environmentalism loads as a separate dimension across Western Europe, that environmentalism has somewhat different social predictors and that it has important associations with party preference that differ from those of other second dimension issues. Our findings have crucial implications. Firstly, not accounting for environmentalism in studies of political behaviour misses an important part of the picture. Secondly, subsuming environmentalism into a broader ‘cultural’ dimension may lead to incomplete conclusions about both social predictors and the electoral consequences of political attitudes and values. Thus, allowing for a separate environmental dimension opens up novel perspectives on political representation in Western democracies.
Dedicated nursing care pathway improved management of opioid‐poisoned patients in the emergency department: A before–after observational study
Authors: Isoardi Katherine , Learmont Benjamin , Horan Benjamin , Isbister Geoffrey
Published: August 2022

Objective

Opioid overdose is increasing and accounts for two‐thirds of poisoning deaths. Opioid induced respiratory depression is life‐threatening and can be under‐recognised even in the hospital setting. We aimed to evaluate the effect of a care pathway on the management of opioid‐poisoned patients.

Methods

This is a before–after observational study following the introduction of a nursing care pathway for opioid‐poisoned patients presenting to ED. Medical records were retrospectively reviewed pre (6‐month period 1 year prior) and post (9‐month period following) the introduction of the pathway. The primary outcome was the proportion of documented episodes of respiratory depression (respiratory rate <10 or oxygen saturation <93% on room air) receiving naloxone. Secondary outcomes were time to naloxone, number of documented observations (first 4 h) and length of stay.

Results

There were 111 patients included in the study, 61 pre‐intervention and 50 post‐intervention (35 followed the pathway). A significantly larger proportion of patients received naloxone for respiratory depression when the pathway was used (134/200 [67%] vs 34/118 [29%], difference 38%, 95% CI 28–48%). The median time to naloxone was similar (pathway 28.5 min vs no pathway 35 min, difference −6.5 min, 95% CI −19 to 12 min). Documentation increased when the pathway was used (12.0 observations/presentation vs 7.5 observations/presentation, difference 4.5 observations/patient, 95% CI 2.1–7.0 observations/patient). Length of stay was similar (pathway 16.7 h vs no pathway 15.3 h, difference 1.4 h, 95% CI −2.4 to 5.9 h).

Conclusions

Following the introduction of a dedicated opioid poisoning nursing care pathway, naloxone delivery and observation documentation increased. A care pathway may improve ED management of opioid poisoning.
Association of serum uric acid with all‐cause and cardiovascular mortality among adults with nonalcoholic fatty liver disease
Authors: Yang Sisi , Ye Ziliang , Liu Mengyi , Zhang Yanjun , Wu Qimeng , Zhou Chun , Zhang Zhuxian , He Panpan , Zhang Yuanyuan , Li Huan , Liu Chengzhang , Qin Xianhui
Published: August 2022

Aim

The association between serum uric acid (SUA) and mortality from cardiovascular diseases (CVDs) in nonalcoholic fatty liver disease (NAFLD) participants remains uncertain. We aim to investigate the relations of SUA with the risk of CVD mortality among adults with and without NAFLD.

Methods

Using data from National Health and Nutrition Examination Survey (NHANES) 1999–2014, a total of 17,858 participants were recruited. Of these, 5767 had a US Fatty Liver Index (USFLI) ≥30 and were classified as having NAFLD. Death information was obtained from the National Death Index until 2015.

Results

During a mean follow‐up of 8.3 years, 427 participants died from CVD. Overall, there was a positive association between SUA and CVD mortality among participants with NAFLD (per SD μmol/L increment, adjusted hazard ratio [HR], 1.40; 95% confidence interval [CI], 1.16–1.68). Accordingly, among those with NAFLD, when SUA was assessed as quartiles, compared with those in the first quartile, a significantly higher risk of CVD mortality was found in participants in the fourth quartile (adjusted HR, 2.69; 95% CI, 1.51–4.80). However, there was no significant association between SUA and CVD mortality among participants without NAFLD (per SD μmol/L increment, adjusted HR, 1.01; 95% CI, 0.83–1.22). Similar trends were found for all‐cause mortality. Similar results were also found when using FLI ≥ 60 to define NAFLD.

Conclusions

In a large and nationally representative sample of US adults, a higher SUA was significantly associated with a higher risk of CVD mortality among participants with NAFLD, but not in those without NAFLD.
Long‐term variability in spawning stock age structure influences climate–recruitment link for Barents Sea cod
Authors: Ottersen Geir , Holt Rebecca E.
Published: August 2022

Fish populations may spawn a vast number of offspring, while only a small and highly variable fraction of a new cohort survives long enough to enter into the fisheries as recruits. It is intuitive that the size and state of the spawning stock, the adult part of the fish population, is important for recruitment. Additionally, environmental conditions can greatly influence survival through vulnerable early life stages until recruitment. To understand what regulates recruitment, an essential part of fish population dynamics, it is thus necessary to explain the impact of fluctuations in both spawning stock and environment, including interactions. Here, we examine if the connection between the environment and recruitment is affected by the state of the spawning stock, including biomass, mean age and age diversity. Specifically, we re‐evaluate the hypothesis stating that recruitment from a spawning stock dominated by young fish and few age classes is more vulnerable to environmental fluctuations. We expand upon earlier work on the Barents Sea stock of Atlantic cod, now with data series extended in time both backwards and forwards to cover the period 1922–2019. While our findings are correlative and cannot prove a specific cause and effect mechanism, they support earlier work and strengthen the evidence for the hypothesis above. Furthermore, this study supports that advice to fisheries management should include considerations of environmental status.
Warming does not delay the start of autumnal leaf coloration but slows its progress rate
Authors: Jiang Nan , Shen Miaogen , Ciais Philippe , Campioli Matteo , Peñuelas Josep , Körner Christian , Cao Ruyin , Piao Shilong , Liu Licong , Wang Shiping , Liang Eryuan , Delpierre Nicolas , Soudani Kamel , Rao Yuhan , Montagnani Leonardo , Hörtnagl Lukas , Paul‐Limoges Eugénie , Myneni Ranga , Wohlfahrt Georg , Fu Yongshuo , Šigut Ladislav , Varlagin Andrej , Chen Jin , Tang Yanhong , Zhao Wenwu
Published: August 2022

Aim

Initiation of autumnal leaf senescence is crucial for plant overwintering and ecosystem dynamics. Previous studies have focused on the advanced stages of autumnal leaf senescence and reported that climatic warming delayed senescence, despite the fundamental differences among the stages of senescence. However, the timing of onset of leaf coloration (DLCO), the earliest visual sign of senescence, has rarely been studied. Here, we assessed the response of DLCO to temperature.

Location

30–75° N in the Northern Hemisphere.

Time period

2000–2018.

Major taxa studied

Deciduous vegetation.

Methods

We retrieved DLCO from high‐temporal‐resolution satellite data, which were then validated by PhenoCam observations. We investigated the temporal changes in DLCO and the relationship between DLCO and temperature by using satellite and ground observations.

Results

DLCO was not significantly (p > .05) delayed between 2000 and 2018 in 94% of the area. DLCO was positively (p < .05) correlated with pre‐DLCO mean daily minimum temperature (Tmin) in only 9% of the area, whereas the end of leaf coloration (DLCE) was positively correlated with pre‐DLCE mean Tmin over a larger area (34%). Further analyses showed that warming slowed the progress of leaf coloration. Interestingly, DLCO was less responsive to pre‐DLCO mean Tmin in areas where daylength was longer across the Northern Hemisphere, particularly for woody vegetation.

Main conclusions

The rate of progress of coloration is more sensitive to temperature than its start date, resulting in an extension of the duration of leaf senescence under warming. The dependence of DLCO response to temperature on daylength indicates stronger photoperiodic control on initiation of leaf senescence in areas with longer daylength (i.e., shorter nights), possibly because plants respond to the length of uninterrupted darkness rather than daylength. This study indicates that the onset of leaf coloration was not responsive to climate warming and provides observational evidence of photoperiod control of autumnal leaf senescence at biome and continental scales.
Outcomes reporting in systematic reviews on non‐surgical root canal treatment: A scoping review for the development of a core outcome set
Authors: Kirkevang Lise‐Lotte , El Karim Ikhlas A. , Duncan Henry Fergus , Nagendrababu Venkateshbabu , Kruse Casper
Published: August 2022

Background

Studies related to non‐surgical root canal treatment are amongst the most frequently performed clinical studies in endodontics. However, heterogeneity in reporting outcomes and lack of standardization is a significant challenge to evidence synthesis and guideline development.

Objectives

The aims of the present scoping review were to (a) identify outcomes reported in systematic reviews evaluating non‐surgical root canal treatment; (b) identify how and when the reported outcomes were measured; (c) assess possible selective reporting bias in the included studies. The information obtained in this study should inform the development of a core outcome set (COS) for non‐surgical root canal treatment.

Methodology

Structured literature searches were performed to identify systematic reviews on non‐surgical root canal treatments published in English between January 1990 and December 2020. Two reviewers undertook study selection and data extraction. Outcomes were categorized according to a healthcare taxonomy into five core areas (survival, clinical/physiological changes, life impact, resource use, and adverse events). The outcome measurement tools and length of follow‐up were recorded.

Results

Seventy‐five systematic reviews were included, of which 40 included meta‐analyses. Most reviews reported on physiological and clinical outcomes, primarily pain and/or radiographic assessment of periapical status, and a variety of measurement tools and scales were used. Few reviews focused on tooth survival, life impact, resources, and adverse events. The heterogeneity amongst the reviews was large on all parameters. Less than 40% of the reviews assessed the risk of selective reporting.

Discussion

Overall aims of the included reviews were highly heterogenic; thus, outcomes and how they were measured also varied considerably. Patient‐centred outcomes and the use of resources were rarely reported on.

Conclusions

Most studies reported on physiological and clinical outcomes, in particular pain and/or radiographic healing. Measurement tools, scales, thresholds, and follow‐up periods varied greatly within each outcome, making comparison across studies complicated. Less than 40% of the reviews assessed risk of selective reporting; thus, selective bias could not be ruled out. The presented information on reported outcomes, measurement tools and scales, and length of follow‐up may guide the planning of future research and inform the development of a COS for non‐surgical root canal treatment.
How toxic is an old friend? A review of the safety of hydroxychloroquine in clinical practice
Authors: Fairley Jessica L. , Nikpour Mandana , Mack Heather G. , Brosnan Maria , Saracino Amanda M. , Pellegrini Marc , Wicks Ian P.
Published: August 2022

Hydroxychloroquine (HCQ) and its close relative chloroquine (CQ) were initially used as antimalarial agents but are now widely prescribed in rheumatology, dermatology and immunology for the management of autoimmune diseases. HCQ is considered to have a better long‐term safety profile than CQ and is therefore more commonly used. HCQ has a key role in the treatment of connective tissue diseases including systemic lupus erythematosus (SLE), where it provides beneficial immunomodulation without clinically significant immunosuppression. HCQ can also assist in managing inflammatory arthritis, including rheumatoid arthritis (RA). Debate around toxicity of HCQ in COVID‐19 has challenged those who regularly prescribe HCQ to discuss its potential toxicities. Accordingly, we have reviewed the adverse effect profile of HCQ to provide guidance about this therapeutic agent in clinical practice.