bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of Adverse Drug Events of Opioids in the United States
Authors: Liu Edward Y. , McCall Kenneth L. , Piper Brian J.
Published: October 2022

The United States (US) is going through an opioid crisis with annual increases in opioid-related mortality. Our study analyzed the adverse drugs events (ADEs) for eleven prescription opioids when correcting for distribution, and their ratios for three periods: 2006-2010, 2011-2016, and 2017-2021 in the US. The opioids included buprenorphine, codeine, fentanyl, hydrocodone, hydromorphone, meperidine, methadone, morphine, oxycodone, oxymorphone, and tapentadol. The Food and Drug Administration Adverse Event Reporting System (FAERS) database consists of reports by MedWatch adverse event forms submitted by healthcare professionals and others (N=667,969), whereas the Automation of Reports and Consolidated Orders System (ARCOS) reports on medically used controlled substances. Oral morphine milligram equivalents (MMEs) were calculated by conversion relative to morphine. The relative ADEs of the select opioids calculated from FAERs, opioid distribution from ARCOS, and the FAERs to ARCOS ratios were analyzed for the eleven opioids. Oxycodone reports peaked in the third period and showed consistently high ADEs. Codeine and meperidine accounted less than five percent of ADEs. The ARCOS distributions were relatively constant over time, but methadone consistently accounted for the largest portion of the total distribution. The FAERS to ARCOS ratios generally increased over time, with meperidine (60.6), oxymorphone (11.1), tapentadol 10.3, and hydromorphone (7.9) most over-represented for ADEs in the third period. Oxymorphone had a 542.2% increase in ratio between the second and third period should be noted. Methadone was under-represented (< .20) in all three periods. These findings indicate the need to further monitor and address the ADEs of select opioids.

Significance

Prescription opioid use in the US is among the highest in the world. This study analyzed both FAERs and ARCOS databases to understand the adverse drugs events. This investigation identified which opioids were overrepresented (e.g. meperidine) and underrepresented (e.g. methadone) for adverse effects relative to the prevalence of use to inform healthcare policies and change the way physicians view and prescribe these opioids.
Genome-wide Analysis of Rare Haplotypes Associated with Breast Cancer Risk: Discovery, Replication, and Generalizability Evaluation
Authors: Wang Fan , Moon Wonjong , Letsou William , Sapkota Yadav , Wang Zhaoming , Im Cindy , Baedke Jessica L. , Robison Leslie , Yasui Yutaka
Published: October 2022

While numerous common variants have been linked to breast cancer (BCa) risk, they explain only partially the total BCa heritability. Inference from the Nordic population-based twin data indicates that rare high-risk loci are the chief determinant of BCa risk. Here, we use haplotypes, rather than single variants, to identify rare high-risk loci for BCa. With computationally phased genotypes from 181,034 white British women in the UK Biobank, we conducted a genome-wide haplotype-BCa association analysis using sliding windows of 5-500 consecutive array-genotyped variants. In the discovery stage, haplotype associations with BCa risk were evaluated retrospectively in the pre-study-enrollment portion of data including 5,487 BCa cases. BCa hazard ratios (HRs) for additive haplotypic effects were estimated using Cox regression. Our replication analysis included women free of BCa at enrollment, of whom 3,524 later developed BCa. This two-stage analysis detected 13 rare loci (frequency <1%), each associated with an appreciable BCa risk increase (discovery: HRs=2.84-6.10, P-value<5×10−8; replication: HRs=2.08-5.61, P-value<0.01). In contrast, the variants that formed these rare haplotypes individually exhibited much smaller effects. Functional annotation revealed extensive cis-regulatory DNA elements in BCa-related cells underlying the replicated rare haplotypes. Using phased, imputed genotypes from 30,064 cases and 25,282 controls in the DRIVE OncoArray case-control study, six of the 13 rare-loci associations proved generalizability (odds ratio estimates: 1.48-7.67, P-value<0.05). This study demonstrates the complementary advantage of utilizing rare haplotypes to capture novel risk loci and possible discoveries of more genetic elements contributing to BCa heritability once large, germline whole-genome sequencing data become available.
Impact of the COVID-19 pandemic on the circulation of other pathogens in England
Authors: Hayes Lauren , Uri Hannah , Bojkova Denisa , Cinatl Jindrich , Wass Mark N. , Michaelis Martin
Published: October 2022

The COVID-19 pandemic and the associated prevention measures did not only impact on the transmission of COVID-19 but also on the spread of other infectious diseases in an unprecedented natural experiment. Here, we analysed the transmission patterns of 22 different infectious diseases during the COVID-19 pandemic in England. Our results show that the COVID-19 prevention measures generally reduced the spread of pathogens that are transmitted via the air and the faecal-oral route. Moreover, the COVID-19 prevention measures resulted in the sustained suppression of vaccine-preventable infectious diseases also after the removal of restrictions, while non-vaccine preventable diseases displayed a rapid rebound. Despite concerns that a lack of exposure to common pathogens may affect population immunity and result in large outbreaks by various pathogens post-COVID-19, only four of the 22 investigated diseases and disease groups displayed higher post-than pre-pandemic levels without an obvious causative relationship. Notably, this included chickenpox for which an effective vaccine is available but not used in the UK, which provides strong evidence supporting the inclusion of the chickenpox vaccination into the routine vaccination schedule in the UK. In conclusion, our findings provide unique, novel insights into the impact of non-pharmaceutical interventions on the spread of a broad range of infectious diseases.
Online survey of treatment experiences for obsessive-compulsive disorder
Authors: Kirkham E.J. , Cao Y. , Król M.
Published: October 2022

Introduction

There is a lack of knowledge about the treatment experiences of people living with obsessive-compulsive disorder (OCD).

Method

Participants with OCD (n= 202) took part in an online survey in which they answered questions about what treatment they had received. They also completed measures of current OCD, anxiety and depression.

Results

Scores above the clinical cut-off for OCD were high (> 70%) across the sample, irrespective of what kind of treatment had been received. Despite this, most participants felt their OCD was better now than it had been pre-treatment. Mean OCD scores were similar between treatment groups (OCD-focused, partly OCD-focused, non-OCD focused, no treatment), though there was some evidence that OCD-focused treatment was associated with lower OCD scores, especially for symptoms of hoarding, neutralising and ordering.

Discussion

These findings contribute to evidence of unmet need in OCD care. Practitioners should be aware that OCD is often a chronic condition which requires specialist care, and may require more than one course of treatment.
Metabolic intervention by low carbohydrate diet suppresses the onset and progression of neuroendocrine tumors
Authors: Chen Yu , Yamamoto Tatsuki , Takahashi Yura , Moro Tomoka , Tajima Tomoko , Sakaguchi Yukiko , Sakata Naoaki , Yokoyama Akihiko , Hijioka Susumu , Sada Akane , Tabata Yuko , Ohki Rieko
Published: October 2022

Insulin signaling often plays a role in the regulation of cancer including tumor initiation, progression, and response to treatment. In addition, the insulin-regulated PI3K-Akt-mTOR pathway plays an important role in the regulation of islet cell proliferation and this pathway is hyperactivated in human non-functional pancreatic neuroendocrine tumors (PanNETs). We therefore investigated the effect of a very low carbohydrate diet (ketogenic diet) on a mouse model that develops non-functional PanNETs to ask how reduced PI3K-Akt-mTOR signaling might affect the development and progression of non-functional PanNET. We found that this dietary intervention resulted in lower PI3K-Akt-mTOR signaling in islet cells and a significant reduction in PanNET formation and progression. We also found that this treatment had a significant effect on the suppression of pituitary NET development. Furthermore, we found that non-functional PanNET patients with lower blood glucose levels tend to have a better prognosis than patients with higher blood glucose levels. This preclinical study shows that a dietary intervention that results in lower serum insulin levels leads to lower insulin signal within the neuroendocrine cells and has a striking suppressive effect on the development and progression of both pancreatic and pituitary NETs.
Possible adaption of the 2022 Monkeypox virus to the human host through gene duplication and loss
Authors: Brinkmann Annika , Kohl Claudia , Pape Katharina , Bourquain Daniel , Thürmer Andrea , Michel Janine , Schaade Lars , Nitsche Andreas
Published: October 2022

Poxviruses are known to evolve slower than RNA viruses, with rearrangements such as gene gain and loss as the main driver for host adaption. In 2022 the world is being challenged by the largest global outbreak so far of Monkeypox virus, and the virus seems to have established itself in the human community. Here we report five MPXV genomes with extensive gene duplication and loss, including duplications of up to 18,000 bp to the opposed genome end, and deletions at the site of insertion of up to 16,000 bp, as a possible adaption to the human host.
Taste receptor T1R3 in nasal cilia detectsStaphylococcus aureusD-amino acids to increase apical glucose uptake and enhance innate immunity
Authors: Carey Ryan M. , Hariri Benjamin M. , Adappa Nithin D. , Palmer James N. , Margolskee Robert F. , Cohen Noam A. , Lee Robert J.
Published: October 2022

Bitter (T2R) and sweet/umami (T1R) taste receptors serve chemosensory roles throughout the body. In airway cilia, T2Rs detect bacterial metabolites to stimulate bactericidal nitric oxide. T1Rs in solitary chemosensory cells detect glucose in airway surface liquid (ASL) and bacterial D-stereoisomer amino acids to regulate antimicrobial peptides. Using differentiated air-liquid interface cultures of primary nasal cells, we show that the T1R3 receptor is also expressed in human and mouse nasal cell cilia. D-amino acids produced at low mM concentrations byStaphylococcus aureusactivate T1R3 to decrease ASL glucose and increase apical glucose uptake by increasing GLUT2 and GLUT10 expression through a β-arrestin pathway. Our data suggests that T1R3 localized to cilia functions as an immune detector for D-amino acids to reduce ASL glucose and potentially limit bacterial growth. Given that glucose protectedS. aureusagainst bactericidal NO produced during T2R activation, the reduced ASL glucose with T1R3 activation may also sensitize bacteria to other innate defenses.

HIGHLIGHTS

Nasal motile cilia express the T1R3 subunit of the sweet taste receptor

S. aureusD-amino acids activate cilia T1R3 to enhance mucosal glucose uptake

Reduced airway surface liquid glucose likely reducesS. aureusgrowth

Reduced airway glucose also sensitizesS. aureusto epithelial NO production
Optical mapping of ground reaction force dynamics in freely behavingDrosophila melanogasterlarvae
Authors: Booth Jonathan H. , Meek Andrew T. , Kronenberg Nils M. , Pulver Stefan R. , Gather Malte C.
Published: October 2022

During locomotion, soft-bodied terrestrial animals solve complex control problems at substrate interfaces, but our understanding of how they achieve this without rigid components remains incomplete. Here, we develop new all-optical methods based on optical interference in a deformable substrate to measure ground reaction forces (GRFs) with micrometre and nanonewton precision in behavingDrosophilalarvae. Combining this with a kinematic analysis of substrate interfacing features, we shed new light onto the biomechanical control of larval locomotion. Crawling in larvae measuring ∼1 mm in length involves an intricate pattern of cuticle sequestration and planting, producing GRFs of 1-7 µN. We show that larvae insert and expand denticulated, feet-like structures into substrates as they move, a process not previously observed in soft bodied animals. These ‘protopodia’ form dynamic anchors to compensate counteracting forces. Our work provides a framework for future biomechanics research in soft-bodied animals and promises to inspire improved soft-robot design.
Development of a High-Throughput Minimum Inhibitory Concentration (HT-MIC) Testing Workflow
Authors: Tiwari Suman , Nizet Oliver , Dillon Nicholas
Published: October 2022

The roots of the minimum inhibitory concentration (MIC) determination go back to the early 1900s. Since then, the test has undergone modifications and advancements in an effort to increase its dependability and accuracy. Although biological investigations use an ever-increasing number of samples, complicated processes and human error sometimes result in poor data quality, which makes it challenging to replicate scientific conclusions. The automation of the few manual steps using protocols decipherable by machine can ease some of the procedural difficulties. Originally relying on manual pipetting and human vision to determine the results, modern broth dilution MIC testing procedures have incorporated microplate readers to enhance sample analysis. However, current MIC testing procedures are unable to simultaneously evaluate a large number of samples efficiently. Here, we have created a workflow using the Opentrons OT-2 robot to enable high-throughput MIC testing. We have further optimized the analysis by incorporating Python programming for MIC assignment to streamline the automation. In this workflow, we performed MIC tests on four different strains, three replicates per strain, and analyzed a total of 1,152 wells. Comparing our our workflow to a conventional plate MIC procedure, we find that the HT-MIC method is 630% faster while simulataneously boasting a 100% accuracy. Our high-throughput MIC workflow can be applied in both academic and clinical settings since it is faster, more efficient, and more accurate than many conventional methods.
Identifying fungal leaf spots on oilseed rape: could pictures help?
Authors: Bousset L. , Ermel M. , Bammé B. , Penaud A. , Carpezat J. , Balesdent MH. , Laval V. , Palerme M. , Parisey N.
Published: October 2022

From sowing in late summer until harvest in following summer, oilseed rape can be infected by several fungi, which foliar symptoms (leaf spots) coexist on the crop. Training an expert at their identification is quick for the typical symptoms with characteristic appearance. However, in many cases the size, colour and morphology are similar and for the atypical symptoms, there is a risk of confusion or in-decidability. Also, scouting the fields for expert training is not possible at all seasons and all diseases might not be seen in all years and all places. The aim of our study was to produce large sets of pictures annotated by several experts, from which tables illustrating the diversity of symptom appearance were chosen. These tables will enable assistance to diagnostic and expert training.
Highly structured habitats mitigate size- and growth-selective mortality of post-settlement juvenile fish
Authors: Kamimura Yasuhiro , Shoji Jun
Published: October 2022

The role of vegetated habitats such as seagrass and macroalgal beds as nurseries is essential for the survival of larval and juvenile fish, although quantitative evaluation of the contribution of these habitats to nursery function is limited. Moreover, growth–survival relationships of larvae and juveniles associated with vegetated habitats have rarely been examined. To quantitatively and qualitatively evaluate the processes affecting juvenile survival in vegetated habitats, we investigated whether there is a correlation between the degree of selection for bigger and faster-growing fish and mortality rates for three cohorts by birth date of post-settlement black rockfish (Sebastes cheni) in a macroalgal bed. We also analyzed relationships between growth rate and experienced temperature by age class to examine the effects of temperature on growth. The latest cohort, which grew under lower vegetation coverage due to a seasonal increase in water temperature, showed higher mortality with evidence of strong selection for bigger and faster-growing fish. The growth–temperature relationships showed that positive effects of temperature on growth weakened after settlement. Therefore, we suggest that macroalgal coverage has a critical role controlling the growth–mortality relationship of post-settlementS. cheni. Furthermore, the negative effects of high temperature on juvenile survival through loss of vegetation may be greater than the positive effects on juvenile growth. These findings will contribute to the management of fisheries resources by increasing the understanding of relationships between survival mechanisms in fish early life stages and vegetation phenology of their habitat under the increasing effects of global warming.
Two closed conformations of CRAF require the 14-3-3 binding motifs and cysteine-rich domain to be intact in live cells
Authors: Okamoto Kenji , Sako Yasushi
Published: October 2022

The protein rapidly accelerated fibrosarcoma (RAF) is a kinase downstream of the membrane protein RAS in the cellular signal transduction system. In the structure of RAF, the N- and C-terminus domains are connected with a flexible linker. The open/close dynamics and dimerization of RAF are thought to regulate its activity, although the details of these conformations are unknown, especially in live cells. In this work, we used alternating laser excitation to measure cytosolic CRAF in live HeLa cells and obtained single-molecule Förster resonance energy transfer (smFRET) distributions of the structural states. We compared the results for wild-type (WT)-CRAF before and after epidermal growth factor (EGF) stimulation, with mutations of the 14-3-3 binding sites and cysteine-rich domain, and an N-terminus truncation. The smFRET distributions of full-length CRAFs were analyzed by global fitting with three beta distributions. Our results suggested that a 14-3-3 dimer bound to two sites on a single CRAF molecule and induced the formation of the autoinhibitory closed conformation. There were two closed conformations, which the majority of WT-CRAF adopted. These two conformations showed different responsiveness to EGF stimulation.
PAM-less Exonuclease-assisted Cas12a for visual detection of Vibrio Species
Authors: Zhang Derek Han , Raykar Siddharth , Ng Kenneth Tsz Chun
Published: October 2022

Foodborne pathogens, includingVibrio spp. and norovirus, cause substantial economic and healthcare burdens worldwide. Rapid and sensitive point-of-care testing on-farm or restaurants for batch inspection of pathogenic contamination in raw food products is essential. Here, we present an easy-to-design, cost-effective PAM-less Exonuclease-assisted Cas12A Nucleic-acid Detection (PECAN) assay paired with nucleic acid amplification systems for rapid and sensitive visual detection of 2 pathogenic Vibrio species:Vibrio parahaemolyticus(TDH) andVibrio Cholerae(ctxA) without protospacer adjacent motif (PAM) site limitation. With T7 exonuclease, PAM-less detection could be achieved with a low concentration of cas12a, costing $0.8 USD per reaction. The system could also be adapted for PAM-less cas12a nucleic acid detection in-field or in-lab for sensitive DNA or RNA detection. We also constructed a low-cost reusable 3D printed heater chassis and reusable sodium acetate heat packs for field use without generating solid waste.
Structural and functional analysis of YopR and identification of an additional key component of the SPβ phage lysis-lysogeny management system
Authors: Kohm Katharina , Jalomo-Khayrova Ekaterina , Basu Syamantak , Steinchen Wieland , Bange Gert , Hertel Robert , Commichau Fabian M. , Czech Laura
Published: October 2022

Prophages need to tightly control their lifestyle to either be maintained within the host genome or enter the lytic cycle. The SPβ prophage present in the genome ofBacillus subtilis168 was recently shown to possess anarbitriumsystem defining its replication stage. Using an historicB. subtilisstrain harboring the heat-sensitive SPβ c2 mutant, we analyzed a key component of the lysis-lysogeny decision system called YopR, which is critical for maintenance of lysogeny. Here, we demonstrate that the heat-sensitive SPβ c2 phenotype is due to a single nucleotide exchange in theyopRgene, rendering the encoded YopRG136Eprotein temperature sensitive. Structural characterization of YopR revealed that the protein is a DNA-binding protein with an overall fold like tyrosine recombinases. Biochemical and functional analyses indicate that YopR has lost the recombinase function and the G136E exchange impairs its higher order structure and DNA binding activity. We further show that the heat-inducible SPβ excision of the c2 mutant still depends on the serine recombinase SprA. Finally, an evolution experiment identified the YosL protein of unknown function as a novel component of the lysis-lysogeny management system, as the presence ofyosLis crucial for the induction of the lytic cycle of SPβ.
The Updated Properties Model (UPM): A topology optimization algorithm for the creation of macro-micro optimized structures with variable stiffness
Authors: Saucedo-Mora Luis , Ben-Yelun Ismael , García-Modet Hugo , Sanz-Gómez Miguel Ángel , Montáns Francisco Javier
Published: October 2022

The design and manufacturing of high value industrial components is suffering a change of paradigm with 3D printing. In this change of paradigm, metamaterials have an important role because when a component is 3D-printed, it is performed from the micro level, where custom structures may be designed to endow the material and the component of special of customized mechanical properties. Topology optimization techniques facilitate the design of both the microstructures and the overall component topology, and today the component topology may be designed assuming a continuous spectrum of mechanical properties facilitated by different locally designed microstructures. However, current topology optimization techniques do not operate directly with the mechanical properties of the material, but through density intermediates, using density-based limits like a minimum or maximum density, assuming an homogeneous base material. We propose here a novel topology optimization algorithm which operates directly on the mechanical properties and energies, without employing density intermediates. The proposed approach reduces the algorithmic complexity since the optimization is performed by the direct iterative update of the mechanical properties, through information taken from its finite element analysis. We show that the proposed methodology can reach similar results as the current techniques based on a gradient descent optimization, eliminating the need for external parameters and, hence, increasing the easy of use and its robustness. The proposed technique is specially suitable for two-level concurrent material-component design using functionally graded metamaterials.
PiDeeL: Pathway-Informed Deep Learning Model for Survival Analysis and Pathological Classification of Gliomas
Authors: Kaynar Gun , Cakmakci Doruk , Bund Caroline , Todeschi Julien , Namer Izzie Jacques , Cicek A. Ercument
Published: October 2022

Online assessment of tumor characteristics during surgery is important and has the potential to establish an intraoperative surgeon feedback mechanism. With the availability of such feedback, surgeons could decide to be more liberal or conservative regarding the resection of the tumor. While there are methods to perform metabolomics-based online tumor pathology prediction, their model complexity and, in turn, the predictive performance is limited by the small dataset sizes. Furthermore, the information conveyed by the feedback provided on the tumor tissue could be improved both in terms of content and accuracy. In this study, we propose a metabolic pathway-informed deep learning model, PiDeeL, to perform survival analysis and pathology assessment based on metabolite concentrations. We show that incorporating pathway information into the model architecture substantially reduces parameter complexity and achieves better survival analysis and pathological classification performance. With these design decisions, we show that PiDeeL improves tumor pathology prediction performance of the state-of-the-art in terms of the Area Under the ROC Curve (AUC-ROC) by 3.38% and the Area Under the Precision-Recall Curve (AUC-PR) by 4.06%. Similarly, with respect to the time-dependent concordance index (c-index), we observe that PiDeeL achieves better survival analysis performance (improvement up to 4.3%) when compared to the state-of-the-art. Moreover, we show that importance analyses performed on input metabolite features as well as pathway-specific hidden-layer neurons of PiDeeL provide insights into tumor metabolism. We foresee that the use of this model in the surgery room will help surgeons adjust the surgery plan on the fly and will result in better prognosis estimates tailored to surgical procedures.

Availability

The code is released athttps://github.com/ciceklab/PiDeeL. The data used in this study is released athttps://zenodo.org/record/7228791.

Contact

cicek@cs.bilkent.edu.tr

Supplementary information

Supplementary data are available atBriefings in Bioinformaticsonline.
Engineering a minimal SilkCatcher/Tag pair compatible with SpyCatcher/Tag pair for the production of native-sized spider silk
Authors: Fan Ruxia , Hakanpää Johanna , Elfving Karoliina , Taberman Helena , Linder Markus B. , Aranko A. Sesilja
Published: October 2022

Protein/peptide pairs, called Catcher/Tag pairs, are applied for biological isopeptide-bond mediated Click-reactions. Covalent protein ligation using Catcher/Tag pairs has turned out to be a valuable tool in biotechnology and biomedicines. It is essential to increase the current toolbox of Catcher/Tag pairs to expand the range of applications further, e.g., for multiple-fragment ligation that requires several orthogonal ligases. We report here engineering of novel Catcher/Tag pairs for protein ligation, aided by a new crystal structure of a minimal CnaB domain fromLactobacillus plantarum. We engineer several split variants, characterize in detail one of them, named SilkCatcher/Tag pair, and show that the newly engineered SilkCatcher/Tag pair is orthogonal and compatible with the widely used SpyCatcher/Tag pair. Finally, we demonstrate the use of the new SilkCatcher/Tag pair in the production of native-sized highly repetitive spider-silk-like proteins with >90% purity, which is not possible with the traditional recombinant production.
KIN: A method to infer relatedness from low-coverage ancient DNA
Authors: Popli Divyaratan , Peyrégne Stéphane , Peter Benjamin M.
Published: October 2022

Genetic kinship of ancient individuals can provide insights into their culture and social hierarchy, and is relevant for downstream genetic analyses. However, estimating relatedness from ancient DNA is difficult due to low-coverage, ascertainment bias, or contamination from various sources. Here, we present KIN, a method to estimate the relatedness of a pair of individuals from the identical-by-descent segments they share. KIN accurately classifies up to 3rd-degree relatives using ≥ 0.05xsequence coverage and differentiates siblings from parent-child. It incorporates additional models to adjust for contamination and detect inbreeding, which improves classification accuracy.
The Western Lake Erie Culture Collection: A promising resource for evaluating the physiological and genetic diversity ofMicrocystisand its associated microbiome
Authors: Yancey Colleen E. , Kiledal E. Anders , Denef Vincent J. , Errera Reagan M. , Evans Jacob T. , Hart Lauren , Isailovic Dragan , James William , Kharbush Jenan K. , Kimbrel Jeffrey A , Li Wei , Mayali Xavier , Nitschky Helena , Polik Catherine , Powers McKenzie A , Premathilaka Sanduni H. , Rappuhn Nicole , Reitz Laura A. , Rivera Sara R. , Zwiers Claire C. , Dick Gregory J.
Published: October 2022

Cyanobacteria harmful algal blooms (cyanoHABs) dominated byMicrocystisspp. have significant public health and economic implications in freshwater bodies around the world. These blooms are capable of producing a variety of cyanotoxins, including microcystins, that affect fishing and tourism industries, human and environmental health, and access to drinking water. In this study, we isolated and sequenced the genomes of 21 unialgalMicrocystiscultures collected from western Lake Erie between 2017-2019. While some cultures isolated in different years have a high degree of genetic similarity (Average Nucleotide Identity >99%), genomic data shows that these cultures also represent much of the breadth of knownMicrocystisdiversity in natural populations. Only 5 isolates contained all the genes required for microcystin synthesis while 2 isolates contained a previously described partialmcyoperon. Microcystin production within cultures was also assessed using Enzyme-Linked Immunosorbent Assay (ELISA) and supported genomic results with high concentrations (up to 900 μg L-1) in cultures with completemcyoperons and no or low toxin detected otherwise. These xenic cultures also contained a substantial diversity of bacteria associated withMicrocystis, which has become increasingly recognized as an essential component of cyanoHAB community dynamics. These results highlight the genomic diversity amongMicrocystisstrains and associated bacteria in Lake Erie, and their potential impacts on bloom development, toxin production, and toxin degradation. This collection significantly increases the availability of environmentally relevantMicrocystisstrains from temperate North America, which is changing rapidly due to climate change.

Highlights

Twenty one xenicMicrocystiscultures were isolated from western Lake Erie and capture the diversity ofMicrocystisstrains observed in natural populations as well as their associated bacteria

Microcystisstrains show variability in core and accessory gene content, and genetically similar strains produce varying concentrations and congeners of microcystins

This collection is a valuable resource for studying strain diversity and interactions betweenMicrocystisand associated bacteria

Our collection increases the availability of environmentally relevant strains from temperate North America, which is historically underrepresented in culture collections.
Structure of the Wnt-Frizzled-LRP6 initiation complex reveals the basis for co-receptor discrimination
Authors: Tsutsumi Naotaka , Hwang Sunhee , Hansen Simon , Waghray Deepa , Wang Nan , Miao Yi , Glassman Caleb R. , Caveney Nathanael A. , Jude Kevin M. , Janda Claudia Y. , Hannoush Rami N. , Garcia K. Christopher
Published: October 2022

Wnt morphogens are critical for embryonic development and tissue regeneration. Canonical Wnts form ternary receptor complexes composed of tissue-specific Frizzled receptors together with the shared LRP5/6 co-receptors to initiate β-catenin signaling. The structure of a ternary complex of an affinity-matured XWnt8-Frizzled8-LRP6 complex elucidates the basis of co-receptor discrimination by canonical Wnts by means of their N-termini and linker domains that engage the LRP6 E1E2 domain funnels. Chimeric Wnts bearing modular linker ‘grafts’ were able to transfer LRP6 domain specificity between different Wnts and enable non-canonical Wnt5a to signal through the canonical pathway. Synthetic peptides comprising the linker domain serve as Wnt-specific antagonists. The structure of the ternary complex provides a topological blueprint for the orientation and proximity of Frizzled and LRP6 within the Wnt cell surface signalosome.
Facilitatory stimulation of the pre-SMA enhances semantic cognition via remote network effects on task-based activity and connectivity
Authors: Martin Sandra , Frieling Regine , Saur Dorothee , Hartwigsen Gesa
Published: October 2022

Background

The continuous decline of executive abilities with age is mirrored by increased neural activity of domain-general networks during task processing. So far, it remains unclear how much domain-general networks contribute to domain-specific processes such as language when cognitive demands increase. The current neuroimaging study explored the potential of intermittent theta-burst stimulation (iTBS) over a domain-general hub to enhance executive and semantic processing in healthy middle-aged to older adults.

Methods

We implemented a cross-over within-subject study design with three task-based neuroimaging sessions per participant. Using an individualized stimulation approach, we stimulated each participant once with effective and once with sham iTBS over the pre-supplementary motor area (pre-SMA), a region of domain-general control. Subsequently, task-specific stimulation effects were assessed in functional MRI using a semantic and a non-verbal executive task with varying cognitive demand.

Results

Effective stimulation increased activation relative to sham stimulation only during semantic processing in visual and dorsal attention networks. Further, iTBS induced increased functional connectivity in task-specific networks for semantic and executive conditions with high cognitive load. Notably, stimulation-induced changes in activation and connectivity related differently to behavior: While increased activation of the parietal dorsal attention network was linked to poorer semantic performance, its enhanced coupling with the pre-SMA was associated with more efficient semantic processing.

Conclusions

iTBS modulates networks in a task-dependent manner and generates effects at regions remote to the stimulation site. These neural changes are linked to more efficient semantic processing, which underlines the general potential of network stimulation approaches in cognitive aging.
The ancestral chromatin landscape of land plants
Authors: Hisanaga Tetsuya , Wu Shuangyang , Schafran Peter , Axelsson Elin , Akimcheva Svetlana , Dolan Liam , Li Fay-Wei , Berger Frédéric
Published: October 2022

Background

In animals and flowering plants specific chromatin modifications define three chromosomal domains: euchromatin comprising transcribed genes, facultative heterochromatin comprising repressed genes, and constitutive heterochromatin comprising transposons. However, recent studies have shown that the correlation between chromatin modifications and transcription vary among different eukaryotic organisms including mosses and liverworts that differ from one another. Mosses and liverworts diverged from hornworts, altogether forming the lineage of bryophytes that shared a common ancestor with all land plants. We aimed to obtain chromatin landscapes in hornworts to establish synapomorphies across bryophytes.

Results

We mapped the chromatin landscape of the model hornwortAnthoceros agrestis.By comparing chromatin landscapes across bryophytes we defined the common chromatin landscape of the ancestor of extant bryophytes. In this group, constitutive heterochromatin was characterized by a scattered distribution across autosomes, which contrasted with the dense compartments of heterochromatin surrounding the centromeres in flowering plants. Topologically associated domains were primarily occupied by transposons with genes at their boundaries and nearly half of the hornwort transposons were associated with facultative heterochromatin and euchromatin.

Conclusions

Most of the features observed in hornworts are also present in liverworts but are distinct from flowering plants. Hence, the ancestral genome of bryophytes was likely a patchwork of units of euchromatin interspersed within facultative and constitutive heterochromatin and each unit contained both transposons and genes sharing the same chromatin state. We propose this genome organization was ancestral to land plants and prevented transposons from being segregated as constitutive heterochromatin around point centromeres as in flowering plants.
Accounting for central place foraging constraints in habitat selection studies
Authors: Benhamou Simon , Courbin Nicolas
Published: October 2022

Habitat selection studies contrast the actual space use with the expected use under the null hypothesis of no preference (hereafter neutral use). Neutral use is most often assimilated to the relative abundance of the different habitat types. This generates a considerable bias when studying habitat selection by foragers that perform numerous back and forth to a central place (CP). Indeed, the increased space use close to the CP with respect to distant places reflects a mechanical effect rather than a true preference for the closest habitats. Yet, correctly estimating habitat selection by CP foragers is of paramount importance for a better understanding of their ecology and efficiency of conservation actions. We show that (1) including the distance to the CP as a covariate in unconditional Resource Selection Functions (RSFs), as did in several studies, is quite inefficient to correct for the bias. Bias can be eliminated only by contrasting the actual use distribution to an appropriate neutral distribution that takes the CP forager behavior into account. (2) The need to specify such an appropriate neutral use distribution can be bypassed by relying on a conditional RSF, where the neutral use is assessed locally without reference to the CP.
R-loop editing by DNA cytosine deaminase APOBEC3B determines the activity of estrogen receptor enhancers
Authors: Zhang Chi , Lu Yu-jing , Chen Bingjie , Bai Zhiyan , Hervieu Alexia , Licciardello Marco P. , Wang Mei , Mitsopoulos Costas , Al-Lazikani Bissan , Totorici Marcello , Rossanese Olivia W. , Workman Paul , Clarke Paul A.
Published: October 2022

Estrogen receptor (ER) activation results in the formation of DNA double strand breaks (DSB), which promote genomic instability and tumour heterogeneity in ER-positive breast cancers. The single-stranded DNA (ssDNA) cytosine deaminase APOBEC3B (A3B) regulates ER activity by inducing DSB at ER enhancers. To delineate how A3B recognises its substrates and unveil the underlying mechanism leading to the formation of ER-induced DSB, we sampled A3B-mediated deamination sites using whole genome sequencing in a human breast cancer cell model lacking base excision repair function. Our genome-wide analysis revealed that C>U conversions carried out by A3B in R-loop structures are processed into DSB in the vicinity of ER promoters or enhancers. A mechanism which required both the processing of A3B-editing sites and R-loops by distinct DNA damage repair mechanisms. In addition, using BioID-enabled mass-spectroscopy proteomics, we identified TDRD3 as a key A3B-binding partner directing the activity of A3B to ER-induced R-loops. This study suggests a function for A3B in sustaining tumour evolution as an adaptive response at the transcriptional and epigenetic level and supports A3B as a promising target to control ER activity in cancer.
A cost-free CURE: Using bioinformatics to identify DNA-binding factors at a specific genomic locus
Authors: Schmidt Casey A. , Hodkinson Lauren J. , Comstra H. Skye , Rieder Leila E.
Published: October 2022

Research experiences provide diverse benefits for undergraduates. Many academic institutions have adopted course-based undergraduate research experiences (CUREs) to improve student access to research opportunities. However, potential instructors of a CURE might still face financial or practical hurdles that prevent implementation. Bioinformatics research offers an alternative that is free, safe, compatible with remote learning, and may be more accessible for students with disabilities. Here, we describe a bioinformatics CURE that leverages publicly available datasets to discover novel proteins that target an instructor-determined genomic locus of interest. We use the free, user-friendly bioinformatics platform Galaxy to map ChIP-seq datasets to a genome, which removes the computing burden from students. Both faculty and students directly benefit from this CURE, as faculty can perform candidate screens and publish CURE results. Students gain not only basic bioinformatics knowledge, but also transferable skills, including scientific communication, database navigation, and primary literature experience. The CURE is flexible and can be expanded to analyze different types of high-throughput data or to investigate different genomic loci in any species.
Clustering of CaV1.3 L-type calcium channels by Shank3
Authors: Yang Qian , Perfitt Tyler L. , Quay Juliana , Hu Lan , Colbran Roger J.
Published: October 2022

Clustering of neuronal L-type voltage-gated Ca2+channels (LTCC) in the plasma membrane is increasingly implicated in creating highly localized Ca2+signaling nanodomains. For example, LTCC activation can increase phosphorylation of the nuclear CREB transcription factor by increasing Ca2+concentrations within a nanodomain close to the channel, without requiring bulk Ca2+increases in the cytosol or nucleus. However, the molecular basis for LTCC clustering is poorly understood. The postsynaptic scaffolding protein Shank3 specifically associates with one of the major neuronal LTCCs, the CaV1.3 calcium channel, and is required for optimal LTCC-dependent excitation-transcription coupling. Here, we co-expressed CaV1.3 α1 subunits with two distinct epitope-tags with or without Shank3 in HEK cells. Co-immunoprecipitation studies using the cell lysates revealed that Shank3 can assemble multiple CaV1.3 α1 subunits in a complex under basal conditions. Moreover, CaV1.3 LTCC complex formation was facilitated by CaVβ subunits (β3 and β2a), which also interact with Shank3. Shank3 interactions with CaV1.3 LTCCs and multimeric CaV1.3 LTCC complex assembly were disrupted following addition of Ca2+and calmodulin (Ca2+/CaM) to cell lysates, perhaps simulating conditions within an activated CaV1.3 LTCC nanodomain. In intact HEK293T cells, co-expression of Shank3 enhanced the intensity of membrane-localized CaV1.3 LTCC clusters under basal conditions, but not after Ca2+channel activation. Live cell imaging studies also revealed that Ca2+influx through LTCCs disassociated Shank3 from CaV1.3 LTCCs clusters and reduced the CaV1.3 cluster intensity. Deletion of the PDZ domain from Shank3 prevented both binding to CaV1.3 and the changes in multimeric CaV1.3 LTCC complex assembly in vitro and in HEK293 cells. Finally, we found that shRNA knock-down of Shank3 expression in cultured rat primary hippocampal neurons reduced the intensity of surface-localized CaV1.3 LTCC clusters in dendrites. Taken together, our findings reveal a novel molecular mechanism contributing to neuronal LTCC clustering under basal conditions.
O2photoreduction at acceptor side of Photosystem I provide photoprotection to conifer thylakoids in early spring
Authors: Bag Pushan , Shutova Tatyana , Shevela Dmitry , Lihavainen Jenna , Nanda Sanchali , Ivanov Alexander G. , Messinger Johannes , Jansson Stefan
Published: October 2022

Green organisms evolve O2via photosynthesis and consume by respiration. Net O2consumption only becomes dominant when photosynthesis is suppressed at night. Here, we show that green thylakoid membranes of Scots pine (Pinus sylvestris L) and Norway spruce (Picea abies) needles demonstrate strong O2consumption even in the presence of light when extremely low temperatures coincide with high solar irradiation during early spring. This phenomenon deviates from the general finding that photosynthetic organisms evolve O2upon illumination. By using different electron transport chain inhibitors, we showed that O2consumption occurred around photosystem (PS) I and correlated with higher abundance of flavodiiron (Flv) A protein in ES thylakoid membranes. Furthermore, by measuring P700 absorption changes, we separated different alternative electron flow pathways and demonstrated that electron scavenging from the acceptor-side of PSI via O2photoreduction is a major alternative pathway in ES. This photoprotection mechanism in vascular plants indicates that conifers have developed an adaptative evolution trajectory for growing in harsh environments.
Rap1 promotes epithelial integrity and cell viability in a growing tissue
Authors: Messer C. Luke , McDonald Jocelyn A.
Published: October 2022

Having intact epithelial tissues is critical for embryonic development and adult homeostasis. How epithelia respond to damaging insults or tissue growth while still maintaining intercellular connections and barrier integrity during development is poorly understood. The conserved small GTPase Rap1 is critical for establishing cell polarity and regulating cadherin-catenin cell junctions. Here, we identified a new role for Rap1 in maintaining epithelial integrity and tissue shape duringDrosophilaoogenesis. Loss of Rap1 activity disrupted the follicle cell epithelium and the shape of egg chambers during a period of major growth. Rap1 was required for proper E-Cadherin localization in the anterior epithelium and for epithelial cell survival. Both Myo-II and the adherens junction-cytoskeletal linker protein α-Catenin were required for normal egg chamber shape but did not strongly affect cell viability. Blocking the apoptotic cascade failed to rescue the cell shape defects caused by Rap1 inhibition. One consequence of increased cell death caused by Rap1 inhibition was the preferential loss of the polar cells, which later in development led to fewer cells forming a properly migrating border cell cluster. Our results thus indicate dual roles for Rap1 in maintaining epithelia and cell survival in a growing tissue during development.
Bacterial motility governs the evolution of antibiotic resistance in spatially heterogeneous environments
Authors: Piskovsky Vit , Oliveira Nuno M.
Published: October 2022

Bacteria evolving in natural and clinical settings experience spatial fluctuations of multiple factors and this heterogeneity is expected to affect bacterial adaptation. Notably, spatial heterogeneity in antibiotic concentrations is believed to accelerate the evolution of antibiotic resistance. However, current literature overlooks the role of cell motility, which is key for bacterial survival and reproduction. Here, we consider a quantitative model for bacterial evolution in antibiotic gradients, where bacteria evolve under the stochastic processes of proliferation, death, mutation and migration. Numerical and analytical results show that cell motility has major effects on bacterial adaptation. If migration is relatively rare, it accelerates adaptation because resistant mutants can colonize neighbouring patches of increasing antibiotic concentration avoiding competition with wild-type cells; but if migration is common throughout the lifespan of bacteria, it decelerates adaptation by promoting genotypic mixing and ecological competition. If migration is sufficiently high, it can limit bacterial survival, and we derive conditions for such a regime. Similar patterns are observed in more complex scenarios, namely where bacteria can bias their motion or switch between motility phenotypes either stochastically or in a density-dependent manner. Overall, our work reveals limits to bacterial adaptation in antibiotic landscapes that are set by cell motility.