bluuebunny/crossref_metadata_2025 huggingface dataset:
New and Increasing Rates of Adverse Events Can be Found in Unstructured Text in Electronic Health Records using the Shakespeare Method
Authors: Bright Roselie A. , Dowdy Katherine , Rankin Summer K. , Blok Sergey V. , Palmer Lee Anne , Bright-Ponte Susan J.
Published: January 2021

Background

Text in electronic health records (EHRs) and big data tools offer the opportunity for surveillance of adverse events (patient harm associated with medical care) (AEs) in the unstructured notes. Writers may explicitly state an apparent association between treatment and adverse outcome (“attributed”) or state the simple treatment and outcome without an association (“unattributed”). We chose to study EHRs from 2006-2008 because of known heparin contamination during this timeframe. We hypothesized that the prevalence of adulterated heparin may have been widespread enough to manifest in EHRs through symptoms related to heparin adverse events, independent of clinicians’ documentation of attributed AEs.

Objective

Use the Shakespeare Method, a new unsupervised set of tools, to identify attributed and unattributed potential AEs using the unstructured text of EHRs.

Methods

We studied 21,287 adult critical care admissions divided into three time periods. Comparisons of period 3 (7/2007 to 6/2008) to period 2 (7/2006 to 6/2007) were used to find admissions notes to review for new or increased clinical events by generating Latent Dirichlet Allocation topics among words in period 3 that were distinct from period 2. These results were further explored with frequency analyses of periods 1 (7/2001 to 6/2006) through 3.

Results

Topics represented unattributed heparin AEs, other medical AEs, rare medical diagnoses, and other clinical events; all were verified with EHRs notes review and frequency analysis. The heparin AEs were not attributed in the notes, diagnosis codes, or procedure codes. Somewhat different from our hypothesis, heparin AEs increased in prevalence from 2001 through 2007, and decreased starting in 2008 (when heparin AEs were being published).

Conclusions

The Shakespeare Method could be a useful supplement to AE reporting and surveillance of structured EHRs data. Future improvements should include automation of the manual review process.
Developing research knowledge through special study module: Notes from year 2 medical students
Authors: Rahman S M Niazur , Alam Nazmun Nahar , Alam Tanbira
Published: January 2021

Introduction

Special Study Module is a mandatory research project implemented in some medical curriculum. For the successful application of evidence-based practice, physicians must understand research methodology before the appraisal of relevant evidence. The objective of this paper is to provide a brief overview of the effectiveness of student research modules in enhancing research understanding.

Methods

Second-year students of undergraduate medical programs were included in this study. At the beginning and after completion of literature review type research projects, the same student cohort completed a questionnaire comprising sections on perceived competency, attitude, and knowledge on research skills. Data from 163 participants who completed both pre and post-survey were analyzed.

Results

Paired t-test revealed significant differences in self-perceived knowledge, attitude, and assessed knowledge of the subjects before and after completing the research modules. Multivariate analysis also displayed a significant increase in self-perceived and assessed knowledge by carrying out the project. No significant association was exhibited by gender and ethnicity.

Conclusions

In summary, the research module improved students’ understanding of research methodology as well as the structure of scientific communication. Further studies to assess the effect of various types of research modules in different study populations are warranted.
PIWI silencing mechanism involving the retrotransposonnimbusorchestrates resistance to infection withSchistosoma mansoniin the snail vector,Biomphalaria glabrata
Authors: Smith Michael , Yadav Swara , Akinyele Olayemi , Pels Nana Adjoa , Horton Daniel , Alsultan Nashwah , Borns Andrea , Cousin Carolyn , Dixon Freddie , Mann Victoria H. , Lee Clarence , Brindley Paul J. , El-Sayed Najib M. , Bridger Joanna M. , Knight Matty
Published: January 2021

Background

Schistosomiasis remains widespread in many regions despite efforts at its elimination. By examining changes in the transcriptome at the host-pathogen interface in the snailBiomphalaria glabrataand the blood flukeSchistosoma mansoni,we previously demonstrated that an early stress response in juvenile snails, manifested by induction of heat shock protein 70 (Hsp 70) and Hsp 90 and of the reverse transcriptase (RT) domain of theB. glabratanon-LTR-retrotransposon,nimbus, were critical forB. glabratasusceptibility toS. mansoni. Subsequently, juvenileB. glabrataBS90 snails, resistant toS. mansoniat 25°C become susceptible by the F2 generation when maintained at 32°C, indicating an epigenetic response.

Methodology/Principal Findings

To better understand this plasticity in susceptibility of the BS90 snail, mRNA sequences were examined fromS. mansoniexposed juvenile BS90 snails cultured either at 25°C (permissive temperature) or 32°C (non-permissive). Comparative analysis of transcriptomes from snails cultured at the non-permissive and permissive temperatures revealed that whereas stress related transcripts dominated the transcriptome of susceptible BS90 juvenile snails at 32°C, transcripts encoding proteins with a role in epigenetics, such as PIWI (BgPiwi), chromobox protein homolog 1 (BgCBx1), histone acetyl transferase histone deacetylase (HDAC) and metallotransferase (MT) were highly expressed in those cultured at 25°C. To further determine a role forBgPiwiinB. glabratasusceptibility toS. mansoni, siRNA corresponding to theBgPiwiencoding transcript was utilized to suppress expression ofBgPiwi, rendering the resistant BS90 juvenile snail susceptible to infection at 25°C. Given transposon silencing activity of PIWI as a facet of its role as guardian of the integrity of the genome, we examined the expression of thenimbusRT encoding transcript at 120 min after infection of resistant BS90piwi-siRNA treated snails. We observed thatnimbusRT was upregulated, indicating that modulation of the transcription of thenimbusRT was associated with susceptibility toS. mansoniinBgPiwi-siRNA treated BS90 snails. Furthermore, treatment of susceptible snails with the RT inhibitor lamivudine, before exposure toS. mansoni, blockedS. mansoniinfection concurrent with downregulation of thenimbusRT transcript and upregulation of theBgPiwiencoding transcript in the lamivudine-treated, schistosome-exposed susceptible snails.

Conclusions and Significance

These findings support a role for the interplay ofBgPiwiandnimbusin the epigenetic modulation of plasticity of resistance/susceptibility in the snail-schistosome relationship.
Proximal and Distal Nephron-specific Adaptation to Furosemide
Authors: Krauson Aram J. , Schaffert Steven , Walczak Elisabeth M. , Nizar Jonathan M. , Holdgate Gwen M. , Iyer Sonali , Elsayed Ragwa , Gaudet Alexandre , Khatri Purvesh , Bhalla Vivek
Published: January 2021

Furosemide, a widely prescribed diuretic for edema-forming states, inhibits sodium reabsorption in the thick ascending limb of the nephron. Tubular adaptation to diuretics has been observed, but the range of mechanisms along the nephron has not been fully explored. Using morphometry, we show that furosemide induces renal tubular epithelial hyperplasia selectively in distal nephron segments. By comparison, we find progressive cellular hypertrophy in proximal and distal nephron segments. We next utilize single cell RNA sequencing of vehicle- and furosemide-treated mice to define potential mechanisms of diuretic resistance. Consistent with distal tubular cell hyperplasia, we detect a net increase in DCT cell number andBirc5, an anti-apoptotic and pro-growth gene, in a subset of DCT cells, as the most prominently up-regulated gene across the nephron. We also map a gradient of cell-specific transcriptional changes congruent with enhanced distal sodium transport. Furosemide stimulates expression of the mitogen IGF-1. Thus, we developed a mouse model of inducible deletion of renal tubular IGF-1 receptor and show reduced kidney growth and proximal, but not distal, tubular hypertrophy by furosemide. Moreover, genes that promote enhanced bioavailability of IGF-1 includingIgfbp1andIgfbp5are significantly and differentially expressed in proximal tubular segments and correspond to IGF-1R-dependent hypertrophy. In contrast, downstream PI3-kinase signaling genes includingPdk1, Akt1, Foxo3, FKBP4, Eif2BP4, andSpp1are significantly and differentially expressed in distal nephron segments and correspond to IGF-1R-independent hypertrophy. These findings highlight novel mechanisms of tubular remodeling and diuretic resistance, provide a repository of transcriptional responses to a common drug, and expand the implications of long-term loop diuretic use for human disease.
Mutational impact and signature of ionizing radiation
Authors: Youk Jeonghwan , Kwon Hyun Woo , Lim Joonoh , Kim Eunji , Kim Ryul , Park Seongyeol , Yi Kijong , Jeon Sara , Choi Jinwook , Na Hyelin , Lee Eun-Seok , Cho Young-Won , Min Dong-Wook , Kim Hyojin , Kang Yeong-Rok , Choi Si Ho , Bae Min Ji , Lee Chang Geun , Kim Joon-Goon , Kim Young Seo , Lee Dong Soo , Kim Tae You , Ku Taeyun , Kim Su Yeon , Lee Joo-Hyeon , Koo Bon-Kyoung , Lee Hyunsook , Yi On Vox , Han Eon Chul , Chang Ji Hyun , Kim Kyung Su , Son Tae Gen , Ju Young Seok
Published: January 2021

Whole-genome sequencing (WGS) of human tumors and normal cells exposed to various carcinogens has revealed distinct mutational patterns that provide deep insights into the DNA damage and repair processes. Although ionizing radiation (IR) is conventionally known as a strong carcinogen, its genome-wide mutational impacts have not been comprehensively investigated at the single-nucleotide level. Here, we explored the mutational landscape of normal single-cells after exposure to the various levels of IR. On average, 1 Gy of IR exposure generated ∼16 mutational events with a spectrum consisting of predominantly small nucleotide deletions and a few characteristic structural variations. In ∼30% of the post-irradiated cells, complex genomic rearrangements, such aschromoplexy, chromothripsis, and breakage-fusion-bridge cycles, were resulted, indicating the stochastic and chaotic nature of DNA repair in the presence of the massive number of concurrent DNA double-strand breaks. These mutational signatures were confirmed in the genomes of 22 IR-induced secondary malignancies. With high-resolution genomic snapshots of irradiated cells, our findings provide deep insights into how IR-induced DNA damage and subsequent repair processes operate in mammalian cells.
Predicting lifestyle and host from positive selection data and genome properties in oomycetes
Authors: Gómez-Pérez Daniel , Kemen Eric
Published: January 2021

Background

Host and niche shifts are a source of genomic and phenotypic diversification as evidenced in parasitism. Exemplary is core metabolism reduction as parasites adapt to a particular host, while the accessory genome often maintains a high degree of diversification. However, selective pressures acting on the genome of organisms that have undergone lifestyle or host change have not been fully investigated.

Results

Here, we developed a comparative genomics approach to study underlying adaptive trends in oomycetes, a eukaryotic phylum with a broad range of economically important plant and animal parasitic lifestyles. Our analysis reveals converging evolution on biological processes for oomycetes that have similar lifestyle. Besides, we find that certain functions, in particular carbohydrate metabolism, transport, and signaling, are important for host and environmental adaption in oomycetes.

Discussion

Given the high correlation between lifestyle and genome properties in our oomycete dataset and the convergent evolution of fungal and oomycete genomes, we have developed a model that predicts plant pathogen lifestyles with high accuracy based on functional annotations. Understanding how genomes and selective pressures correlate with lifestyle may be crucial to identify new emerging diseases and pandemic threats.
Single cell label-free probing of chromatin dynamics during B lymphocyte maturation
Authors: Morrish Rikke , Yim Kevin Ho Wai , Pagliara Stefano , Palombo Francesca , Chahwan Richard , Stone Nicholas
Published: January 2021

Large-scale intracellular signalling during developmental growth or in response to environmental alterations are largely orchestrated by chromatin within the cell nuclei. Chemical and conformational modifications of the chromatin architecture are critical steps in the regulation of differential gene expression and ultimately cell fate determination. Therefore, establishing chemical properties of the nucleus could provide key markers for phenotypic characterisation of cellular processes on a scale of individual cells.

Raman microscopy is a sensitive technique that is capable of probing single cell chemical composition - and sub-cellular regions - in a label-free optical manner. As such, it has great potential in both clinical and basic research. However, perceived limitations of Raman spectroscopy such as low signal intensity and the difficulty in linking alterations in vibrational signals directly with ensuing biological effects have hampered advances in the field. Here we use immune B lymphocyte development as a model to assess chromatin and transcriptional changes using confocal Raman microscopy in combination with microfluidic devices and correlative transcriptomics, thereby linking changes in chemical and structural properties to biological outcomes. Live B lymphocytes were assessed before and after maturation. Multivariate analysis was applied to distinguish cellular components within each cell. The spectral differences between non-activated and activated B lymphocytes were then identified, and their correlation with known intracellular biological changes were assessed in comparison to conventional RNA-seq analysis. Our data shows that spectral analysis provides a powerful tool to study gene activation that can complement conventional molecular biology techniques and opens the way for mapping the dynamics in the biochemical makeup of individual cells.
Hybridization enables the fixation of selfish queen genotypes in eusocial colonies
Authors: Weyna Arthur , Romiguier Jonathan , Mullon Charles
Published: January 2021

A eusocial colony typically consists of two main castes: queens that reproduce and sterile workers that help them. This division of labour however is vulnerable to genetic elements that favour the development of their carriers into queens. Several factors, such as intra-colonial relatedness, can modulate the spread of such caste-biasing genotypes. Here we investigate the effects of a notable yet understudied ecological setting: where larvae produced by hybridization develop into sterile workers. Using mathematical modelling, we show that the coevolution of hybridization with caste determination readily triggers an evolutionary arms race between non-hybrid larvae that increasingly develop into queens, and queens that increasingly hybridize to produce workers. Even where hybridization reduces worker function and colony fitness, this race can lead to the loss of developmental plasticity and to genetically hard-wired caste determination. Overall, our results may help understand the repeated evolution towards remarkable reproductive systems (e.g. social hybridogenesis) observed in many ant species.
The lethal triad: SARS-CoV-2 Spike, ACE2 and TMPRSS2. Mutations in host and pathogen may affect the course of pandemic
Authors: Calcagnile Matteo , Forgez Patricia , Alifano Marco , Alifano Pietro
Published: January 2021

Variants of SARS-CoV-2 have been identified rapidly after the beginning of pandemic. One of them, involving the spike protein and called D614G, represents a substantial percentage of currently isolated strains. While research on this variant was ongoing worldwide, on December 20th2020 the European Centre for Disease Prevention and Control reported a Threat Assessment Brief describing the emergence of a new variant of SARS-CoV-2, named B.1.1.7, harboring multiple mutations mostly affecting the Spike protein. This viral variant has been recently associated with a rapid increase in COVID-19 cases in South East England, with alarming implications for future virus transmission rates. Specifically, of the nine amino acid replacements that characterize the Spike in the emerging variant, four are found in the region between the Fusion Peptide and the RBD domain (namely the already known D614G, together with A570D, P681H, T716I), and one, N501Y, is found in the Spike Receptor Binding Domain – Receptor Binding Motif (RBD-RBM). In this study, by usingin silicobiology, we provide evidence that these amino acid replacements have dramatic effects on the interactions between SARS-CoV-2 Spike and the host ACE2 receptor or TMPRSS2, the protease that induces the fusogenic activity of Spike. Mostly, we show that these effects are strongly dependent on ACE2 and TMPRSS2 polymorphism, suggesting that dynamics of pandemics are strongly influenced not only by virus variation but also by host genetic background.
Phylogenetic analyses of SARS-CoV-2 B.1.1.7 lineage suggest a single origin followed by multiple exportation events versus convergent evolution
Authors: Vrancken B. , Dellicour S. , Smith D.M. , Chaillon A
Published: January 2021

Disclaimer

The authors have withdrawn this manuscript because it will need to be fully actualized to properly acknowledge the contribution of several genomic data contributors, including the unique contribution of the COG-UK consortium. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding authors
Neuromodulation of Behavioral Specialization: Tachykinin Signaling Inhibits Task-specific Behavioral Responsiveness in Honeybee Workers
Authors: Han Bin , Wei Qiaohong , Wu Fan , Hu Han , Ma Chuan , Meng Lifeng , Zhang Xufeng , Feng Mao , Fang Yu , Rueppell Olav , Li Jianke
Published: January 2021

Behavioral specialization is key to the success of social insects and often compartmentalized among colony members leading to division of labor. Response thresholds to task-specific stimuli proximally regulate behavioral specialization but their neurobiological regulation is not understood. Here, we show that response thresholds to task-relevant stimuli correspond to the specialization of three behavioral phenotypes of honeybee workers. Quantitative neuropeptidome comparisons suggest two tachykinin-related peptides (TRP2 and TRP3) as candidates for the modification of these response thresholds. Based on our characterization of their receptor binding and downstream signaling, we then confirm the functional role of tachykinins: TRP2 injection and RNAi cause consistent, opposite effects on responsiveness to task-specific stimuli of each behaviorally specialized phenotype but not to stimuli that are unrelated to their tasks. Thus, our study demonstrates that TRP-signaling regulates the degree of task-specific responsiveness of specialized honeybee workers and may control the context-specificity of behavior in animals more generally.
Differential gene expression associated with a floral scent polymorphism in the evening primroseOenothera harringtonii(Onagraceae)
Authors: Bechen Lindsey L. , Johnson Matthew G. , Broadhead Geoffrey T. , Levin Rachel A. , Overson Rick P. , Jogesh Tania , Fant Jeremie B. , Raguso Robert A. , Skogen Krissa A. , Wickett Norman J.
Published: January 2021

Background

Plant volatiles play an important role in both plant-pollinator and plant-herbivore interactions. Intraspecific polymorphisms in volatile production are ubiquitous, but studies that explore underlying differential gene expression are rare.Oenothera harringtoniipopulations are polymorphic in floral emission of the monoterpene (R)-(-)-linalool; some plants emit (R)-(-)-linalool (linalool+ plants) while others do not (linalool-plants). However, the genes associated with differential production of this floral volatile inOenotheraare unknown. We used RNA-Seq to broadly characterize differential gene expression involved in (R)-(-)-linalool biosynthesis. To identify genes that may be associated with the polymorphism for this trait, we used RNA-Seq to compare gene expression in six differentOenothera harringtoniitissues from each of three linalool+ and linalool-plants.

Results

Three clusters of differentially expressed genes were enriched for terpene synthase activity: two were characterized by tissue-specific upregulation and one by upregulation only in plants with flowers that produce (R)-(-)-linalool. A molecular phylogeny of all terpene synthases identified two putative (R)-(-)-linalool synthase transcripts inOenothera harringtonii, a single allele of which is found exclusively in linalool+ plants.

Conclusions

By using a naturally occurring polymorphism and comparing different tissues, we were able to identify genes putatively involved in the biosynthesis of (R)-(-)-linalool. Expression of these genes in linalool-plants suggests a regulatory polymorphism, rather than a population-specific loss-of-function allele. Additional terpene biosynthesis-related genes that are up-regulated in plants that emit (R)-(-)-linalool may be associated with herbivore defense, suggesting a potential economy of scale between plant reproduction and defense.
Inter-domain Horizontal Gene Transfer of Nickel-binding Superoxide Dismutase
Authors: Sutherland Kevin M. , Ward Lewis M. , Colombero Chloé-Rose , Johnston David T.
Published: January 2021

The ability of aerobic microorganisms to regulate internal and external concentrations of the reactive oxygen species (ROS) superoxide directly influences the health and viability of cells. Superoxide dismutases (SODs) are the primary regulatory enzymes that are used by microorganisms to degrade superoxide. SOD is not one, but three separate, non-homologous enzymes that perform the same function. Thus, the evolutionary history of genes encoding for different SOD enzymes is one of convergent evolution, which reflects environmental selection brought about by an oxygenated atmosphere, changes in metal availability, and opportunistic horizontal gene transfer (HGT). In this study we examine the phylogenetic history of the protein sequence encoding for the nickel-binding metalloform of the SOD enzyme (SodN). A comparison of organismal and SodN protein phylogenetic trees reveals several instances of HGT, including multiple inter-domain transfers of thesodNgene from the bacterial domain to the archaeal domain. Nearly half of the archaeal members withsodNlive in the photic zone of the marine water column. ThesodNgene is widespread and characterized by apparent vertical gene transfer in some sediment-associated lineages within the Actinobacteriota (Actinobacteria) and Chloroflexota (Chloroflexi) phyla, suggesting the ancestralsodNlikely originated in one of these clades before expanding its taxonomic and biogeographic distribution to additional microbial groups in the surface ocean in response to decreasing iron availability. In addition to decreasing iron quotas, nickel-binding SOD has the added benefit of withstanding high reactant and product ROS concentrations without damaging the enzyme, making it particularly well suited for the modern surface ocean.
Community RNA-Seq: Multi-kingdom responses to living versus decaying root inputs in soil
Authors: Nuccio Erin E. , Nguyen Nhu H. , da Rocha Ulisses Nunes , Mayali Xavier , Bougoure Jeremy , Weber Peter , Brodie Eoin , Firestone Mary , Pett-Ridge Jennifer
Published: January 2021

Roots are the primary source of organic carbon inputs to most soils. Decomposition is a multi-trophic process involving multiple kingdoms of microbial life, but typically microbial ecology studies focus on one or two major lineages in isolation. We used Illumina shotgun RNA sequencing to conduct PCR-independent SSU rRNA community analysis (“community RNA-Seq”) to simultaneously study the bacteria, archaea, fungi, and microfauna surrounding both living and decomposing roots of the annual grass,Avena fatua. Plants were grown in13CO2-labeled microcosms amended with15N-root litter. We identified rhizosphere substrate preferences for13C-exudates versus15N-litter using NanoSIMS microarray imaging (Chip-SIP). When litter was available, rhizosphere and bulk soil had significantly more Amoebozoa, which are potentially important yet often overlooked top-down drivers of detritusphere community dynamics and nutrient cycling. Bulk soil containing litter was depleted in Actinobacteria but had significantly more Bacteroidetes and Proteobacteria. While Actinobacteria were abundant in the rhizosphere, Chip-SIP showed Actinobacteria preferentially incorporated litter relative to root exudates, indicating this group’s more prominent role in detritus elemental cycling in the rhizosphere. Our results emphasize that decomposition is a multi-trophic process involving cross-kingdom interactions, and the trajectory of carbon through this soil food web likely impacts the fate of carbon in soil.
Biodegradable and Biocompatible Graphene-based Scaffolds for Functional Neural Tissue Engineering: A Strategy Approach Using Dental Pulp Stem Cells and Biomaterials
Authors: Mansouri Negar , Al-Sarawi Said , Losic Dusan , Mazumdar Jagan , Clark Jillian , Gronthos Stan , O’Hare Doig Ryan
Published: January 2021

Neural tissue engineering aims to restore function of nervous system tissues using biocompatible cell-seeded scaffolds. Graphene-based scaffolds combined with stem cells deserve special attention to enhance tissue regeneration in a controlled manner. However, it is believed that minor changes in scaffold biomaterial com-position, internal porous structure, and physicochemical properties can impact cellular growth and adhesion. The current work aims to investigatein vitrobiological effects of 3D graphene oxide (GO)/sodium alginate (GOSA) and reduced GOSA (RGOSA) scaffolds on dental pulp stem cells (DPSCs) in terms of cell viability and cytotoxicity. Herein, the effects of the 3D scaffolds, coating conditions, and serum supplementation on DPSCs functions are explored extensively. Biodegradation analysis revealed that addition of GO enhanced the degradation rate of composite scaffolds. Compared to the 2D surface, the cell viability of 3D scaffolds was higher (p <0.0001), highlighting the optimal initial cell adhesion to the scaffold surface and cell migration through pores. Moreover, the cytotoxicity study indicated that the incorporation of graphene supported higher DPSCs viability. It is also shown that when the mean pore size of scaffold increases, DPSCs activity decreases. In terms of coating conditions, poly-l-lysine (PLL) was the most robust coating reagent that improved cell-scaffold adherence and DPSCs metabolism activity. The cytotoxicity of GO-based scaffolds showed that DPSCs can be seeded in serum-free media without cytotoxic effects. This is critical for human translation as cellular transplants are typically serum-free. These findings suggest that proposed 3D GO-based scaffolds have favourable effects on the biological responses of DPSCs.
Multi-omics analysis of glucose-mediated signaling by a moonlighting Gβ protein Asc1/RACK1
Authors: Li Shuang , Li Yuanyuan , Rushing Blake R. , McRitchie Susan L. , Jones Janice C. , Sumner Susan J. , Dohlman Henrik G.
Published: January 2021

G proteins were originally discovered through efforts to understand the effects of hormones, such as glucagon and epinephrine, on glucose metabolism. On the other hand, many cellular metabolites, including glucose, serve as ligands for G protein-coupled receptors. Here we investigate the consequences of glucose-mediated receptor signaling, and in particular the role of a Gα subunit Gpa2 and a non-canonical Gβ subunit, known as Asc1 in yeast and RACK1 in animals. Asc1/RACK1 is of particular interest because it has multiple, seemingly unrelated, functions in the cell. The existence of such “moonlighting” operations has complicated the determination of phenotype from genotype. Through a comparative analysis of individual gene deletion mutants, and by integrating transcriptomics and metabolomics measurements, we have determined the relative contributions of the Gα and Gβ protein subunits to glucose-initiated processes in yeast. We determined that Gpa2 is primarily involved in regulating sugar metabolism while Asc1 is primarily involved in amino acid metabolism. Both proteins are involved in regulating purine metabolism. Of the two subunits, Gpa2 regulates a greater number of gene transcripts and was particularly important in determining the amplitude of response to glucose addition. We conclude that the two G protein subunits regulate distinct but complementary processes downstream of the glucose-sensing receptor, as well as processes that lead ultimately to changes in cell growth and metabolism.

AUTHOR SUMMARY

Despite the societal importance of glucose fermentation in yeast, the mechanisms by which these cells detect and respond to glucose have remained obscure. Glucose detection requires a cell surface receptor coupled to a G protein that is comprised of two subunits, rather than the more typical heterotrimer: an α subunit Gpa2 and the β subunit Asc1 (or RACK1 in humans). Asc1/RACK1 also serves as a subunit of the ribosome, where it regulates the synthesis of proteins involved in glucose fermentation. This manuscript uses global metabolomics and transcriptomics to demonstrate the distinct roles of each G protein subunit in transmitting the glucose signal. Whereas Gpa2 is primarily involved in the metabolism of sugars, Asc1/RACK1 contributes to production of amino acids necessary for protein synthesis and cell division. These findings reveal the initial steps of glucose signaling and several unique and complementary functions of the G protein subunits. More broadly, the integrated approach used here is likely to guide efforts to determine the topology of complex G protein and metabolic signaling networks in humans.
Intracranial brain stimulation modulates fMRI-based network switching
Authors: Pedersen Mangor , Zalesky Andrew
Published: January 2021

The extent to which functional MRI (fMRI) reflects direct neuronal changes remains unknown. Using 160 simultaneous electrical stimulation (es-fMRI) and intracranial brain stimulation recordings acquired in 26 individuals with epilepsy (with varying electrode locations), we tested whether brain networks dynamically change during intracranial brain stimulation, aiming to establish whether switching between brain networks is reduced after intracranial brain stimulation. As the brain spontaneously switches between a repertoire of intrinsic functional network configurations and the rate of switching is typically increased in brain disorders, we hypothesised that intracranial stimulation would reduce the brain’s switching rate, thus potentially normalising aberrant brain network dynamics. To test this hypothesis, we quantified the rate that brain regions changed networks over time in response to brain stimulation, usingnetwork switchingapplied to multilayer modularity analysis of time-resolved es-fMRI connectivity. Network switching and synchrony was decreased after the first brain stimulation followed by a more consistent pattern of network switching over time. This change was commonly observed in cortical networks and adjacent to the electrode targets. Our results suggest that neuronal perturbation is likely to modulate large-scale brain networks, and multilayer network modelling may be used to inform the clinical efficacy of brain stimulation in epilepsy.
Structure and dynamics of semaglutide and taspoglutide bound GLP-1R-Gs complexes
Authors: Zhang Xin , Belousoff Matthew J. , Liang Yi-Lynn , Danev Radostin , Sexton Patrick M. , Wootten Denise
Published: January 2021

The glucagon-like peptide-1 receptor (GLP-1R) regulates insulin secretion, carbohydrate metabolism and appetite, and is an important target for treatment of type II diabetes and obesity. Multiple GLP-1R agonists have entered into clinical trials, such as semaglutide, progressing to approval. Others, including taspoglutide, failed through high incidence of side-effects or insufficient efficacy. GLP-1R agonists have a broad spectrum of signalling profiles. However, molecular understanding is limited by a lack of structural information on how different GLP-1R agonists engage with the GLP-1R. In this study, we determined cryo-electron microscopy (cryo-EM) structures of GLP-1R-Gs protein complexes bound with semaglutide and taspoglutide. These revealed similar peptide binding modes to that previously observed for GLP-1. However, 3D variability analysis of the cryo-EM micrographs revealed different motions within the bound peptides and the receptor relative to when GLP-1 is bound. This work provides novel insights into the molecular determinants of peptide engagement with the GLP-1R.
Modeling Oyster Reef Reproductive Sustainability: Analyzing Gamete Viability, Hydrodynamics, and Reef Structure to Facilitate Restoration ofCrassostrea virginica
Authors: Weissberg Justin , Pagano Vinny
Published: January 2021

The eastern oyster is a keystone species and ecosystem engineer. However, restoration efforts of wild oysters are often unsuccessful, in that they do not produce a robust population of oysters that are able to successfully reproduce. Furthermore, the dynamics of wild oyster fertilization is not yet well understood. Through conducting an experiment predicated on quantifying the influence of elementary aspects of fertilization kinetics—sperm concentration, gamete age, and success rate—we found that, as stochastic as the mating process may seem, there are correlations which fundamentally serve as the framework for assessing long-term sustainability, reef structure, and hydrodynamic parameters in relation to fertilization. We then focused on mathematically defining a procedure which simulated a concentration distribution of a single sperm and egg release where there existed conditions necessary for breeding to take place. We found a very significant impact of both gamete age and sperm concentration on fertilization rate (p < 0.0001). Our hydrodynamic model demonstrates that distance can also drastically influence broadcast spawning. This could be used as a foundation for developing a flexible model for wild oyster fertilization based on placement, initial seawater conditions, and size of the starting population. The results of this research could be implemented into a more user-friendly program which would accept multiple variables as inputs and output the probability of fertilization given arbitrary values. By accounting for environmental deviations, this generalization would increase its compatibility with the public and actualize the project’s intended purpose: enhance the planning of oyster reef restoration projects.
Fis connects two sensory pathways, quorum sensing and surface sensing, to control motility inVibrio parahaemolyticus
Authors: J.G. Tague , Regmi A. , Gregory G.J. , Boyd E.F.
Published: January 2021

Fis (Factor forInversionStimulation) is a global regulator that is highly expressed during exponential growth and undetectable in stationary growth. Quorum sensing (QS) is a global regulatory mechanism that controls gene expression in response to cell density and growth phase. InV. parahaemolyticus, a marine species and a significant human pathogen, the QS regulatory sRNAs, Qrr1 to Qrr5, negatively regulate the high cell density QS master regulator OpaR. OpaR is a positive regulator of capsule polysaccharide (CPS) formation required for biofilm formation and a repressor of swarming motility. InVibrio parahaemolyticus, we showed, using genetics and DNA binding assays, that Fis bound directly to the regulatory regions of theqrrgenes and was a positive regulator of these genes. In the Δfismutant,opaRexpression was induced and a robust CPS and biofilm was produced, while swarming motility was abolished. Expression analysis and promoter binding assays showed that Fis was a direct activator of both the lateral flagellumlafoperon and the surface sensingscrABCoperon, both required for swarming motility. Inin vitrogrowth competition assays, Δfiswas outcompeted by wild type in minimal media supplemented with intestinal mucus, and we showed that Fis directly modulated catabolism gene expression. Inin vivocolonization competition assays, Δfiswas outcompeted by wild type, indicating Fis is required for fitness. Overall, these data demonstrate a direct role for Fis in QS, motility, and metabolism inV. parahaemolyticus.

IMPORTANCE

In this study, we examined the role of Fis in modulating expression of the five-quorum sensing regulatory sRNAs,qrr1toqrr5, and showed that Fis is a direct positive regulator of QS, which oppositely controls CPS and swarming motility inV. parahaemolyticus. The Δfisdeletion mutant was swarming defective due to a requirement for Fis in lateral flagella and surface sensing gene expression. Thus, Fis links QS and surface sensing to control swarming motility and, indirectly, CPS production. Fis was also required for cell metabolism, acting as a direct regulator of several carbon catabolism loci. Bothin vitroandin vivocompetition assays showed that the Δfismutant had a significant defect compared to wild type. Overall, our data demonstrates that Fis plays a critical role inV. parahaemolyticusphysiology that was previously unexamined.
Individual level prediction of emerging suicide events in the pharmacologic treatment of bipolar disorder
Authors: Luo Sean X. , Ciarleglio Adam , Galfalvy Hanga , Grunebaum Michael , Sher Leo , Mann J. John , Oquendo Maria A.
Published: January 2021

Background

Patients with bipolar disorder have a high lifetime risk of suicide. Predicting, preventing and managing suicidal behavior are major goals in clinical practice. Changes in suicidal thoughts and behavior are common in the course of treatment of bipolar disorder.

Methods

Using a dataset from a randomized clinical trial of bipolar disorder treatment (N=98), we tested predictors of future suicidal behavior identified through a review of literature and applied marginal variable selection and machine learning methods. The performance of the models was assessed using the optimism-adjusted C statistic.

Results

Number of prior hospitalizations, number of prior suicide attempts, current employment status and Hamilton Depression Scale were identified as predictors and a simple logistic regression model was constructed. This model was compared with a model incorporating interactions with treatment group assignment, and more complex variable selection methods (LASSO and Survival Trees). The best performing models had average optimism-adjusted C-statistics of 0.67 (main effects only) and 0.69 (Survival Trees). Incorporating medication group did not improve prediction performance of the models.

Conclusions

These results suggest that models with a few predictors may yield a clinically meaningful way to stratify risk of emerging suicide events in patients who are undergoing pharmacologic treatment for bipolar disorder.

Significance Statement

This study aims to find out whether suicide events that occur during the pharmacological treatment of bipolar disorder, a severe psychiatric disorder that is highly associated with suicide behavior, can be predicted. Using existing methods, we developed and compared several predictive models. We showed that these models performed similarly to predictive models of other outcomes, such as treatment efficacy, in unipolar and bipolar depression. This suggests that suicide events during bipolar disorder may be a feasible target for individualized interventions in the future.
Optimising SARS-CoV-2 pooled testing strategies on social networks for low-resource settings
Authors: Mazzitello K I , Jiang Y , Arizmendi C M
Published: January 2021

Controlling the COVID-19 pandemic is an urgent global challenge. The rapid geographic spread of SARS-CoV-2 directly reflects the social structure. Before effective vaccines and treatments are widely available, we have to rely on alternative, non-pharmaceutical interventions, including frequency testing, contact tracing, social distancing, mask wearing, and hand-washing, as public health practises to slow down the spread of the disease. However frequent testing is the key in the absence of any alternative. We propose a network approach to determine the optimal low resources setting oriented pool testing strategies that identifies infected individuals in a small number of tests and few rounds of testing, at low prevalence of the virus. We simulate stochastic infection curves on societies under quarantine. Allowing some social interaction is possible to keep the COVID-19 curve flat. However, similar results can be strategically obtained searching and isolating infected persons to preserve a healthier social structure. Here, we analyze which are the best strategies to contain the virus applying an algorithm that combine samples and testing them in groups [1]. A relevant parameter to keep infection curves flat using this algorithm is the dairy frequency of testing at zones where a high infection rate is reported. On the other hand, the algorithm efficiency is low for random search of infected people.
Real-time optical analysis of a colorimetric LAMP assay for SARS-CoV-2 in saliva with a handheld instrument improves accuracy compared to endpoint assessment
Authors: Diaz Lena M. , Johnson Brandon E. , Jenkins Daniel M.
Published: January 2021

Controlling the course of the COVID-19 pandemic will require widespread deployment of consistent and accurate diagnostic testing of the novel coronavirus SARS-CoV-2. Ideally, tests should detect a minimum viral load, be minimally invasive, and provide a rapid and simple readout. Current FDA-approved RT-qPCR-based standard diagnostic approaches require invasive nasopharyngeal swabs and involve laboratory-based analyses that can delay results. Recently, a loop mediated isothermal nucleic acid amplification (LAMP) test that utilizes colorimetric readout received FDA approval. This approach utilizes a pH indicator dye to detect drop in pH from nucleotide hydrolysis during nucleic acid amplification. This method has only been approved for use with RNA extracted from clinical specimens collected via nasopharyngeal swabs. In this study, we developed a quantitative LAMP-based strategy to detect SARS-CoV-2 RNA in saliva. Our detection system distinguished positive from negative sample types using a handheld instrument that monitors optical changes throughout the LAMP reaction. We used this system in a streamlined LAMP testing protocol that could be completed in less than two hours to directly detect inactivated SARS-CoV-2 in minimally processed saliva that bypassed RNA extraction, with a limit of detection (LOD) of 50 genomes/reaction. The quantitative method correctly detected virus in 100% of contrived clinical samples spiked with inactivated SARS- CoV-2 at either 1X (50 genomes/reaction) or 2X (100 genomes/reaction) of the LOD. Importantly the quantitative method was based on dynamic optical changes during the reaction so was able to correctly classify samples that were misclassified by endpoint observation of color.
Validation of the German version of the Life-Space Assessment LSA-D
Authors: Mümken Sandra A. , Gellert Paul , Stollwerck Malte , O’Sullivan Julie L. , Kiselev Jörn
Published: January 2021

Objectives

To develop a German version of the original University of Alabama at Birmingham (UAB) Study of Aging Life-Space Assessment (LSA-D) for measurement of community mobility in older adults within the past 4 weeks and to evaluate its psychometric properties for urban and rural populations of older adults.

Design

Cross-sectional validation study.

Setting

Two study centres in urban and rural German outpatient hospital settings.

Participants

In total N=83 community-dwelling older adults were recruited (n=40 from urban and n=43 from rural areas; mean age was 78.5 (SD=5.4); 49% male).

Primary and secondary outcome measures

The final version of the translated LSA-D was related with questions about activities and instrumental activities of daily living (ADL/iADL; primary hypothesis), Timed-Up&Go-Test (TUG), self-rated health, balance confidence and history of falls, use of transportation, and sociodemographic factors to obtain construct validity. Secondary outcome measures of health included handgrip strength, screening of cognitive function and comorbidities. To assess conduct construct validity, correlations between LSA-D and all health measures were examined for total sample, urban and rural subsamples using bivariate regression and multiple adjusted regression models. Posthoc analyses included different LSA-D scoring methods for each region. All parameters were estimated using non-parametric bootstrapping procedure.

Results

In the multiple adjusted model for the total sample, number of ADL/iADL limitations (β=-.26; 95%CI=-.42/-.08), TUG (β=-.37; 95%CI=-.68/-.14), living in shared living arrangements (β=.22; 95%CI=.01/.44) and history of falls in the past 6 months (β=-.22; 95%CI=-.41/-.05) showed significant associations with the LSA-D composite score, while living in urban area (β=-.19; 95%CI=-.42/.03) and male gender (β=.15; 95%CI=-.04/.35) were not significant.

Conclusion

The LSA-D is a valid tool for measuring life-space mobility in German community-dwelling older adults within the past four weeks in ambulant urban and rural settings.

Trial registration number

DRKS00019023

Strengths and limitations of this study

German validation of the original UAB Life-Space Assessment (LSA-D) for community dwelling older adults in urban and rural settings

Using bootstrapped bivariate and multiple adjusted regression models to attain construct validity of the LSA-D

Recruitment had to be stopped shortly before reaching the calculated sample size due to the decision to restrict in face-to-face research to contain the outbreak of the Covid-19 pandemic in March 2020