bluuebunny/crossref_metadata_2025 huggingface dataset:
Lung cancer in the French West Indies: role of sugarcane work and other occupational exposures
Authors: Cabréra Léïla , Auguste Aviane , Michineau Léah , Joachim Clarisse , Deloumeaux Jacqueline , Luce Danièle
Published: July 2022

Objective

To study the role of occupational exposures in lung cancer risk in the French West Indies, with special attention to some specific activities, such as sugarcane work, that can only be studied in a limited number of populations.

Methods

We used data from a population-based case-control study that included 147 incident lung cancer cases and 405 controls. Smoking history and a detailed occupational history with a description of tasks and substances were collected by questionnaire during face-to-face interviews. Odds ratios (OR) adjusted for sex, age, region, smoking status and cigarette pack-years and 95% confidence intervals (95% CI) were estimated by unconditional logistic regression.

Results

Significantly increased risks of lung cancer were found in sugarcane farm workers (OR=2.7; 95% CI 1.1-6.6) and more generally in the sugarcane growing sector (OR=2.5; 95% CI 1.0-6.3) and to a lesser extent in rum production. Elevated risks of lung cancer were also observed among other agricultural workers, painters, warehouse porters, labourers, maintenance and motor vehicle repair workers. Exposure to herbicides in sugarcane cultivation was associated with an increased risk of lung cancer (OR=2.6; 95% CI 0.9-7.6).

Conclusion

These results showed that occupational exposures contributed to lung cancer risk in the French West Indies, and highlighted the role of exposures related to sugarcane work.
Performance evaluation of the LumiraDx SARS-CoV-2 & Flu A/B Test in diagnosing COVID-19 and influenza in patients with respiratory symptoms
Authors: Ellis Jayne , Guest Poppy , Lawson Vicki , Loecherbach Julia , Lindner Nigel , McCulloch Andrew
Published: July 2022

Introduction

Coronavirus disease 2019 (COVID-19) and influenza share similar symptoms, which hampers diagnosis. Given that they require different containment and treatment strategies, fast and accurate distinction between the two infections is needed. This study evaluates the sensitivity and specificity of the LumiraDx SARS-CoV-2 & Flu A/B Test for simultaneous detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A/B from a single nasal swab.

Methods

Nasal samples were collected from patients as part of the ASPIRE (NCT04557046) and INSPIRE (NCT04288921) studies at point-of-care testing sites in the USA. ASPIRE study participants were included after developing COVID-19 symptoms in the last 14 days or following a positive SARS-CoV-2 test in the last 48 hours. INSPIRE study participants were included after developing influenza symptoms in the last 4 days. Samples were extracted into proprietary buffer and analysed using the LumiraDx SARS-CoV-2 & Flu A/B Test. A reference sample was taken from each subject, placed into universal transport medium and tested using reference SARS-CoV-2 and influenza reverse transcription polymerase chain reaction (RT-PCR) tests. The test and reference samples were compared using the positive percent agreement (PPA) and negative percent agreement (NPA), together with their 95% confidence intervals (CI).

Results

Analysis of the data from the ASPIRE (N=124) and INSPIRE (N=159) studies revealed high levels of agreement between the LumiraDx SARS-CoV-2 & Flu A/B Test and the reference tests in detecting SARS-CoV-2 (PPA=95.5% [95% CI: 84.9%, 98.7%]; NPA=96.0% [95% CI: 90.9%, 98.3%]), influenza A (PPA=83.3% [95% CI: 66.4%, 92.7%]; NPA=97.7% [95% CI: 93.4%, 99.2%]) and influenza B (PPA=80.0% [95% CI: 62.7%, 90.5%]; NPA=95.3% [95% CI: 90.2%, 97.9%]).

Conclusions

The LumiraDx SARS-CoV-2 & Flu A/B Test shows a high agreement with the reference RT-PCR tests while simultaneously detecting and differentiating between SARS-CoV-2 and influenza A/B.

Trial registration, ClinicalTrials.gov identifier: NCT04557046 and NCT04288921
Perisomatic Features Enable Efficient and Dataset Wide Cell-Type Classifications Across Large-Scale Electron Microscopy Volumes
Authors: Elabbady Leila , Seshamani Sharmishtaa , Mu Shang , Mahalingam Gayathri , Schneider-Mizell Casey , Bodor Agnes L , Bae J. Alexander , Brittain Derrick , Buchanan JoAnn , Bumbarger Daniel J. , Castro Manuel A. , Dorkenwald Sven , Halageri Akhilesh , Jia Zhen , Jordan Chris , Kapner Dan , Kemnitz Nico , Kinn Sam , Lee Kisuk , Li Kai , Lu Ran , Macrina Thomas , Mitchell Eric , Mondal Shanka Subhra , Nehoran Barak , Popovych Sergiy , Silversmith William , Takeno Marc , Torres Russel , Turner Nicholas L , Wong William , Wu Jingpeng , Yin Wenjing , Yu Szi-chieh ,   The MICrONS Consortium, Seung H. Sebastian , Reid R. Clay , Maçarico Da Costa Nuno , Collman Forrest
Published: July 2022

Mammalian neocortex contains a highly diverse set of cell types. These types have been mapped systematically using a variety of molecular, electrophysiological and morphological approaches. Each modality offers new perspectives on the variation of biological processes underlying cell type specialization. Cellular scale electron microscopy (EM) provides dense ultrastructural examination and an unbiased perspective into the subcellular organization of brain cells, including their synaptic connectivity and nanometer scale morphology. It also presents a clear challenge for analysis to identify cell-types in data that contains tens of thousands of neurons, most of which have incomplete reconstructions. To address this challenge, we present the first systematic survey of the somatic region of all cells within a cubic millimeter of cortex using quantitative features obtained from EM. This analysis demonstrates a surprising sufficiency of the perisomatic region to identify cell-types, including types defined primarily based on their connectivity patterns. We then describe how this classification facilitates cell type specific connectivity characterization and locating cells with rare connectivity patterns in the dataset.
Integrating pharmacogenomics data-driven prediction with bulk and single-cell RNAseq to demonstrate the efficacy of an NAMPT inhibitor against aggressive, taxane-resistant, and stem-like cells in lethal prostate cancer
Authors: Mazumder Suman , Ghosh Taraswi Mitra , Mukherjee Ujjal K. , Chakravarti Sayak , Amiri Farshad , Hemmati Farnaz , Mistriotis Panagiotis , Elhussin Isra , Salam Ahmad-bin , Dean-Colomb Windy , Li Feng , Yates Clayton , Arnold Robert D. , Mitra Amit K.
Published: July 2022

Metastatic prostate cancer is the second leading cause of cancer deaths in US men. Resistance to standard medical castration and secondary taxane-based chemotherapy is nearly universal. Further, presence of cancer stem-like cells (EMT/epithelial to mesenchymal transdifferentiation) and neuroendocrine PCa (NEPC) subtypes significantly contribute to aggressive/advanced/lethal variants of PCa (AVPC).

In this study, first we used single-cell RNA sequencing (scRNAseq) analysis to demonstrate that ARlow PCa cells in metastatic prostate cancer, including castration-sensitive tumors, harbored signatures of EMT, and ‘cancer stemness’. Next, we introduced a novel pharmacogenomics data-driven computational approach and identified several potential agents that can be re-purposed as novel secondary drugs (“secDrugs”) to treat advance variants of Prostate cancer. Using scRNAseq as a biomarker-based drug screen, we demonstrated that a majority of the single-cell subclones in mCRPC and mCSPC cell lines also showed significantly high expression of the NAMPT pathway genes, indicating that the secDrug FK866, which targets NAMPT, is potentially effective against drug-resistant and stem-cell-like subpopulation cluster. Next, we showed significant in vitro cytotoxicity of FK866 as single-agent and in combination with the taxanes or Enzalutamide against models of clinically-advanced PCa. We performed bulk- and single-cell RNAseq to identify several pathways underlining FK866 mechanism of action and found that in addition to NAMPT inhibition, FK866 regulates tumor metastasis, cell migration, invasion, DNA repair machinery, redox homeostasis, autophagy, as well as cancer stemness–related genes HES1 and CD44. Further, we performed a microfluidic chip-based cell migration assay that demonstrated that FK866 reduces cancer cell invasion and motility, indicating abrogation of metastasis. Finally, using multiple PCa patient datasets, we showed that FK866 is potentially capable of reversing expression of several genes associated with biochemical recurrence and inter-ethnic differences, including IFITM3 and LTB4R.

Thus, using FK866 as a proof-of-concept drug, we introduced a novel, universally applicable preclinical drug development pipeline to circumvent subclonal aggressiveness, drug resistance, and stemness in lethal PCa.
Cleavage of protein kinase c δ by caspase-3 mediates pro-inflammatory cytokine-induced apoptosis in pancreatic islets
Authors: Collins Jillian , Piscopio Robert A. , Reyland Mary E. , Johansen Chelsea G. , Benninger Richard K. P. , Farnsworth Nikki L.
Published: July 2022

In type 1 diabetes (T1D), autoreactive immune cells infiltrate the pancreas and secrete pro-inflammatory cytokines that initiate cell death in insulin producing islet β-cells. Protein kinase C δ (PKCδ) plays a role in mediating cytokine-induced β-cell death; however, the exact mechanisms are not well understood. To address this, we utilized an inducible β-cell specific PKCδ KO mouse as well as a small peptide specific inhibitor of PKCδ. We identified a role for PKCδ in mediating cytokine-induced β-cell death and have shown that inhibiting PKCδ protects pancreatic β-cells from cytokine-induced apoptosis in both mouse and human islets. We determined that cytokines induced nuclear translocation and activity of PKCδ and that caspase-3 cleavage of PKCδ may be required for cytokine-mediated islet apoptosis. Further, cytokine-activated PKCδ increases activity both of pro-apoptotic Bax with acute treatment and JNK with prolonged treatment. Overall, our results suggest that PKCδ mediates cytokine-induced apoptosis via nuclear translocation, cleavage by caspase-3, and upregulation of pro-apoptotic signaling in pancreatic β-cells. Combined with the protective effects of PKCδ inhibition with δV1-1, the results of this study will aid in the development of novel therapies to prevent or delay β-cell death and preserve β-cell function in T1D.
A de novo transcriptome assembly of the annelid worm Hediste diversicolor
Authors: Samico Rodrigo , Machado André M. , Domingues Marcos , Hagemann Andreas , Valente Luísa , Malzahn Arne , Gomes-dos-Santos André , Ruivo Raquel , Monroig Óscar , Castro L. Filipe C.
Published: July 2022

The development of Next-Generation Sequencing (NGS) technologies has revolutionized multiple fields of Biology. The ability to sequence DNA and RNA in an automated, parallel and low-cost approach, was key to boost the applicability and acquisition efficiency of omics resources. In this context, the availability of these tools has become indispensable towards our understanding of biodiversity, deepening our knowledge on the distinct complexity levels, from cells to ecosystems.

In this study we comprehensively characterised and annotated a whole-body transcriptome of Hediste diversicolor. This annelid worm species belongs to the family Nereididae and inhabits estuarine and lagoon areas on the Atlantic coasts of Europe and North America. Ecologically, this species plays an important role in benthic food webs. The ability of rework sediments through bioturbation activity makes this species essential to the estuarine mechanisms.

Here, we used Illumina next-generation sequencing technology, to sequence a total 105 million (M) paired-end (PE) raw reads and produce the first multi-tissue transcriptome assembly of an adult of H. diversicolor. This transcriptome contains 69,335 transcripts with a N50 transcript length of 2,313 bp and a BUSCO gene completeness of 97.7% and 96% (S: 88.2%; D: 7.8%) in Eukaryota and Metazoa lineage-specific profile libraries. Our findings offer a valuable resource for multiple biological studies using this species.
Tardigrade small heat shock proteins can limit desiccation-induced protein aggregation
Authors: Hibshman Jonathan D. , Carra Serena , Goldstein Bob
Published: July 2022

Small heat shock proteins (sHSPs) are chaperones known for their response to heat stress. While sHSPs have well-characterized roles in heat tolerance, potential roles for sHSPs in desiccation tolerance have not been as thoroughly explored. We identified nine sHSPs from the genome of the tardigrade Hypsibius exemplaris, each containing a conserved alpha-crystallin domain flanked by disordered regions. Many of these sHSPs are highly expressed and in some cases are upregulated during desiccation. We found that tardigrade sHSPs were sufficient to improve desiccation tolerance when expressed in E. coli. Purification and subsequent analysis of two sHSPs, HSP21 and HSP24.6, revealed that these proteins can form large complexes in vitro, similar to oligomeric assemblies documented for other sHSPs. These proteins limited heat-induced aggregation of the model enzyme citrate synthase. Heterologous expression of HSP24.6 improved bacterial heat shock survival, and the protein significantly reduced heat-induced aggregation of soluble bacterial protein. Thus, HSP24.6 likely chaperones against protein aggregation to promote survival of heat stress. Furthermore, HSP21 and HSP24.6 also limited desiccation-induced aggregation and loss of function of citrate synthase. This suggests a mechanism by which tardigrade sHSPs promote desiccation tolerance: by limiting desiccation-induced protein aggregation, thereby maintaining proteostasis and supporting survival. These results suggest that sHSPs, classical chaperones, provide a mechanism of general stress resistance that can also be deployed to support survival during anhydrobiosis.
Prediction error neurons in mouse cortex are molecularly targetable cell types
Authors: O’Toole Sean M. , Oyibo Hassana K. , Keller Georg B.
Published: July 2022

Predictive processing postulates the existence of prediction error neurons in cortex. Functionally, both negative and positive prediction error neurons have been identified in layer 2/3 of visual cortex, but whether they correspond to transcriptionally defined subpopulations is unclear. Here we used the activity-dependent, photoconvertible marker CaMPARI2 to tag neurons in layer 2/3 of visual cortex during stimuli and behaviors designed to trigger prediction errors. We performed single-cell RNA-sequencing on these populations and found that previously annotated Adamts2 and Rrad layer 2/3 cell types were enriched when photolabeling for negative or positive prediction error responses respectively. Finally, we validated these results functionally by designing artificial promoters for use in AAV vectors to express genetically encoded calcium indicators. Thus, positive and negative prediction error responses mapped onto transcriptionally distinct cell types in layer 2/3 that can be targeted using AAV vectors.
Optogenetically induced reward and ‘frustration’ memory in larval Drosophila
Authors: Thoener Juliane , Weiglein Aliće , Gerber Bertram , Schleyer Michael
Published: July 2022

Humans and animals alike form oppositely valenced memories for stimuli that predict the occurrence versus the termination of a reward: appetitive ‘reward’ memory for stimuli associated with the occurrence of a reward and aversive ‘frustration’ memory for stimuli that are associated with its termination. We characterize these memories in larval Drosophila using a combination of Pavlovian conditioning, optogenetic activation of the dopaminergic central-brain DAN-i1864 neuron, and high-resolution video-tracking. This reveals their dependency on the number of training trials and the duration of DAN-i1864 activation, their temporal stability, and the parameters of locomotion that are modulated during memory expression. Together with previous results on ‘punishment’ versus ‘relief’ learning by DAN-f1 neuron activation, this reveals a 2×2 matrix of timing-dependent memory valence for the occurrence/ termination of reward/ punishment. These findings should aid the understanding and modelling of how brains decipher the predictive, causal structure of events around a target reinforcing occurrence.
Temporal progression along discrete coding states during decision-making in the mouse gustatory cortex
Authors: Lang Liam , Camera Giancarlo La , Fontanini Alfredo
Published: July 2022

The mouse gustatory cortex (GC) is involved in taste-guided decision-making in addition to sensory processing. Rodent GC exhibits metastable neural dynamics during ongoing and stimulus-evoked activity, but how these dynamics evolve in the context of a taste-based decision-making task remains unclear. Here we employ analytical and modeling approaches to i) extract metastable dynamics in ensemble spiking activity recorded from the GC of mice performing a perceptual decision-making task; ii) investigate the computational mechanisms underlying GC metastability in this task; and iii) establish a relationship between GC dynamics and behavioral performance. Our results show that activity in GC during perceptual decision-making is metastable and that this metastability may serve as a substrate for sequentially encoding sensory, abstract cue, and decision information over time. Perturbations of the model’s metastable dynamics indicate that boosting inhibition in different coding epochs differentially impacts network performance, explaining a counterintuitive effect of GC optogenetic silencing on mouse behavior.
Single Photon smFRET. III. Application to Pulsed Illumination
Authors: Safar Matthew , Saurabh Ayush , Sarkar Bidyut , Fazel Mohamadreza , Ishii Kunihiko , Tahara Tahei , Sgouralis Ioannis , Pressé Steve
Published: July 2022

Förster resonance energy transfer (FRET) using pulsed illumination has been pivotal in leveraging lifetime information in FRET analysis. However, there remain major challenges in quantitative single photon, single molecule FRET (smFRET) data analysis under pulsed illumination including: 1) simultaneously deducing kinetics and number of system states; 2) providing uncertainties over estimates, particularly uncertainty over the number of system states; 3) taking into account detector noise sources such as crosstalk, and the instrument response function contributing to uncertainty; in addition to 4) other experimental noise sources such as background. Here, we implement the Bayesian nonparametric framework described in the first companion manuscript that addresses all aforementioned issues in smFRET data analysis specialized for the case of pulsed illumination. Furthermore, we apply our method to both synthetic as well as experimental data acquired using Holliday junctions.

Why It Matters

In the first companion manuscript of this series, we developed new methods to analyze noisy smFRET data. These methods eliminate the requirement ofa priorispecifying the dimensionality of the physical model describing a molecular complex’s kinetics. Here, we apply these methods to experimentally obtained datasets with samples illuminated by laser pulses at regular time intervals. In particular, we study conformational dynamics of Holliday junctions.
Metheor: Ultrafast DNA methylation heterogeneity calculation from bisulfite read alignments
Authors: Lee Dohoon , Koo Bonil , Yang Jeewon , Kim Sun
Published: July 2022

Motivation

Phased DNA methylation states within bisulfite sequencing reads are valuable source of information that can be used to estimate epigenetic diversity across cells as well as epigenomic instability in individual cells. Various measures capturing the heterogeneity of DNA methylation states have been proposed for a decade. However, in routine analyses on DNA methylation, this heterogeneity is often overlooked by computing average methylation levels at CpG sites. In this study, to facilitate the application of the DNA methylation heterogeneity measures in downstream epigenomic analyses, we present a Rust-based, extremely fast and lightweight bioinformatics toolkit called Metheor.

Results

We benchmark the performance of Metheor against existing code implementation for DNA methylation heterogeneity measures in three different scenarios of simulated bisulfite sequencing datasets. Metheor was shown to dramatically reduce the execution time up to 300-fold and memory footprint up to 60-fold, while producing the same results with the original implementation.

Availability

Source code for Metheor is at https://github.com/dohlee/metheor and is freely available for non-commercial users.

Contact

sunkim.bioinfo@snu.ac.kr
Emergence of Small Colony Variants (SCVs) is an adaptive strategy used byPseudomonas aeruginosato palliate O2limitations
Authors: Besse Alison , Groleau Marie-Christine , Déziel Eric
Published: July 2022

The ability to generate a subpopulation of Small Colony Variants (SCVs) is a conserved feature ofPseudomonas aeruginosaand could represent a key adaptive strategy to colonize and persist in multiple niches. However, very little is known about the role of the SCV phenotype, the conditions that promote its emergence and its possible involvement in an adaptive strategy. In the present work, we investigated thein vitroselective conditions promoting the emergence of SCVs from the prototypical strain PA14, which readily forms SCVs in non-agitated standing cultures. We found that O2limitations, which cause a redox imbalance, is the main factor selecting for the SCV phenotype, which promotes survival of the populationviaformation of a biofilm at the air-liquid interface to access the electron acceptor. When this selective pressure is relieved by aeration or supplementation of an alternative electron acceptor, SCVs are barely detectable. We also observed that SCV emergence contributes to redox rebalancing, suggesting that it is involved in an adaptive strategy. We conclude that selection for the SCV phenotype is an adaptive solution adopted byP. aeruginosato access poorly available O2.

IMPORTANCE

The bacteriumP. aeruginosais an opportunistic pathogen that thrives in many environments. It poses a significant health concern, notably because it is a causative agent of nosocomial infections and the most prevalent pathogen found in the lungs of people with cystic fibrosis. In infected hosts, its persistence is often related to the emergence of an alternative phenotype known as Small Colony Variant (SCV). Identification of conditions selecting for the SCV phenotype contributes to knowledge regarding adaptive mechanisms exploited byP. aeruginosato survive in multiple niches and persist during infections. Hindering this adaptation strategy could help controlP. aeruginosapersistent infections.
Striatal Dopamine Binding in Anhedonia: A Simultaneous [11C]Raclopride Positron Emission Tomography and Functional Magnetic Resonance Imaging Investigation
Authors: Phillips Rachel D. , Walsh Erin C. , Zürcher Nicole R. , Lalush David , Kinard Jessica , Tseng Chieh-En , Cernasov Paul , Kan Delia , Cummings Kaitlin , Kelley Lisalynn , Campbell David , Dillon Daniel G. , Pizzagalli Diego A. , Izquierdo-Garcia David , Hooker Jacob , Smoski Moria , Dichter Gabriel S.
Published: July 2022

Background

Anhedonia is hypothesized to be associated with blunted mesocorticolimbic dopamine (DA) functioning in samples with major depressive disorder. The purpose of this study was to examine linkages between striatal DA binding, reward circuitry functioning, anhedonia, and, in an exploratory fashion, self-reported stress, in a transdiagnostic anhedonic sample.

Methods

Participants with (n=25) and without (n=12) clinically impairing anhedonia completed a reward-processing task during simultaneous positron emission tomography and magnetic resonance (PET-MR) imaging with [11C]raclopride, a DA D2/D3 receptor antagonist that selectively binds to striatal DA receptors.

Results

Relative to controls, the anhedonia group exhibited increased [11C]raclopride binding potential (ΔBPND) in response to rewards, interpreted as decreased task-related DA release, in the left putamen, caudate, and nucleus accumbens and right putamen and pallidum. There were no group differences in task-related brain activation (fMRI) during reward processing after correcting for multiple comparisons. General functional connectivity (GFC) findings revealed blunted fMRI connectivity between PET-derived striatal seeds and target regions (i.e., bilateral caudate, putamen, pallidum, medial prefrontal cortex, anterior cingulate cortex, and thalamus) in the anhedonia group. Associations were identified between anhedonia severity and the magnitude of task-related DA release to rewards in the left putamen, but not mesocorticolimbic GFC. We did not find evidence of associations between self-reported stress and striatal DA response to rewards, mesocorticolimbic fMRI activation or GFC in the anhedonic sample.

Conclusions

Results provide evidence for reduced striatal DA functioning during reward processing and blunted mesocorticolimbic network functional connectivity in a transdiagnostic sample with clinically significant anhedonia.
Fragment size and diversity of mulches affect their decomposition, nutrient dynamics, and soil microbiology
Authors: Gaitanis Dimitrios , Lukac Martin , Tibbett Mark
Published: July 2022

Plant-based mulch has been proposed as a sustainable way of maintaining soil fertility. However, the role of mulch diversity, quality, and size in decomposition dynamics, and their effect on crop yield are not fully explored. We investigated how mulch quality, proxied by the constituent plant species diversity, and residue size drive mulch decomposition, crop nutrition, and yield.

A rhizotron experiment was set up with barley as a model crop, with the addition of mulch of two particle sizes (1.5 and 30 cm) and four different plant residue mixes (17, 12, 6, and 1 species) in a fully factorial design. Soil nutrient dynamics were measured at advanced decomposition stages, together with residue quality, arbuscular mycorrhizal fungal (AMF) root colonization, and crop yield.

Residue mass loss was significantly affected by its chemical composition. Long residues retained significantly higher C and N content, than short residues. Crop yield was not affected by residue type or size. Residue size significantly affected barley growth rate, influencing seed protein content. Soil available K was significantly increased by residues with a higher initial C:N ratio. Short residues resulted in higher soil Zn. Residues of higher diversity resulted in higher AMF root colonization of the barley plants.

Generally, long residue mulches maintain soil fertility for a longer period than short ones, without a deleterious effect on crop yield. Further investigation should evaluate the effect of continuous application of long residue mulches on soil fertility and microbial populations.
Evolutionary consequences of nascent multicellular life cycles
Authors: Pentz Jennifer T. , MacGillivray Kathryn , DuBose James G. , Conlin Peter L. , Reinhardt Emma , Libby Eric , Ratcliff William C.
Published: July 2022

A key step in the evolutionary transition to multicellularity is the origin of multicellular groups as biological individuals capable of adaptation. Comparative work, supported by theory, suggests clonal development should facilitate this transition, though this hypothesis has never been tested in a single model system. We evolved 20 replicate populations of otherwise isogenic clonally-reproducing ‘snowflake’ yeast (Δace2/Δace2) and aggregative ‘floc’ yeast (GAL1p::FLO1/ GAL1p::FLO1) with daily selection for rapid growth in liquid media, which favors faster cell division, followed by selection for rapid sedimentation, which favors larger multicellular groups. While both genotypes adapted to this regime, growing faster and having higher survival during the group-selection phase, there was a stark difference in evolutionary dynamics. Aggregative floc yeast obtained nearly all of their increased fitness from faster growth, not improved group survival; indicating that selection acted primarily at the level of cells. In contrast, clonal snowflake yeast mainly benefited from higher group-dependent fitness, indicating a shift in the level of biological individuality from cells to groups. Through genome sequencing and mathematical modeling, we show that the genetic bottlenecks in a clonal life cycle also drive much higher rates of genetic drift—a result with complex implications for this evolutionary transition. Our results highlight the central role that early multicellular life cycles play in the process of multicellular adaptation.
Buying time: detecting Vocs in SARS-CoV-2 via co-evolutionary signals
Authors: Barrett Christopher , Bura Andrei C. , He Qijun , Huang Fenix W. , Li Thomas J. X. , Reidys Christian M.
Published: July 2022

We present a novel framework facilitating the rapid detection of variants of interest (VOI) and concern (VOC) in a viral multiple sequence alignment (MSA). The framework is purely based on the genomic sequence data, without requiring prior established biological analysis. The framework’s building blocks are sets of co-evolving sites (motifs), identified via co-evolutionary signals within the MSA. Motifs form a weighted simplicial complex, whose vertices are sites that satisfy a certain nucleotide diversity. Higher dimensional simplices are constructed using distances quantifying the co-evolutionary coupling of pairs and in the context of our method maximal motifs manifest as clusters. The framework triggers an alert via a cluster with a significant fraction of newly emerging polymorphic sites. We apply our method to SARS-CoV-2, analyzing all alerts issued from November 2020 through August 2021 with weekly resolution for England, USA, India and South America. Within a week at most a handful of alerts, each of which involving on the order of 10 sites are triggered. Cross referencing alerts with a posteriori knowledge of VOI/VOC-designations and lineages, motif-induced alerts detect VOIs/VOCs rapidly, typically weeks earlier than current methods. We show how motifs provide insight into the organization of the characteristic mutations of a VOI/VOC, organizing them as co-evolving blocks. Finally we study the dependency of the motif reconstruction on metric and clustering method and provide the receiver operating characteristic (ROC) of our alert criterion.
Genetic variation in correlated regulatory region of Immunity
Authors: Avalos Diana , Rey Guillaume , Ribeiro Diogo M. , Ramisch Anna , Dermitzakis Emmanouil T. , Delaneau Olivier
Published: July 2022

Studying the interplay between genetic variation, epigenetic changes and regulation of gene expression in immune cells is important to understand the modification of cellular states in various conditions, including immune diseases. Here, we built cis maps of regulatory regions with coordinated activity – Cis Regulatory Domains (CRDs) – in neutrophils, monocytes and T cells. For this, we leveraged (i) whole-genome sequencing (WGS), (ii) chromatin immunoprecipitation sequencing (ChIP-seq), (iii) DNA methylation (450k arrays), and (iv) transcriptional profiles (RNA-seq) from the BLUEPRINT consortium, for up to 200 individuals.

Our study uncovers 9287, 7666 and 5480 histone CRDs (hCRDs) and 6053, 6112, 5701 methyl CRDs (mCRDs) in monocytes, neutrophils and T-cells, respectively. We discovered 15294 hCRD-gene and 6185 mCRD-gene associations (5% FDR). Only 33% of hCRD-gene associations and 37% of mCRD-gene associations were shared between cell-types, revealing the dynamic nature of regulatory interactions and how similarly located regulatory regions modulate the activity of different genes on different cell types. We mapped Quantitative Trait Loci associated with CRD activity (CRD-QTLs) and found that 89% and 70% of these hCRDs and mCRDs are under genetic control highlighting the importance of genetic variation to study the coordination of cellular regulatory programs. We found CRD-QTLs to be enriched in celltype-specific transcription factor binding sites, such as SPI1, STAT3, RFX1, SOX4, ATF3 for neutrophils and monocytes and TCF4 and BCL11A for T-cells, in line with the Human protein Atlas.

We integrated PCHi-C data, which showed that most significant associations discovered within gene-CRD associations and co-expressed genes associated with the same CRD, involving large genomic distances, tend to happen between genomic regions in close spatial proximity. Finally, we mapped trans regulatory associations between CRDs, which enabled the discovery of 207 trans-eQTLs across cell types. Overlapping our hits with trans eQTLs from eQTLGen Consortium meta-analysis in whole blood revealed 52 trans-eQTLs shared between the two studies. Overall, we show that mapping functional regulatory units using population genomics data allows discovering important mechanisms in the regulation of gene expression in immune cells and gain a greater understanding of cell-type specific regulatory mechanisms of immunity.
PTPN22 R620W Gene Editing in T Cells Enhances Low Avidity TCR Responses
Authors: Anderson Warren , Barahmand-pour-Whitman Fariba , Linsley Peter S , Cerosaletti Karen , Buckner Jane H , Rawlings David J
Published: July 2022

A genetic variant in the genePTPN22(R620W, rs2476601) is strongly associated with increased risk for multiple autoimmune diseases and has been linked to altered TCR regulation. Here, we utilize Crispr/Cas9 gene editing with donor DNA repair templates in human cord blood-derived, naive T cells to generatePTPN22risk edited, non-risk edited (silent modification), or knock out T cells from the same donor.PTPN22risk edited cells exhibited increased activation marker expression following non-specific TCR engagement, findings that mimicked PTPN22 KO cells. Next, using lentiviral delivery of T1D patient-derived islet-antigen specific TCRs, we demonstrate that loss of PTPN22 function led to enhanced signaling in T cells expressing a lower avidity self-reactive TCR. In this setting, loss of PTPN22 mediated enhanced proliferation and Th1 skewing. Importantly, expression of the risk variant in association with a lower avidity TCR also increased proliferation relative to PTPN22 non-risk T cells. Together, these findings suggest that, in primary human T cells,PTPN22rs2476601 contributes to autoimmunity risk by permitting increased TCR signaling in mildly self-reactive T cells, thereby potentially expanding the self-reactive T cell pool and skewing this population toward an inflammatory phenotype.
Prophages and plasmids display opposite trends in the types of accessory genes they carry
Authors: Takeuchi Nobuto , Hamada-Zhu Sophia , Suzuki Haruo
Published: July 2022

2

Mobile genetic elements (MGEs), such as phages and plasmids, often possess accessory genes encoding bacterial functions, facilitating bacterial evolution. Are there evolutionary rules governing the arsenal of accessory genes MGEs carry? If such rules exist, they might be reflected in the types of accessory genes different MGEs carry. To test this hypothesis, we compare prophages and plasmids with respect to the frequencies at which they carry antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in the genomes of 21 pathogenic bacterial species using public databases. Our results indicate that prophages tend to carry VFGs more frequently than ARGs in three species, whereas plasmids tend to carry ARGs more frequently than VFGs in nine species. InEscherichia coli, where these trends are detected, prophage-borne VFGs encode a much narrower range of functions than do plasmid-borne VFGs, typically involved in damaging host cells or modulating host immunity. In the species where the above trends were not detected, ARGs and VFGs are barely found in prophages and plasmids. These results indicate that MGEs differentiate in the types of accessory genes they carry depending on their infection strategies, suggesting an evolutionary rule governing horizontal gene transfer mediated by MGEs.
Arabidopsis latent virus 1, a comovirus widely spread in Arabidopsis thaliana collections
Authors: Verhoeven Ava , Kloth Karen J. , Kupczok Anne , Oymans Geert H. , Damen Janna , Rijnsburger Karin , Jiang Zhang , Deelen Cas , Sasidharan Rashmi , van Zanten Martijn , van der Vlugt René A.A.
Published: July 2022

Transcriptome studies of Illumina RNA-seq datasets of different Arabidopsis thaliana natural accessions and T-DNA mutants revealed the presence of two virus-like RNA sequences which showed the typical two segmented genome characteristics of a comovirus.

This comovirus did not induce any visible symptoms in infected Arabidopsis plants cultivated under standard laboratory conditions. Hence it was named Arabidopsis latent virus 1 (ArLV1). Virus infectivity in Arabidopsis plants was confirmed by RT-qPCR, transmission electron microscopy and mechanical inoculation. ArLV1 can also mechanically infect Nicotiana benthamiana, causing distinct mosaic symptoms.

A bioinformatics investigation of Arabidopsis RNA-Seq repositories, including nearly 6500 Sequence Read Archives (SRAs) in the NCBI SRA database, revealed the presence of ArLV1 in 25% of all archived natural Arabidopsis accessions and in 8.5% of all analyzed SRAs. ArLV1 could also be detected in Arabidopsis plants collected from the wild.

ArLV1 is highly seed-transmissible with up to 40% incidence on the progeny derived from infected Arabidopsis plants. This has likely led to a worldwide distribution in the model plant Arabidopsis with yet unknown effects on plant performance in a substantial number of studies.

Plain language summary

We identified Arabidopsis latent virus 1 (ArLV1), a comovirus that infects the model plant Arabidopsis thaliana without causing any visible symptoms. It is efficiently spread by transmission via seeds to the plant progeny. ArLV1 is infectious to Arabidopsis plants and another model plant, Nicotiana benthamiana. By analyzing public sequencing data, we found that ArLV1 is widely spread in Arabidopsis laboratory collections worldwide. Moreover, it was also detected in wild Arabidopsis plants collected from different locations in the Netherlands and Spain, suggesting that it is a virus that naturally occurs in Arabidopsis.
Nodulin 16 of Lotus japonicus (Nlj16) regulates the recruitment of Leghemoglobin (LegH) to the infected nodule cell membrane during symbiotic nitrogen fixation
Authors: Ghosh Amit , Das Aniruddho , Ashrafi Md Azimuddin , Saha Sudeshna , Molla Firoz , DasGupta Maitrayee , Siddhanta Anirban
Published: July 2022

Nitrogenase that catalyses anaerobic symbiotic nitrogen fixation (SNF) in legumes is synthesized by rhizobium. Legume root cells express nodulin proteins after infection with rhizobia. Nodulins have been classified as early and late, reflecting the time points of their expression. Leghemoglobin (LegH), which is a classic example of a late nodulin, sequesters oxygen inside the nodule to protect the nitrogenase from oxygen toxicity to sustain SNF. Previous data from our laboratory demonstrated that phosphorylated LegH at S45 showed compromised oxygen sequestration in vitro due to structural disruption of the porphyrin binding pocket responsible for its oxygen binding. Moreover, we have demonstrated by using co-immunoprecipitation that LegH interacts both in vitro with Nodulin 16 of Lotus japonicus (Nlj16), another late nodulin. Fluorescence Immunohistochemistry (IHC) data shows that both LegH and Nlj16 are localized in the membrane and cytosol of infected cells. Notably, serine phosphorylation of LegH and interaction of Nlj16 with LegH respectively reduces and increases its in vitro oxygen sequestration ability. In this report, to further elucidate the spatio-temporal regulation of this interaction, we generated hairy root transgenic Lotus japonicus plants where Nlj16 has been knocked down by using siRNA. Most interestingly, our data shows that the membrane localization of LegH is obliterated in the Nlj16 knocked-down root cells infected with the cognate Rhizobia suggesting a distinct role of Nlj16 in its recruitment to the membrane of nodule cells.
On specialists and generalists: niche range strategies across the tree of life
Authors: von Meijenfeldt F. A. Bastiaan , Hogeweg Paulien , Dutilh Bas E.
Published: July 2022

Generalists can survive in many environments whereas specialists have a limited distribution. Although a classical concept in ecology, niche breadth has remained challenging to quantify because it depends on an objective definition of the environment. Here, by defining the environment of a microbe as the community it resides in, we integrated information from over 22 thousand environmental sequencing samples to derive a quantitative social niche breadth score for all microbial taxa. At the level of genera, we explored niche range strategies across the tree of life. We found that generalists include opportunists that stochastically dominate local communities, while specialists are stable but low in abundance. Generalists have a more diverse and open pan genome than specialists, but we found no global correlation between niche breadth and genome size. Instead, we observed two distinct evolutionary strategies, where specialists have relatively small genomes in habitats with low local diversity, but relatively large genomes in habitats with high local diversity. Together, our global analysis shines a new, data-driven light on microbial niche range strategies.
Shared and distinct neural activity during anticipation and outcome of win and loss: A meta-analysis of the monetary incentive delay task
Authors: Chen Yu , Chaudhary Shefali , Li Chiang-Shan R.
Published: July 2022

Reward and punishment motivate decision making and behavioral changes. Numerous studies have examined regional activities during anticipation and outcome of win and loss in the monetary incentive delay task (MIDT). However, the great majority of studies reported findings of anticipation or outcome and of win or loss alone. It remains unclear how the neural correlates share and differentiate amongst these processes. We conducted an Activation Likelihood Estimation meta-analysis of 77 studies of the MIDT (5,779 subjects), including 24 published since the most recent meta-analysis, to identify and, with conjunction and subtraction, contrast regional responses to win anticipation, loss anticipation, win outcome, and loss outcome. Win and loss anticipation engaged a shared network of bilateral anterior insula (AI), striatum, thalamus, supplementary motor area (SMA), and precentral gyrus. Win and loss outcomes did not share regional activities. Win and loss outcome each engaged higher activity in medial orbitofrontal cortex (mOFC) and dorsal anterior cingulate cortex. Bilateral striatum and right occipital cortex responded to both anticipation and outcome of win, and right AI to both phases of loss. Win anticipation vs. outcome engaged higher activity in bilateral AI, striatum, SMA and precentral gyrus and right thalamus, and lower activity in bilateral mOFC and posterior cingulate cortex as well as right inferior frontal and angular gyri. Loss anticipation relative to outcome involved higher activity in bilateral striatum and left AI. These findings collectively suggest shared and distinct regional responses during monetary wins and losses. Delineating the neural correlates of these component processes may facilitate empirical research of motivated behavior and dysfunctional approach and avoidance in psychopathology.

Highlights

Win and loss anticipation both engaged the fronto-striatal-thalamic network.

Win and loss outcomes shared no regional activities.

The mOFC and dACC play distinct roles each in processing win and loss outcome.

Win and loss anticipation engaged bilateral AI; loss outcome only the right AI.

Win/loss anticipation vs. outcome engaged predominantly right/left AI.
Subcellular Redox Responses Reveal Different Cu-dependent Antioxidant Defenses between Mitochondria and Cytosol
Authors: Zhang Yuteng , Wen Meng-Hsuan , Qin Guoting , Cai Chengzhi , Chen Tai-Yen
Published: July 2022

Excess intracellular Cu perturbs cellular redox balance and thus causes diseases. However, the relationship between cellular redox status and Cu homeostasis and how such an interplay is coordinated within cellular compartments has not yet been well established. Using combined approaches of organelle-specific redox sensor Grx1-roGFP2 and non-targeted proteomics, we investigate the real-time Cu-dependent antioxidant defenses of mitochondria and cytosol in live HEK293 cells. The Cu-dependent real-time imaging experiments show that CuCl2 treatment results in increased oxidative stress in both cytosol and mitochondria. In contrast, subsequent Cu depletion by BCS, a Cu chelating reagent, lowers oxidative stress in mitochondria but causes even higher oxidative stress in the cytosol. The proteomic data reveal that several mitochondrial proteins, but not cytosolic ones, undergo significant abundance change under Cu treatments. The proteomic analysis also shows that proteins with significant changes are related to mitochondrial oxidative phosphorylation and glutathione synthesis. The differences in redox behaviors and protein profiles in different cellular compartments reveal distinct mitochondrial and cytosolic response mechanisms upon Cu-induced oxidative stress. These findings provide insights into how redox and Cu homeostasis interplay by modulating specific protein expressions at the subcellular levels, shedding light on understanding the effects of Cu-induced redox misregulation on the diseases.

Graphical abstract
Engineering Toxoplasma transgenic tissue cysts
Authors: Hong David D. , Brooks Krista , Goerner Amber L. , Vizcarra Edward A. , Loges Luiza N. , Wilson Emma H. , White Michael W.
Published: July 2022

Current approaches to find therapeutic solutions to treat and prevent reactivation of toxoplasmosis have suffered from limited accessibility to the relevant Toxoplasma stages and a lack of accurate in vitro developmental models. The loss of developmental competency in vitro that is exacerbated during the generation of transgenic tachyzoites is also a major impediment to understanding the molecular basis of bradyzoite recrudescence, which is the central feature of reactivation. We have developed an innovative ex vivo model of bradyzoite recrudescence and applied this method to successfully modify Toxoplasma genes while avoiding the problems caused by continuous in vitro cell culture. We present four protocols required to engineer in vivo transgenic tissue cysts: 1) the reliable production of in vivo tissue cysts and excysted bradyzoites, 2) the use of fast-growing parasites from ex vivo bradyzoite infections to successfully generate transgenic tissue cysts in mice, 3) the cloning of transgenic bradyzoites via single cyst infections, and finally, 4) the long term cold storage and recovery of transgenic tissue cysts in brain tissue homogenates. We demonstrated these protocols by knocking out the Toxoplasma HXGPRT gene and the gene encoding the ApiAP2 transcription factor, AP2IX-9 in tissue cysts from mice. Unexpectedly, the knockout of the AP2IX-9 gene in the Type II ME49EW strain eliminated one of the three developmental pathways initiated by the bradyzoite; host-dependent bradyzoite to bradyzoite replication.