bluuebunny/crossref_metadata_2025 huggingface dataset:
The impact of environmental mycobiomes on geographic variation in COVID-19 mortality
Authors: Ladau Joshua , Abuabara Katrina , Walker Angelica M. , Joachimiak Marcin P. , Bansal Ishan , Wu Yulun , Hoffman Elijah B. , Kuo Chaincy , Falco Nicola , Streich Jared , van der Laan Mark J. , Wainwright Haruko M. , Brodie Eoin L. , Hess Matthias , Jacobson Daniel , Brown James B.
Published: December 2021

Mortality rates during the COVID-19 pandemic have varied by orders of magnitude across communities in the United States1. Individual, socioeconomic, and environmental factors have been linked to health outcomes of COVID-192,3,4,5. It is now widely appreciated that the environmental microbiome, composed of microbial communities associated with soil, water, atmosphere, and the built environment, impacts immune system development and susceptibility to immune-mediated disease6,7,8. The human microbiome has been linked to individual COVID-19 disease outcomes9, but there are limited data on the influence of the environmental microbiome on geographic variation in COVID-19 across populations10. To fill this knowledge gap, we used taxonomic profiles of fungal communities associated with 1,135 homes in 494 counties from across the United States in a machine learning analysis to predict COVID-19 Infection Fatality Ratios (the number of deaths caused by COVID-19 per 1000 SARS-CoV-2 infections1; ‘IFR’). Here we show that exposure to increased fungal diversity, and in particular indoor exposure to outdoor fungi, is associated with reduced SARS-CoV-2 IFR. Further, we identify seven fungal genera that are the predominant drivers of this protective signal and may play a role in suppressing COVID-19 mortality. This relationship is strongest in counties where human populations have remained stable over at least the previous decade, consistent with the importance of early-life microbial exposures11. We also assessed the explanatory power of 754 other environmental and socioeconomic factors, and found that indoor-outdoor fungal beta-diversity is amongst the strongest predictors of county-level IFR, on par with the most important known COVID-19 risk factors, including age12. We anticipate that our study will be a starting point for further integration of environmental mycobiome data with population health information, providing an important missing link in our capacity to identify vulnerable populations. Ultimately, our identification of specific genera predicted to be protective against COVID-19 mortality may point toward novel, proactive therapeutic approaches to infectious disease.
Machine learning identified distinct serum lipidomic signatures in hospitalized COVID-19-positive and COVID-19-negative patients
Authors: Castañé Helena , Iftimie Simona , Baiges-Gaya Gerard , Rodríguez-Tomàs Elisabet , Jiménez-Franco Andrea , López-Azcona Ana Felisa , Garrido Pedro , Castro Antoni , Camps Jordi , Joven Jorge
Published: December 2021

Background

Lipids are involved in the interaction between viral infection and the host metabolic and immunological response. Several studies comparing the lipidome of COVID-19-positive hospitalized patients vs. healthy subjects have already been reported. It is largely unknown, however, whether these differences are specific to this disease. The present study compared the lipidomic signature of hospitalized COVID-19-positive patients with that of healthy subjects, and with COVID-19-negative patients hospitalized for other infectious/inflammatory diseases. Potential COVID-19 biomarkers were identified.

Methods

We analyzed the lipidomic signature of 126 COVID-19-positive patients, 45 COVID-19-negative patients hospitalized with other infectious/inflammatory diseases and 50 healthy volunteers. Results were interpreted by machine learning.

Results

We identified acylcarnitines, lysophosphatidylethanolamines, arachidonic acid and oxylipins as the most altered species in COVID-19-positive patients compared to healthy volunteers. However, we found similar alterations in COVID-19-negative patients. By contrast, we identified lysophosphatidylcholine 22:6-sn2, phosphatidylcholine 36:1 and secondary bile acids as the parameters that had the greatest capacity to discriminate between COVID-19-positive and COVID-19-negative patients.

Conclusion

This study shows that COVID-19 infection shares many lipid alterations with other infectious/inflammatory diseases, but differentiating them from the healthy population. Also, we identified some lipid species the alterations of which distinguish COVID-19-positive from Covid-19-negative patients. Our results highlight the value of integrating lipidomics with machine learning algorithms to explore the pathophysiology of COVID-19 and, consequently, improve clinical decision making.
Previous visceral leishmaniasis relapses outperform immunological or clinical signs as predictors of further relapses in patients co-infected with HIV-1
Authors: Takele Yegnasew , Mulaw Tadele , Adem Emebet , Womersley Rebecca , Kaforou Myrsini , Franssen Susanne Ursula , Levin Michael , Taylor Graham Philip , Müller Ingrid , Cotton James Anthony , Kropf Pascale
Published: December 2021

Visceral leishmaniasis (VL) and HIV co-infection (VL/HIV) has emerged as a significant public health problem in Ethiopia, with up to 30% of VL patients co-infected with HIV. These patients suffer from recurrent VL relapses and increased mortality. Our aim was to assess whether VL/HIV co-infected patients with a previous history of VL relapses (recurrent VL/HIV) have a poorer prognosis as compared to HIV patients presenting with their first episode of VL (primary VL/HIV). Our results show that recurrent VL/HIV patients have a higher parasite load, higher mortality and that their relapse-free survival is significantly shorter. The poorer prognosis of recurrent VL/HIV patients is accompanied by lower weight gain and lower recovery of all blood cell lineages, as well as lower production of IFNγ, lower CD4+ T cell counts and higher expression levels of PD1 on T cells. Furthermore, our results show that prior history of VL relapse is an important risk factor for future relapse. Both CD4+ T cell count and parasite load were also associated with a higher risk of VL relapse, but neither of these was independently associated with relapse risk after adjustment for previous VL relapse history.

We propose that in addition to the current treatments, novel interventions should be considered at the time of VL diagnosis in VL/HIV patients; and suggest that improved anti-leishmanial and antiretroviral treatments, as well as immune therapy, through PD1/PDL-1 blockade and/or through IFNγ administration, could result in more efficient parasite killing and thereby reduce the relapse rate and improve survival.
Link between aging and atheroprotection in Mif-deficient atherosclerotic mice
Authors: Krammer Christine , Yang Bishan , Reichl Sabrina , Bolini Verena , Schulte Corinna , Noels Heidi , Bounkari Omar El , Kapurniotu Aphrodite , Weber Christian , Mohanta Sarajo , Bernhagen Jürgen
Published: December 2021

Abstract

Atherosclerosis is a lipid-triggered chronic inflammatory condition of our arteries and the main underlying pathology of myocardial infarction and stroke. Pathogenesis is age-dependent, but the mechanistic links between disease progression, age, and atherogenic cytokines and chemokines are incompletely understood. Here, we studied the chemokine-like inflammatory cytokine macrophage migration inhibitory factor (MIF) in atherogenic Apoe−/− mice across different stages of aging and cholesterol-rich high-fat diet (HFD). MIF promotes atherosclerosis by mediating atherogenic monocyte and T-cell recruitment, amplifying lesional inflammation, and suppressing atheroprotective B-cell responses. However, age-related links between atherogenesis and MIF and its role in advanced atherosclerosis in aged mice have not been systematically explored. We compared effects of global Mif-gene deficiency in 30-, 42-, and 48-week-old Apoe−/− mice on HFD for 24, 36, or 42 weeks, respectively, and in 52-week-old mice on a 6-week HFD. While a regio-specific atheroprotective phenotype of Mif-deficiency was observed in the 30/24-week-old group, atheroprotection was not detected in the 48/42- and 52/6-week-old groups, suggesting that atheroprotection afforded by global Mif-gene deletion differs across aging stages and atherogenic diet duration. We identify a combination of mechanisms that could explain this phenotype: i) Mif-deficiency promotes lesional Trem2+ macrophage numbers in younger but not aged mice; ii) Mif-deficiency favors formation of lymphocyte-rich stage-I/II ATLOs in younger mice but ATLO numbers equalize with those in Apoe−/− controls in the older mice; and iii) plasma anti-oxLDL-IgM antibody levels are decreased in aged Mif-deficient mice. Of note, these three markers (Trem2+ macrophages, ATLOs, anti-oxLDL-IgM antibodies) have been previously linked to atheroprotection. Together, our study thus suggests that regio-specific atheroprotection due to global Mif-gene deficiency in atherogenic Apoe−/− mice is lost upon advanced aging and identifies mechanisms that could explain this phenotype shift. These observations may have implications for translational MIF- directed strategies.
Genome editing excisase origins illuminated by somatic genome of Blepharisma
Authors: Singh Minakshi , Brandon Seah Kwee Boon , Emmerich Christiane , Singh Aditi , Woehle Christian , Huettel Bruno , Byerly Adam , Stover Naomi Alexandra , Sugiura Mayumi , Harumoto Terue , Swart Estienne Carl
Published: December 2021

Massive DNA excision occurs regularly in ciliates, ubiquitous microbial eukaryotes with somatic and germline nuclei in the same cell. Tens of thousands of internally eliminated sequences (IESs) scattered throughout a copy of the ciliate germline genome are deleted during development of the streamlined somatic genome. Blepharisma represents one of the two earliest diverging ciliate classes, and, unusually, has dual pathways of somatic nuclear development, making it ideal for investigating the functioning and evolution of these processes. Here, we report the somatic genome assembly of Blepharisma stoltei strain ATCC 30299 (41 Mb), arranged as numerous alternative telomere-capped minichromosomes. This genome encodes eight PiggyBac transposase homologs liberated from transposons. All are subject to purifying selection, but just one, the putative IES excisase, has a complete catalytic triad. We propose PiggyBac homologs were ancestral excisases that enabled evolution of extensive, natural genome editing.
The ColR/S two-component system is a conserved determinant of host association across Pseudomonas species
Authors: Wiesmann Christina L. , Zhang Yue , Alford Morgan , Thoms David , Dostert Melanie , Wilson Andrew , Pletzer Daniel , Hancock Robert E. W. , Haney Cara H.
Published: December 2021

Members of the bacterial genus Pseudomonas form mutualistic, commensal and pathogenic associations with diverse hosts. The prevalence of host association across the genus suggests that symbiosis may be a conserved ancestral trait and that distinct symbiotic lifestyles may be more recently evolved. Here we show that the ColR/S two-component system, part of the Pseudomonas core genome, is functionally conserved between Pseudomonas aeruginosa and Pseudomonas fluorescens. Using plant rhizosphere colonization and virulence in a murine abscess model, we show that colR is required for commensalism with plants and virulence in animals. Comparative transcriptomics revealed that the ColR regulon has diverged between P. aeruginosa and P. fluorescens and deleting components of the ColR regulon revealed strain-specific, but not hostspecific, requirements for ColR-dependent genes. Collectively, our results suggest that ColR/S allows Pseudomonas to sense and respond to a host, but that the ColR-regulon has diverged between Pseudomonas strains with distinct lifestyles.
Simulated visual hallucinations in virtual reality enhance cognitive flexibility
Authors: Rastelli Clara , Greco Antonino , Kenett Yoed N. , Finocchiaro Chiara , De Pisapia Nicola
Published: December 2021

Historically, psychedelic drugs are known to modulate cognitive flexibility, a central aspect of cognition permitting adaptation to changing environmental demands. Despite proof suggesting phenomenological similarities between artificially-induced and actual psychedelic altered perception, experimental evidence is still lacking about whether the former is also able to modulate cognitive flexibility. To address this, we measure participants’ cognitive flexibility through behavioral tasks after the exposure to virtual reality panoramic videos and their hallucinatory-like counterparts generated by the DeepDream algorithm. Results show that the estimated semantic network has a flexible structure when preceded by altered videos. Crucially, following the simulated psychedelic exposure, individuals also show an attenuated contribution of the automatic process and chaotic dynamics underlying the decision process. This suggests that simulated altered perceptual phenomenology enhances cognitive flexibility, presumably due to a reorganization in the cognitive dynamics that facilitates the exploration of uncommon decision strategies and inhibits automated choices.
The blackgrass genome reveals patterns of divergent evolution of non-target site resistance to herbicides
Authors: Cai Lichun , Comont David , MacGregor Dana , Lowe Claudia , Beffa Roland , Saski Christopher , Neve Paul
Published: December 2021

Globally, weedy plants result in more crop yield loss than plant pathogens and insect pests combined. Much of the success of weeds rests with their ability to rapidly adapt in the face of human-mediated environmental management and change. The evolution of resistance to herbicides is an emblematic example of this rapid adaptation. Here, we focus on Alopecurus myosuroides (blackgrass), the most impactful agricultural weed in Europe. To gain insights into the evolutionary history and genomic mechanisms underlying adaptation in blackgrass, we assembled and annotated its large, complex genome. We show that non-target site herbicide resistance is oligogenic and likely evolves from standing genetic variation. We present evidence for divergent selection of resistance at the level of the genome in wild, evolved populations, though at the transcriptional level, resistance mechanisms are underpinned by similar patterns of up-regulation of stress- and defence-responsive gene families. These gene families are expanded in the blackgrass genome, suggesting that the large, duplicated, and dynamic genome plays a role in enabling rapid adaptation in blackgrass. These observations have wide significance for understanding rapid plant adaptation in novel stressful environments.
Combined SHP2 and ERK inhibition for the treatment of KRAS-driven Pancreatic Ductal Adenocarcinoma
Authors: Ciecielski Katrin J. , Mulero-Sánchez Antonio , Berninger Alexandra , Cañas Laura Ruiz , Bosma Astrid , Görgülü Kıvanç , Wu Nan , Diakopoulos Kalliope N. , Kaya-Aksoy Ezgi , Ruess Dietrich A. , Kabacaoğlu Derya , Schmidt Fränze , Heinemann Larissa , Fan Yuhui , Thijssen Bram , van de Ven Marieke , Proost Natalie , Kossatz Susanne , Weber Wolfgang A. , Sainz Bruno , Bernards Rene , Algül Hana , Lesina Marina , Mainardi Sara
Published: December 2021

Mutant KRAS is present in over 90% of pancreatic as well as 30-40% of lung and colorectal cancers and is one of the most common oncogenic drivers. Despite decades of research and the recent emergence of isoform-specific KRASG12C-inhibitors, most mutant KRAS isoforms, including the ones frequently associated with pancreatic ductal adenocarcinoma (PDAC), cannot be targeted directly. Moreover, targeting single RAS downstream effectors induces adaptive mechanisms leading to tumor recurrence or resistance. We report here on the combined inhibition of SHP2, a non-receptor tyrosine phosphatase upstream of KRAS, and ERK, a serine/threonine kinase and a key molecule downstream of KRAS in PDAC. This combination shows synergistic anticancer activity in vitro, superior disruption of the MAPK pathway, and significantly increased apoptosis induction compared to single-agent treatments. In vivo, we demonstrate good tolerability and efficacy of the combination. Concurrent inhibition of SHP2 and ERK induces significant tumor regression in multiple PDAC mouse models. Finally, we show evidence that 18F-FDG PET scans can be used to detect and predict early drug responses in animal models. Based on these compelling results, we will investigate this drug combination in a clinical trial (SHERPA, SHP2 and ERK inhibition in pancreatic cancer, NCT04916236), enrolling patients with KRAS-mutant PDAC.
Effects of habitat destruction on coevolving metacommunities
Authors: Gawecka Klementyna A. , Pedraza Fernando , Bascompte Jordi
Published: December 2021

Habitat destruction is a growing threat to biodiversity and ecosystem services. The ecological consequences of habitat loss and fragmentation involve reductions in species abundance and even the extinction of species and interactions. However, we do not yet understand how habitat loss can alter the coevolutionary trajectories of the remaining species or how coevolution, in turn, affects their response to habitat loss. To investigate this, we develop a spatially explicit model which couples metacommunity and coevolutionary dynamics. We show that, by changing the size, composition and structure of local networks, habitat destruction increases the diversity of coevolutionary outcomes across the landscape. Furthermore, we show that while coevolution dampens the negative effects of habitat destruction in mutualistic networks, its effects on the persistence of antagonistic communities are less predictable.
Comparative Analysis and Data Provenance for 1,113 Bacterial Genome Assemblies
Authors: Yarmosh David A. , Lopera Juan G. , Puthuveetil Nikhita P. , Combs Patrick Ford , Reese Amy L. , Tabron Corina , Pierola Amanda E. , Duncan James , Greenfield Samuel R. , Marlow Robert , King Stephen , Riojas Marco A. , Bagnoli John , Benton Briana , Jacobs Jonathan L.
Published: December 2021

The quality and traceability of microbial genomics data in public databases is deteriorating as they rapidly expand and struggle to cope with data curation challenges. While the availability of public genomic data has become essential for modern life sciences research, the curation of the data is a growing area of concern that has significant real-world impacts on public health epidemiology, drug discovery, and environmental biosurveillance research1–6. While public microbial genome databases such as NCBI’s RefSeq database leverage the scalability of crowd sourcing for growth, they do not require data provenance to the original biological source materials or accurate descriptions of how the data was produced7. Here, we describe the de novo assembly of 1,113 bacterial genome references produced from authenticated materials sourced from the American Type Culture Collection (ATCC), each with full data provenance. Over 98% of these ATCC Standard Reference Genomes (ASRGs) are superior to assemblies for comparable strains found in NCBI’s RefSeq database. Comparative genomics analysis revealed significant issues in RefSeq bacterial genome assemblies related to genome completeness, mutations, structural differences, metadata errors, and gaps in traceability to the original biological source materials. For example, nearly half of RefSeq assemblies lack details on sample source information, sequencing technology, or bioinformatics methods. We suggest there is an intrinsic connection between the quality of genomic metadata, the traceability of the data, and the methods used to produce them with the quality of the resulting genome assemblies themselves. Our results highlight common problems with “ reference genomes” and underscore the importance of data provenance for precision science and reproducibility. These gaps in metadata accuracy and data provenance represent an “ elephant in the room” for microbial genomics research, but addressing these issues would require raising the level of accountability for data depositors and our own expectations of data quality.
Computational analysis of the effect of SARS-CoV-2 variant Omicron Spike protein mutations on dynamics, ACE2 binding and propensity for immune escape
Authors: Teruel Natalia , Crown Matthew , Bashton Matthew , Najmanovich Rafael
Published: December 2021

The recently reported Omicron (B.1.1.529) SARS-CoV-2 variant has a large number of mutations in the Spike (S) protein compared to previous variants. Here we evaluate the potential effect of Omicron S mutations on S protein dynamics and ACE2 binding as contributing factors to infectivity as well as propensity for immune escape. We define a consensus set of mutations from 77 sequences assigned as Omicron in GISAID as of November 25. We create structural models of the Omicron S protein in the open and closed states, as part of a complex with ACE2 and for each of 77 complexes of S bound to different antibodies with known structures. We have previously utilized Dynamical Signatures (DS) and the Vibrational Entropy Score (VDS) to evaluate the propensity of S variants to favour the open state. Here, we introduce the Binding Influence Score (BIS) to evaluate the influence of mutations on binding affinity based on the net gain or loss of interactions within the protein-protein interface. BIS shows excellent correlation with experimental data (Pearson correlation coefficient of 0.87) on individual mutations in the ACE2 interface for the Alpha, Beta, Gamma, Delta and Omicron variants combined. On the one hand, the DS of Omicron highly favours a more rigid open state and a more flexible closed state with the largest VDS of all variants to date, suggesting a large increase in the chances to interact with ACE2. On the other hand, the BIS shows that apart from N501Y, all other mutations in the interface reduce ACE2 binding affinity. VDS and BIS show opposing effects on the overall effectiveness of Omicron mutations to promote binding to ACE2 and therefore initiate infection. To evaluate the propensity for immune escape we calculated the net change of favourable and unfavourable interactions within each S-antibody interface. The net change of interactions shows a positive score (a net increase of favourable interactions and decrease of unfavourable ones) for 41 out of 77 antibodies, a nil score for 15 and a negative score for 21 antibodies. Therefore, in only 28% of S-antibody complexes (21/77) we predict some level of immune escape due to a weakening of the interactions with Omicron S. Considering that most antibody epitopes and the mutations are within the S-ACE2 interface our results suggest that mutations within the RBD of Omicron may give rise to only partial immune escape, which comes at the expense of reduced ACE2 binding affinity. However, this reduced ACE2 affinity appears to have been offset by increasing the occupancy of the open state of the Spike protein.
Caveats to deep learning approaches to RNA secondary structure prediction
Authors: Flamm Christoph , Wielach Julia , Wolfinger Michael T. , Badelt Stefan , Lorenz Ronny , Hofacker Ivo L.
Published: December 2021

Machine learning (ML) and in particular deep learning techniques have gained popularity for predicting structures from biopolymer sequences. An interesting case is the prediction of RNA secondary structures, where well established biophysics based methods exist. The accuracy of these classical methods is limited due to lack of experimental parameters and certain simplifying assumptions and has seen little improvement over the last decade. This makes RNA folding an attractive target for machine learning and consequently several deep learning models have been proposed in recent years. However, for ML approaches to be competitive for de-novo structure prediction, the models must not just demonstrate good phenomenological fits, but be able to learn a (complex) biophysical model. In this contribution we discuss limitations of current approaches, in particular due to biases in the training data. Furthermore, we propose to study capabilities and limitations of ML models by first applying them on synthetic data (obtained from a simplified biophysical model) that can be generated in arbitrary amounts and where all biases can be controlled. We assume that a deep learning model that performs well on these synthetic, would also perform well on real data, and vice versa. We apply this idea by testing several ML models of varying complexity. Finally, we show that the best models are capable of capturing many, but not all, properties of RNA secondary structures. Most severely, the number of predicted base pairs scales quadratically with sequence length, even though a secondary structure can only accommodate a linear number of pairs.
Childhood trajectories of internalising and externalising problems associated with a polygenic risk score for neuroticism in a UK birth cohort study
Authors: Costantini Ilaria , Sallis Hannah , Tilling Kate , Major-Smith Daniel , Pearson Rebecca M , Kounali Daphne-Zacharenia
Published: December 2021

Neuroticism represents a personality disposition towards experiencing negative emotions more frequently and intensely. Longitudinal studies suggest that neuroticism increases risk of several psychological and physical problems. Improved understanding of how this trait manifests in early life could help inform preventative strategies in those liable to neuroticism.

This study explored how a polygenic risk score (PRS) for neuroticism is expressed from infancy to late childhood across various psychological outcomes and how it associates with trajectories of internalising and externalising problems from ages 4-11 in the Avon Longitudinal Study of Parents and Children (N=5,279). We employed multivariable linear and ordinal regression models to estimate associations between a child neuroticism PRS and psychological outcomes. A three-level mixed-effect model was employed to characterise child internalising and externalising trajectories and estimate how a child PRS associated with both their overall levels and rates of change.

We found evidence that the PRS for neuroticism was associated with a more sensitive temperament in early infancy in addition to higher emotional and behavioural problems and a higher risk of being diagnosed with a variety of clinical disorders, particularly anxiety disorders, in childhood. We also found strong evidence that the PRS for neuroticism was associated with overall levels of internalising and externalising trajectories, with a larger magnitude of effect on the internalising trajectory. The PRS was also associated with slower rates of reduction of internalising problems.

Our findings using a large, well-characterised birth cohort study suggest that phenotypic manifestations of a PRS for adult neuroticism can be detected as early as in infancy and that this PRS associates with several mental health problems and differences in emotional trajectories across childhood.
Vaccines provide disproportional protection to the increased hospitalisation risk posed by the Delta variant of SARS-CoV2: a meta-analysis
Authors: Simons Mirre J P
Published: December 2021

Variants of SARS-CoV2 that achieved global dominance (Alpha and Delta) have been associated with increased hospitalisation risk. A quantification of this risk across studies is currently lacking for Delta. Furthermore, how risk for severe disease changes in both vaccinated and unvaccinated individuals is important as the underlying risks determine public health impact. The surplus risk of Delta versus Alpha on hospitalisation was determined using random-effects meta-analysis. Infection with the Delta compared to the Alpha variant increased hospitalisation risk (unvaccinated: log HR 0.62, CI: 0.41 – 0.84, P < 0.0001; linear HR 1.87). This finding should inform our response to future variants of concern, currently Omicron. SARS-CoV2 variants that achieve dominance, have achieved this through a higher rate of infection and this evolutionary trajectory has also come with a correlated higher risk of severe disease. The surplus risk posed by Delta was significantly lower however in the vaccinated (model estimate -0.40, CI: -0.73 – -0.07, P = 0.017). Vaccination thus provided a disproportionate level of protection to hospitalisation with the Delta variant and provides further rationale for vaccination for SARS-CoV2 as a durable public health measure.
Potential severity, mitigation, and control of Omicron waves depending on pre-existing immunity and immune evasion
Authors: Bartha Ferenc A. , Boldog Péter , Tekeli Tamás , Vizi Zsolt , Dénes Attila , Röst Gergely
Published: December 2021

We assess the potential consequences of the upcoming SARS-CoV-2 waves caused by the Omicron variant. Our results suggest that even in those regions where the Delta variant is controlled at the moment by a combination of non-pharmaceutical interventions and population immunity, a significant Omicron wave can be expected. We stratify the population according to prior immunity status, and characterize the possible outbreaks depending on the population level of pre-existing immunity and the immune evasion capability of Omicron. We point out that two countries having similar effective reproduction numbers for the Delta variant can experience very different Omicron waves in terms of peak time, peak size and total number of infections among the high risk population.
Comparison of extraction methods for intracellular metabolomics
Authors: Andresen Carolin , Boch Tobias , Gegner Hagen M. , Mechtel Nils , Narr Andreas , Birgin Emrullah , Rasbach Erik , Rahbari Nuh , Trumpp Andreas , Poschet Gernot , Hübschmann Daniel
Published: December 2021

Measurements of metabolic compounds inside cells or tissues are of high informative potential since they represent the endpoint of biological information flow and a snapshot of the integration of many regulatory processes. However, it requires careful extraction to quantify their abundance. Here we present a comprehensive study using ten extraction protocols on four human sample types (liver tissue, bone marrow, HL60 and HEK cells) targeting 630 metabolites of different chemical classes. We show that the extraction efficiency and stability is highly variable across protocols and tissues by using different quality metrics including the limit of detection and variability between replicates as well as the sum of concentration as a global estimate of extraction stability. The profile of extracted metabolites depends on the used solvents - an observation which has implications for measurements of different sample types and metabolic compounds of interest. To identify the optimal extraction method for future metabolomics studies, the benchmark dataset was implemented in an easy-to-use, interactive and flexible online resource (R/shiny app MetaboExtract).
Namco: A microbiome explorer
Authors: Dietrich Alexander , Matchado Monica Steffi , Zwiebel Maximilian , Ölke Benjamin , Lauber Michael , Lagkouvardos Ilias , Baumbach Jan , Haller Dirk , Brandl Beate , Skurk Thomas , Hauner Hans , Reitmeier Sandra , List Markus
Published: December 2021

16S rRNA gene profiling is currently the most widely used technique in microbiome research and allows for studying microbial diversity, taxonomic profiling, phylogenetics, functional and network analysis. While a plethora of tools have been developed for the analysis of 16S rRNA gene data, only a few platforms offer a user-friendly interface and none comprehensively covers the whole analysis pipeline from raw data processing down to complex analysis. We introduce Namco, an R shiny application that offers a streamlined interface and serves as a one-stop solution for microbiome analysis. We demonstrate Namco’s capabilities by studying the association between a rich fibre diet and the gut microbiota composition. Namco helped to prove the hypothesis that butyrate-producing bacteria are prompted by fibre-enriched intervention. Namco provides a broad range of features from raw data processing and basic statistics down to machine learning and network analysis, thus covering complex data analysis tasks that are not comprehensively covered elsewhere. Namco is freely available athttps://exbio.wzw.tum.de/Namco/.

Impact statement

Amplicon sequencing is a key technology of microbiome research and has yielded many insights into the complexity and diversity of microbiota. To fully leverage these data, a wide range of tools have been developed for raw data processing, normalization, statistical analysis and visualization. These tools are mostly available as R packages but cannot be easily linked in an automated pipeline due to the heterogeneous characteristics of microbiome data. Instead, user-friendly tools for explorative analysis are needed to give biomedical researchers without experience in scripting languages the possibility to fully exploit their data. Several tools for microbiome data analysis have been proposed in recent years which cover a broad range of functionality but few offer a user-friendly and beginner-friendly interface while covering the entire value whole value chain from raw data processing down to complex analysis. With Namco(https://exbio.wzw.tum.de/namco/), we present a beginner-friendly one-stop solution for microbiome analysis that covers upstream analyses like raw data processing, taxonomic binning and downstream analyses like basic statistics, machine learning and network analysis, among other features.
Dynamic interplay between structural variations and 3D chromosome organization in pancreatic cancer
Authors: Du Yongxing , Gu Zongting , Li Zongze , Yuan Zan , Zhao Yue , Zheng Xiaohao , Bo Xiaochen , Chen Hebing , Wang Chengfeng
Published: December 2021

Structural variations (SVs) are the greatest source of variation in the genome and can lead to oncogenesis. However, the identification and interpretation of SVs in human pancreatic cancer remain largely undefined due to technological limitations. Here, we investigate the spectrum of SVs and three-dimensional (3D) chromatin architecture in human pancreatic ductal epithelial cell carcinogenesis by using state-of-the-art long- read single-molecule real-time (SMRT) and high-throughput chromosome conformation capture (Hi-C) sequencing techniques. We find that the 3D genome organization is remodeled and correlated with gene expressional change. The bulk remodeling effect of cross-boundary SVs in the 3D genome partly depends on intercellular genomic heterogeneity. Meanwhile, contact domains tend to minimize these disrupting effects of SVs within local adjacent genomic regions to maintain overall stability of 3D genome organization. Moreover, our data also demonstrates complex genomic rearrangements involving two key driver genes CDKN2A and SMAD4, and elucidates their influence on cancer-related gene expression from both linear view and 3D perspective. Overall, this study provides a valuable resource and highlights the impact, complexity and dynamicity of the interplay between SVs and 3D genome organization, which further expands our understanding of pathogenesis of SVs in human pancreatic cancer.
Intact rDNA arrays of Potentilla-origin detected in Erythronium nucleus suggest recent eudicot-to-monocot horizontal transfer
Authors: Bartha László , Mandáková Terezie , Kovařík Aleš , Bulzu Paul-Adrian , Rodde Nathalie , Mahelka Václav , Lysak Martin A. , Fustier Margaux-Alison , Šafář Jan , Cápal Petr , Keresztes Lujza , Banciu Horia L.
Published: December 2021

The occurrence of horizontal gene transfer (HGT) in Eukarya is increasingly gaining recognition. Nuclear-to-nuclear jump of DNA between plant species at high phylogenetic distance and devoid of intimate association (e.g., parasitism) is still scarcely reported. Within eukaryotes, components of ribosomal DNA (rDNA) multigene family have been found to be horizontally transferred in protists, fungi and grasses. However, in neither case HGT occurred between phylogenetic families, nor the transferred rDNA remained tandemly arrayed and transcriptionally active in the recipient organism. This study aimed to characterize an alien eudicot-type of 45S nuclear rDNA, assumingly transferred horizontally to the genome of monocot European Erythronium (Liliaceae). Genome skimming coupled by PacBio HiFi sequencing of a BAC clone were applied to determine DNA sequence of the alien rDNA. A clear phylogenetic signal traced the origin of the alien rDNA of Erythronium back to the Argentea clade of Potentilla (Rosaceae) and deemed the transfer to have occurred in the common ancestor of E. dens-canis and E. caucasicum. Though being discontinuous, transferred rDNA preserved its general tandemly arrayed feature in the host organism. Southern blotting, molecular cytogenetics, and sequencing of a BAC clone derived from flow-sorted nuclei indicated integration of the alien rDNA into the recipient’s nuclear genome. Unprecedently, dicot-type alien rDNA was found to be transcribed in the monocot Erythronium albeit much less efficiently than the native counterpart. This study adds a new example to the growing list of naturally transgenic plants while holding the scientific community continually in suspense about the mode of DNA transfer.

Significance Statement

Ribosomal DNA is an essential component of all cellular genomes. In plants, accidental movement of rDNA via horizontal gene transfer has only been reported in sexually incompatible grasses (monocots) where it involved non-functional rDNA units. In this study, we propose that evolutionary trajectories of eudicots and monocots were bypassed by the jump of rDNA from a Potentilla species (Rosaceae) to a common ancestor of Erythronium dens-canis and E. caucasicum (Liliaceae). The alien eudicot-type rDNA appeared relatively well conserved in the examined host Erythronium genome, being able to be expressed while preserving its general tandemly repeated feature, evidences that have no match in earlier literature.
A mixture of innate cryoprotectants is key for freeze tolerance and cryopreservation of a drosophilid fly larva
Authors: Kučera Lukáš , Moos Martin , Štětina Tomáš , Korbelová Jaroslava , Vodrážka Petr , Marteaux Lauren Des , Grgac Robert , Hůla Petr , Rozsypal Jan , Faltus Miloš , Šimek Petr , Sedlacek Radislav , Koštál Vladimír
Published: December 2021

Insects that naturally tolerate internal freezing produce complex mixtures of multiple cryoprotectants (CPs). Better knowledge on composition of these mixtures, and on mechanisms of how the individual CPs interact, could inspire development of laboratory CP formulations optimized for cryopreservation of cells and other biological material. Here we identify and quantify (using high resolution mass spectrometry) a range of putative CPs in larval tissues of a subarctic fly,Chymomyza costatathat survives long-term cryopreservation in liquid nitrogen. The CPs (proline, trehalose, glutamine, asparagine, glycine betaine, glycerophosphoethanolamine, glycerophosphocholine, and sarcosine) accumulate in hemolymph in a ratio of 313:108:55:26:6:4:3:0.5 mmol.L-1. Using calorimetry, we show that the artificial mixtures, mimicking the concentrations of major CPs’ in hemolymph of freeze-tolerant larvae, suppress the melting point of water and significantly reduce the ice fraction. We demonstrate in a bioassay that mixtures of CPs administered through the diet act synergistically rather than additively to enable cryopreservation of otherwise freeze-sensitive larvae. Using MALDI-MSI, we show that during slow extracellular freezing trehalose becomes concentrated in partially dehydrated hemolymph where it stimulates transition to the amorphous glass phase. In contrast, proline moves to the boundary between extracellular ice and dehydrated hemolymph and tissues where it likely forms a layer of dense viscoelastic liquid. We propose that amorphous glass and viscoelastic liquids may protect macromolecules and cells from thermomechanical shocks associated with freezing and transfer into and out of liquid nitrogen.

Summary statement

The composition of natural cryoprotectant mixture of the extremely freeze-tolerant insect is revealed. Components of the mixture work in synergy and behave differently during organismal freezing and cryopreservation.
Chromosome-scale haplotype-phased genome assemblies of the male and female lines of wild asparagus (Asparagus kiusianus), a dioecious plant species
Authors: Shirasawa Kenta , Ueta Saki , Murakami Kyoko , Abdelrahman Mostafa , Kanno Akira , Isobe Sachiko
Published: December 2021

Asparagus kiusianus is a disease-resistant dioecious plant species and a wild relative of garden asparagus (A. officinalis). To enhance A. kiusianus genomic resources, advance plant science, and facilitate asparagus breeding, we determined the genome sequences of the male and female lines of A. kiusianus. Genome sequence reads obtained with a linked-read technology were assembled into four haplotype-phased contig sequences (~1.6 Gb each) for the male and female lines. The contig sequences were aligned onto the chromosome sequences of garden asparagus to construct pseudomolecule sequences. Approximately 55,000 potential protein-encoding genes were predicted in each genome assembly, and ~70% of the genome sequence was annotated as repetitive. Comparative analysis of the genomes of the two species revealed structural and sequence variants between the two species as well as between the male and female lines of each species. Genes with high sequence similarity with the male-specific sex determinant gene in A. officinalis, MSE1/AoMYB35/AspTDF1, were presented in the genomes of the male line but absent from the female genome assemblies. Overall, the genome sequence assemblies, gene sequences, and structural and sequence variants determined in this study will reveal the genetic mechanisms underlying sexual differentiation in plants, and will accelerate disease-resistance breeding in garden asparagus.
The African Swine Fever Isolate ASFV-Kenya-1033-IX is highly virulent and stable after growth in the wild boar cell line WSL
Authors: Hemmink Johanneke D. , Abkallo Hussein M. , Henson Sonal P. , Khazalwa Emmanuel M. , Oduor Bernard , Lacasta Anna , Okoth Edward , Fuchs Walter , Bishop Richard P. , Steinaa Lucilla
Published: December 2021

In this study, we describe an African swine fever genotype IX virus (ASFV-Kenya-1033-IX), which was isolated from a domestic pig in Western Kenya during a reported outbreak, including efficiency of virus replication, in vivo virulence, and genome stability in pulmonary alveolar macrophages (PAM) and in a wild boar cell line (WSL). The ASFV-Kenya-1033-IX stock, which underwent multiple passages in WSL (more than 20), retained its ability to replicate in primary macrophages and it also retained the virulence in vivo. At the genomic level, only a few single nucleotide differences were observed between the macrophage and WSL-grown virus. Thus, we propose that the WSL cell line is suitable to produce live attenuated ASFV vaccine candidates based on this isolate and probably of similar viruses. The genome sequences for ASFV-Kenya-1033-IX grown in macrophages and in WSL cells was submitted to GenBank and a challenge model based on this isolate was set up, which will aid the development of vaccines against genotype IX ASFV circulating in Eastern and Central Africa.
DNMT3A knockouts in human iPSCs prevent de novo DNA methylation and reveal growth advantage during hematopoietic differentiation
Authors: Cypris Olivia , Franzen Julia , Frobel Joana , Glück Philipp , Kuo Chao-Chung , Schmitz Stephani , Nüchtern Selina , Zenke Martin , Wagner Wolfgang
Published: December 2021

DNA methyltransferase 3A (DNMT3A) is a frequently mutated gene in many hematological malignancies, indicating that it may be essential for hematopoietic differentiation. Here, we addressed the functional relevance of DNMT3A for differentiation of human induced pluripotent stem cells (iPSCs) by knocking out exon 2, 19, or 23. Exon 19-/- and 23-/- lines revealed absence of almost the entire de novo DNA methylation during mesenchymal and hematopoietic differentiation. Yet, differentiation was only slightly reduced in exon 19-/- and increased in exon 23-/- lines, whereas there was no significant impact on gene expression in hematopoietic progenitors (iHPCs). Notably, DNMT3A-/- iHPCs recapitulate some DNA methylation differences of acute myeloid leukemia with DNMT3A mutations. Furthermore, multicolor genetic barcoding revealed competitive growth advantage of exon 23-/- iHPCs. Our results demonstrate that de novo DNA methylation during hematopoietic differentiation of iPSCs is almost entirely dependent on DNMT3A and exon 23-/- iHPCs even gained growth advantage.
Exceptions to the rule: Why does resistance evolution not undermine antibiotic therapy in all bacterial infections?
Authors: Bhattacharya Amrita , Aluquin Anton , Kennedy David A
Published: December 2021

Antibiotic resistance poses one of the greatest public health challenges of the 21st century. Yet not all pathogens are equally affected by resistance evolution. Why? Here we examine what underlies variation in antibiotic resistance across human bacterial pathogens and the drugs used to treat them. We document the observed prevalence of antibiotic resistance for ‘pathogen x drug’ combinations across 57 different human bacterial pathogens and 53 antibiotics from 15 drug classes used to treat them. Using AIC-based model selection we analyze 14 different traits of bacteria and antibiotics that are believed to be important in resistance evolution. Using these data, we identify the traits that best explain observed variation in resistance evolution. Our results show that nosocomial pathogens and indirectly transmitted pathogens are significantly associated with increased prevalence of resistance whereas zoonotic pathogens, specifically those with wild animal reservoirs, are associated with reduced prevalence of resistance. We found partial support for associations between drug resistance and gram classification, human microbiome reservoirs, horizontal gene transfer, and documented human-to human transfer. Global drug use, time since drug discovery, mechanism of drug action, and environmental reservoirs did not emerge as statistically robust predictors of drug resistance in our analyses. To the best of our knowledge this work is the first systematic analysis of resistance across such a wide range of human bacterial pathogens, encompassing the vast majority of common bacterial pathogens. Insights from our study may help guide public health policies and future studies on resistance control.