bluuebunny/crossref_metadata_2025 huggingface dataset:
Long-term sequelae of Pneumococcal Sepsis in children: a systematic review
Authors: Ogunbameru Adeteju , Miranda Rafael Neves , Bielecki Joanna , Sander Beate
Published: March 2021

Background

Long-term sequelae associated with pneumococcal sepsis (PS) in pediatric patients in existing literature is currently unclear.

Aim

To review the evidence on sequelae and prognostic factors associated with PS among pediatric patients.

Method

We conducted a systematic review following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses reporting guidelines. We screened six databases from their inception to January 15, 2021. Study population were neonates, infants, children and adolescents less than 18 years old with suspected or confirmed PS disease. Outcomes included sequelae types, prognostic factors, pooled death estimate and length of hospital stay (LOS) for survivors and deceased patients. Quality of studies was assessed using Joanna Briggs Institute appraisal checklists.

Results

We screened 981 abstracts, and 24 full-text articles for final review. Septic shock was the most prevalent physical sequelae reported (13%, n=1492 patients). No functional, cognitive or neurological sequelae were reported in included studies. Meta-analysis of pooled mortality estimate was 14.6% (95%CI: 9.9 −19.4%). Prognostic factors associated with increased risk of PS sequelae and death included pediatric risk of mortality score ≥ 10 and co-infection with meningitis. LOS for survivors and non-survivors ranged between 5-30 days and 1-30 days. Nine included studies met at least 50% of the quality assessment criteria.

Conclusion

Physical sequelae and death are the PS sequelae types currently identified in existing literature. Lack of information about other possible sequelae types suggests the long-term consequences of PS disease maybe underreported, especially in resource-limited settings. Future studies should consider exploring reasons for the existing of this knowledge gap.
OCD.py - Characterizing immunoglobulin inter-domain orientations
Authors: Hoerschinger Valentin J. , Fernández-Quintero Monica L. , Waibl Franz , Kraml Johannes , Bujotzek Alexander , Georges Guy , Liedl Klaus R.
Published: March 2021

Inter-domain orientations between immunoglobulin domains are important for the modeling and engineering of novel antibody therapeutics. Previous tools to describe these orientations are applicable only to the variable domains of antibodies and T-cell receptors. We present the “Orientation of Cylindrical Domains (OCD)” tool, which employs a transferable approach to calculate inter-domain orientations for all immunoglobulin domains. Based on a reference structure, the OCD tool automatically builds a suitable reference coordinate system for each domain. Through alignment, the reference coordinate systems are transferred onto the sample to calculate six measures which fully characterize the inter-domain orientation.

Availability and implementation

The OCD approach is implemented as a stand-alone Python script, OCD.py, which can handle multiple types of data input for the analysis of single structures and molecular dynamics trajectories alike. OCD.py is available athttps://github.com/liedllab/OCDunder MIT license.

Supplementary Information

Supplementary information and data are available atBioinformaticsonline.
The inflammasome-activated cytokine IL-1β is targeted for ubiquitylation and proteasomal degradation to limit its inflammatory potential
Authors: Vijayaraj Swarna L. , Feltham Rebecca , Rashidi Maryam , Frank Daniel , Liu Zhengyang , Simpson Daniel S. , Ebert Gregor , Vince Angelina , Herold Marco J. , Kueh Andrew , Pearson Jaclyn S. , Dagley Laura F. , Murphy James M. , Webb Andrew I. , Lawlor Kate E. , Vince James E.
Published: March 2021

Interleukin-1β (IL-1β) is activated by inflammasome-associated caspase-1 in rare autoinflammatory conditions and in wide-spread diseases. Therefore, IL-1β activity must be fine-tuned to enable antimicrobial responses whilst limiting collateral damage. Here we report that precursor IL-1β is rapidly turned over by the proteasome and this correlates with its decoration by K11-, K63- and K48-linked ubiquitin chains. The ubiquitylation of IL-1β is not just a degradation signal triggered by inflammasome priming and activating stimuli, but also limits IL-1β cleavage by caspase-1. We further demonstrate that IL-1β K133 is modified by ubiquitin and forms a salt bridge with IL-1β D129. Loss of IL-1β K133 ubiquitylation, or disruption of the K133:D129 electrostatic interaction, stabilizes IL-1β. Accordingly,IL-1βK133R/K133Rmice display increased precursor IL-1β upon inflammasome priming and increased bioactive IL-1β, bothin vitroand following LPS injectionin vivo. These findings reveal new mechanisms for limiting IL-1β activity and safeguarding against damaging inflammation.
Immunoinformatic Approach for the identification of T Cell and B Cell Epitopes in the Surface Glycoprotein and Designing a Potent Multiepitope Vaccine Construct Against SARS-CoV-2 including the new UK variant
Authors: Selvaraj Gracy Fathima , Ramesh Kiruba , Padmanabhan Padmapriya , Gopalan Vidya , Govindan Karthikeyan , Chandran Aswathi , Srinivasan Sivasubramanian , Krishnasamy Kaveri
Published: March 2021

The emergence of a novel coronavirus in China in late 2019 has turned into a SARS-CoV-2 pandemic affecting several millions of people worldwide in a short span of time with high fatality. The crisis is further aggravated by the emergence and evolution of new variant SARS-CoV-2 strains in UK during December, 2020 followed by their transmission to other countries. A major concern is that prophylaxis and therapeutics are not available yet to control and prevent the virus which is spreading at an alarming rate, though several vaccine trials are in the final stage. As vaccines are developed through various strategies, their immunogenic potential may drastically vary and thus pose several challenges in offering both arms of immunity such as humoral and cell-mediated immune responses against the virus. In this study, we adopted an immunoinformatics-aided identification of B cell and T cell epitopes in the Spike protein, which is a surface glycoprotein of SARS-CoV-2, for developing a new Multiepitope vaccine construct (MEVC). MEVC has 575 amino acids and comprises adjuvants and various cytotoxic T-lymphocyte (CTL), helper T-lymphocyte (HTL), and B-cell epitopes that possess the highest affinity for the respective HLA alleles, assembled and joined by linkers. The computational data suggest that the MEVC is non-toxic, non-allergenic and thermostable with the capability to elicit both humoral and cell-mediated immune responses. The population coverage of various countries affected by COVID-19 with respect to the selected B and T cell epitopes in MEVC was also investigated. Subsequently, the biological activity of MEVC was assessed by bioinformatic tools using the interaction between the vaccine candidate and the innate immune system receptors TLR3 and TLR4. The epitopes of the construct were analyzed with that of the strains belonging to various clades including the new variant UK strain having multiple unique mutations in S protein. Due to the advantageous features, the MEVC can be testedin vitrofor more practical validation and the study offers immense scope for developing a potential vaccine candidate against SARS-CoV-2 in view of the public health emergency associated with COVID-19 disease caused by SARS-CoV-2.
Comparative Genomics of two Inbred Lines of the Potato Cyst NematodeGlobodera rostochiensisreveals disparate Effector Family-specific Diversification Patterns
Authors: van Steenbrugge Joris J.M. , van den Elsen Sven , Holterman Martijn , Sterken Mark G. , Thorpe Peter , Goverse Aska , Smant Geert , Helder Johannes
Published: March 2021

Background

Potato cyst nematodes belong to the most harmful pathogens in potato, and durable management of these soil-borne parasites largely depends on host-plant resistances. These resistances are pathotype specific. The currentGlobodera rostochiensispathotype scheme that defines five pathotypes (Ro1 - Ro5) is for fundamental and practical reasons barely useful. As a result, resistant potato varieties are worldwide used in a non-informed manner.

Results

We generated two novel reference genomes ofG. rostochiensisinbred lines derived from a Ro1 and a Ro5 population. These genome sequences comprise 173 and 189 scaffolds respectively, marking a ≈ 24-fold reduction in fragmentation as compared to the current reference genome. We provide copy number variations for 18 effector families. Four dorsal gland effector families were investigated in more detail. SPRYSECs, known to be implicated in immune suppression, constitute by far the most diversified family with 60 and 99 variants in Ro1 and Ro5 distributed over 18 and 26 scaffolds. In contrast, CLEs, effectors involved in feeding site induction, show strong physical clustering. The 10 and 16 variants cluster on respectively 2 and 1 scaffolds. Given that pathotypes are defined by their effectoromes, we pinpoint the disparate nature of the contributing effector families in terms of sequence diversification and loss and gain of variants.

Conclusion

Two novel reference genomes allow for nearly complete inventories of effector diversification and physical organisation within and between pathotypes. Combined with insights we provide on effector family-specific diversification patterns, this constitutes a solid basis for an effectorome-based virulence scheme for this notorious pathogen.
scite: a smart citation index that displays the context of citations and classifies their intent using deep learning
Authors: Nicholson J.M. , Mordaunt M. , Lopez P. , Uppala A. , Rosati D. , Rodrigues N.P. , Grabitz P. , Rife S.C.
Published: March 2021

Citation indices are tools used by the academic community for research and research evaluation which aggregate scientific literature output and measure scientific impact by collating citation counts. Citation indices help measure the interconnections between scientific papers but fall short because they only display paper titles, authors, and the date of publications, and fail to communicate contextual information about why a citation was made. The usage of citations in research evaluation without due consideration to context can be problematic, if only because a citation that disputes a paper is treated the same as a citation that supports it. To solve this problem, we have used machine learning and other techniques to develop a “smart citation index” called scite, which categorizes citations based on context. Scite shows how a citation was used by displaying the surrounding textual context from the citing paper, and a classification from our deep learning model that indicates whether the statement provides supporting or disputing evidence for a referenced work, or simply mentions it. Scite has been developed by analyzing over 23 million full-text scientific articles and currently has a database of more than 800 million classified citation statements. Here we describe how scite works and how it can be used to further research and research evaluation.
Replication kinetic, cell tropism and associated immune responses in SARS-CoV-2 and H5N1 virus infected human iPSC derived neural models
Authors: Bauer Lisa , Lendemeijer Bas , Leijten Lonneke , Embregts Carmen W. E. , Rockx Barry , Kushner Steven A. , de Vrij Femke M.S. , van Riel Debby
Published: March 2021

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection is associated with a wide variety of neurological complications. Even though SARS-CoV-2 is rarely detected in the central nervous system (CNS) or cerebrospinal fluid, evidence is accumulating that SARS-CoV-2 might enter the CNS via the olfactory nerve. However, what happens after SARS-CoV-2 enters the CNS is poorly understood. Therefore, we investigated the replication kinetics, cell tropism, and associated immune responses of SARS-CoV-2 infection in different types of neural cultures derived from human induced pluripotent stem cells (hiPSCs). SARS-CoV-2 was compared to the neurotropic and highly pathogenic H5N1 influenza A virus. SARS-CoV-2 infected a minority of individual mature neurons, without subsequent virus replication and spread, despite ACE2, TMPRSS2 and NPR1 expression in all cultures. However, this sparse infection did result in the production of type-III-interferons and IL-8. In contrast, H5N1 virus replicated and spread very efficiently in all cell types in all cultures. Taken together, our findings support the hypothesis that neurological complications might result from local immune responses triggered by virus invasion, rather than abundant SARS-CoV-2 replication in the CNS.
Early Spring Snowmelt and Summer Droughts Strongly Impair the Resilience of Key Microbial Communities in Subalpine Grassland Ecosystems
Authors: Hafeez Farhan , Bernard Lionel , Poly Franck , Clément Jean-Christophe , Pommier Thomas
Published: March 2021

Subalpine grassland ecosystems are important from biodiversity, agriculture, and touristic perspectives but their resilience to seasonally occurring climatic extremes is increasingly challenged with climate change, accelerating their vulnerability to tipping points. Microbial communities, which are central in ecosystem functioning, are usually considered as more resistant and highly resilient to such extreme events due to their functional redundancy and strong selection in residing habitats. To investigate this, we explored soil microbial responses upon recurrent summer droughts associated with early snowmelt in subalpine grasslands mesocosms set-up at the Lautaret Pass (French Alps). Potential respiration, nitrification and denitrification were monitored over a period of two growing seasons along with quantification of community gene abundances of total bacteria as well as (de)nitrifiers. Results revealed that droughts had a low and short-term adverse impact on bacterial total respiration supporting their hypothesized high resilience, i.e., resistance and ability to recover. Nitrification and abundances of the corresponding functional guilds showed relatively strong resistance to summer droughts but declined in response to early snowmelt. This triggered a cascading effect on denitrification but also on abundances of denitrifying communities which recovered from all climatic extremes except from the summer droughts where nitrifiers were collapsed. Denitrification and respective functional groups faced high impact of applied stresses with strong reduction in abundance and activity of this specialized community. Although, consequently lower microbial competition for nitrate may be positive for plant biomass production, warnings exist when considering the potential nitrogen leaching from these ecosystems as well as risks of greenhouses gases emission such as N2O.
Age-related neurodegeneration and cognitive impairments of NRMT1 knockout mice are preceded by misregulation of RB and expansion of the neural stem cell population
Authors: Catlin James , Marziali Leandro N. , Rein Benjamin , Yan Zhen , Feltri M. Laura , Schaner Tooley Christine E.
Published: March 2021

N-terminal methylation is an important post-translational modification that regulates protein/DNA interactions and plays a role in many cellular processes, including DNA damage repair, mitosis, and transcriptional regulation. Our generation of a constitutive knockout mouse for the N-terminal methyltransferase NRMT1, demonstrated its loss results in severe developmental abnormalities and premature aging. As premature aging is often accompanied by neurodegeneration, we more specifically examined how NRMT1 loss affects neural pathology and cognitive behaviors. Here we find thatNrmt1-/-mice exhibit postnatal enlargement of the lateral ventricles, age-dependent striatal and hippocampal neurodegeneration, memory impairments, and hyperactivity. These morphological and behavior abnormalities are preceded by alterations in neural stem cell (NSC) development. Depletion of quiescent NSC pools inNrmt1-/-mice is concurrent with expansion of intermediate progenitor and neuroblast pools. These phenotypes are similar to those seen with loss of the NRMT1 target retinoblastoma protein (RB), and we see that NRMT1 loss leads to derepression of RB target genes and abnormal RB phosphorylation and degradation. As also seen with RB loss, neurons inNrmt1-/-mice fail to exit cell cycle and ultimately undergo NOXA-mediated apoptosis, indicating that early misregulation of RB inNrmt1-/-mice promotes premature NSC proliferation and contributes to subsequent neurodegenerative phenotypes.
Functional development of a V3-specific broadly neutralizing antibody isolated from a case of HIV superinfection
Authors: Shipley Mackenzie M. , Prasad Vidya Mangala , Doepker Laura E. , Dingens Adam , Ralph Duncan , Harkins Elias , Dhar Amrit , Arenz Dana , Chohan Vrasha , Weight Haidyn , Mandaliya Kishor , Bloom Jesse D. , Matsen Frederick A. , Lee Kelly K. , Overbaugh Julie M.
Published: March 2021

Stimulating broadly neutralizing antibodies (bnAbs) directly from germline remains a barrier for HIV vaccines. HIV superinfection elicits bnAbs more frequently than single infection, providing clues of how to elicit such responses. We used longitudinal antibody sequencing and structural studies to characterize bnAb development from a superinfection case. Mature bnAb QA013.2 bound both initial transmitted and superinfecting virus, but its inferred naïve bound only the superinfecting strain and was not neutralizing. QA013.2 requires residues spanning FWRH1-CDRH1 to attain breadth, which is uncommon for V3-specific bnAbs. A 4.15 Å cryo-EM structure of QA013.2 bound to heterologous native-like trimer showed recognition of V3 signatures (N301, N332, and GDIR). Antigenic profiling revealed that viral escape was achieved not only by changes in the structurally-defined epitope, but also by mutations in V1. These results highlight shared and distinct properties of QA013.2 relative to other V3-specific bnAbs in the setting of sequential, diverse antigenic variants.
Super interactive promoters provide insight into cell type-specific regulatory networks in blood lineage cell types
Authors: Lagler Taylor M. , Yang Yuchen , Harigaya Yuriko , Sankaran Vijay G. , Hu Ming , Reiner Alexander P. , Raffield Laura M. , Wen Jia , Li Yun
Published: March 2021

Existing studies of chromatin conformation have primarily focused on potential enhancers interacting with gene promoters. By contrast, the interactivity of promotersper se, while equally critical to understanding transcriptional control, has been largely unexplored, particularly in a cell type-specific manner for blood lineage cell types. In this study, we leverage promoter capture Hi-C data across a compendium of blood lineage cell types to identify and characterize cell type-specific super-interactive promoters (SIPs). Notably, promoter-interacting regions (PIRs) of SIPs are more likely to overlap with cell type-specific ATAC-seq peaks and GWAS variants for relevant blood cell traits than PIRs of non-SIPs. Further, SIP genes tend to express at a higher level in the corresponding cell type, and show enriched heritability of relevant blood cell trait(s). Importantly, this analysis shows the potential of using promoter-centric analyses of chromatin spatial organization data to identify biologically important genes and their regulatory regions.
Alternative LC-MS/MS Platforms and Data Acquisition Strategies for Proteomic Genotyping of Human Hair Shafts
Authors: Goecker Zachary C. , Legg Kevin M. , Salemi Michelle R. , Herren Anthony W. , Phinney Brett S. , McKiernan Heather E. , Parker Glendon J.
Published: March 2021

Protein is a major component of all biological evidence. Proteomic genotyping is the use of genetically variant peptides that contain single amino acid polymorphisms to infer the genotype of matching non-synonymous single nucleotide polymorphisms for the individual who originated the protein sample. This can be used to statistically associate an individual to evidence found at a crime scene. The utility of the inferred genotype increases as the detection of genetically variant peptides increases, which is the direct result of technology transfer to mass spectrometry platforms typically available. Digests of single (2 cm) human hair shafts from three European and two African subjects were analyzed using data dependent acquisition on a Q-Exactive™ Plus Hybrid Quadrupole-Orbitrap™ system, data independent acquisition and a variant of parallel reaction monitoring on a Orbitrap Fusion™ Lumos™ Tribrid™ system, and multiple reaction monitoring on an Agilent 6495 triple quadrupole system. In our hands, average genetically variant peptide detection from a selected 24 genetically variant peptide panel increased from 6.5 ± 1.1 and 3.1 ± 0.8 using data dependent and independent acquisition to 9.5 ± 0.7 and 11.7 ± 1.7 using parallel reaction monitoring and multiple reaction monitoring (p < 0.05). Parallel reaction monitoring resulted in a 1.3-fold increase in detection sensitivity, and multiple reaction monitoring resulted in a 1.6-fold increase in detection sensitivity. This increase in biomarker detection has a functional impact on the statistical association of a protein sample and an individual. Increased biomarker sensitivity, using Markov Chain Monte Carlo modeling, produced a median estimated random match probability of over 1 in 10 trillion from a single hair using targeted proteomics. For parallel reaction monitoring and multiple reaction monitoring, detected genetically variant peptides were validated by the inclusion of stable isotope labeled peptides in each sample, which served also as a detection trigger. This research accomplishes two aims: the demonstration of utility for alternative analytical platforms in proteomic genotyping, and the establishment of validation methods for the evaluation of inferred genotypes.

Highlights

Test four mass spectrometry configurations to optimize detection of genetically variant peptides

Technology transfer of proteomic genotyping assays

Improved sensitivity results in higher level of forensic discrimination for human identification using multiple reaction monitoring

Graphical Abstract
Retinal factors of visual sensitivity in the human fovea
Authors: Domdei Niklas , Reiniger Jenny L. , Holz Frank G. , Harmening Wolf
Published: March 2021

Humans direct their gaze towards visual objects of interest such that the retinal images of fixated objects fall onto the fovea, a small anatomically and physiologically specialized region of the retina displaying highest visual fidelity. One striking anatomical feature of the fovea is its non-uniform cellular topography, with a steep decline of cone photoreceptor density and outer segment length with increasing distance from its center. We here assessed in how far the specific cellular organization of the foveola is reflected in visual function. Increment sensitivity to small spot visual stimuli (1 x 1 arcmin, 543 nm light) was recorded psychophysically in 4 human participants at 17 locations placed concentric within a 0.2-degree diameter around the preferred retinal locus of fixation with adaptive optics scanning laser ophthalmoscopy based microstimulation. While cone density as well as maximum outer segment length differed significantly among the four tested participants, the range of observed threshold was similar, yielding an average increment threshold of 3.3 ± 0.2 log10 photons at the cornea. Thresholds were correlated with retinal eccentricity, as well as cone density and outer segment length. Biophysical simulation allowed to develop a model of foveal sensitivity based on these parameters, explaining at least 37% of the observed threshold variability. Based on high reproducibility in replicate testing, the residual variability is assumed to be caused by individual cone and bipolar cell weighting at the specific target locations.
Spatial representation by ramping activity of neurons in the retrohippocampal cortex
Authors: Tennant Sarah A. , Clark Harry , Hawes Ian , Tam Wing Kin , Hua Junji , Yang Wannan , Gerlei Klara Z. , Wood Emma R. , Nolan Matthew F.
Published: March 2021

Neurons in the retrohippocampal cortices play crucial roles in spatial memory. Many retrohippocampal neurons have firing fields that are selectively active at specific locations, with memory for rewarded locations associated with reorganisation of these firing fields. Whether this is the sole strategy for representing spatial memories is unclear. Here, we demonstrate that during a spatial memory task retrohippocampal neurons encode location through ramping activity that extends within segments of a linear track approaching and following a reward, with the rewarded location represented by offsets or switches in the slope of the ramping activity. These ramping representations could be maintained independently of trial outcome and cues that mark the reward location, indicating that they result from recall of the track structure. During recordings in an open arena, neurons that generated ramping activity during the spatial memory task were more numerous than grid or border cells, with a majority showing spatial firing that did not meet criteria for classification as grid or border representations. Encoding of rewarded locations through offsets and switches in the slope of ramping activity also emerged in recurrent neural networks trained to solve a similar location memory task. Impaired performance of these networks following disruption of outputs from ramping neurons is consistent with this coding strategy supporting navigation to recalled locations of behavioural significance. We hypothesise that retrohippocampal ramping activity mediates readout of learned models for goal-directed navigation.
Predicting Cellular Drug Sensitivity using Conditional Modulation of Gene Expression
Authors: Connell Will , Keiser Michael
Published: March 2021

Selecting drugs most effective against a tumor’s specific transcriptional signature is an important challenge in precision medicine. To assess oncogenic therapy options, cancer cell lines are dosed with drugs that can differentially impact cellular viability. Here we show that basal gene expression patterns can be conditioned by learned small molecule structure to better predict cellular drug sensitivity, achieving anR2of 0.7190±0.0098 (a 5.61% gain). We find that 1) transforming gene expression values by learned small molecule representations outperforms raw feature concatenation, 2) small molecule structural features meaningfully contribute to learned representations, and 3) an affine transformation best integrates these representations. We analyze conditioning parameters to determine how small molecule representations modulate gene expression embeddings. This ongoing work formalizesin silicocellular screening as a conditional task in precision oncology applications that can improve drug selection for cancer treatment.
The brown algaeSaccharina japonicaandSargassum horneriexhibit species-specific responses to synergistic stress of ocean acidification and eutrophication
Authors: Liu Yuxin , Cao Jiazhen , Chu Yaoyao , Liu Yan , Wang Qiaohan , Gong Qingli , Li Jingyu
Published: March 2021

Ocean acidification and eutrophication are two important environmental stressors. They inevitably impact marine macroalgae, and hence the coastal ecosystem of China.Saccharina japonica, as the main culture species in China, is suffering the harmful golden tide caused bySargassum horneri. However, it remains unclear whether the detrimental effects ofS. hornerionS. japonicacultivation become more severe in future acidified and eutrophic scenario. In this study, we respectively investigated the effects ofpCO2(400 μatm and 1000 μatm) and nutrients (non-enriched and enriched seawater) on the growth, photosynthesis, respiration, chlorophyll contents, and tissue nitrogen ofS. japonicaandS. horneri. Results indicated that enrichment of nutrients contributedS. hornerito utilize HCO3-. The carbon acquisition pathway shifted from HCO3-to CO2inS. japonica, whileS. horneriremained using HCO3-regulated by nutrient enrichment.S. horneriexhibited better photosynthetic traits thanS. japonica, with a higher level of net photosynthetic rate and chlorophyll contents at elevatedpCO2and enriched nutrients. Tissue nitrogen also accumulated richly in the thalli ofS. horneriunder higherpCO2and nutrients. Significant enhancement in growth was only detected inS. horneriunder synergistic stress. Together,S. hornerishowed competitive dominance in current study. These findings suggest that increasing risk of golden tide in acidified and eutrophic ocean can most likely result in great damage toS. japonicacultivation.
Machine learning methods trained on simple models can predict critical transitions in complex natural systems
Authors: Deb Smita , Sidheekh Sahil , Clements Christopher F. , Krishnan Narayanan C. , Dutta Partha S.
Published: March 2021

1. Sudden transitions from one stable state to a contrasting state occur in complex systems ranging from the collapse of ecological populations to climatic change, with much recent work seeking to develop methods to predict these unexpected transitions from signals in time series data. However, previously developed methods vary widely in their reliability, and fail to classify whether an approaching collapse might be catastrophic (and hard to reverse) or non-catastrophic (easier to reverse) with significant implications for how such systems are managed.

2. Here we develop a novel detection method, using simulated outcomes from a range of simple mathematical models with varying nonlinearity to train a deep neural network to detect critical transitions - the Early Warning Signal Network (EWSNet).

3. We demonstrate that this neural network (EWSNet), trained on simulated data with minimal assumptions about the underlying structure of the system, can predict with high reliability observed real-world transitions in ecological and climatological data. Importantly, our model appears to capture latent properties in time series missed by previous warning signals approaches, allowing us to not only detect if a transition is approaching but critically whether the collapse will be catastrophic or non-catastrophic.

4. The EWSNet can flag a critical transition with unprecedented accuracy, overcoming some of the major limitations of traditional methods based on phenomena such as Critical Slowing Down. These novel properties mean EWSNet has the potential to serve as a universal indicator of transitions across a broad spectrum of complex systems, without requiring information on the structure of the system being monitored. Our work highlights the practicality of deep learning for addressing further questions pertaining to ecosystem collapse and have much broader management implications.
Pyrolyzed substrates induce aromatic compound metabolism in the post-fire fungus,Pyronema domesticum
Authors: Fischer Monika S. , Stark Frances Grace , Berry Timothy D. , Zeba Nayela , Whitman Thea , Traxler Matthew F.
Published: March 2021

Wildfires represent a fundamental and profound disturbance in many ecosystems, and their frequency and severity are increasing in many regions of the world. Fire affects soil by removing carbon in the form of CO2and transforming remaining surface carbon into pyrolyzed organic material (PyOM). Fires also generate substantial necromass at depths where the heat kills soil organisms but does not catalyze the formation of PyOM.Pyronemaspecies strongly dominate soil fungal communities within weeks to months after fire. However, the carbon pool (i.e. necromass or PyOM) that fuels their rise in abundance is unknown. We used aPyronema domesticumisolate from the catastrophic 2013 Rim Fire (CA, USA) to ask ifP. domesticumis capable of metabolizing PyOM.P. domesticumgrew readily on agar media where the sole carbon source was PyOM (specifically, pine wood PyOM produced at 750 °C). Using RNAseq, we investigated the response ofP. domesticumto PyOM and observed a comprehensive induction of genes involved in the metabolism and mineralization of aromatic compounds, typical of those found in PyOM. Lastly, we used13C-labeled 750 °C PyOM to demonstrate thatP. domesticumis capable of mineralizing PyOM to CO2. Collectively, our results indicate a robust potential forP. domesticumto liberate carbon from PyOM in post-fire ecosystems and return it to the bioavailable carbon pool.

IMPORTANCE

Fires are increasing in frequency and severity in many regions across the world. Thus, it’s critically important to understand how our ecosystems respond to inform restoration and recovery efforts. Fire transforms the soil, removing many nutrients while leaving behind both nutritious necromass and complex pyrolyzed organic matter, which is often recalcitrant. Filamentous fungi of the genusPyronemastrongly dominate soil fungal communities soon after fire. While Pyronema are key pioneer species in post-fire environments, the nutrient source that fuels their rise in abundance is unknown. In this manuscript, we used a P. domesticum isolate from the catastrophic 2013 Rim Fire (CA, USA) to demonstrate thatP. domesticummetabolizes pyrolyzed organic material, effectively liberating this complex pyrolyzed carbon and returning it to the bioavailable carbon pool. The success of Pyronema in post-fire ecosystems has the potential to kick-start growth of other organisms and influence the entire trajectory of post-fire recovery.
Overexpression of the RNA-binding protein NrdA affects global gene expression and secondary metabolism inAspergillusspecies
Authors: Kadooka Chihiro , Izumitsu Kosuke , Asai Teigo , Mori Kazuki , Okutsu Kayu , Yoshizaki Yumiko , Takamine Kazunori , Goto Masatoshi , Tamaki Hisanori , Futagami Taiki
Published: March 2021

RNA-binding protein Nrd1 plays a role in RNA polymerase II transcription termination. In this study, we showed that the orthologous NrdA is important in global mRNA expression and secondary metabolism inAspergillusspecies. We constructed annrdAconditional expression strain using the Tet-On system inAspergillus luchuenesismut.kawachii. Downregulation ofnrdAcaused a severe growth defect, indicating that NrdA is essential for the proliferation ofA. kawachii. Parallel RNA-sequencing and RNA immunoprecipitation-sequencing analysis identified potential NrdA-interacting transcripts, corresponding to 32% of the predicted protein coding genes ofA. kawachii. Subsequent gene ontology analysis suggested that overexpression of NrdA affects the production of secondary metabolites. To clarify this, we constructed NrdA-overexpressing strains ofAspergillus nidulans,Aspergillus fumigatus, andAspergillus oryzae. Overexpression of NrdA reduced the production of sterigmatocystin and penicillin inA. nidulans, as well as that of helvolic acid and pyripyropene A inA. fumigatus. Moreover, it increased the production of kojic acid and reduced production of penicillin inA. oryzae. These effects were accompanied by almost consistent transcriptional changes in the relevant genes. Collectively, these results suggest that NrdA is the essential RNA-binding protein, which plays a significant role in global gene expression and secondary metabolism inAspergillusspecies.

IMPORTANCE

Nrd1, a component of the Nrd1–Nab3–Sen1 complex, is an essential RNA-binding protein involved in transcriptional termination in yeast. However, its role in filamentous fungi has not been studied. In this study, we characterized an orthologous NrdA in theAspergillusspecies, identified potential NrdA-interacting mRNA, and investigated the effect of overexpression of NrdA on mRNA expression inAspergillus luchuensismut.kawachii. The results indicated that NrdA controls global gene expression involved in versatile metabolic pathways, including the secondary metabolic process. We demonstrated that NrdA overexpression significantly affected the production of secondary metabolites inAspergillus nidulans,Aspergillus oryzae, andAspergillus fumigatus. Our findings are of importance to the fungal research community because the secondary metabolism is an industrially and clinically important aspect for theAspergillusspecies.
Faecal shedding models for SARS-CoV-2 RNA among hospitalised patients and implications for wastewater-based epidemiology
Authors: Hoffmann Till , Alsing Justin
Published: March 2021

The concentration of SARS-CoV-2 RNA in faeces is not well established, posing challenges for wastewater-based surveillance of COVID-19 and risk assessments of environmental transmission. We develop versatile hierarchical models for faecal RNA shedding and apply them to data collected in six studies. We find that the mean number of gene copies per mL of faeces is 1.9 × 106(2.3 × 105–2.0 × 10895% credible interval) among unvaccinated hospitalised patients. Using Bayesian model comparison, we find no evidence for a subpopulation of patients who do not shed RNA: limits of quantification can account for negative stool samples. Our models indicate that hospitalised patients represent the tail of the shedding profile with a half-life of 34 hours (28–43 95% credible interval), suggesting that wastewater-based surveillance signals are more indicative of incidence than prevalence and can be a leading indicator of clinical presentation. Shedding among inpatients cannot explain high RNA concentrations observed in wastewater, consistent with more abundant shedding during the early infection course. We show that the models generalise and can predict summary statistics of held-out clinical datasets. However, shedding prior to hospitalisation cannot be constrained due to lack of samples, and information on viral variants was not available.
Geospatial approach to investigate spatial clustering and hotspots of blood lead levels in children within Kabwe, Zambia
Authors: Moonga Given , Chisola Moses N , Berger Ursula , Nowak Dennis , Yabe John , Nakata Hokuto , Nakayama Shouta , Ishizuka Mayumi , Bose-O’Reilly Stephan
Published: March 2021

Background

Communities around Kabwe/Zambia are exposed to lead due to deposits from an old lead (Pb) and zinc (Zn) mining site. Children are particularly more vulnerable than adults, presenting with greatest risk of health complications because of their increased oral uptake due to their hand to mouth activities. Spatial analysis of childhood lead exposure is useful in identifying specific areas with highest risk of pollution. The objective of the current study was to use a geospatial approach investigate spatial clustering and hotspots of blood lead levels in children within Kabwe.

Methods

We analysed data on blood lead levels (BLL) for 363 children below the age of 15 from Kabwe town. We used spatial autocorrelation methods involving the global Moran’s I and local Getis-Ord Gi*statistic in ArcMap 10.5.1, to test for spatial dependency among the blood lead levels in children.

Results

BLL in children from Kabwe are spatially autocorrelated with a Moran’s Index of 0.62 (p<0.001). We found distinct hot spots in communities close to the old lead and zinc-mining site, lying on its western side. We observed lower levels of BLL in areas distant to the mine and located at its eastern side. This pattern suggests a possible association between BLL and distance from the abandoned lead and zinc mine, and prevailing winds.

Conclusion

Using geocoded data, we found clustering of childhood blood lead and identified distinct hot spot areas with particular high lead levels for Kabwe town. The geospatial approach used is especially valuable in resource-constrained settings like Zambia, where the precise identification of the locations of risk areas allows to initiate targeted remedial and treatment programs.
GlucoCEST MRI for the early evaluation response to chemotherapeutic and metabolic treatments in a murine triple negative breast cancer: a comparison with [18F]F-FDG-PET
Authors: Capozza Martina , Anemone Annasofia , Dhakan Chetan , Peruta Melania Della , Bracesco Martina , Zullino Sara , Villano Daisy , Terreno Enzo , Longo Dario Livio , Aime Silvio
Published: March 2021

Purpose

Triple-negative breast cancer (TNBC) patients have usually poor outcome after chemotherapy and early prediction of therapeutic response would be helpful. [18F]F-FDG-PET/CT acquisitions are often carried out to monitor variation in metabolic activity associated to response to the therapy, despite moderate accuracy and radiation exposure limit its application. The glucoCEST technique relies on the use of unlabelled D-glucose to assess glucose uptake with conventional MRI scanners and is currently under active investigations at clinical level. This work aims at validating the potential of MRI-glucoCEST in monitoring early therapeutic responses in a TNBC tumor murine model.

Procedures

Breast tumor (4T1) bearing mice were treated with doxorubicin or dichloroacetate for one week. PET/CT with [18F]F-FDG and MRI-glucoCEST were performed at baseline and after 3 cycles of treatment. Metabolic changes measured with [18F]F-FDG-PET and glucoCEST were compared and evaluated with changes in tumor volumes.

Results

Doxorubicin treated mice showed a significant decrease in tumor growth when compared to the control group. GlucoCEST imaging provided early metabolic response after three cycles of treatment, conversely, no variations were detect by in [18F]F-FDG uptake. Dichloroacetate treated mice did not show any decrease either in tumor volume or in tumor metabolic activity as assessed by both glucoCEST and [18F]F-FDG-PET.

Conclusions

Early metabolic changes during doxorubicin treatment can be predicted by glucoCEST imaging that appears more sensitive than [18F]F-FDG-PET in reporting on early therapeutic response. These findings support the view that glucoCEST may be a sensitive technique for monitoring metabolic response, but future studies are needed to explore the accuracy of this approach in other tumor types and treatments.
Fast holographic scattering compensation for deep tissue biological imaging
Authors: May Molly A. , Barré Nicolas , Kummer Kai K. , Kress Michaela , Ritsch-Marte Monika , Jesacher Alexander
Published: March 2021

Scattering in biological tissues is a major barrier for in vivo optical imaging of all but the most superficial structures. Progress toward overcoming the distortions caused by scattering in turbid media has been made by shaping the excitation wavefront to redirect power into a single point in the imaging plane. However, fast, non-invasive determination of the required wavefront compensation remains challenging. Here, we introduce a quickly converging algorithm for non-invasive scattering compensation, termed DASH, in which holographic phase stepping interferometry enables new phase information to be updated after each measurement. This leads to rapid improvement of the wavefront correction, forming a focus after just one measurement iteration and achieving an order of magnitude higher signal enhancement at this stage than the previous state-of-the-art. Using DASH, we demonstrate two-photon fluorescence imaging of microglia cells in highly turbid mouse hippocampal tissue down to a depth of 530 μm.
Noncanonical mRNA decay by the endoplasmic-reticulum stress sensor IRE1α promotes cancer-cell survival
Authors: Le Thomas Adrien , Ferri Elena , Marsters Scot , Harnoss Jonathan M. , Modrusan Zora , Li Weihan , Rudolph Joachim , Wang Weiru , Wu Thomas D. , Walter Peter , Ashkenazi Avi
Published: March 2021

Eukaryotic IRE1 mitigates endoplasmic-reticulum (ER) stress by orchestrating the unfolded-protein response (UPR). IRE1 spans the ER membrane, and signals through a cytosolic kinase-endoribonuclease module. The endoribonuclease generates the transcription factor XBP1s by intron excision between similar RNA stem-loop endomotifs, and depletes select cellular mRNAs through regulated IRE1-dependent decay (RIDD). Paradoxically, mammalian RIDD seemingly targets only mRNAs with XBP1-like endomotifs, while in flies RIDD exhibits little sequence restriction. By comparing nascent and total IRE1α-controlled mRNAs in human breast cancer cells, we discovered not only canonical endomotif-containing RIDD substrates, but also many targets lacking recognizable motifs—degraded by a process we coin RIDDLE, for RIDD lacking endomotif. IRE1α displayed two basic endoribonuclease modalities: endomotif-specific cleavage, minimally requiring dimers; and endomotif-independent promiscuous processing, requiring phospho-oligomers. An oligomer-deficient mutant that did not support RIDDLE failed to rescue cancer-cell viability. These results link IRE1α oligomers, RIDDLE, and cell survival, advancing mechanistic understanding of the UPR.
Single cell RNA sequencing of theStrongylocentrotus purpuratuslarva reveals the blueprint of major cell types and nervous system of a non-chordate deuterostome
Authors: Paganos Periklis , Voronov Danila , Musser Jacob , Arendt Detlev , Arnone Maria I.
Published: March 2021

Identifying the molecular fingerprint of organismal cell types is key for understanding their function and evolution. Here, we use single cell RNA sequencing (scRNA-seq) to survey the cell types of the sea urchin early pluteus larva, representing an important developmental transition from non-feeding to feeding larva. We identify 21 distinct cell clusters, representing cells of the digestive, skeletal, immune, and nervous systems. Further subclustering of these reveal a highly detailed portrait of cell diversity across the larva, including the identification of neuronal cell types. We then validate important gene regulatory networks driving sea urchin development and reveal new domains of activity within the larval body. Focusing on neurons that co-expressPdx-1andBrn1/2/4, we identify an unprecedented number of genes shared by this population of neurons in sea urchin and vertebrate endocrine pancreatic cells. Using differential expression results from Pdx-1 knockdown experiments, we show that Pdx1 is necessary for the acquisition of the neuronal identity of these cells. We hypothesize that a network similar to the one orchestrated by Pdx1 in the sea urchin neurons was active in an ancestral cell type and then inherited by neuronal and pancreatic developmental lineages in sea urchins and vertebrates.
Establishment of Developmental Gene Silencing by Ordered Polycomb Complex Recruitment in Early Zebrafish Embryos
Authors: Hickey Graham J.M. , Wike Candice , Nie Xichen , Guo Yixuan , Tan Mengyao , Murphy Patrick , Cairns Bradley R.
Published: March 2021

Vertebrate embryos achieve developmental competency during zygotic genome activation (ZGA) by establishing chromatin states that silence yet poise developmental genes for subsequent lineage-specific activation. Here, we reveal how developmental gene poising is establishedde novoin preZGA zebrafish embryos. Poising is established at promoters and enhancers that initially contain open/permissive chromatin with ‘Placeholder’ nucleosomes (bearing H2A.Z, H3K4me1, and H3K27ac), and DNA hypomethylation. Silencing is initiated by the recruitment of Polycomb Repressive Complex 1 (PRC1), and H2Aub1 deposition by catalytic Rnf2 during preZGA and ZGA stages. During postZGA, H2Aub1 enables Aebp2-containing PRC2 recruitment and H3K27me3 deposition. Notably, preventing H2Aub1 (via Rnf2 inhibition) eliminates recruitment of Aebp2-PRC2 and H3K27me3, and elicits transcriptional upregulation of certain developmental genes during ZGA. However, upregulation is independent of H3K27me3 – establishing H2Aub1 as the critical silencing modification at ZGA. Taken together, we reveal the logic and mechanism for establishing poised/silent developmental genes in early vertebrate embryos.

Impact Statement

De novopolycomb domains are formed in zebrafish early embryos by focal histone H2Aub1 deposition by Rnf2-PRC1 – which imposes transcription silencing – followed by subsequent recruitment of Aebp2-PRC2 and H3K27me3 deposition.