bluuebunny/crossref_metadata_2025 huggingface dataset:
Microbiome compositions and fecal metabolite concentrations predict post-operative infection in liver transplant recipients
Authors: Lehmann Christopher J , Dylla Nicholas P , Odenwald Matthew , Nayak Ravi , Khalid Maryam , Boissiere Jaye , Cantoral Jackelyn , Adler Emerald , Stutz Matthew R , Cruz Mark Dela , Moran Angelica , Lin Huaiying , Sundararajan Anitha , Sidebottom Ashley M. , Pamer Eric G , Aronsohn Andrew , Fung John , Baker Talia B , Kacha Aalok
Published: February 2023

Background

Liver transplantation (LT) is associated with postoperative infections caused by antibiotic-resistant bacterial pathogens that reside in the intestine. An intact intestinal microbiome suppresses expansion of enteric pathogens, however patients with severe liver disease often have reduced microbiome diversity and increased density of antibiotic-resistantEnterococcusandEnterobacteralesspecies. (1–4) Experimental models have demonstrated that metabolites produced by the intestinal microbiome, including short chain fatty acids (SCFAs), secondary bile acids and indole compounds, enhance host epithelial and immune defenses against enteric pathogens.(5–10) Microbiome derived metabolites likely contribute to resistance against infectious diseases in LT patients, however, this remains uninvestigated.

Methods

We prospectively enrolled 107 liver transplant candidates and determined peri-transplant fecal microbiome compositions including relative and absolute fecal metabolite concentrations.

Results

Fecal microbiomes in LT recipients ranged from highly diverse to complete loss of diversity resulting in expansion ofEnterococcusand/orEnterobacteralesspecies that were associated with postoperative infection. Gas chromatographic (GC-) and liquid chromatographic (LC-) Mass spectrometric analyses revealed decreased concentrations of SCFAs, secondary bile acids, and indole compounds in fecal samples with low microbiome diversity and associated expansion ofEnterococcusandEnterobacteralespopulations.

Conclusion

Fecal metabolite abundances accurately predicted LT patients with reduced microbial diversity and those who developed postoperative infection.
Re-weightingMC1R, ASIPandIRF4risk variants optimises polygenic risk scores for keratinocyte cancer stratification in solid organ transplant recipients
Authors: Seviiri Mathias , Law Matthew H. , Olsen Catherine M. , Whiteman David C. , Green Adele C. , MacGregor Stuart
Published: February 2023

Introduction

Solid organ transplant recipients (SOTRs) are at much higher risk of developing squamous cell carcinoma (SCC) and basal cell carcinoma (BCC), compared to the general population. Previous studies have derived genetics-based predictors (polygenic risk scores, PRS) of SCC and BCC risk in SOTRs by assuming that genetic risk variants act in the same way in the general population as in SOTRs, but this assumption has not been fully tested.

Objective

To investigate whether known genetic risk variants for SCC and BCC have different effect sizes in SOTRs versus in non-transplantees, and if a re-weighted PRS would improve risk prediction.

Methods

We conducted genome-wide association studies for SCC and BCC separately in the non-transplant general population and in SOTRs, and compared the risks associated with selected common genetic variants for KC risk in SOTR vs non-transplant individuals from the UK Biobank. For regions with an increased log odds ratio in SOTRs, PRSs including these weights were validated in the QSkin study, and applied to the Australian STAR SOTR cohort.

Results

Effect sizes for functional variants in MC1R (rs1805007),ASIP(rs6059655), andIRF4(rs12203592) were much more strongly associated with the risk of KC in SOTRs than in non-transplantees. The proportional increase in the effect sizes ranged from 1.9-fold for rs6059655 and BCC risk (SOTRs log (OR)=0.49, 95%CI=0.00-0.98 vs log (OR)=0.26, 95%CI=0.24-0.30 in non-transplantees) to as high as 4.8-fold for rs1805007 and SCC risk (SOTR log (OR)=0.88, 95% CI=0.41-1.35 vs log (OR)=0.18, 95% CI=0.12-0.24 in non-transplantees). PRS with SOTR derived weights for these SNPs showed improved SCC/BCC risk stratification in the STAR Cohort, with the optimised PRS reclassifying 19% of SCC cases vs 8% using the standard PRS, and 18% of BCC cases vs 12% using the standard PRS.

Conclusion

Effect sizes for SCC and BCC risk for genetic variants in theMC1R, ASIP and IRF4genes are elevated in SOTRs, and correctly weighting these variants improves risk stratification based on polygenic risk.
The timing of transcription of RpoS-dependent genes varies across multiple stresses inEscherichia coliK-12
Authors: Adams Josephine , Hoang Johnson , Petroni Emily , Ashby Ethan , Hardin Johanna , Stoebel Daniel M.
Published: February 2023

The alternative sigma factor RpoS regulates transcription of over 1000 genes inEscherichia coliin response to many different stresses. RpoS levels rise continuously after exposure to stress, and the consequences of changing levels of RpoS for the temporal patterns of expression of RpoS-regulated genes have not been described. We measured RpoS levels at various times during the entry to stationary phase, or in response to high osmolarity or low temperature, and found that the time required to reach maximum levels varied by several hours. We quantified the transcriptome across these stresses using RNA-seq. The number of differentially expressed genes differed among stresses, with 1379 DE genes identified in stationary phase, 633 in high osmolarity, and 302 in cold shock. To quantify the timing of gene expression, we fit sigmoid or double sigmoid models to differentially expressed genes in each stress. During the entry into stationary phase, genes whose expression rose earlier tended to be those that had been found to respond most strongly to low levels of RpoS. The timing of individual gene’s expression was not correlated across stresses. Taken together, our results demonstrateE. coliactivates RpoS with different timing in response to different stresses, which in turn generates a unique pattern of timing of the transcription response to each stress.

Importance

Bacteria adapt to changing environments by altering the transcription of their genes. Specific proteins can regulate these changes. This study explored how a single protein called RpoS controls how many genes change expression during adaptation to three stresses. We found that: 1) RpoS is responsible for activating different genes in different stresses; 2) that during a stress, the timing of gene activation depends on the what stress it is, and; 3) that how much RpoS a gene needs in order to be activated can predict when that gene will be activated during the stress of stationary phase.
Amino acid substitutions in norovirus VP1 dictate cell tropism via an attachment process dependent on membrane mobility
Authors: Mills Jake T. , Minogue Susanna C. , Snowden Joseph S. , Arden Wynter K.C. , Rowlands David J. , Stonehouse Nicola J. , Wobus Christiane E. , Herod Morgan R.
Published: February 2023

Viruses interact with receptors on the cell surface to initiate and co-ordinate infection. The distribution of receptors on host cells can be a key determinant of viral tropism and host infection. Unravelling the complex nature of virus-receptor interactions is, therefore, of fundamental importance to understanding viral pathogenesis. Noroviruses are non-enveloped, icosahedral, positive-sense RNA viruses of global importance to human health, with no approved vaccine or antiviral agent available. Here we use murine norovirus as a model for the study of molecular mechanisms of virus-receptor interactions. We show that variation at a single amino acid residue in the major viral capsid protein had a key impact on the interaction between virus and receptor. This variation did not affect virion production or virus growth kinetics, but a specific amino acid was rapidly selected through evolution experiments, and significantly improved cellular attachment when infecting immune cells in suspension. However, reducing plasma membrane mobility counteracted this phenotype, providing insight into for the role of membrane fluidity and receptor recruitment in norovirus cellular attachment. When the infectivity of a panel of recombinant viruses with single amino acid variations was comparedin vivo, there were significant differences in the distribution of viruses in a murine model, demonstrating a role in cellular tropismin vivo. Overall, these results highlight the importance of lipid rafts and virus-induced receptor recruitment in viral infection, as well as how capsid evolution can greatly influence cellular tropism, within-host spread and pathogenicity.

Importance

All viruses initiate infection by utilising receptors to attach to target host cells. These virus-receptor interactions can therefore dictate viral replication and pathogenesis. Understanding the nature of virus-receptor interactions could also be important to developing novel therapies. Noroviruses are non-enveloped icosahedral viruses of medical importance. They are a common cause of acute gastroenteritis with no approved vaccine or therapy and are a tractable model for studying fundamental virus biology. In this study, we utilise the murine norovirus model system to show that variation in a single amino acid of the major capsid protein can alone can affect viral infectivity through improved attachment to suspension cells. Reducing plasma membrane mobility reduced infectivity, providing an insight into the importance of membrane mobility for receptor recruitment. Furthermore, variation at this site was able to change viral distribution in a murine model, illustrating how in-host capsid evolution can influence viral infectivity and immune evasion.
Host and transmission route ofEnterocytozoon hepatopenaei(EHP) from dragonfly to shrimp
Authors: Kumar Dewangan Naresh , Pang Jianhu , Zhao Caiyuan , Cao Changsheng , Yin Bin , Weng Shaoping , He Jianguo
Published: February 2023

Enterocytozoon hepatopenaei(EHP) is a shrimp pathogen that causes huge economic losses. In the present study, the hosts of EHP were investigated using polymerase chain reaction (PCR) in an aquaculture farm located in Maoming, China. EHP was detected inLitopenaeus vannamei,Penaeus monodon, crab, false mussel, and three dragonfly species (Anax parthenope,Pantala flavescens, andIschnura senegalensis). In the histopathological examination using hematoxylin–eosin staining, EHP spores were found in nymphs and adult dragonflies naturally infected with EHP that were collected from the shrimp farm. Fluorescence in situ hybridization results showed a positive signal for EHP infection in the fat body of dragonfly nymphs. Immature and mature microsporidian spores and late sporogonial plasmodium were observed in the cytoplasm of dragonfly nymphs using transmission electron microscopy. The transmission of EHP from shrimp to dragonfly nymphs was confirmed via cohabitation challenge experiments in which EHP-free dragonfly nymphs were cohabited with EHP-infected shrimp, and the transmission of EHP from dragonfly nymphs to shrimp was demonstrated via the cohabitation of EHP-infected dragonfly nymphs with EHP-free shrimp and oral administration challenge experiments. This study confirms that dragonflies can act as natural EHP hosts, and a novel EHP horizontal transmission route exists between dragonflies and shrimp.

Author summary

To the authors’ knowledge, this study presents the first report of microsporidia (EHP) infecting both crustaceans and insects (A. parthenope,P. flavescens, andI. senegalensis). The horizontal transmission of EHP between dragonfly nymphs and shrimp was confirmed through cohabitation and oral administration challenge experiments. EHP has become a globally significant threat to shrimp aquaculture. The findings of the present study will help to design prevention strategies, such as the use of nets to prevent dragonflies from entering shrimp ponds.
A cleaved METTL3 potentiates the METTL3-WTAP interaction and breast cancer progression
Authors: Yan Chaojun , Xiong Jingjing , Zhou Zirui , Li Qifang , Gao Chuan , Zhang Mengyao , Yu Liya , Li Jinpeng , Hu Ming-Ming , Zhang Chen-Song , Cai Cheguo , Zhang Haojian , Zhang Jing
Published: February 2023

N6-methyladenosine (m6A) methylation of RNA by the methyltransferase complex (MTC), with core components including METTL3-METTL14 heterodimers andWilms’ tumor 1-associated protein(WTAP), contributes to breast tumorigenesis, but the underlying regulatory mechanisms remain elusive. Here, we identify a novel cleaved form METTL3a (residues 239-580 of METTL3). We find that METTL3a is required for the METTL3-WTAP interaction, RNA m6A deposition, as well as cancer cell proliferation. Mechanistically, we find that METTL3a is essential for the METTL3-METTL3 interaction, which is a prerequisite step for recruitment of WTAP in MTC. Analysis of m6A sequencing data shows that depletion of METTL3a globally disrupts m6A deposition, and METTL3a mediates mTOR activation via m6A-mediated suppression of TMEM127 expression. Moreover, we find that METTL3 cleavage is mediated by proteasome in an mTOR-dependent manner, revealing positive regulatory feedback between METTL3a and mTOR signaling. Our findings reveal METTL3a as an important component of MTC, and suggest the METTL3a-mTOR axis as a potential therapeutic target for breast cancer.
Elasticity of Whole Blood Clots Measured via Volume Controlled Cavity Expansion
Authors: Varner Hannah , Sugerman Gabriella P. , Rausch Manuel K. , Cohen Tal
Published: February 2023

Measuring and understanding the mechanical properties of blood clots can provide insights into disease progression and the effectiveness of potential treatments. However, several limitations hinder the use of standard mechanical testing methods to measure the response of soft biological tissues, like blood clots. These tissues can be difficult to mount, and are inhomogeneous, irregular in shape, scarce, and valuable. To remedy this, we employ in this work Volume Controlled Cavity Expansion (VCCE), a technique that was recently developed, to measure local mechanical properties of soft materials in their natural environment. Through a highly controlled volume expansion of a water bubble at the tip of an injection needle, paired with simultaneous measurement of the resisting pressure, we obtain a local signature of whole blood clot mechanical response. Comparing this data with predictive theoretical models, we find that a 1-term Ogden model is sufficient to capture the nonlinear elastic response observed in our experiments and produces shear modulus values that are comparable to values reported in the literature. Moreover, we find that bovine whole blood stored at 4°C for greater than 2 days exhibits a statistically significant shift in the shear modulus from 2.53 ± 0.44 kPa on day 2 (N= 13) to 1.23 ± 0.18 kPa on day 3 (N= 14). In contrast to previously reported results, our samples did not exhibit viscoelastic rate sensitivity within strain rates ranging from 0.22 – 21.1 s−1. By surveying existing data on whole blood clots for comparison, we show that this technique provides highly repeatable and reliable results, hence we propose the more widespread adoption of VCCE as a path forward to building a better understanding of the mechanics of soft biological materials.

Graphical Abstract

Highlights

Volume controlled cavity expansion overcomes common obstacles to testing biological samples

Whole blood clot elasticity is well captured by the Ogden hyperelastic material model

Shear modulus strain-rate sensitivity was not observed in clots for moderate rates
Truly dorsal: nonlinear integration of motion signals is required to account for the responses of pattern cells in rat visual cortex
Authors: Matteucci Giulio , Marotti Rosilari Bellacosa , Zattera Benedetta , Zoccolan Davide
Published: February 2023

The defining feature of advanced motion processing in the primate dorsal stream is the existence of pattern cells – specialized cortical neurons that integrate local motion signals into pattern-invariant representations of global direction. Pattern cells have also been reported in rodent visual cortex, but it is unknown whether the tuning of these neurons results from truly integrative, nonlinear mechanisms or trivially arises from linear receptive fields (RFs) with a peculiar geometry. Here we show that pattern cells in rat visual cortical areas V1 and LM process motion direction in a way that cannot be explained by the linear spatiotemporal structure of their RFs. Instead, their tuning properties are consistent with those of units in a state-of-the-art neural network model of the dorsal stream. This suggests that similar cortical processes underly motion representation in primates and rodents. The latter could thus serve as powerful model systems to unravel the underlying circuit-level mechanisms.
MotorNet: a Python toolbox for controlling differentiable biomechanical effectors with artificial neural networks
Authors: Codol Olivier , Michaels Jonathan A. , Kashefi Mehrdad , Pruszynski J. Andrew , Gribble Paul L.
Published: February 2023

Artificial neural networks (ANNs) are a powerful class of computational models for unravelling neural mechanisms of brain function. However, for neural control of movement, they currently must be integrated with software simulating biomechanical effectors, leading to limiting impracticalities: (1) researchers must rely on two different platforms and (2) biomechanical effectors are not generally differentiable, constraining researchers to reinforcement learning algorithms despite the existence and potential biological relevance of faster training methods. To address these limitations, we developed MotorNet, an open-source Python toolbox for creating arbitrarily complex, differentiable, and biomechanically realistic effectors that can be trained on user-defined motor tasks using ANNs. MotorNet is designed to meet several goals: ease of installation, ease of use, a high-level user-friendly API, and a modular architecture to allow for flexibility in model building. MotorNet requires no dependencies outside Python, making it easy to get started with. For instance, it allows training ANNs on typically used motor control models such as a two joint, six muscle, planar arm within minutes on a typical desktop computer. MotorNet is built on PyTorch and therefore can implement any network architecture that is possible using the PyTorch framework. Consequently, it will immediately benefit from advances in artificial intelligence through PyTorch updates. Finally, it is open source, enabling users to create and share their own improvements, such as new effector and network architectures or custom task designs. MotorNet’s focus on higher order model and task design will alleviate overhead cost to initiate computational projects for new researchers by providing a standalone, ready-to-go framework, and speed up efforts of established computational teams by enabling a focus on concepts and ideas over implementation.
Nanojunctions: Specificity of Ca2+signalling requires nano-scale architecture of intracellular membrane contact sites
Authors: Fameli Nicola , van Breemen Cornelis , Groschner Klaus
Published: February 2023

Specificity of control over virtually all essential cellular functions by Ca2+is based on the existence of separated, autonomic signaling modules. Spatiotemporal definition of Ca2+signals involves the assembly of signaling complexes within the nano-architecture of contact sites between the sarco/endoplasmic (SR/ER) reticulum and the plasma membrane (PM). While the requirement of precise spatial assembly and positioning of the junctional signaling elements is well documented, the role of the nano-scale membrane architecture itself, as an ion reflecting confinement of the signaling unit, remains as yet elusive. Utilizing the NCX1/SERCA2-mediated ER Ca2+refilling process as a junctional signalling paradigm, we provide here the first evidence for an indispensable cellular function of the junctional membrane architecture. Our stochastic modeling approach demonstrates that junctional ER Ca2+refilling operates exclusively at nano-scale membrane spacing, with a strong inverse relationship between junctional width and signaling efficiency. Our model predicts a breakdown of junctional Ca2+signaling with loss of reflecting membrane confinement, irrespective of the spatial positioning of the molecular signaling elements. Alterations in the molecular and nano-scale membrane organization at organelle-PM contacts are suggested as new concept in pathophysiology.
Substrate evaporation drives collective construction in termites
Authors: Facchini G. , Rathery A. , Douady S. , Sillam-Dussès D. , Perna A.
Published: February 2023

Termites build complex nests which are an impressive example of self-organization. We know that the coordinated actions involved in the construction of these nests by multiple individuals are primarily mediated by signals and cues embedded in the structure of the nest itself. However, to date there is still no scientific consensus about the nature of the stimuli that guide termite construction, and how they are sensed by termites. In order to address these questions, we studied the early building behavior ofCoptotermes gestroitermites in artificial arenas, decorated with topographic cues to stimulate construction. Pellet collections were evenly distributed across the experimental setup, compatible with a collection mechanism that is not affected by local topography, but only by the distribution of termite occupancy (termites pick pellets at the positions where they are). Conversely, pellet depositions were concentrated at locations of high surface curvature and at the boundaries between different types of substrate. The single feature shared by all pellet deposition regions was that they correspond to local maxima in the evaporation flux. We can show analytically and we confirm experimentally that evaporation flux is directly proportional to the local curvature of nest surfaces. Taken together, our results indicate that surface curvature is sufficient to organize termite building activity, and that termites likely sense curvature indirectly through substrate evaporation. Our findings reconcile the apparently discordant results of previous studies.
Design and Validation of an Open Loop Controlled Positive-Displacement Pump for Vascular Flow Modelling
Authors: O’Brien Thomas
Published: February 2023

Realistic vascular flow-rates are highly patient dependent. There is a need, when evaluating vascular medical devices, to study variable physiological flow-rates corresponding to specific patients. This study presents an experimental analysis of a positive-displacement piston pump designed for generating patient-specific vascular flow-rate wave-forms. Open loop control is used to drive a positive-displacement piston pump according to user-input physiological wave-forms. Transient and frequency analyses are performed for simple and complex inputs. Theoretical analysis of the system shows that it may be modelled as a linear first order system and the response of the system for various inputs shows that the real system approximates a linear first order response, however, higher order effects are noted. These higher order effects do not have any particular detrimental effect on the generation of physiologically realistic flow-rate waveforms.
Proliferating cell nuclear antigen involves in temperature stress tolerance ofUlva prolifera
Authors: He Hongyan , Yang Juanjuan , He Yuan , Li Zhiyong , Fu Caiwei , Zhang Dongren , Li Mengru , Lu Aiming , Dong Jingwei , Liu Jiasi , Gu Huiyue , Shen Songdong
Published: February 2023

Ulva proliferais the dominant species of “green tide”, and has higher tolerance to environmental stresses such as temperature. However, the molecular mechanisms are still unclear. Here, transcriptome analysis, Western blot and RT-qPCR analysis ofU. proliferasuggested that, under temperature stresses (4°C, 36°C), the expression ofPCNAandCyclinAwas promoted, and the MAPK signaling was activated. Besides, the results showed that PCNA interacted with CyclinA. Interestingly, the expression ofmiR-2916, which was predicted to bind PCNA at -552∼-772, was negatively correlated with the expression ofPCNAunder temperature stresses (4°C, 36°C). In addition, the results showed that low temperature (4°C) had no obvious effect on the survival, the formation of cell walls, and the division of protoplasts. However, high temperature (36°C) had obvious effect on them. PCNA inhibitors increased the sensitivity of the protoplasts under temperature stresses. Together, our results suggested PCNA regulating the proliferation in response to the temperature stress ofU. proliferawas associated with miR-2916/PCNA/CyclinA/MAPK pathway. In conclusion, the study preliminarily illuminates the molecular mechanism in response to temperature stress ofU. prolifera, and may provide a new insight for prevention of green tide.
NTpred: A robust and precise machine learning framework for in-silico identification of Tyrosine nitration sites in protein sequences
Authors: Datta Sourajyoti , Asim Muhammad Nabeel , Dengel Andreas , Ahmed Sheraz
Published: February 2023

Post-translational modifications (PTMs) either enhance a protein’s activity in various sub-cellular processes, or degrade their activity which leads towards failure of intracellular processes. Tyrosine nitration (NT) modification degrades protein’s activity that initiate and propagate various diseases including Neurodegenerative, Cardiovascular, Autoimmune diseases, and Carcinogenesis. Identification of NT modification support development of novel therapies and drug discoveries for associated diseases. Identification of NT modification in biochemical labs is expensive, time consuming, and error-prone. To supplement this process, several computational approaches have been proposed. However these approaches remain fail to precisely identify NT modification, due to the extraction of irrelevant, redundant and less discriminative features from protein sequences. The paper in hand presents NTpred framework competent in extracting comprehensive features from raw protein sequences using four different sequence encoders. To reap the benefits of different encoders, it generates four additional feature spaces by fusing different combinations of individual encodings. Furthermore, it eradicates irrelevant and redundant features from eight different feature spaces through a Recursive Feature Elimination process. Selected features of four individual encodings and four feature fusion vectors are used to train eight different Gradient Boosted Tree classifiers. The probability scores from the trained classifiers are utilized to generate a new probabilistic feature space, that is utilized to train a Logistic Regression classifier. On BD1 benchmark dataset, the proposed framework outperform existing best performing predictor in 5-fold cross validation and independent test evaluation with combined improvement of 13.7% in MCC and 20.1% in AUC. Similarly, on BD2 benchmark dataset, the proposed framework outperform existing best performing predictor with combined improvement of 5.3% in MCC and 1.0% in AUC.
Respiratory virus concentrations in human excretions that contribute to wastewater: A systematic review
Authors: Lowry Sarah A. , Wolfe Marlene K. , Boehm Alexandria B.
Published: February 2023

Concentrations of nucleic acids from a range of respiratory viruses including human influenza A and B, respiratory syncytial virus (RSV), metapneumovirus, parainfluenza virus, rhinovirus, and seasonal coronaviruses in wastewater solids collected from wastewater treatment plants correlate to clinical data on disease occurrence in the community contributing to the wastewater. Viral nucleic acids enter wastewater from various excretions including stool, urine, mucus, sputum, and saliva deposited in toilets or other drains in buildings. In order to relate the measured concentrations in wastewater at a treatment plant to actual number of infections in a community, concentrations of the viral nucleic acids in these human excretions are needed as inputs to a mass balance model. In this study, we carried out a systematic review and meta-analysis to characterize the concentrations and presence of influenza A and B, respiratory syncytial virus (RSV), metapneumovirus, parainfluenza virus, rhinovirus, and seasonal coronaviruses in stool, urine, mucus, sputum, and saliva. The systematic review protocol can be accessed athttps://doi.org/10.17605/OSF.IO/ESVYC. We identified 220 data sets from 50 unique articles that met inclusion criteria and reported information on viral concentrations and presence in these excretions. Data were unevenly distributed across virus type (with the most available for influenza) and excretion type (with the most available for respiratory excretions). The majority of data sets only reported the presence or absence of the virus in an excretion in a cross-sectional study design. There is a need for more concentration data, including longitudinal data, across all respiratory virus and excretion types. Such data would allow quantitatively linking virus wastewater concentrations to numbers of infected individuals.
Crane fly semiochemical overrules plant control over cyanobiont inAzollasymbioses
Authors: Güngör Erbil , Savary Jérôme , Adema Kelvin , Dijkhuizen Laura W. , Keilwagen Jens , Himmelbach Axel , Mascher Martin , Koppers Nils , Bräutigam Andrea , Hove Charles van , Riant Olivier , Nierzwicki-Bauer Sandra , Schluepmann Henriette
Published: February 2023

Semiochemicals from insects that restrict plant symbiont dinitrogen fixation had not been known. Here we report on a the glycosylated triketide δ-lactone only found inNephrotoma cornicinacrane flies, cornicinine, that causes chlorosis in the floating-fern symbioses from the genusAzolla.

Cornicinine was chemically synthesized, as well as its aglycone and diastereoisomer. Only the glycosylated trans-A form was active: 500 nM cornicinine in the growth medium turned the dinitrogen-fixing cyanobacterial filaments fromNostoc azollaeinside the host leaf cavities into akinete-like cells. Cornicinine further inhibited akinete germination inAzollasporelings, precluding re-establishment of the symbiosis during sexual reproduction. It did not affect the plantArabidopsis thalianaor several free-living cyanobacteria from the generaAnabaenaorNostoc. Chlorosis occurred in hosts on nitrogen with and devoid of cyanobiont. Cornicinine, therefore, targeted host mechanisms resulting in coordinate cyanobiont differentiation.

Sequence profiling of messenger RNA from isolated leaf cavities confirmed high NH4-assimilation and proanthocyanidin biosynthesis in this trichome-rich tissue. Leaf-cavity transcripts in ferns grown on cornicinine reflected activation of Cullin-RING ubiquitin-ligase pathways, known to mediate metabolite signaling and plant elicitation consistent with the chlorosis phenotype. Transcripts accumulating when akinetes are induced, in leaf cavities of ferns on cornicinine and in megasporocarps, were consistent with increased JA-oxidase, sulfate transport and exosome formation.

The work begins to uncover molecular mechanisms of cyanobiont differentiation in a seed-free plant symbiosis important for wetland ecology or circular crop-production today, that once caused massive CO2draw-down during the Eocene geological past.

Significance

Coordinated differentiation of host and filamentous cyanobacteria underlies the development of ecologically important symbioses; this includes the floating fernsAzollawhich share their wetland habitat withNephrotoma cornicinacraneflies containing the glycosylated triketide δ-lactone semiochemical, cornicinine. Cornicinine overrules cyanobiont differentiation thus inhibiting symbiosis N2-fixation and sexual reproduction; its mode of action resembles plant elicitation as suggested by transcriptional profiling of cells lining the cyanobiont cavities using a new release of the fern host genome.
Updating TCGA glioma classification through integration of molecular profiling data following the 2016 and 2021 WHO guidelines
Authors: de Mendonça Mónica Leiria , Coletti Roberta , Gonçalves Céline S. , Martins Eduarda P. , Costa Bruno M. , Vinga Susana , Lopes Marta B.
Published: February 2023

The understanding of glioma disease has been evolving drastically with dedicated research into the genetic and molecular profiling of glioma tumour tissue. Molecular biomarkers have gained progressive and substantial importance in providing diagnostic information, leading to groundbreaking changes in the tumour classification system, criteria and taxonomy standardised by the 2016 and 2021 editions of the World Health Organization Classification of Tumours of the Central Nervous System’s guidelines (WHO-2016 and WHO-2021, respectively). Some of the insights into glioma disease derived from extensive research on open-source multi-omics databases, such as the Cancer Genome Atlas (TCGA). However, given the substantial changes in glioma classification, retrospective databases may harbour outdated diagnostic annotations, suboptimal for further research. Here we propose two methods for updating the tumour classification of TCGA glioma samples in accordance with WHO-2016 and WHO-2021 guidelines, through the integration of curated molecular profiling information. Our methods allowed for the diagnostic update of 98% and 87% of evaluated TCGA glioma cases according to WHO-2016 and -2021, respectively, and highlighted changes in patient-specific diagnosis across both guidelines’ editions. Our reclassification pipelines are provided in R scripts, facilitating direct reproduction or tailoring upon new releases of WHO guidelines.
Structural basis of bifunctional CTP/dCTP synthase
Authors: Guo Chen-Jun , Zhang Zherong , Zhong Jiale , Liu Ji-Long
Published: February 2023

Nucleotides are important molecules of life. According to the sugar, nucleotides can be divided into nucleotides and deoxynucleotides, which are the basic components of RNA and DNA respectively. CTP synthase (CTPS) catalyzes the last step in the de novo synthesis of CTP, which can form cytoophidia in cells from all three domains of life. We have recently found that CTPS combines with NTPs to form filaments, and solved the structures of CTPS bound with NTPs. Previous biochemical studies have shown that CTPS can also serve as dCTPS, i.e. CTPS/dCTPS can not only bind UTP, ATP and GTP to generate CTP, but also bind deoxynucleotides to generate dCTP. However, the structural basis of the bifunctional enzyme CTPS/dCTPS binding deoxynucleotide is not clear. In this study, we find that CTPS/dCTPS can form filaments bound with deoxynucleotides. Biochemically, we compare the binding and reaction characteristics of the corresponding nucleotides/deoxynucleotides and CTPS/dCTPS. Using cryo-electron microscopy, we solve the the structure of CTPS/dCTPS bound with deoxynucleotides at near-atomic resolution. This study not only provides a structural basis for understanding the catalysis and regulation of bifunctional CTPS/dCTPS, but also opens a door for further exploration the compartmentation of CTPS/dCTPS inside a cell.
Dual-wield NTPases: a novel protein family mined from AlphaFold DB
Authors: Sakuma Koya , Koike Ryotaro , Ota Motonori
Published: February 2023

AlphaFold protein structure database (AlphaFold DB) archives a vast number of predicted models. We conducted systematic data mining against AlphaFold DB and discovered an uncharacterized P-loop NTPase family. The structure of the protein family was surprisingly novel, showing an atypical topology for P-loop NTPases, noticeable two-fold symmetry and two pairs of independent putative active sites. Our findings show that structural data mining is a powerful approach to identifying undiscovered protein families.
S1000: A better taxonomic name corpus for biomedical information extraction
Authors: Luoma Jouni , Nastou Katerina , Ohta Tomoko , Toivonen Harttu , Pafilis Evangelos , Jensen Lars Juhl , Pyysalo Sampo
Published: February 2023

Motivation

The recognition of mentions of species names in text is a critically important task for biomedical text mining. While deep learning-based methods have made great advances in many named entity recognition tasks, results for species name recognition remain poor. We hypothesize that this is primarily due to the lack of appropriate corpora.

Results

We introduce the S1000 corpus, a comprehensive manual re-annotation and extension of the S800 corpus. We demonstrate that S1000 makes highly accurate recognition of species names possible (F-score=93.1%), both for deep learning and dictionary-based methods.

Availability

All resources introduced in this study are available under open licenses fromhttps://jensenlab.org/resources/s1000/. The webpage contains links to a Zenodo project and two GitHub repositories associated with the study.

Contact

sampo.pyysalo@utu.fi,lars.juhl.jensen@cpr.ku.dk

Supplementary information

Supplementary data are available atBioinformaticsonline.
Tracing cancer evolution and heterogeneity using Hi-C
Authors: Erdmann-Pham Dan Daniel , Batra Sanjit Singh , Turkalo Timothy K. , Durbin James , Blanchette Marco , Yeh Iwei , Shain Hunter , Bastian Boris C. , Song Yun S. , Rokhsar Daniel S. , Hockemeyer Dirk
Published: February 2023

Chromosomal rearrangements can initiate and drive cancer progression, yet it has been challenging to evaluate their impact, especially in genetically heterogeneous solid cancers. To address this problem we developed HiDENSEC, a new computational framework for analyzing chromatin conformation capture in heterogeneous samples, which can infer somatic copy number alterations, characterize large-scale chromosomal rearrangements, and estimate cancer cell fractions. We validated HiDENSEC within silicoandin vitrocontrols, and then characterized chromosome-scale evolution during melanoma progression in formalin-fixed tumor samples from three patients. The resulting comprehensive annotation of the genomic events includes copy number neutral translocations that disrupt tumor suppressor genes such as NF1, whole chromosome arm exchanges that result in loss of CDKN2A, and whole-arm copy-number neutral loss of homozygosity involving PTEN. These findings show that large-scale chromosomal rearrangements occur throughout cancer evolution and characterizing these events yields insights into drivers of melanoma progression.
Crosstalk between Rac and Rho GTPase activity mediated by Arhgef11 and Arhgef12 coordinates cell protrusion-retraction cycles
Authors: Nanda Suchet , Calderon Abram , Duong Thanh-Thuy , Koch Johannes , Sachan Arya , Xin Xiaoyi , Solouk Djamschid , Wu Yao-Wen , Nalbant Perihan , Dehmelt Leif
Published: February 2023

Rho GTPase crosstalk is thought to play a key role in the spatio-temporal coordination of cytoskeletal dynamics during cell migration. Here, we directly investigated crosstalk between the major Rho GTPases Rho, Rac and Cdc42 by combining acute activity perturbation with activity measurements in individual, mammalian cells. As expected for their proposed mutual inhibition, we confirmed that Rho inhibits Rac activity. However, surprisingly, we found that Rac strongly stimulates Rho activity. We hypothesized that this crosstalk might play a role in mediating the tight spatio-temporal coupling between cell protrusions and retractions that are typically observed during mesenchymal cell migration. Using new, improved activity sensors for endogenous Rho GTPases, we find that Rac activation is tightly and precisely coupled to local cell protrusions, followed by Rho activation during retraction. In a screen for potential crosstalk mediators, we find that a subset of the Rho activating Lbc-type GEFs, in particular Arhgef11 and Arhgef12, are enriched at transient cell protrusions and retractions. Furthermore, via an optogenetic approach, we show that these Lbc GEFs are recruited to the plasma membrane by active Rac, suggesting that they might link cell protrusion and retraction by mediating Rac/Rho activity crosstalk. Indeed, depletion of these GEFs impaired cell protrusion-retraction dynamics, which was accompanied by a decrease in migration distance and an increase in migration directionality. Thus, our study shows that Arhgef11 and Arhgef12 facilitate effective exploratory cell migration by coordinating the central cell morphogenic processes of cell protrusion and retraction by coupling the activity of the associated small GTPases Rac and Rho.
STRategy: A support system for collecting and analyzing short tandem repeats for forensic science
Authors: Kulthammanit Nuttachai , Sukawutthiya Poonyapat , Noh Hasnee , Vongpaisarnsin Kornkiat , Wichadakul Duangdao
Published: February 2023

Short tandem repeats (STRs) are short repeated sequences commonly found in the human genome. They provide many advantages to forensic sciences, such as identifying individuals, estimating the likelihood of kinship, and analyzing mixtures. Next-generation sequencing (NGS) technologies, e.g., ForenSeq Signature Prep, have been proposed for sequencing STRs, obtaining the sequence of each locus and SNPs, and inferring length-based alleles. However, even though the sequenced STRs from ForenSeq offer more insights into the STRs, which lead to the genetic analysis of population and sub-population structures, no open-source software platform enables the collection and management of STR data from NGS and incorporates related analysis tools in one place.

Here, we introduce STRategy, a standalone web-based application supporting essential STR data management and analysis capabilities. The analyzed data will be visualized in various forms, for example, charts, maps, and pattern alignments. The system implemented a role-based access control that allows users to search or access specific data depending on their responsibilities. It enables public users to search for data. In addition, they can view statistical data, for example, detailed alleles and genetic variation. Lab users can add, update, and see the information of individuals and explore pattern alignments for a specific locus within the population. Administrators can customize the system, for example, configure maps according to the samples’ geographic data, and manage reference STR repeat motifs.

We designed and developed the STRategy using software engineering principles for flexible extension and easy deployment utilizing the Docker container. The source code is publicly available athttps://github.com/cucpbioinfo/STRategy. Also, we deployed a showcase system on a cloud computing service where its URL is included on the GitHub repository. The current version only supports the ForenSeq sample detail report files.
A quantitative autonomous bioluminescence reporter system with a wide dynamic range for Plant Synthetic Biology
Authors: Calvache Camilo , Vazquez-Vilar Marta , Moreno-Giménez Elena , Orzaez Diego
Published: February 2023

Engineered autonomous bioluminescence (EAB) offers many potential applications in Plant Synthetic Biology, notably asin vivoreporter system. Current EAB reporter configurations are limited for quantitative applications due to low dynamic range. We reconfigured theNeonothopanus nambifungal bioluminescence (NeoLuc) pathway to serve as a high-throughput and inexpensive reporter for quantitative analysis of gene expression. We showed that by configuring the first committed step in the pathway (HispS) as the transcriptional entry point instead of the fungal luciferase, the dynamic range of the output increased dramatically, equaling that of the FLuc/RLuc reporter, and outperforming it in high throughput capacity. Furthermore, the inclusion of an enhanced GFP as normalizer allowed transient ratiometric measurements inN. benthamiana. Fast and rich datasets generated by the NeoLuc/eGFP system enabled us to undertake the optimization of new challenging synthetic gene circuits, including a complex agrochemical/optogenetic dual input switch for tight control of engineered metabolic pathways.
Predicting Individual Traits From T1-weighted Anatomical MRI Using the Xception CNN Architecture
Authors: Baratz Zvi , Assaf Yaniv
Published: February 2023

Modeling individual traits is a long-standing goal of neuroscientific research, as it allows us to gain a more profound understanding of the relationship between brain structure and individual variability. In this article, we used the Keras-Tuner library to evaluate the performance of a tuned Xception convolutional neural network (CNN) architecture in predicting sex and age from a sample of 4,049 T1-weighted anatomical MRI scans originating from 1,594 participants. In addition, we used the same tuning procedure to predict the big five inventory (BFI) personality traits for 415 participants (represented by 1,253 scans), and compared the results with those generated by applying transfer learning (TL) based on the models for sex and age. To minimize the effects of preprocessing procedures, scans were subjected exclusively to brain extraction and linear registration with the 2 mm MNI152 template. Our results suggest that CNNs trained with hyperparameter optimization could be used as an effective and accessible tool for predicting subject traits from anatomical MRI scans, and that TL shows potential for application across target domains. While BFI scores were not found not be predictable from T1-weighted scans, further research is required to assess other preprocessing and prediction workflows.
Near-atomic resolution reconstructions fromin siturevitrified cryo samples
Authors: Bongiovanni Gabriele , Harder Oliver F. , Voss Jonathan M. , Drabbels Marcel , Lorenz Ulrich J.
Published: February 2023

We have recently introduced a microsecond time-resolved version of cryo-electron microscopy (cryo-EM) to enable the observation of the fast conformational motions of proteins. Our technique involves locally melting a cryo sample with a laser beam to allow the proteins to undergo dynamics in liquid phase. When the laser is switched off, the sample cools within just a few microseconds and revitrifies, trapping particles in their transient configurations, in which they can subsequently be imaged. We have previously described two alternative implementations of the technique, using either an optical microscope or performing revitrification experimentsin situ. Here, we show that it is possible to obtain near-atomic resolution reconstructions fromin siturevitrified cryo samples. Moreover, the resulting map is indistinguishable from that obtained from a conventional sample within our spatial resolution. Interestingly, we observe that revitrification leads to a more homogeneous angular distribution of the particles, suggesting that revitrification may potentially be used to overcome issues of preferred particle orientation.

Synopsis

Near-atomic resolution reconstructions can be obtained fromin situmelted and revitrified cryo samples. Revitrification results in a more homogeneous angular distribution.
Genetic consequences of effective and suboptimal dosing with mutagenic drugs in a hamster model of SARS-CoV-2 infection
Authors: Illingworth Christopher J. R. , Guerra-Assuncao Jose A. , Gregg Samuel , Charles Oscar , Pang Juanita , Roy Sunando , Abdelnabi Rana , Neyts Johan , Breuer Judith
Published: February 2023

Mutagenic antiviral drugs have shown promising results against multiple viruses, yet concerns have been raised about whether their use might promote the emergence of new and harmful viral variants. Here, we examine the genetic consequences of effective and suboptimal dosing of favipiravir and molnupiravir in the treatment of SARS-CoV-2 infection in a hamster model. We identify a dose-dependent effect upon the mutational load in a viral population, with molnupiravir having a greater potency than favipiravir per mg/kg of treatment. The emergence of de novo variants was largely driven by stochastic processes, with evidence of compensatory adaptation but not of the emergence of drug resistance or novel immune phenotypes. Effective doses for favipiravir and molunpiravir correspond to similar levels of mutational load. Combining both drugs had an increased impact on both efficacy and mutational load. Our results suggest the potential for mutational load to provide a marker for clinical efficacy.