bluuebunny/crossref_metadata_2025 huggingface dataset:
Parasite and pathogen prevalence in our closest animal companions is determined by accessibility of sanitation services
Authors: Chalkowski Kayleigh , Lepczyk Christopher A. , Wilson Alan E. , Valenta Kim , Sipley Breanna , Brownlee Joi , Morgan Abbey M. , Santos Scott R. , Willoughby Janna R. , Zohdy Sarah
Published: March 2022

Despite the critical role parasites play in ecosystem functioning and their considerable influence on human society, little is known about their variations in abundance on a global scale. This gap in knowledge is amplified by a lack of holistic understanding on how the abundance of parasites of wildlife and humans varies across environmental and socioeconomic gradients, despite a need to integrate study of parasites across social and environmental spheres. Free-roaming companion animals (e.g., domestic cats (Felis catus) and dogs (Canis lupus familiaris)) share pathogens and have frequent contact with humans and wildlife. Thus, they are an effective model to understand how parasite and pathogen prevalence of humans and wildlife varies across environmental and socioeconomic gradients. Through a global systematic review and analysis of socioeconomic and environmental variables, including per capita GDP, income disparity, sanitation, biodiversity, island habitation, and latitude, we find that sanitation and island habitation best explained free-roaming companion animal parasite and pathogen prevalence. Sanitation was significantly associated with parasite and pathogen prevalence in free-roaming companion animals, such that for every 10% increase in the proportion of the human population with improved sanitation access, parasite and pathogen prevalence in free-roaming companion animals decreased by 12% (5-19%, 95% C.L.; p = 0.0023). Since companion animals share many parasites with humans and wildlife, these results suggest that actionable interventions to improve sanitation access could reduce parasite and pathogen exposure risks from companion animals to humans and wildlife.

Significance Statement

In addition to playing a critical role in ecosystem functioning, parasites also influence human health, behavior, and society. Further, parasites are also impacted by human activities, as much as by ecological phenomena in natural environments. Despite these dualities, little is known about their variations in abundance on a global scale across environmental and socioeconomic gradients. Using free-roaming companion animals (e.g., domestic cats (Felis catus) and dogs (Canis lupus familiaris)) as a model system, we find that access to safely managed sanitation services is strongly associated with parasite and pathogen prevalence. This finding underscores improvements to sanitation as an actionable One Health intervention that could reduce parasite and pathogen exposure risks from companion animals to humans and wildlife.
Oil accumulation in leaves driven by a native promoter-gene fusion created using CRISPR/Cas9 mediated genomic deletion
Authors: Bhunia Rupam Kumar , Menard Guillaume , Eastmond Peter J.
Published: March 2022

Achieving gain-of-function phenotypes without inserting foreign DNA is an important challenge for plant biotechnologists. Here we show that a gene can be brought under the control of a promoter from an upstream gene by deleting the intervening genomic sequence using dual-guide CRISPR/Cas9. We fuse the promoter of a non-essential photosynthesis-related gene to DIACYLGLYCEROL ACYLTRANSFERASE 2 (DGAT2) to drive oil biosynthesis in leaves of a lipase deficient sugar-dependent 1 mutant. DGAT2 expression is enhanced more than twenty-fold and the triacylglycerol content increases by around thirty-fold. This strategy offers a transgene-free route to engineering gain-of-function traits such as high lipid forage to increase the productivity and sustainability of ruminant farming.
Kaempferol over-accumulation in the flavonoid 3’ hydroxylase tt7 mutant disrupts seed coat outer integument differentiation and compromises seed longevity
Authors: Niñoles R , Arjona P. , Hashim A. , Bueso E. , Serrano R. , Molina I. , Gadea J
Published: March 2022

Seeds slowly accumulate damage during storage, which ultimately results in germination failure. The seed coat is the barrier between the embryo and the external environment, and its composition is critical for seed longevity. Flavonols accumulates in the outer integument, but the effect of altering flavonol composition on outer integument development has not been explored.

Genetic, biochemical, ultrastructural and transcriptomics assays on a battery of loss-of-function mutants in the flavonoid biosynthesis pathway were used to study the effect of altered flavonoid composition in seed development and seed longevity.

Controlled deterioration assays indicate that loss-of-function of the flavonoid 3’ hydroxylase TT7 gene dramatically affects seed longevity and seed development. Seed outer integument differentiation is compromised from nine days after pollination in tt7 seeds, with a defective suberine layer and incomplete degradation of seed-coat starch. These distinctive phenotypes are not shared by other mutants showing also altered flavonoid composition. Double-mutant analysis indicate that over-accumulation of kaempferol is the primary cause of the observed phenotypes. Expression analysis suggest that the tt7 flavonoid pattern affects transcriptional and non-transcriptional levels of regulation.

The increase of kaempferols in the seed coat influences seed development. This positions TT7 as an essential player modulating seed coat development and seed longevity.
Myosin essential light chain 1sa decelerates actin and thin filament gliding on β-myosin molecules
Authors: Osten Jennifer , Mohebbi Maral , Uta Petra , Matinmehr Faramarz , Wang Tianbang , Kraft Theresia , Amrute-Nayak Mamta , Scholz Tim
Published: March 2022

The β-myosin heavy chain expressed in ventricular myocardium and the myosin heavy chain (MyHC) in slow-twitch skeletal soleus muscle type-I fibers are both encoded by MYH7. Thus, these myosin molecules are deemed equivalent. However, some reports suggested variations in the light chain composition between soleus and ventricular myosin, which could influence functional parameters such as maximum velocity of shortening. To test for functional differences of the actin gliding velocity on immobilized myosin molecules we made use of the in vitro motility assay.

We found that ventricular myosin moved actin filaments with approx. 0.9 μm/s significantly faster than soleus myosin (0.3 μm/s). Unregulated actin filaments are not the native interaction partner of myosin and are believed to slow down movement. Yet, using native thin filaments purified from soleus or ventricular tissue, the gliding velocity of soleus and ventricular myosin remained significantly different. When comparing the light chain composition of ventricular and soleus β-myosin a difference became evident. Soleus myosin contains not only the “ventricular” essential light chain (ELC) MLC1sb/v, but also an additional longer and more positively charged MLC1sa. Moreover, we revealed that on a single muscle fiber level, a higher relative content of MLC1sa was associated with significantly slower actin gliding.

We conclude that the ELC MLC1sa decelerates gliding velocity presumably by a decreased dissociation rate from actin associated with a higher actin affinity compared to MLC1sb/v. Such ELC/actin interactions might also be relevant in vivo as differences between soleus and ventricular myosin persisted when native thin filaments were used.

Compared to the “ventricular” essential myosin light chain MLC1sb/v, the longer and more positively charged MLC1sa present in slow-twitch soleus muscle fibers decelerates actin filament gliding on β-myosin molecules presumably by a decreased dissociation rate from actin filaments.
Biodiversity effects on seedling biomass growth are modulated by light environment across functional groups
Authors: Anujan Krishna , Shabnam Alisha , Ali Irfan , Kumar G Ashok , Sankaran Mahesh , Krishnadas Meghna , Naeem Shahid
Published: March 2022

Tree biodiversity has the potential to ensure consistency in the functioning of forest ecosystems, not just over space, but over long-timescales by maintaining composition through recruitment. However, for continued buffering in the face of global environmental change, the sensitivity of biodiversity-ecosystem functioning relationships to heterogeneous environments needs to be understood.

Seedling recruitment in carbon-rich tropical forests is a result of biotic and abiotic drivers but their combined outcomes at the community-level remain poorly understood. Although biodiversity in seedling communities can potentially increase their growth and biomass accumulation, abiotic drivers like light can alter this effect through divergent effects on constituent species and functional groups. In forests with high baseline heterogeneity in microclimates, these processes can enhance or constrain regeneration.

We tested the effects and interactions between species richness and canopy cover on the growth of seedling communities consisting of tropical broad-leaved evergreen and deciduous forest species using a fully crossed manipulated experiment in the Andaman Islands, India and compared these with field observations from a long-term forest plot in the same landscape.

We show that in the critical seedling establishment phase, species richness and light increase community biomass independently. Accounting for variation across species, individual species on average accumulated more biomass in communities with both higher light and higher diversity.

We also show that overyielding in species rich communities fits expectations from a model of complementarity with non-random overyielding than selection or spatial insurance effects.

Synthesis Taken together, our results show that the potential for biodiversity to increase ecosystem functioning in seedling communities is modulated by light. Further understanding on the interaction of biodiversity with multiple abiotic drivers and their effect on regeneration dynamics is crucial for predicting future ecosystem functioning.
Remodeled Connexin 43 hemichannels alter cardiac excitability and promote arrhythmias
Authors: Lillo Mauricio A. , Muñoz Manuel F. , Gaul-Muller Kelli , Shirokova Natalia , Xie Lai-Hua , Fraidenraich Diego , Contreras Jorge E.
Published: March 2022

Connexin-43 (Cx43) is the most abundant protein forming gap junction channels (GJCs) in cardiac ventricles. In multiple cardiac pathologies, including hypertrophy and heart failure, Cx43 is found remodeled at the lateral side of the intercalated discs of ventricular cardiomyocytes. Remodeling of Cx43 has been long linked to spontaneous ventricular arrhythmia, yet the mechanisms by which arrhythmias develop are still debated. Using a model of a dystrophic cardiomyopathy, we previously showed that remodeled Cx43 function as aberrant hemichannels (non-forming GJCs) that alter cardiomyocyte excitability and, consequently, promote arrhythmias. Here, we aim to evaluate if opening of remodeled Cx43 can serve as a general mechanism to alter cardiac excitability independent of cellular dysfunction associated with a particular cardiomyopathy. To address this issue, we used a genetically modified Cx43 knock-in mouse (S3A) that promotes cardiac remodeling of Cx43 protein without apparent cardiac dysfunction. Importantly, when S3A mice were subjected to cardiac stress using the β-adrenergic agonist isoproterenol (Iso), they displayed acute and severe arrhythmias, which were not observed in WT mice. Pre-treatment of S3A mice with the Cx43 hemichannel blocker, Gap19, prevented Iso-induced abnormal electrocardiographic behavior. At the cellular level, when compared with WT, Iso-treated S3A cardiomyocytes showed increased membrane permeability and greater plasma membrane depolarization, which subsequently leads to triggered activity. These cellular dysfunctions were also prevented by Cx43 hemichannel blockers. Our results support the notion that opening of remodeled Cx43 hemichannels, regardless of the type of cardiomyopathy, is sufficient to mediate cardiac stress-induced arrhythmogenicity.
Gapless provides combined scaffolding, gap filling and assembly correction with long reads
Authors: Schmeing Stephan , Robinson Mark D
Published: March 2022

Continuity, correctness and completeness of genome assemblies are important for many biological projects. Long reads represent a major driver towards delivering high-quality genomes, but not everybody can achieve the necessary coverage for good long-read-only assemblies. Therefore, improving existing assemblies with low-coverage long reads is a promising alternative. The improvements include correction, scaffolding and gap filling. However, most tools perform only one of these tasks and the useful information of reads that supported the scaffolding is lost when running separate programs successively. Therefore, we propose a new tool for combined execution of all three tasks using PacBio or Oxford Nanopore reads. gapless is available at: https://github.com/schmeing/gapless.
Probing function in ligand-gated ion channels without measuring ion transport
Authors: Godellas Nicole E. , Grosman Claudio
Published: March 2022

Although the functional properties of ion channels are most accurately assessed using electrophysiological approaches, a number of experimental situations call for alternative methods. Here, working on members of the pentameric ligand-gated ion-channel (pLGIC) superfamily, we focused on the practical implementation of, and the interpretation of results from, equilibrium-type ligand-binding assays. Ligand-binding studies of pLGICs are—by no means—new, but the lack of uniformity in published protocols, large disparities between the results obtained for a given parameter by different groups, and a general disregard for constraints placed on the experimental observations by simple theoretical considerations suggested that a thorough analysis of this classic technique was in order. To this end, we present a detailed practical and theoretical study of this type of assay using radiolabeled α-bungarotoxin, unlabeled small-molecule cholinergic ligands, the human homomeric α7-AChR, and extensive calculations in the framework of a realistic five-binding-site reaction scheme. Furthermore, we show examples of the practical application of this method to tackle two long-standing questions in the field: whether ligand-binding affinities are sensitive to binding-site occupancy, and whether mutations to amino-acid residues in the transmembrane domain can affect the channel’s affinities for ligands that bind to the extracellular domain.
ezQTL: A Web Platform for Interactive Visualization and Colocalization of Quantitative Trait Loci and GWAS
Authors: Zhang Tongwu , Klein Alyssa , Sang Jian , Choi Jiyeon , Brown Kevin M
Published: March 2022

Genome-wide association studies (GWASs) have identified thousands of genomic loci associated with complex diseases and traits, including cancer. The vast majority of common trait-associated variants identified via GWAS fall in non-coding regions of the genome, posing a challenge in elucidating the causal variants, genes, and mechanisms involved. Expression quantitative trait locus (eQTL) and other molecular QTL studies have been valuable resources in identifying candidate causal genes from GWAS loci through statistical colocalization methods. While QTL colocalization is becoming a standard analysis in post-GWAS investigation, an easy web tool for users to perform formal colocalization analyses with either user-provided or public GWAS and eQTL datasets has been lacking. Here, we present ezQTL, a web-based bioinformatic application to interactively visualize and analyze genetic association data such as GWAS and molecular QTLs under different linkage disequilibrium (LD) patterns (1000 Genomes Project, UK Biobank, or user-provided data). This application allows users to perform data quality control for variants matched between different datasets, LD visualization, and two-trait colocalization analyses using two state-of-the-art methodologies (eCAVIAR and HyPrColoc), including batch processing. ezQTL is a free and publicly available cross-platform web tool, which can be accessed online at https://analysistools.cancer.gov/ezqtl.
Inter-microscope comparability of dental microwear texture data obtained from different optical profilometers
Authors: Winkler Daniela E. , Kubo Mugino O.
Published: March 2022

Dental microwear texture analysis has become a well-established approach for dietary inference and reconstruction of mammals and other tetrapods, both extant and extinct. As the amount of available data grows immensely, researchers could benefit from combining data gathered by others to perform meta-analyses. However, different devices used to capture three-dimensional surface scans for DMTA are known to produce variation even when measuring the same surface. Here we compare DMTA data of 36 guinea pigs that received different diets in a controlled feeding experiment, measured on a confocal disc-scanning and a confocal laser-scanning microscope. We are testing different pre-analysis filtering protocols to mitigate differences. We find inter-microscopes and filter-related differences for the majority of analysed 41 DMTA parameters. Certain microscope-specific filter routines resulted in less differences than other pre-analysis protocols. We further identify DMTA parameters which were stable regardless of microscope or pre-analysis treatment. Overall, the results obtained on both microscopes show the same dietary differentiation between guinea pig feeding groups, which supports that DMTA is a suitable method to obtain repeatable, objective dietary inferences. We finally propose a roadmap to enhance data exchange and inter-lab comparability and collaboration in the future.
Evaluation of systemic immune response in patients with inflammatory complications of large joint replacements
Authors: Mamonova I.A. , Babushkina I.V. , Ulyanov V.Yu. , Bondarenko A.S. , Shpinyak S.P.
Published: March 2022

We studied the features of systemic immunity in patients with inflammatory complications of their knee replacements and used the factor analysis to find immune characteristics associated with the progress of the pathological condition. The components indicative of changes related to the development of cell and humoral immune response in patients were isolated. Our findings present prospects for the development of new diagnostic techniques ensuring higher precision in searching for adequate surgical methods.
Cultural adaptation of the person-centered maternity care scale at governmental health facilities in Cambodia
Authors: Naito Yuko Takahashi , Fukuzawa Rieko , Afulani Patience A. , Kim Rattana , Aiga Hirotsugu
Published: March 2022

Background

In Cambodia, the importance of valuing women’s childbirth experiences in improving quality of care has been understudied. This is largely because of absence of reliable Khmer tools for measuring women’s intrapartum care experiences. Generally, cross-cultural development of those tools often involves translation from a source language into a target language. Yet, few earlier studies considered Cambodian cultural context. Thus, we developed the Cambodian version of the Person-Centered Maternity Care (PCMC) scale, by culturally adapting its original to Cambodian context for ensuring cultural equivalence and content validity.

Methods

Three rounds of cognitive interviewing with 20 early postpartum women were conducted at two governmental health facilities in Cambodia. Cognitive interviewing was composed of structured questionnaire pretesting and qualitative probing. The issues identified in the process of transcribing and translating audio-recorded cognitive interviews were iteratively discussed among study team members, and further analyzed.

Results

A total of 14 issues related to cultural adaptations were identified in the 31 translated questions for the Cambodian version of the PCMC scale. Our study identified three key findings: (i) discrepancies between the WHO recommendations on intrapartum care and Cambodian field realities; (ii) discrepancies in recognition on PCMC between national experts and local women; and (iii) challenges in correctly collecting and interpreting less-educated women’s views on intrapartum care.

Conclusion

Not only women’s verbal data but also their non-verbal data and cultural contexts should be comprehensively counted, when reflecting Cambodian women’s intrapartum practice realities in the translated version. This is the first study that attempted to develop the tool for measuring Cambodian women’s experiences during childbirth, by addressing cross-cultural issues.
Stem cell regulators control a G1 duration gradient in the plant root meristem
Authors: Echevarria Clara , Desvoyes Bénédicte , Marconi Marco , Franco-Zorrila José Manuel , Lee Laura , Umeda Masaaki , Sablowski Robert , Birnbaum Kenneth D. , Wabnik Krzysztof , Gutierrez Crisanto
Published: March 2022

In meristems, where new plant organs initiate, key stem cell regulators have been identified, but their link to cell cycle progression remains unclear. Here, we show that the root meristem has a positional gradient of G1 duration that ranges from ∼2 h near the meristem boundary to more than 20 h in stem cells and early derivatives. Mutants in the PLETHORA (PLT) genes shortened G1 length and flattened its gradient. Computer modeling of an incoherent feed-forward loop (IFFL) predicted the inference of a negative regulatory pathway. We propose that PLT genes play opposing roles, maintaining meristem and stem cell activity and inhibiting G1 progression through the CDK inhibitor KRP5, a PLT target, and RBR1. This establishes a previously undescribed proximal-distal feature of the root meristem in which a G1 duration gradient is shaped by stem cell and meristem maintenance regulators.
Putting life history theory to the test - the estimation of reproductive values from field data
Authors: Borger Mirjam J. , Komdeur Jan , Richardson David S. , Weissing Franz J.
Published: March 2022

Quantifying fitness is important to understand adaptive evolution. Reproductive values are useful for making fitness comparisons involving different categories of individuals, like males and females. By definition, the reproductive value of a category is the expectedper capitacontribution of the members of that category to the gene pool of future generations. Life history theory reveals how reproductive values can be determined via the estimation of life-history parameters, but this requires intricate algebraic calculations. Recently, a more intuitive, pedigree-based method has become popular, which estimates the genetic contributions of individuals to future generations by tracking their descendants down the pedigree. Here we compare both methods. We implement various life-history scenarios (for which the “true” reproductive values can be calculated) in individual-based simulations, use the simulation data to estimate reproductive values with both methods, and compare the results with the true target values. We show that the pedigree-based estimation of reproductive values is either systematically biased (and hence inaccurate), or very imprecise. This holds even for simple life histories and under idealized conditions. In contrast, the traditional algebraic method estimates reproductive values with high accuracy and precision.

Lay Summary

To study evolution in empirical systems it is important to accurately and precisely measure fitness. Here, using simulations, we compare two methods for estimating fitness and test their accuracy and precision. One estimates life-history parameters and calculates a fitness proxy using complex algebra. The other method estimates genetic contribution to future generations by tracking descendants down the pedigree. We conclude that the pedigree method is unreliable, while the algebraic method is accurate and precise.
Tradeoffs in bacterial physiology determine the efficiency of antibiotic killing
Authors: Bren Anat , Glass David S. , Kohanim Yael Korem , Mayo Avi , Alon Uri
Published: March 2022

Antibiotics can kill or stop the growth of bacteria, and their effectiveness depends on many factors. It is important to understand the relation between bacterial physiology, the environment and antibiotic action. While many of the mechanistic details of antibiotic action are known, the connection between death rate and bacterial physiology is poorly understood. Death rate in antibiotics has often been shown to rise linearly with growth rate; however, it remains unclear how environmental factors, in concert with whole-cell physiological properties, affect bactericidal activity. To address this, we developed a high-throughput assay to precisely measure antibiotic-mediated bacterial death. We found that death rate is linear in growth rate, but the slope depends on environmental conditions. Specifically, stressors lower the death rate compared to a non-stressed environment with the same growth rate. To understand the role of stress, we developed a mathematical model of bacterial death based on resource allocation that takes into account a newly defined stress-response sector; we identify this sector using RNA-seq. Our model accurately predicts the death rate and minimal inhibitory concentration of antibiotics across a wide range of conditions, including a previously unknown increase in the stress response and protection from death at very low levels of cAMP. The present death-growth model suggests conditions that may improve antibiotic efficacy.
URB597 induces aggression in adult Lister Hooded rats
Authors: Warren William G. , Hale Ed , Papagianni Eleni P. , Cassaday Helen J. , Stevenson Carl W. , Stubbendorff Christine
Published: March 2022

The endocannabinoid system has been implicated in both social and cognitive processing. The endocannabinoid metabolism inhibitor, URB597, dose-dependently improves non-social memory in adult Wistar and Sprague Dawley rats, whereas its effect on social interaction (SI) is affected by both rat strain and drug dose. Lister Hooded rats consistently respond differently to drug treatment in general compared with albino strains. This study sought to investigate the effects of different doses of URB597 on social and non-social memory in Lister Hooded rats, as well as analysing the behavioural composition of the SI.

Males were tested for novel object recognition (NOR), social preference (between an object and an unfamiliar rat), social novelty recognition (for a familiar vs unfamiliar rat) and SI with an unfamiliar rat. URB597 (0.1 or 0.3 mg/kg) or vehicle was given 30 minutes before testing. During SI testing, total interaction time was assessed along with time spent on aggressive and explorative behaviours.

Lister Hooded rats displayed expected non-social and social memory and social preference, which was not affected by URB597. During SI, URB597 did not affect total interaction time. However, the high dose increased aggression, compared to vehicle, and decreased anogenital sniffing, compared to the low dose of URB597. In summary, URB597 did not affect NOR, social preference or social recognition memory but did have subtle behavioural effects during SI in Lister hooded rats.

These findings highlight the importance of considering strain as well as the composition of behaviour when investigating drug effects on social behaviour.
Multi-omics profiling of collagen-induced arthritis mouse model reveals early metabolic dysregulation via SIRT1 axis
Authors: Li Lingzi , Freitag Janina , Asbrand Christian , Munteanu Bogdan , Wang Bei-Tzu , Zezina Ekaterina , Didier Michel , Thill Gilbert , Rocher Corinne , Herrmann Matthias , Biesemann Nadine
Published: March 2022

Rheumatoid arthritis (RA) is characterized by joint infiltration of immune cells and synovial inflammation which leads to progressive disability. Current treatments improve the disease outcome, but the unmet medical need is still high. New discoveries over the last decade have revealed the major impact of cellular metabolism on immune cell functions. So far, a comprehensive understanding of metabolic changes during disease development, especially in the diseased microenvironment, is still limited. Therefore, we studied the longitudinal metabolic changes during the development of murine arthritis integrating metabolomics and bulk RNA-seq data. We identified an early change in macrophage pathways which was accompanied by oxidative stress, a drop in NAD+ level and induction of glucose transporters. We discovered inhibition of SIRT1, a NAD-dependent histone deacetylase and confirmed its dysregulation in human macrophages and synovial tissue of RA patients. Mining this database should enable the discovery of novel metabolic targets and therapy opportunities in RA.
Structural basis for APE1 processing DNA damage in the nucleosome
Authors: Weaver Tyler M. , Hoitsma Nicole M. , Spencer Jonah J. , Gakhar Lokesh , Schnicker Nicholas J. , Freudenthal Bret D.
Published: March 2022

Genomic DNA is continually exposed to endogenous and exogenous factors that promote DNA damage. Eukaryotic genomic DNA is packaged into nucleosomes, which present a barrier to accessing and effectively repairing DNA damage. The mechanisms by which DNA repair proteins overcome this barrier to repair DNA damage in the nucleosome and protect genomic stability is unknown. Here, we determine how the base excision repair (BER) endonuclease AP-endonuclease 1 (APE1) recognizes and cleaves DNA damage in the nucleosome. Kinetic assays determined that APE1 cleaves solvent-exposed AP sites in the nucleosome with 3 - 6 orders of magnitude higher efficiency than occluded AP sites. A cryo-electron microscopy structure of APE1 bound to a nucleosome containing a solvent-exposed AP site identified that APE1 uses a DNA sculpting mechanism for AP site recognition, where APE1 bends the nucleosomal DNA to access the AP site. Notably, additional biochemical and structural characterization of occluded AP sites identified contacts between the nucleosomal DNA and histone octamer that prevent efficient processing of the AP site by APE1. These findings provide a rationale for the position-dependent activity of BER proteins in the nucleosome and suggests the ability of BER proteins to sculpt nucleosomal DNA drives efficient BER in chromatin.
Determinants of multiheme cytochrome extracellular electron transfer uncovered by systematic peptide insertion
Authors: Campbell Ian J. , Atkinson Joshua T. , Carpenter Matthew D. , Myerscough Dru , Su Lin , Ajo-Franklin Caroline Marie , Silberg Jonathan J.
Published: March 2022

The multiheme cytochrome MtrA enables microbial respiration by transferring electrons across the outer membrane to extracellular electron acceptors. While structural studies have identified residues that mediate MtrA binding to hemes and to other cytochromes that facilitate extracellular electron transfer (EET), the relative importance of these interactions for EET is not known. To better understand EET, we evaluated how insertion of an octapeptide across all MtrA backbone locations affects Shewanella oneidensis MR-1 respiration on Fe(III). EET efficiency was found to be inversely correlated with insertion proximity to the heme prosthetic groups. Mutants with decreased EET also arose from insertions in a subset of the regions that make residue-residue contacts with the porin MtrB, while all sites contacting the extracellular MtrC presented high peptide insertion tolerance. MtrA variants having peptide insertions within the CXXCH motifs that coordinate heme cofactors retained some ability to support respiration on Fe(III), although these variants presented significantly decreased EET. Furthermore, the fitness of cells expressing different MtrA variants under Fe(III)-respiring conditions correlated with anode reduction. The peptide-insertion profile, which represents the first comprehensive sequence-structure-function map for a multiheme cytochrome, implicates MtrA as a strategic protein engineering target for regulating EET.
Type I interferons govern Zika virus resistance of human macrophages and microglia
Authors: Hanrath Aidan T. , Hatton Catherine F. , Gothe Florian , Browne Cathy , Vowles Jane , Leary Peter , Cockell Simon J. , Cowley Sally A. , James William S. , Hambleton Sophie , Duncan Christopher J. A.
Published: March 2022

The role of the human type I interferon (IFN-I) system in restricting Zika virus (ZIKV) is uncertain. Here, genetic and pharmacological ablation of IFN-I signalling enhanced ZIKV replication and cytopathicity in macrophages and microglia, key cells in ZIKV transmission and pathogenesis. Thus, despite the extensive IFN-I countermeasures employed by ZIKV, IFN-I dictates the outcome of infection in macrophages. Therapeutic manipulation of the IFN-I system may bring clinical benefit in ZIKV.
Tailoring CRISPR-Cas Immunity for the Degradation of Antibiotic Resistance Genes
Authors: Li Xin , Bao Nan , Yan Zhen , Yuan Xian-Zheng , Wang Shu-Guang , Xia Peng-Fei
Published: March 2022

The evolution and dissemination of antibiotic resistance genes (ARGs) are prompting severe health and environmental issues. While environmental processes are key barriers preventing the spread of ARGs, they are often sources of ARGs at the same time, as ARGs may be required and accumulate in the biological treatment units. An upgrading of environmental biotechnology is imperative and urgent. ARGs confer antibiotic resistance based on the DNA sequences rather than the chemistry of DNA molecules. An ARG can be considered degraded if its sequence was disrupted. Therefore, we present here that CRISPR-Cas immunity, an archaeal and bacterial immune system for eliminating invading foreign DNAs, can be repurposed and tailored for the degradation of ARGs. By deploying an artificial IncP machinery, the designed system, namely VADER, can be successfully delivered via bacterial conjugation. Then, we propose a new sector for ARG degradation to be implemented as a complement to the biological units in the framework of environmental processes. In this endeavor, a prototype conjugation reactor at a 10-mL-scale was devised, and 100% of the target ARG were eliminated in the transconjugated microbes receiving VADER in the reactor. By generating a nexus of synthetic biology and environmental biotechnology, we believe that our work is not only an enterprise for tackling ARG problems but also a potential solution for managing undesired genetic materials in general in the future.

Importance

Antibiotic resistance has been causing severe health problems and leading to millions of deaths in recent years. Environmental processes, especially the wastewater treatment sector, are important to barrier the spread of antibiotic resistance from the pharmaceutical industry, hospitals, or civil sewage. However, they have been identified as the source of antibiotic resistance at the same time, as antibiotic resistance with its main cause antibiotic resistance genes (ARGs) may be required and accumulate in the biological treatment units, leading to the dissemination of ARGs. Here, we transplanted the CRISPR-Cas system, an immune system via programmable DNA cleavage, to environmental biotechnology for tackling the antibiotic resistance dilemma thereof, and we propose a new sector in environmental processes specialized in ARG removal with a reactor inhabiting the CRISPR-Cas system per se. Our study provides a new angle to resolve public health issues via the implementation of synthetic biology at the process level.
Epithelial monolayer development and tight junction assembly on nanopillar arrays
Authors: Yeste Jose , Illa Xavi , Shashikanth Nitesh , Guimerà-Brunet Anton , Villa Rosa , Turner Jerrold R
Published: March 2022

Nanostructured materials provide an outstanding opportunity to both stimulate and measure cellular processes. In the context of tight junctions, it was previously reported that transient application of a nanotopographic surface over the apical brush border membrane of epithelial monolayers triggers redistribution of ZO-1, claudins, and F-actin that increases paracellular macromolecular flux. In excitable tissues, nanomaterials have been used to apply and measure electrical signals, such action potentials. As a first step towards translating these technologies for use in analysis of epithelial function, we sought to culture monolayers composed of transporting epithelia over nanopillar arrays without perturbing cellular structure or function. Madin-Darby Canine kidney I (MDCK I) cells were cultured on collagen-coated silicon chips with ∼1 μm diameter nanopillar arrays. Fluorescence and scanning electron microscopy were used to assess the impact of height on nanopillar-epithelial interactions. Monolayers formed over and were largely unaffected by short nanopillars. These nanopillars were located beneath basal epithelial surfaces and were not preferentially located within lateral intercellular spaces or beneath ZO-1-containing junctions. In contrast, tall nanopillars that exceeded cell height disrupted MDCK I monolayer growth. Cells interacted with, encircled, and extended cytoplasm over the top of tall nanopillars, and dense ZO-1 and F-actin accumulations occasionally surrounded apical membranes adjacent to nanopillars. Finally, when grown over arrays composed of nanopillars 1 – 2 μm shorter than cells, MDCK I frequently grew between nanopillars. As a result, nanopillars were more commonly present within lateral intercellular spaces beneath junctions. Apical complex structure was intact, as assessed by fluorescence microscopy of ZO-1, occludin, claudin-2, F-actin, and E-cadherin. Apical microvilli were also unaffected. We therefore show that conditions can be defined to allow growth of mature, correctly assembled epithelial monolayers with nanopillars localized to lateral intercellular spaces. This sets the stage for application of nanotechnologies for perturbation and analysis of epithelial biology.
Stretching of long double-stranded DNA and RNA described by the same model
Authors: Afanasyev Alexander Y. , Onufriev Alexey V.
Published: March 2022

We propose a bead-spring model that accurately reproduces a variety of experimental force-extension curves of long double-stranded DNA and RNA, including torsionally constrained and unconstrained DNA, and negatively supercoiled DNA. A key feature of the model is a specific non-convex energy function of the spring. We provide an algorithm for obtaining five required parameters of the model from experimental force-extension curves. In the plateau region of the force-extension curves, our molecular dynamics simulations show that the polymer separates into a mix of weakly and strongly stretched states without forming macroscopically distinct phases.
The characterization of multiple novel paramyxovirus species highlights the diverse nature of the subfamily Orthoparamyxovirinae
Authors: Vanmechelen Bert , Meurs Sien , Horemans Marie , Loosen Arne , Maes Tibe Joly , Laenen Lies , Vergote Valentijn , Koundouno Fara Raymond , Magassouba N’faly , Konde Mandy Kader , Condé Ibrahima Sory , Carroll Miles W. , Maes Piet
Published: March 2022

The subfamily Orthoparamyxovirinae is a group of single-stranded, negative-sense RNA viruses that contains many human, animal and zoonotic pathogens. While there are currently only 34 recognized member species in this subfamily, recent research has revealed that much of its diversity remains to be characterized. Using a newly developed nested PCR-based screening assay, we report here the discovery of fifteen orthoparamyxoviruses in rodents and shrews from Belgium and Guinea, thirteen of which are believed to represent new species. Using nanopore sequencing, complete genomes could be determined for almost all of these viruses, enabling a detailed evaluation of their genome characteristics. While most viruses are thought to belong to the rapidly expanding genus Jeilongvirus, we also identify novel members of the genera Narmovirus, Henipavirus and Morbillivirus. Together with other recently discovered orthoparamyxoviruses, both the henipaviruses and the morbillivirus discovered here appear to form distinct rodent-/shrew-borne clades within their respective genera, clustering separately from all currently classified member species. In the case of the henipaviruses, a comparison of the different members of this clade revealed the presence of a secondary conserved open reading frame, encoding for a transmembrane protein, within the F gene, the biological relevance of which remains to be established. While the characteristics of the viruses described here shed further light on the complex evolutionary origin of paramyxoviruses, they also illustrate that the diversity of this group of viruses in terms of genome organization appears to be much larger than previously assumed.

Data availability

The genome sequences generated in this study have been submitted to GenBank (accession numbers OK623353-OK623368).
IPMK modulates insulin-mediated suppression of hepatic glucose production
Authors: Jung Ik-Rak , Anokye-Danso Frederick , Jin Sunghee , Ahima Rexford S. , Kim Sangwon F.
Published: March 2022

Hepatic glucose production is crucial for the maintenance of normal glucose homeostasis. Although hepatic insulin resistance contributes to excessive glucose production, its mechanism is not well understood. Here, we show that inositol polyphosphate multikinase (IPMK), a key enzyme in inositol polyphosphate biosynthesis, plays a role in regulating hepatic insulin signaling and gluconeogenesis both in vitro and in vivo.IPMK-deficient hepatocytes exhibit decreased insulin-induced activation of Akt-FoxO1 signaling. The expression of mRNA levels of phosphoenolpyruvate carboxykinase 1 (Pck1) and glucose 6-phosphatase (G6pc), key enzymes mediating gluconeogenesis, are increased in IPMK-deficient hepatocytes compared to wild type (WT) hepatocytes. Importantly, re-expressing IPMK restores insulin sensitivity and alleviates glucose production in IPMK-deficient hepatocytes. Moreover, hepatocyte-specific IPMK deletion exacerbates hyperglycemia and insulin sensitivity in mice fed a high-fat diet (HFD), accompanied by an increase in hepatic glucose production during pyruvate tolerance test and reduction in Akt phosphorylation in IPMK deficient liver. Our results demonstrate that IPMK mediates insulin signaling and gluconeogenesis and may be potentially targeted for treatment of diabetes.

Highlights

IPMK expression is reduced in livers of HFD-fed mice.

Hepatocyte-specific deletion of IPMK in mice aggravated HFD-induced insulin resistance.

Loss of IPMK decreased insulin-induced activation of Akt-FoxO1 signaling, leading to the increase of glucose production in hepatocytes.
Small non-coding RNA landscape of extracellular vesicles from a post-traumatic model of equine osteoarthritis
Authors: Anderson James R , Jacobsen Stine , Walters Marie , Bundgaard Louise , Diendorfer Andreas , Hackl Matthias , Clarke Emily J , James Victoria , Peffers Mandy J
Published: March 2022

Extracellular vesicles comprise an as yet inadequately investigated intercellular communication pathway in the field of early osteoarthritis. We hypothesised that small non-coding RNA expression pattern in synovial fluid and plasma would change during progression of experimental osteoarthritis. In this study, we used small RNA sequencing to provide a comprehensive overview of the temporal expression profiles of small non-coding transcripts carried by EVs derived from plasma and synovial fluid for the first time in a post-traumatic model of equine osteoarthritis. Additionally, we characterised synovial fluid and plasma-derived extracellular vesicles with respect to quantity, size, and surface markers. The differential expression of seven microRNAs in plasma and synovial fluid-derived extracellular vesicles; miR-451, miR-25, miR-215, miR-92a, miR-let-7c, miR-486-5p, miR-23a and four snoRNAs; U3, snord15, snord46, snord58 represent potential biomarkers for early OA. Bioinformatics analysis of the differentially expressed microRNAs in synovial fluid highlighted that in early OA these related to the inhibition of cell cycle, cell cycle progression, DNA damage and cell proliferation but increased cell viability, and differentiation of stem cells. Plasma and synovial fluid-derived extracellular vesicle small non-coding signatures have been established for the first time in a temporal model of osteoarthritis. These could serve as novel biomarkers for the evaluation of osteoarthritis progression or act as potential therapeutic targets.
Injury-induced pulmonary tuft cells are heterogenous, arise independent of key Type 2 cytokines, and are dispensable for dysplastic repair
Authors: Barr Justinn , Gentile Maria Elena , Lee Sunyoung , Kotas Maya E. , de Mello Costa Maria Fernanda , Holcomb Nicolas P. , Jaquish Abigail , Palashikar Gargi , Matsumoto Ichiro , Margolskee Robert , Cohen Noam A. , Sun Xin , Vaughan Andrew E.
Published: March 2022

While the lung bears significant regenerative capacity, severe viral pneumonia can chronically impair lung function by triggering dysplastic remodeling. The connection between these enduring changes and chronic disease remains poorly understood. We recently described the emergence of tuft cells within Krt5+ dysplastic regions after influenza injury. Using bulk and single cell transcriptomics, we characterized and delineated multiple distinct tuft cell populations that arise following influenza clearance. Distinct from intestinal tuft cells which rely on Type 2 immune signals for their expansion, neither IL-25 nor IL-4Rα signaling are required to drive tuft cell development in dysplastic/injured lungs. Furthermore, tuft cells were also observed upon bleomycin injury, suggesting that their development may be a general response to severe lung injury. While intestinal tuft cells promote growth and differentiation of surrounding epithelial cells, in the lungs of tuft cell deficient mice, Krt5+ dysplasia still occurs, goblet cell production is unchanged, and there remains no appreciable contribution of Krt5+ cells into more regionally appropriate alveolar Type 2 cells. Together, these findings highlight unexpected differences in signals necessary for lung tuft cell amplification and establish a framework for future elucidation of tuft cell functions in pulmonary health and disease.
Towards a bionic IoT: environmental monitoring using smartphone interrogated plant sensors
Authors: Guo Yunlong , Canning John , Chaczko Zenon
Published: March 2022

The utilisation of plants directly as quantifiable natural sensors is proposed. A case study measuring surface wettability of Aucuba japonica, or Japanese Laurel, plants using a novel smartphone field interrogator is demonstrated. This plant has been naturalised globally from Asia. Top-down contact angle measurements map wettability on-site and characterise a range of properties impacting plant health, such as aging, solar and UV exposure, and pollution. Leaves at an early age or in the shadow of trees are found to be hydrophobic with contact angle θ ~ 99°, while more mature leaves under sunlight are hydrophilic with θ ~ 79°. Direct UVA irradiation at λ = 365 nm is shown to accelerate aging, changing contact angle of one leaf from slightly hydrophobic at θ ~ 91° to be hydrophilic with θ ~ 87 ° after 30 min. Leaves growing beside a road with heavy traffic are observed to be substantially hydrophilic, as low as θ ~ 47°, arising from increased wettability with particulate accumulation on the leaf surface. Away from the road, the contact angle increases as high as θ ~ 96°. The results demonstrate that contact angle measurements using a portable diagnostic IoT edge device can be taken into the field for environmental detection, pollution assessment and more. Using an internet connected smartphone combined with a plant sensor allows multiple measurements at multiple locations together in real-time, potentially enabling tracking of parameter change anywhere where plants are present or introduced. This hybrid integration of widely distributed living organic systems with the internet marks the beginning of a new bionic internet-of-things (b-IoT).