bluuebunny/crossref_metadata_2025 huggingface dataset:
Belowground plant responses to root herbivory depend on the composition and structure of their root-colonising arbuscular mycorrhizal fungi
Authors: Ng Anna , Wilson Bree A.L. , Frew Adam
Published: March 2022

There is growing interest in managing arbuscular mycorrhizal (AM) fungi in agriculture to support plant production. These fungi can support crop growth and nutrient uptake but also affect plant-herbivore interactions. Our knowledge of how native AM fungal diversity and community composition influence these interactions is limited, while our understanding of this in relation to root-herbivory is lacking altogether.

To begin to address these knowledge gaps, plants were grown with no AM fungi or were inoculated with native fungal communities sourced from either a crop field (field community), a sclerophyll forest (forest community), or a crop field in fallow (fallow community). We then explored how the composition and structure (species richness and relative abundance) of root-colonising AM fungal communities was associated with the growth and belowground nutrient responses of a major crop (Sorghum bicolor) to attack from a root-feeding insect (Dermolepida albohirtum).

DNA metabarcoding revealed plants associated with three distinct root-colonising AM fungal communities. Fungal taxon richness in roots was highest in the field community and lowest in the fallow community. Both the field and fallow communities were dominated by the putatively ruderal genera Glomus and Claroideoglomus, while the forest-derived community contained greater proportions of Paraglomus and Ambispora.

In response to root herbivory, plants without AM fungi and plants colonised by the forest community exhibited root biomass losses of 61% and 44%, respectively. Similarly, these two groups also had reductions of 59% and 65% in their root phosphorus content, respectively, when subjected to the root herbivore. In contrast, plants associating with communities harbouring greater proportions of Glomus and Claroideoglomus (the field and fallow communities) did not exhibit reductions in root biomass or nutrient content.

Our results show that plant responses to root-herbivory vary with root-colonising AM fungal community composition and structure. In a community context, our findings suggest that stronger associations with the genera Claroideoglomus and Glomus may potentially support crop tolerance-associated responses belowground. There is an urgent need for more exploration of how natural assemblages of AM fungi differentially mediate plant-herbivore interactions if we are to effectively manage soil fungi in sustainable agricultural systems.
Orthogonal synthetases for polyketide precursors
Authors: Fricke Riley , Swenson Cameron V. , Roe Leah Tang , Hamlish Noah , Ad Omer , Smaga Sarah , Gee Christine L. , Schepartz Alanna
Published: March 2022

The absence of orthogonal aminoacyl-tRNA synthetases that accept non-L-α-amino acids is the primary bottleneck hindering the in vivo translation of sequence-defined hetero-oligomers. Here we report PylRS enzymes that accept α-hydroxy acids, α-thio acids, N-formyl-L-α-amino acids, and α-carboxyl acid monomers (malonic acids) that are formally precursors to polyketide natural products. These monomers are all accommodated and accepted by the translation apparatus in vitro. High-resolution structural analysis of the complex between one such PylRS enzyme and a meta-substituted 2-benzylmalonate derivative reveals an active site that discriminates pro-chiral carboxylates and accommodates the large size and distinct electrostatics of an α-carboxyl acid substituent. This work emphasizes the potential of PylRS-derived enzymes for acylating tRNA with monomers whose α-substituent diverges significantly from the α-amine embodied in proteinogenic amino acids. These enzymes could act in synergy with natural or evolved ribosomes to generate diverse sequence-defined non-protein hetero-oligomers.
Rac1 controls cell turnover and mammary gland reversibility in post-partum involution
Authors: Mironov Aleksander , Fisher Matthew , Elsayed Randa , Karabulutoglu Melis , Akhtar Nasreen
Published: March 2022

Cell turnover in adult tissues is essential for maintaining tissue homeostasis over a lifespan and for inducing the morphological changes associated with the reproductive cycle. However, the underlying mechanisms that coordinate the balance of cell death and proliferation remain unsolved. Using the mammary gland we have discovered that Rac1 acts as a nexus to control cell turnover. Post-lactational tissue regression is characterized by the death of milk secreting alveoli, but the process is reversible within the first 48h if feeding recommences. In mice lacking epithelial Rac1, alveolar regression was delayed. This defect did not result from failed cell death but rather increased cell turnover. Fitter progenitor cells inappropriately divided, regenerating the alveoli but cell death also concomitantly accelerated. We discovered that progenitor cell hyperproliferation was linked to non-autonomous effects of Rac1 deletion on the macrophageal niche with heightened inflammation. Moreover, loss of Rac1 impaired cell death with autophagy but switched the cell death route to apoptosis. Finally, mammary gland reversibility failed in the absence of Rac1 as the regenerated alveoli failed to recommence lactation upon re-suckling.
Genetic structure analysis on leopard cat reveals the effects of habitat fragmentation on subpopulation differentiation in Beijing
Authors: Teng Yang , Yang Jing , Ju Longfei , Gai Lixin , Li Jian , Gao Fuli , Bao Weidong
Published: March 2022

In the face of habitat shrinkage and segregation, the survival of wild cats looks bleak. Interpreting the population genetic structure during habitat fragmentation is critical to planning effective management strategies. To reveal the segregation effects of road construction and human settlement on population genetic structure, we noninvasively analyzed fecal DNA samples from leopard cats (Prionailurus bengalensis) from five nature reserves in mountainous areas around Beijing. We focused on molecular microsatellite markers and the mitochondrial control region. A total of 112 individual leopard cats were identified among 601 samples of scat, and generally moderate population genetic diversity was detected. Microsatellite marker–based gene flow (Nm) and STRUCTURE analyses showed no obvious discrepancies among the subpopulations; however, the calculation of genetic distance and construction of a phylogenetic tree of the mitochondrial control region revealed a trend toward differentiation from the other subpopulations in the Songshan subpopulation, which indicates habitat fragmentation effects. Because the isolated Songshan subpopulation may evolve independently, we suggest that its genetic structure be monitored every 5 years to detect any changes and that individuals be introduced as needed to maintain the viability of this subpopulation.
Image segmentation and separation of spectrally similar dyes in fluorescence microscopy by dynamic mode decomposition of photobleaching kinetics
Authors: Wüstner Daniel
Published: March 2022

Background

Image segmentation in fluorescence microscopy is often based on spectral separation of fluorescent probes (color-based segmentation) or on significant intensity differences in individual image regions (intensity-based segmentation). These approaches fail, if dye fluorescence shows large spectral overlap with other employed probes or with strong cellular autofluorescence.

Results

Here, a novel model-free approach is presented which determines bleaching kinetics based on dynamic mode decomposition (DMD) and uses the inferred photobleaching kinetics to distinguish different probes or dye molecules from autofluorescence. DMD is a data-driven computational method for detecting and quantifying dynamic events in complex spatiotemporal data. Here, DMD is used to determine photobleaching characteristics of a fluorescent sterol probe, dehydroergosterol (DHE), compared to that of cellular autofluorescence in the nematode Caenorhabditis elegans. It is shown that decomposition of those dynamic modes allows for precise image segmentation, thereby separating probe from autofluorescence without invoking a particular model for the bleaching process. In a second application, DMD of dye-specific photobleaching is used to separate two green-fluorescent dyes, an NBD-tagged sphingolipid and Alexa488-transferrin, thereby assigning them to different cellular compartments.

Conclusions

Data-based decomposition of dynamic modes can be employed to analyze spatially varying photobleaching of fluorescent probes in cells and tissues for image segmentation, discrimination of probe from autofluorescence and image denoising. The new method should find wide application in analysis of dynamic fluorescence imaging data.
Rate-distortion theory of neural coding and its implications for working memory
Authors: Jakob Anthony M.V. , Gershman Samuel J.
Published: March 2022

Rate-distortion theory provides a powerful framework for understanding the nature of human memory by formalizing the relationship between information rate (the average number of bits per stimulus transmitted across the memory channel) and distortion (the cost of memory errors). Here we show how this abstract computational-level framework can be realized by a model of neural population coding. The model reproduces key regularities of visual working memory, including some that were not previously explained by population coding models. We verify a novel prediction of the model by reanalyzing recordings of monkey prefrontal neurons during an oculomotor delayed response task.
IntegronFinder 2.0: identification and analysis of integrons across Bacteria, with a focus on antibiotic resistance in Klebsiella
Authors: Néron Bertrand , Littner Eloi , Haudiquet Matthieu , Perrin Amandine , Cury Jean , Rocha Eduardo P.C.
Published: March 2022

Integrons are mobile genetic elements that contain multiple cassettes encoding accessory genes whose order is shuffled by a specific integrase. Integrons within mobile genetic elements often contain multiple antibiotic resistance genes that they spread among nosocomial pathogens and contribute to the current antibiotic resistance crisis. However, most integrons are presumably sedentary and encode a much broader diversity of functions. IntegronFinder is a widely used software to identify novel integrons in bacterial genomes, but has aged and lacks some useful functionalities to handle very large datasets of draft genomes or metagenomes. Here, we present IntegronFinder version 2. We have updated the code, improved its efficiency and usability, adapted the output to incomplete genome data, and added a few novel functions. We describe these changes and illustrate the relevance of the program by analyzing the distribution of integrons across more than 20,000 fully sequenced genomes. We also take full advantage of its novel capabilities to analyze close to 4 thousandKlebsiella pneumoniaegenomes for the presence of integrons and antibiotic resistance genes within them. Our data shows thatK. pneumoniaehas a large diversity of integrons and the largest mobile integron in our database of plasmids. The pangenome of these integrons contains a total of 165 different gene families with most of the largest families being related with resistance to numerous types of antibiotics. IntegronFinder is a free and open-source software available athttps://github.com/gem-pasteur/Integron_Finder.
Multiscale structural anisotropy in pulvinus motor organs of the sensitive plant Mimosa pudica
Authors: Sleboda David A. , Geitmann Anja , Sharif-Naeini Reza
Published: March 2022

Pulvini are joint-like motor organs that power active leaf movement in many plants. Multiple structural specializations spanning subcellular, cellular, and tissue scales of pulvinus organization have been described; however, the impacts of multiscale mechanics on pulvinus physiology remain poorly understood. To investigate the influence of multiscale morphology on turgor-induced deformation, we visualized Mimosa pudica pulvinus morphology at multiple hierarchical scales of organization and used osmotic perturbations to experimentally swell pulvini in incremental states of dissection. We observed directional cellulose microfibril reinforcement, oblong, spindle-shaped primary pit fields, and flattened, disk-like cell geometries in the parenchyma of M. pudica. Consistent with these observations, isolated parenchyma tissues displayed highly anisotropic swelling behaviors indicating a high degree of mechanical anisotropy. Swelling behaviors at higher scales of pulvinus organization were also influenced by the presence of the pulvinus epidermis, which displayed oblong epidermal cells oriented transverse to the pulvinus long axis. Our findings indicate that structural specializations spread across multiple hierarchical scales of organization guide hydraulic deformation of pulvini, suggesting that multiscale mechanics are crucial to the translation of cell-level turgor variations into organ-scale pulvinus motion in vivo.
A2A Receptor contributes to tumor progression in P2X7 null mice
Authors: De Marchi Elena , Pegoraro Anna , Turiello Roberta , Di Virgilio Francesco , Morello Silvana , Adinolfi Elena
Published: March 2022

ATP and adenosine are key constituents of the tumor niche where they exert opposite and complementary roles. ATP promotes tumor growth but also immune eradicating responses mainly via the P2X7 receptor (P2X7R), while adenosine acts as a potent immune suppressor and facilitates neovascularization thanks to A2A receptor (A2AR) activity. However, studies exploring the interplay between P2X7R and A2AR in the tumor microenvironment are as yet missing. Here we investigated tumor growth in C57/bl6 P2X7 null mice inoculated with B16-F10 melanoma cells, showing that several pro-inflammatory cytokines (IL1-β, TNF-α, IL-6, IL-12, IL-17, IFN-γ) were significantly decreased while the immune suppressant TGF-β was almost three-fold increased. Interestingly, tumors growing in P2X7-null mice also upregulated tumor-associated and splenic A2AR, suggesting that immunosuppression associated to lack of the P2X7R might depend upon A2AR overexpression. Immunohistochemical analysis showed that tumor cells A2AR expression was increased, especially around necrotic areas, and that VEGF and the endothelial marker CD31 were also upregulated. The A2AR antagonist SCH-58261 reduced tumor growth similarly in the P2X7 WT, or null mice strain. However, SCH-58261only reduced VEGF in the P2X7-KO mice, thus supporting the hypothesis of an A2AR mediated increase in vascularisation in P2X7-null host. SCH-58261 administration also significantly reduced intratumor TGF-β, thus supporting a key immune suppressive role of A2AR in our model. This study shows a novel direct correlation between P2X7R and A2AR in oncogenesis and paves the way for new combined therapies promoting anti-cancer immune responses and reducing tumor vascularization.
Time-Dependent Increase in Susceptibility and Severity of Secondary Bacterial Infection during SARS-CoV-2 Infection
Authors: Smith Amanda P. , Williams Evan P. , Plunkett Taylor R. , Selvaraj Muneeswaran , Lane Lindey C. , Zalduondo Lillian , Xue Yi , Vogel Peter , Channappanavar Rudragouda , Jonsson Colleen B. , Smith Amber M.
Published: March 2022

Secondary bacterial infections can exacerbate SARS-CoV-2 infection, but their prevalence and impact remain poorly understood. Here, we established that a mild to moderate SARS-CoV-2 infection increased the risk of pneumococcal coinfection in a time-dependent, but sexindependent, manner in the transgenic K18-hACE mouse model of COVID-19. Bacterial coinfection was not established at 3 d post-virus, but increased lethality was observed when the bacteria was initiated at 5 or 7 d post-virus infection (pvi). Bacterial outgrowth was accompanied by neutrophilia in the groups coinfected at 7 d pvi and reductions in B cells, T cells, IL-6, IL-15, IL-18, and LIF were present in groups coinfected at 5 d pvi. However, viral burden, lung pathology, cytokines, chemokines, and immune cell activation were largely unchanged after bacterial coinfection. Examining surviving animals more than a week after infection resolution suggested that immune cell activation remained high and was exacerbated in the lungs of coinfected animals compared with SARS-CoV-2 infection alone. These data suggest that SARS-CoV-2 increases susceptibility and pathogenicity to bacterial coinfection, and further studies are needed to understand and combat disease associated with bacterial pneumonia in COVID-19 patients.
Maximize crop production and environmental sustainability: insights from an ecophysiological model of plant-pest interactions and multi-criteria decision analysis
Authors: Zaffaroni Marta , Bevacqua Daniele
Published: March 2022

Satisfying the demand for agricultural products while also protecting the environment from negative impacts of agriculture is a major challenge for crop management. We used an ecophysiological model of plant-pest interaction and multi-criteria decision analysis to optimize crop management when considering two contrasting objectives: (1) maximizing crop production and (2) minimizing environmental impact related to fertilization, irrigation and pesticide deployment. The model provides an indicator of crop production for 27 management scenarios, obtained combining three levels of fertilization, irrigation and pesticide use, respectively. We computed the environmental impact relevant to each management scenario by means of a weighted sum of costs assigned to fertilization, irrigation and pesticide use. We identified the optimal scenarios with respect to the considered objectives analysing the Pareto front. These scenarios were mostly characterized by high fertilization and no pesticide use. We evaluated the multi-functionality of the optimal scenarios by mean of the Gini coefficient: the scenario better assuring the equality between the two objectives was characterized by high fertilization, intermediate irrigation and no pesticide. Although our results remain qualitative and not immediately transferable to agronomic practices, our analytical framework provides a useful tool to evidence trade-offs among two contrasting objectives and provide solutions to act in an efficient way by leaving a certain degree of freedom to the political decision maker.
BRAF-V600E-Mediated Erk Activation Promotes Sustained Cell Cycling and Broad Transcriptional Changes in Neonatal Cardiomyocytes
Authors: Strash Nicholas , DeLuca Sophia , Janer Carattini Geovanni L. , Chen Yifan , Scherba Jacob , Jain Mehul , Naseri Ramona , Wu Tianyu , Bursac Nenad
Published: March 2022

Mitogens capable of promoting cardiomyocyte proliferation represent important targets for functional heart regeneration following myocardial infarction. We previously described an ERK-dependent pro-proliferative tissue phenotype following overexpression of constitutively-active (ca) human ERBB2 in both neonatal rat ventricular myocytes (NRVMs) and human iPSC-derived cardiomyocytes (hiPSC-CMs). Since ERBB2 canonically regulates multiple other pathways in addition to ERK, it is unclear whether ERK activation alone can drive CM proliferation. Here, we activated ERK in a targeted fashion by CM-specific lentiviral expression of a constitutively active mutant of BRAF, BRAF-V600E (caBRAF), in cultured NRVMs and examined the effects on engineered NRVM tissue proliferation, morphology, and function. caBRAF expression induced ERK activation, tissue growth, loss of contractile function, and increased tissue stiffness, all of which were sustained for at least 4 weeksin vitro. From bulk RNA-sequencing analysis of engineered tissues, we found that caBRAF had broad transcriptomic effects on CMs and induced a shift to glycolytic metabolism. Together, this work shows that direct ERK activation is sufficient to modulate CM cycling and functional maturation in a cell-autonomous fashion and could offer a potential target for cardiac regenerative therapies.
IGF2BP1/IMP1 deletion enhances a facultative stem cell state via regulation ofMAP1LC3B
Authors: Parham Louis R. , Williams Patrick A. , Chatterji Priya , Acheampong Kofi K. , Danan Charles H. , Katada Kay , Ma Xianghui , Simon Lauren A. , Naughton Kaitlyn E. , Mizuno Rei , Karakasheva Tatiana , McMillan Emily A. , Whelan Kelly A. , Brady Donita C. , Shaffer Sydney M. , Hamilton Kathryn E.
Published: March 2022

Homeostatic tissue maintenance requires coordinated regulation of metabolic processes including macroautophagy/autophagy. Autophagy dysregulation underlies numerous human diseases. Our prior work revealed that the RNA binding protein IGF2BP1/IMP1 binds transcripts encoding autophagy-related proteins. Furthermore, Imp1 deletion in gastrointestinal epithelial cells in mice was associated with enhanced autophagy flux and improved recovery from tissue injury. In the current study, we evaluated molecular mechanisms underlying IMP1 modulation of autophagy. We provide a mechanism of direct IMP1 regulation of MAP1LC3B that is dependent upon IMP1 phosphorylation or cell stress, suggesting dynamic modulation of Imp1-mediated autophagy repression that facilitates tissue regeneration. More broadly, our study supports a new mechanism by which tissue regeneration is modulated post-transcriptionally via cell state rather than changes in stem or other cell lineages. This new mechanism may be particularly important in gastrointestinal epithelial cells, where autophagy is essential for tissue recovery following injury, or in diseases such as inflammatory bowel disease where defective autophagy is implicated.
Sleep and circadian rhythm disruption alters the lung transcriptome to predispose to viral infection
Authors: Taylor Lewis , Von Lendenfeld Felix , Ashton Anna , Sanghani Harshmeena , Tam Eric , Usselmann Laura , Veretennikova Maria , Dallmann Robert , McKeating Jane A , Vasudevan Sridhar , Jagannath Aarti
Published: March 2022

Sleep and circadian rhythm disruption (SCRD), as encountered during shift work, increases the risk of respiratory viral infection including SARS-CoV-2. However, the mechanism(s) underpinning higher rates of respiratory viral infection following SCRD remain poorly characterised. To address this, we investigated the effects of acute sleep deprivation on the mouse lung transcriptome. Here we show that sleep deprivation profoundly alters the transcriptional landscape of the lung, causing the suppression of both innate and adaptive immune systems, disrupting the circadian clock, and activating genes implicated in SARS-CoV-2 replication, thereby generating a lung environment that promotes viral infection and associated disease pathogenesis. Our study provides a mechanistic explanation of how SCRD increases the risk of respiratory viral infections including SARS-CoV-2 and highlights therapeutic avenues for the prevention and treatment of COVID-19.
RdRp-scan: A Bioinformatic Resource to Identify and Annotate Divergent RNA Viruses in Metagenomic Sequence Data
Authors: Charon Justine , Buchmann Jan P. , Sadiq Sabrina , Holmes Edward C.
Published: March 2022

Despite a rapid expansion in the number of known RNA viruses following the advent of metagenomic sequencing, the identification and annotation of highly divergent RNA viruses remains challenging, particularly from poorly characterized hosts and environmental samples. Protein structures are more conserved than primary sequence data, such that structure-based comparisons provide an opportunity to reveal the viral “dusk matter”: viral sequences with low, but detectable, levels of sequence identity to known viruses with available protein structures. Here, we present a new open computational and resource – RdRp-scan – that contains a standardized bioinformatic toolkit to identify and annotate divergent RNA viruses in metagenomic sequence data based on the detection of RNA dependent RNA polymerase (RdRp) sequences. By combining RdRp-specific Hidden Markov models (HMM) and structural comparisons we show that RdRp-scan can efficiently detect RdRp sequences with identity levels as low as 10% to those from known viruses and not identifiable using standard sequence-to-sequence comparisons. In addition, to facilitate the annotation and placement of newly detected and divergent virus-like sequences into the known diversity of RNA viruses, RdRp-scan provides new custom and curated databases of viral RdRp sequences and core motif, as well as pre-built RdRp alignments. In parallel, our analysis of the sequence diversity detected by RdRp-scan revealed that while most of the taxonomically unassigned RdRps fell into pre-established clusters, some sequences cluster into potential new orders of RNA viruses related to the Wolframvirales and Tolivirales. Finally, a survey of the conserved A, B and C RdRp motifs within the RdRp-scan sequence database revealed additional variations of both sequence and position, which might provide new insights into the structure, function and evolution of viral RdRps.
Synaptotagmin 1 mediates toxicity of botulinum neurotoxin type A
Authors: Joensuu Merja , Lanoue Vanessa , Syed Parnayan , Wallis Tristan P. , Rae James , Blum Ailisa , Gormal Rachel , Small Christopher , Sanders Shanley , Jiang Anmin , Mahrhold Stefan , Krez Nadja , Cousin Michael , Cooper-White Ruby , Cooper-White Justin J. , Collins Brett M. , Parton Robert G. , Balistreri Giuseppe , Rummel Andreas , Meunier Frédéric A.
Published: March 2022

The extreme neurotoxicity of botulinum neurotoxins (BoNTs), broadly used as a therapeutics, is mediated by their direct binding to two plasma membrane receptors: polysialogangliosides (PSGs) and serotype-dependently either synaptotagmin 1/2 (Syt1/2) or synaptic vesicle glycoprotein 2 (SV2). Here, we demonstrate that although BoNT/A serotype binds directly to PSG and SV2, its neurotoxicity depends on Syt1. Using single-molecule superresolution microscopy of pathological concentrations of BoNT/A holotoxins, we demonstrate that the toxin binds to a preassembled PSG-Syt1 complex that forms nanoclusters with SV2 on the plasma membrane of hippocampal neurons. This coincidental interaction controls the selective endocytic targeting of BoNT/A into synaptic vesicles, leading to incapacitation of neuronal communication. Our results suggest that Syt1-SV2 plasma membrane nanoclusters may acts as a common target for various BoNT serotypes.

One-Sentence Summary

BoNT/A hijacks an intrinsic tripartite PSG-Syt1-SV2 endocytic sorting mechanism to incapacitate neuronal communication
dSeqSb: A systems biology approach to decipher dynamics of host-pathogen interactions using temporal dual RNA-seq data
Authors: Dinarvand Mojdeh , Kock Forrest , Al Mouiee Daniel , Vuong Kaylee , Vijayan Abhishek , Tanzim Afia Fariha , Azad AKM , Penesyan Anahit , Castaño-Rodríguez Natalia , Vafaee Fatemeh
Published: March 2022

Infection triggers a dynamic cascade of reciprocal events between host and pathogen wherein the host activates complex mechanisms to recognise and kill pathogens while the pathogen adjusts its virulence and fitness to avoid eradication by the host. The interaction between the pathogen and the host results in large-scale changes in gene expression in both organisms. Dual RNA-seq, the simultaneous detection of host and pathogen transcripts, has become a leading approach to unravel complex molecular interactions between the host and the pathogen and is particularly informative for intracellular organisms. The amount of in vitro and in vivo dual RNA-seq data is rapidly growing which demands computational pipelines to effectively analyse such data. In particular, holistic, systems-level, and temporal analyses of dual RNA-seq data are essential to enable further insights into the host-pathogen transcriptional dynamics and potential interactions. Here, we developed an integrative network-driven bioinformatics pipeline, dRNASb, a systems biology-based computational pipeline to analyse temporal transcriptional clusters, incorporate molecular interaction networks (e.g., protein-protein interactions), identify topologically and functionally key transcripts in host and pathogen, and associate host and pathogen temporal transcriptome to decipher potential between-species interactions. The pipeline is applicable to various dual RNA-seq data from different species and experimental conditions. As a case study, we applied dRNASb to analyse temporal dual RNA-seq data of Salmonella-infected human cells, which enabled us to uncover genes contributing to the infection process and their potential functions and to identify potential host-pathogen interactions between host and pathogen genes. Overall, dRNASb has the potential to identify key genes involved in bacterial growth or host defence mechanisms for future uses as therapeutic targets.
Neuronal miR-138 represses HSV-2 lytic infection by regulating viral and host genes with mechanistic differences compared to HSV-1
Authors: Chen Siyu , Deng Yue , Chen Hongjia , Lin Yuqi , Yang Xuewei , Sun Boqiang , Pan Dongli
Published: March 2022

Herpes simplex virus 2 (HSV-2) establishes latent infection in dorsal root ganglion (DRG) neurons after productive (lytic) infection in peripheral tissues. A neuron-specific microRNA, miR-138, favors HSV-1 latency by repressing viral ICP0, and host Oct-1 and Foxc1 genes, yet the role of miR-138 in HSV-2 infection was unknown. The ICP0 mRNAs of HSV-1, HSV-2 and chimpanzee herpesvirus each have one to two canonical miR-138 binding sites. The sites are 100% conserved in 308 HSV-1 and 300 HSV-2 published sequences of clinical isolates. In co-transfection assays, miR-138 repressed HSV-2 ICP0 expression through the seed region and surrounding interactions that are different from HSV-1. An HSV-2 mutant with disrupted miR-138 binding sites on ICP0 showed increased ICP0 expression in Neuro-2a cells. Photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation confirmed miR-138 binding to HSV-2 ICP0, and identified UL19 and UL20 as additional targets, whose expression was repressed by miR-138 during co-transfection. In Neuro-2a cells, transfected miR-138 and its antagomir decreased and increased HSV-2 replication, respectively, and knockout experiment showed that miR-138’s host targets OCT-1 and FOXC1 were important for HSV-2 replication. In primary mouse DRG neurons, both ICP0 and FOXC1 positively regulated HSV-2 replication, but both overexpressed and endogenous miR-138 suppressed HSV-2 replication primarily by repressing ICP0 expression. Thus, miR-138 can suppress HSV-2 neuronal replication through multiple viral and host pathways. These results reveal functional similarities and mechanistic differences in how miR-138 regulates HSV-1 and HSV-2 infection and indicate an evolutionary advantage of using miR-138 to repress lytic infection in neurons.

Importance

Herpes simplex virus 1 (HSV-1) and HSV-2 are closely related viruses with major differences. Both viruses establish latency in neurons from which they reactivate to cause disease. A key aspect of HSV latency is repression of productive infection in neurons. Based on previous work with HSV-1, we investigated the role of a neuron-specific microRNA, miR-138, in HSV-2 infection, and established it as a repressor of HSV-2 productive infection in neuronal cells. This repression is mediated mainly by targeting viral ICP0 and host Foxc1 mRNAs, but other pathways also contribute. Despite functional conservation of the role of miR-138 between HSV-1 and HSV-2, many molecular mechanisms differ including how miR-138 represses ICP0 expression and miR-138 targeting of HSV-2 but not HSV-1 UL19 and UL20. To our knowledge, this study provides the first example of host microRNA regulation of HSV-2 infection.
Real-Time Flow Cytometry to assess qualitative and quantitative responses of oral pathobionts during exposure to antiseptics
Authors: Chatzigiannidou I. , Heyse J. , Props R. , Rubbens P. , Teughels W. , Van de Wiele T. , Boon N.
Published: March 2022

Antiseptics are widely used in oral healthcare to prevent or treat oral diseases, such as gingivitis and periodontitis. However, the incidence of bacteria being tolerant to standard antiseptics has sharply increased over the last few years. This stresses the urgency for surveillance against tolerant organisms, as well as the discovery of novel antimicrobials. Traditionally, susceptibility to antimicrobials is assessed by broth micro-dilution or disc diffusion assays, both of which are time-consuming, labor-intensive and provide limited information on the mode of action of the antimicrobials. The above-mentioned limitations highlight the need for the development of new methods to monitor and further understand antimicrobial susceptibility. Here, we used real-time flow cytometry, combined with membrane permeability staining, as a quick and sensitive technology to study the quantitative and qualitative response of two oral pathobionts to different concentrations of chlorhexidine, cetylpyridinium chloride or triclosan. Apart from the real-time monitoring of cell damage, we further applied a phenotypic fingerprint method to differentiate between the bacterial subpopulations that arose due to treatment. We quantified the pathobiont damage rate of different antiseptics at different concentrations within 15 minutes of exposure and identified the conditions under which the bacteria were most susceptible. Moreover, we detected species-specific and treatment-specific phenotypic subpopulations. This proves that real-time flow cytometry can provide information on the susceptibility of different microorganisms in a short time frame while differentiating between antiseptics and thus could be a valuable tool in the discovery of novel antimicrobial compounds while at the same time deciphering their mode of action.
Transcriptomic clustering of critically ill COVID-19 patients
Authors: López-Martínez Cecilia , Martín-Vicente Paula , Gómez de Oña Juan , López-Alonso Inés , Gil-Peña Helena , Cuesta-Llavona Elías , Fernández-Rodríguez Margarita , Crespo Irene , Salgado del Riego Estefanía , Rodríguez-García Raquel , Parra Diego , Fernández Javier , Rodríguez-Carrio Javier , Dávalos Alberto , Chapado Luis A , Coto Eliecer , Albaiceta Guillermo M , Amado-Rodríguez Laura
Published: March 2022

Infections caused by SARS-CoV-2 may cause a severe disease, termed COVID-19, with significant mortality. Host responses to this infection, mainly in terms of systemic inflammation, have emerged as key pathogenetic mechanisms, and their modulation is the only therapeutic strategy that has shown a mortality benefit. Herein, we used peripheral blood transcriptomes of critically-ill COVID-19 patients obtained at admission in an Intensive Care Unit (ICU), to identify two transcriptomic clusters characterized by expression of either interferon-related or immune checkpoint genes, respectively. These profiles have different ICU outcome, in spite of no major clinical differences at ICU admission. A transcriptomic signature was used to identify these clusters in an external validation cohort, yielding similar results. These findings reveal different underlying pathogenetic mechanisms and illustrate the potential of transcriptomics to identify patient endotypes in severe COVID-19, aimed to ultimately personalize their therapies.
Duration of viable virus shedding in SARS-CoV-2 omicron variant infection
Authors: Boucau Julie , Marino Caitlin , Regan James , Uddin Rockib , Choudhary Manish C. , Flynn James P. , Chen Geoffrey , Stuckwisch Ashley M. , Mathews Josh , Liew May Y. , Singh Arshdeep , Lipiner Taryn , Kittilson Autumn , Melberg Meghan , Li Yijia , Gilbert Rebecca F. , Reynolds Zahra , Iyer Surabhi L. , Chamberlin Grace C. , Vyas Tammy D. , Goldberg Marcia B. , Vyas Jatin M. , Li Jonathan Z. , Lemieux Jacob E. , Siedner Mark J. , Barczak Amy K.
Published: March 2022

Clinical features of SARS-CoV-2 Omicron variant infection, including incubation period and transmission rates, distinguish this variant from preceding variants. However, whether the duration of shedding of viable virus differs between omicron and previous variants is not well understood. To characterize how variant and vaccination status impact shedding of viable virus, we serially sampled symptomatic outpatients newly diagnosed with COVID-19. Anterior nasal swabs were tested for viral load, sequencing, and viral culture. Time to PCR conversion was similar between individuals infected with the Delta and the Omicron variant. Time to culture conversion was also similar, with a median time to culture conversion of 6 days (interquartile range 4-8 days) in both groups. There were also no differences in time to PCR or culture conversion by vaccination status.
Viral cultures, Polymerase Chain Reaction Cycle Threshold Values and Viral Load Estimation for SARS-CoV-2 Infectious Potential Assessment in Hematopoietic Stem Cell and Solid Organ Transplant Patients: A Systematic Review
Authors: Jefferson Tom , Spencer Elizabeth A. , Conly John M. , Rosca Elena C. , Maltoni Susanna , Brassey Jon , Onakpoya Igho J. , Evans David H. , Heneghan Carl J. , Plüddemann Annette
Published: March 2022

Background

Organ transplant recipients are at increased vulnerability to SARS-CoV-2 due to immunosuppression and may pose a continued transmission risk especially within hospital settings. Detailed case reports including symptoms, viral load and infectiousness, defined by the presence of replication-competent viruses in culture, provide an opportunity to examine the relationship between clinical course, burden and contagiousness, and provide guidance on release from isolation.

Objectives

We performed a systematic review to investigate the relationship in transplant recipients between serial SARS-CoV-2 RT-PCR cycle threshold (Ct) value or cycle of quantification value (Cq), or other measures of viral burden and the likelihood and duration of the presence of infectious virus based on viral culture including the influence of age, sex, underlying pathologies, degree of immunosuppression, and/or vaccination on this relationship.

Methods

We searched LitCovid, medRxiv, Google Scholar and WHO Covid-19 databases, from 1 November 2019 until 31 December 2021. We included studies reporting relevant data for transplantees with SARS-CoV-2 infection: results from serial RT-PCR testing and viral culture data from the same respiratory samples. We assessed methodological quality using five criteria, and synthesised the data narratively and graphically.

Results

We included 10 case reports and case series reporting on 38 transplantees. We observed a relationship between proxies of viral burden and likelihood of shedding replication-competent SARS-CoV-2. Two individuals shed replication-competent viruses over 100 days after infection onset. Lack of standardisation of testing and reporting platforms precludes establishing a definitive viral burden cut-off. However, most transplantees stopped shedding competent viruses when the RT-PCR cycle threshold was above 30 despite differences across platforms.

Conclusions

Viral burden is a reasonable proxy for infectivity when considered within the context of the clinical status of each patient. Standardised study design and reporting are essential to standardise guidance based on an increasing evidence base.
Efficacy of bladder training in adults with overactive bladder: A systematic review protocol
Authors: Lopes Rocha Anna Karoline , Monteiro Silvia Elizate , Volpato Maria P. , Paula e Silva Dinah Verleun de , Valim Lilian , Riccetto Cássio , Botelho Simone
Published: March 2022

Introduction

The aim of this systematic review will be to investigate and update whether bladder training can promote improvement of symptoms of overactive bladder syndrome with or without urgency urinary incontinence in adults.

Methods

We will perform a systematic review according to the Cochrane methodology of randomized controlled trials. An overall search strategy will be developed and adapted for each database. A bibliographic search will be conducted in eight databases - PubMed, PEDro, SciELO, LILACS, Cochrane Library, Web of Science, EMBASE, CINAHL, by manual searching. The MeSH terms will be “Bladder Training”, “Bladder Drill”, “Bladder Re-education”, “Bladder Retraining”, “Bladder Discipline”, “Overactive Bladder”, “Bladder, Overactive”, “Overactive Urinary Bladder”, “Urinary Bladder”, “Overactive, Urinary Bladder”, “Bladder, Urinary”, “Urinary Bladder Disease”, “Bladder Disease”, “Bladder Detrusor Muscle” and “Detrusor Muscle, Bladder”. Meta-analysis, if plausible, will be performed by the software Review Manager 5.4. Primary outcomes: symptoms of overactive bladder syndrome (urinary urgency with daytime voiding frequency, nocturia with or without urgency urinary incontinence), and cure/improvement assessed by instruments. Secondary outcomes: quality of life, functional assessment, validated scale/questionnaire and adverse events. Quality assessment will be performed by Cochrane instrument and quality of evidence will be assessed by GRADE.

Discussion

This study is a review of randomized controlled studies to analyze the efficacy of bladder training in improving the symptoms of adults with overactive bladder syndrome. The study design of randomized controlled trials for a higher level of scientific evidence was chosen. The aim is to obtain results that allow further studies and evidence that this intervention generates beneficial effects in the sample studied.

Trial registration

Systematic review registration

PROSPERO CRD42022301522.
Racial/Ethnic Disparities in the Observed COVID-19 Case Fatality Rate Among the U.S. Population
Authors: Schumm L. Philip , Giurcanu Mihai C. , Locey Kenneth J. , Ortega Jean Czerlinski , Zhang Zhenyu , Grossman Robert L.
Published: March 2022

Purpose

During the initial 12 months of the pandemic, racial and ethnic disparities in COVID-19 death rates received considerable attention but it has been unclear whether disparities in death rates were due to disparities in case fatality rates (CFRs), incidence rates or both. We examined differences in observed COVID-19 case fatality rates (CFRs) between U.S. Whites, Blacks/African Americans and Latinx during this period.

Methods

Using data from the COVID Tracking Project (CTP) and the CDC’s COVID-19 Case Surveillance Public Use dataset, we calculated CFR ratios comparing minority groups to Whites, both overall and separately by age group. We also used a model of monthly COVID-19 deaths to estimate CFR ratios, adjusting for age, gender, and differences across states and time.

Results

Overall Blacks and Latinx had lower CFRs than Whites. However, when adjusting for age, Blacks and Latinx had higher CFRs than Whites among those younger than 65. CFRs varied substantially across states and time.

Conclusions

Disparities in COVID-19 case fatality among U.S. Blacks and Latinx under age 65 were evident during the first year of the pandemic. Understanding racial/ethnic differences in COVID-19 CFRs is challenging due to limitations in available data.
Cyclin CLB2 mRNA localization and protein synthesis link cell cycle progression to bud growth
Authors: Maekiniemi Anna , Savakis Philipp , Snoep Jacky L , Seiler Markus , van Rossum Kelly , van Niekerk David D. , Zarnack Kathi , Singer Robert H , Tutucci Evelina
Published: March 2022

Clb2 is a conserved mitotic B-type cyclin, the levels of which are finely controlled to drive progression through the cell cycle. While it is known thatCLB2transcription and Clb2 protein degradation are important for precise control of its expression, it remains unclear whether the synthesis of Clb2 is also regulated. To address whether and how Clb2 expression levels respond to cell growth changes and adapt cell cycle progression, we combined single-cell and single-molecule imaging methods to measureCLB2mRNA and protein expression throughout theSaccharomyces cerevisiaecell cycle. We found that theCLB2mRNA was efficiently localized to the yeast bud as soon as this compartment was formed, but strikingly the Clb2 protein accumulated in the mother nucleus. TheCLB2mRNA localization in the yeast bud by the She2-3 complex did not control protein localization but rather promotedCLB2translation. Moreover,CLB2mRNA bud localization and protein synthesis were coupled and dependent on a single secondary structure -a ZIP code- located in the coding sequence. In aCLB2ZIP code mutant, mRNA localization was impaired and Clb2 protein synthesis decreased, resulting in changes in cell cycle distribution and increased size of daughter cells at birth. Finally, while in WT cells the Clb2 protein concentration followed bud growth, this relationship was impaired in the ZIP code mutant. We propose that S. cerevisiae couples the control ofCLB2mRNA bud localization and protein synthesis to coordinate cell growth and cell cycle progression. This mechanism extends our knowledge of CLB2 expression regulation, and constitutes a novel function for mRNA localization.
The laminin-keratin link shields the nucleus from mechanical deformation and signalling
Authors: Kechagia Zanetta , Sáez Pablo , Gómez-González Manuel , Zamarbide Martín , Andreu Ion , Koorman Thijs , Beedle Amy E.M. , Derksen Patrick W.B. , Trepat Xavier , Arroyo Marino , Roca-Cusachs Pere
Published: March 2022

The mechanical properties of the extracellular matrix (ECM) dictate tissue behaviour. In epithelial tissues, laminin is both a very abundant ECM component, and a key supporting element. Here we show that laminin hinders the mechanoresponses of breast epithelial cells by shielding the nucleus from mechanical deformation. Coating substrates with laminin-111, unlike fibronectin or collagen I, impairs cell response to substrate rigidity, and YAP nuclear localization. Blocking the laminin-specific integrin β4 increases nuclear YAP ratios in a rigidity dependent manner, without affecting cell forces or focal adhesions. By combining mechanical perturbations and mathematical modelling, we show that β4 integrins establish a mechanical linkage between the substrate and the keratin cytoskeleton, which stiffens the network and shields the nucleus from actomyosin-mediated mechanical deformation. In turn, this affects nuclear YAP mechanoresponses and chromatin methylation. Our results demonstrate a mechanism by which tissues can regulate their sensitivity to mechanical signals.
An amyloidosis-associated polymorphism does not alter LECT2 stability in vitro
Authors: Belonogov Liudmila , Taylor Paris E. , Wong Sherry , Morgan Gareth J.
Published: March 2022

Amyloid fibrils formed from leukocyte chemotactic factor 2 (LECT2), a secreted human cytokine, are associated with kidney failure in the disease amyloid LECT2 (ALECT2) amyloidosis. This rare disease was recognized in 2008 and has a variable prevalence worldwide. The mechanisms which lead to ALECT2 fibril deposition are not known and there are no treatments other than kidney transplant. The LECT2 gene harbors a single nucleotide polymorphism that leads to either a valine or isoleucine residue at position 40 of the mature protein. Most of the individuals diagnosed with ALECT2 amyloidosis are homozygous for valine at this position, which led us to hypothesize that the valine-containing variant of LECT2 protein is less stable and more prone to aggregation than the isoleucine-containing variant. Here, we investigate the structure, stability and aggregation of both variants of recombinant LECT2. Both variants have similar structures in solution; unfold in similar concentrations of urea; and aggregate at similar rates under native-like conditions, forming structures that bind to thioflavin T. Chelation of the structural zinc ion destabilizes both variants to a similar extent, and increases the rate at which they aggregate. We do not observe a consistent difference in stability or aggregation between the variants of LECT2, so we suggest that the presence of the valine residue at position 40 does not determine whether an individual is at increased risk of ALECT2 amyloidosis.