bluuebunny/crossref_metadata_2025 huggingface dataset:
Smallpox vaccination induces a substantial increase in commensal skin bacteria that promote pathology and enhance immunity
Authors: Shmeleva Evgeniya V. , de Agüero Mercedes Gomez , Wagner Josef , Enright Anton J. , Macpherson Andrew J. , Ferguson Brian J. , Smith Geoffrey L.
Published: July 2021

Interactions between pathogens, host microbiota and the immune system influence many physiological and pathological processes. In the 20th century, widespread dermal vaccination with vaccinia virus (VACV) led to the eradication of smallpox but how VACV interacts with the microbiota and whether this influences the efficacy of vaccination are largely unknown. Here we report that intradermal vaccination with VACV induces a large increase in the number of commensal bacteria in infected tissue, which enhance recruitment of inflammatory cells, promote tissue damage and increase immunity. Treatment of vaccinated specific-pathogen-free (SPF) mice with antibiotic, or infection of genetically-matched germ-free (GF) animals caused smaller lesions without alteration in virus titre. Tissue damage correlated with enhanced neutrophil and T cell infiltration and levels of pro-inflammatory tissue cytokines and chemokines. One month after vaccination, GF mice had reduced VACV-neutralising antibodies compared to SPF mice; while numbers of VACV-specific CD8+ T cells were equal in all groups of animals. Thus, skin microbiota may provide an adjuvant-like stimulus during vaccination with VACV. This observation has implications for dermal vaccination with live vaccines.

Author Summary

Smallpox was caused by variola virus and was eradicated by widespread dermal vaccination with vaccinia virus (VACV), a related orthopoxvirus of unknown origin. Eradication was declared in 1980 without an understanding of the immunological correlates of protection, or knowledge of the effect of smallpox vaccination on the local microbiota. Here we demonstrate that intradermal infection of mice with VACV induces a ∼1000-fold expansion of commensal skin bacteria that influence the recruitment of inflammatory cells into the infected tissue and enhance the size of the vaccination lesion. Antibiotic treatment reduced lesion size without changing virus titres. The bacterial expansion also contributes to the level of neutralizing antibodies at one month post vaccination, because genetically matched germ-free mice developed lower neutralizing antibodies than specific pathogen free controls. Thus, dermal infection by VACV enhanced bacterial growth and these bacteria promote pathology and enhance the antibody response. This finding has implication for dermal vaccination with live vaccines.
Localization of infection in neonatal rhesus macaques after oral viral challenge
Authors: Taylor Roslyn A. , McRaven Michael D. , Carias Ann M. , Anderson Meegan R. , Matias Edgar , Araínga Mariluz , Allen Edward J. , Rogers Kenneth A. , Gupta Sandeep , Kulkarni Viraj , Lakhashe Samir , Lorenzo-Redondo Ramon , Thomas Yanique , Strickland Amanda , Villinger Francois J , Ruprecht Ruth M. , Hope Thomas J.
Published: July 2021

While vertical transmission of human immunodeficiency virus (HIV) can occur in utero and during delivery and through breastfeeding. We utilized Positron Emission Tomography (PET) imaging coupled with fluorescent microscopy of 64Cu-labeled photoactivatable-GFP-HIV (PA-GFP-BaL) to determine how HIV virions distribute and localize in neonatal rhesus macaques two and four hours after oral viral challenge. Our results show that by four hours after oral viral exposure, HIV virions localize to and penetrate the rectal mucosa. We also used a dual viral challenge with a non-replicative viral vector and a replication competent SHIV-1157ipd3N4 to examine viral transduction and dissemination at 96 hours. Our data show that while SHIV-1157ipd3N4 infection can be found in the oral cavity and upper gastrointestinal (GI) tract, the small and large intestine contained the largest number of infected cells. Moreover, we found that T cells were the biggest population of infected immune cells. Thus, thanks to these novel technologies, we are able to visualize and delineate of viral distribution and infection throughout the entire neonatal GI tract during acute viral infection.

Author Summary

Approximately 1.8 million children are currently living with human immunodeficiency virus (HIV). While mother-to-child HIV transmission can occur in utero and during delivery, it most commonly occurs through breastfeeding, creating the need to understand how the virus moves throughout the body and infects the infant once breast milk is consumed. Here, we used multiple imaging techniques and PCR to determine how HIV distributes throughout the gastrointestinal tract after oral viral exposure and in which tissues and cell types become acutely infected. We found that HIV rapidly spreads throughout and penetrates the entire gastrointestinal tract as early as four hours after exposure. We also found that the intestine contained the largest number of infected cells at 96 hours and that most cells infected were T cells. Our study shows that these imaging technologies allow for the examination of viral distribution and infection in a rhesus macaque model.
Quantitative Single-Molecule Imaging with Statistical Machine Learning
Authors: Boonkird Artittaya , Nino Daniel F. , Milstein Joshua N.
Published: July 2021

Single-molecule localization microscopy (SMLM) is a super-resolution technique capable of rendering nanometer scale images of cellular structures. Recently, much effort has gone into developing SMLM into a quantitative method capable of determining the abundance and stoichiometry of macromolecular complexes. These methods often require knowledge of the complex photophysical properties of photoswitchable flourophores. We previously developed a simpler method built upon the observation that most photswitchable fluorophores emit an exponentially distributed number of blinks before photobleaching, but its utility was limited by the need to calibrate for the blinking distribution. Here we extend this method by incorporating a machine learning technique known as Expectation-Maximization (EM) and apply it to a statistical mixture model of monomers, dimers and trimers. We show that the protomer fractions and the underlying single-fluorophore blinking distributions can be inferred, simultaneously, from SMLM datasets, obviating the need for an additional calibration and greatly expanding the applicability of this technique. To illustrate the utility of our approach, we benchmark the method on both simulated datasets and experimental datasets assembled from dSTORM images of Alexa-647 labeled DNA nanostructures.
Nest relief in the cryptically-incubating semipalmated sandpiper is quick, but vocal
Authors: Bulla Martin , Muck Christina , Tritscher Daniela , Kempenaers Bart
Published: August 2021

Biparental care requires coordination between parents. Such coordination might prove difficult if opportunities to communicate are scarce, which might have led to the evolution of elaborate and noisy nest relief rituals in species facing a low risk of predation. However, whether such conspicuous rituals also evolved in species that avoid predation by relying on crypsis remains unclear. Here, we used a continuous monitoring system to describe nest relief behavior during incubation in an Arctic-breeding shorebird with passive nest defense, the semipalmated sandpiper (Calidris pusilla). We then explored whether nest relief behavior provides information about parental cooperation and predicts incubation effort. We found that incubating parents vocalized twice as much before the arrival of their partner than during other times of incubation. In 75% of nest reliefs, the incubating parent left the nest only after its partner had returned and initiated the nest relief. In these cases, exchanges were quick (25s, median) and shortened over the incubation period by 0.1 – 1.4s per day (95%CI), suggesting that parents became more synchronized. However, nest reliefs were not cryptic. In 90% of exchanges, at least one parent vocalized, and in 20% of nest reliefs the incubating parent left the nest only after its returning partner called instantaneously. In 30% of cases, the returning parent initiated the nest relief with a call; in 39% of these cases, the incubating partner replied. If the partner replied, the next off-nest bout was 1 – 4hr (95%CI) longer than when the partner did not reply, which corresponds to an 8 – 45% increase. Our results indicate that incubating semipalmated sandpipers, which rely on crypsis to avoid nest predation, have quick but acoustically conspicuous nest reliefs. Our results also suggest that vocalizations during nest reliefs may be important for the division of parental duties.

LAY SUMMARY

Biparental care requires coordination between parents. In species where both parents incubate and nests are visible, parents often perform complex nest relief rituals. Is this also the case in species where nests are cryptic?

We video-recorded nest relief behavior at nests of cryptically incubating semipalmated sandpipers.

Parents relieved each other quickly, but they vocalized frequently. In 20% of nest reliefs the incubating parent left only after its returning partner called instantaneously. In 30% of cases the returning parent initiated the nest relief with a call. If the partner replied, its next off-nest bout was 1 – 4hr longer than when the partner did not reply, which corresponds to an 8 – 45% increase.

Our results suggest that vocalizations during nest relief may be important for the division of parental duties. Further work in sandpipers and other taxa is needed to elucidate the role of parental vocalization in coordinating and synchronizing parental duties.
Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates
Authors: Nunn Adam , Rodríguez-Arévalo Isaac , Tandukar Zenith , Frels Katherine , Contreras-Garrido Adrián , Carbonell-Bejerano Pablo , Zhang Panpan , Ramos-Cruz Daniela , Jandrasits Katharina , Lanz Christa , Brusa Anthony , Mirouze Marie , Dorn Kevin , Jarvis Brice , Sedbrook John , Wyse Donald L. , Otto Christian , Langenberger David , Stadler Peter F. , Weigel Detlef , Marks M. David , Anderson James A. , Becker Claude , Chopra Ratan
Published: August 2021

Thlaspi arvense (field pennycress) is being domesticated as a winter annual oilseed crop capable of improving ecosystems and intensifying agricultural productivity without increasing land use. It is a selfing diploid with a short life cycle and is amenable to genetic manipulations, making it an accessible field-based model species for genetics and epigenetics. The availability of a high quality reference genome is vital for understanding pennycress physiology and for clarifying its evolutionary history within the Brassicaceae. Here, we present a chromosome-level genome assembly of var. MN106-Ref with improved gene annotation, and use it to investigate gene structure differences between two accessions (MN108 and Spring32-10) that are highly amenable to genetic transformation. We describe small RNAs, pseudogenes, and transposable elements, and highlight tissue specific expression and methylation patterns. Resequencing of forty wild accessions provides insights into genome-wide genetic variation as well as QTL regions for flowering time and a seedling color phenotype. Altogether, these data will serve as a tool for pennycress improvement in general and for translational research across the Brassicaceae.
A robust method of extraction and GC-MS analysis of Monophenols exhibited UV-B mediated accumulation in Arabidopsis
Authors: Lingwan Maneesh , Masakapalli Shyam Kumar
Published: August 2021

Studies on specialised metabolites like phenolics are of immense interest owing to their significance to agriculture, nutrition and health. In plants, phenolics accumulate and exhibits spatial and temporal regulations in response to growth conditions. Robust methodologies aimed at efficient extraction of plant phenolics, their qualitative and quantitative analysis is desired. We optimised the analytical and experimental bottlenecks that captured free, ester, glycoside and wall-bound phenolics after acid or alkali treatments of the tissue extracts and subsequent GC-MS analysis. Higher recovery of phenolics from the methanolic extracts was achieved by through a) Ultrasonication assisted extraction along with Methyl tert-butyl ether (MTBE) enrichment b) nitrogen gas drying and c) their derivatisation using MSTFA for GC-MS analysis. The optimised protocol was tested on Arabidopsis rosette exposed to UV-B radiation (280-315 nm) which triggered enhanced levels of 11 monophenols and might be attributed to photoprotection and other physiological roles. Interestingly, coumaric acid (308 m/z) and caffeic acid (396 m/z) levels were enhanced by 12-14 folds under UV-B. Other phenolics such as cinnamic acid (220 m/z), hydroxybenzoic acid (282 m/z), vanillic acid (312 m/z, gallic acid (458 m/z), ferulic acid (338 m/z), benzoic acid (194 m/z), hydroxycinnamic acid (368 m/z) and protocatechuic acid (370 m/z) also showed elevated levels by about 1 to 4 folds. Notably, vanillin (253 m/z) was detected only in the UV-B exposed tissues. The protocol also comprehensively captured the variations in the levels of ester, glycoside and wall-bounded phenolics with high reproducibility and sensitivity. The robust method of extraction and GC-MS analysis can readily be adopted for studying phenolics in plant systems.
The role of muscle stem cells and fibro-adipogenic progenitors in female pelvic floor muscle regeneration following birth injury
Authors: Sesillo Francesca Boscolo , Rajesh Varsha , Wong Michelle , Duran Pamela , Baynes Brittni , Laurent Louise C. , Christman Karen L. , Sacco Alessandra , Alperin Marianna
Published: July 2021

Pelvic floor muscle (PFM) injury during childbirth is a key risk factor for subsequent pelvic floor disorders that affect millions of women worldwide. Muscle stem cells (MuSCs) play a central role in the regeneration of injured skeletal muscles, where they activate, proliferate, and differentiate to assure myogenesis needed for muscle recovery. For robust regenerative function, MuSCs require the support of fibro-adipogenic progenitors (FAPs) and immune cells. To elucidate the role of MuSCs, FAPs, and immune infiltrate in female PFM regeneration, we used radiation to perturb the system and followed PFM recovery in a simulated birth injury (SBI) rat model. Non-irradiated and irradiated rats were euthanized at 3,7, 10, and 28 days after SBI; PFMs were harvested and prepared for immunohistochemistry. Cross sectional area (CSA) of all PFM myofibers 28 days after injury in irradiated animals was significantly lower relative to non-irradiated injured controls, indicating impairment of PFM recovery. Following SBI in non-irradiated animals, the number of MuSCs and FAPs expanded significantly at 7 and 3 days after injury, respectively; this expansion did not occur in irradiated animals at the same time points. CSA of embryonic myosin heavy chain (eMyHC, marker of newly regenerated myofibers) positive fibers was also significantly smaller following SBI in irradiated muscles compared to PFMs from non-irradiated injured controls at 7 days. Our results demonstrate that loss of function and decreased expansion of MuSCs and FAPs associated with irradiation results in impaired PFM recovery, signifying essential roles for MuSCs and FAPs in the regenerative process of female PFMs after birth injury. These findings can inform the identification of novel preventative and therapeutic targets and the development of new treatments for PFM dysfunction and associated pelvic floor disorders.
Plant-associated microbiomes promote nutrient turnover in impoverished substrates of a biodiversity hotspot
Authors: Camargo Antonio P. , Correa de Souza Rafael Soares , Jose Juliana , Gerhardt Isabel R. , Dante Ricardo A. , Mukherjee Supratim , Huntemann Marcel , Kyrpides Nikos C. , Carazzolle Marcelo F. , Arruda Paulo
Published: August 2021

The substrates of the Brazilian campos rupestres have extremely low concentrations of key nutrients, mainly phosphorus, imposing severe restrictions to plant growth. Regardless, this ecosystem harbors enormous biodiversity which raises the question of how nutrients are cycled and acquired by the biosphere. To uncover the nutrient turnover potential of plant-associated microorganisms in the campos rupestres, we investigated the compositions and functions of microbiomes associated with two species of the Velloziaceae family that grow over distinct substrates (soil and rock). Amplicon, metagenomic, and metagenome-assembled genome sequence data showed that the campos rupestres harbor a novel assemblage of plant-associated prokaryotes and fungi. Compositional analysis revealed that the plant-associated soil and rock communities differed in taxonomic structure but shared a core of highly efficient colonizers that were strongly coupled with nutrient mobilization. Investigation of functional and abundance data revealed that the plant hosts actively recruit communities by exuding organic compounds and that the root-associated microbiomes possess a diverse repertoire of phosphorus turnover mechanisms. We also showed that the microbiomes of both plant species encompass novel populations capable of mobilizing nitrogen and that the substrate strongly influences the dynamics of this cycle. Our results show that the interplay between plants and their microbiomes shapes nutrient turnover in the campos rupestres. We highlight that investigation of microbial diversity is fundamental to understand plant fitness in stressful environments.
Social selectivity and social motivation in voles
Authors: Beery Annaliese K. , Lopez Sarah A. , Blandino Katrina L. , Lee Nicole S. , Bourdon Natalie S. , Ahern Todd H.
Published: July 2021

Selective relationships are fundamental to humans and many other animals, but relationships between mates, family members, or peers may be mediated differently. We examined connections between social reward and social selectivity, aggression, and oxytocin receptor signaling pathways in rodents that naturally form enduring, selective relationships with mates and peers (prairie voles) or peers (meadow voles). Female prairie and meadow voles worked harder to access familiar vs. unfamiliar individuals, regardless of sex, and huddled extensively with familiar subjects. Male prairie voles also displayed strongly selective huddling preferences for familiar animals, but worked hardest to repeatedly access females vs. males, with no difference in effort by familiarity. This demonstrates a fundamental disconnect between motivation and social selectivity in males, and reveals a striking sex difference in pathways underlying social monogamy. Meadow voles exhibited social preferences but low social motivation, consistent with tolerance rather than reward supporting social groups in this species. Natural variation in oxytocin receptor genotype was associated with oxytocin receptor density, and both genotype and receptor binding predicted individual variation in prosocial and aggressive behaviors. These results provide a basis for understanding species, sex, and individual differences in the mechanisms underlying the role of social reward in social preference.
A Computational Model of the Effect of Short-Term Monocular Deprivation on Binocular Rivalry in the Context of Amblyopia
Authors: Seeliger Norman , Triesch Jochen
Published: August 2021

Treatments for amblyopia focus on vision therapy and patching of one eye. Predicting the success of these methods remains difficult, however. Recent research has used binocular rivalry to monitor visual cortical plasticity during occlusion therapy, leading to a successful prediction of the recovery rate of the amblyopic eye. The underlying mechanisms and their relation to neural homeostatic plasticity are not known. Here we propose a spiking neural network to explain the effect of short-term monocular deprivation on binocular rivalry. The model reproduces perceptual switches as observed experimentally. When one eye is occluded, inhibitory plasticity changes the balance between the eyes and leads to longer dominance periods for the eye that has been deprived. The model suggests that homeostatic inhibitory plasticity is a critical component of the observed effects and might play an important role in the recovery from amblyopia.
Ageing-associated myelin dysfunction drives amyloid deposition in mouse models of Alzheimer’s disease
Authors: Depp Constanze , Sun Ting , Sasmita Andrew Octavian , Spieth Lena , Berghoff Stefan A. , Steixner-Kumar Agnes A. , Subramanian Swati , Möbius Wiebke , Göbbels Sandra , Saher Gesine , Zampar Silvia , Wirths Oliver , Thalmann Maik , Saito Takashi , Saido Takaomi , Krueger-Burg Dilja , Kawaguchi Riki , Willem Michael , Haass Christian , Geschwind Daniel , Ehrenreich Hannelore , Stassart Ruth , Nave Klaus-Armin
Published: August 2021

The prevalence of Alzheimer’s disease (AD), the leading cause of dementia, shows a strict age-dependency, but why ageing constitutes the main risk factor for this disease is still poorly understood. Brain ageing affects oligodendrocytes1 and the structural integrity of myelin sheaths2, the latter associated with secondary neuroinflammation3. Since oligodendrocytes support axonal and neuronal health4–7, we hypothesised that ageing-associated loss of myelin integrity could be an upstream risk factor for neuronal amyloid-β (Aβ) deposition, the primary neuropathological hallmark of AD. Here, we show that in AD mouse models different genetically induced defects of myelin integrity or demyelinating injuries are indeed potent drivers of amyloid deposition in vivo, quantified by whole brain light sheet microscopy. Conversely, the lack of myelin in the forebrain provides protection against plaque deposition. Mechanistically, we find that myelin dysfunction causes the accumulation of the Aβ producing machinery within axonal swellings and increases cortical amyloid precursor protein (APP) cleavage. Surprisingly, AD mice with dysfunctional myelin lack plaque-corralling microglia but show a disease-associated microglia (DAM)-like signature as revealed by bulk and single cell transcriptomics. These activated microglia, however, are primarily engaged with myelin, preventing the protective reactions of microglia to Aβ plaques. Our data suggest a working model, in which age-dependent structural defects of myelin promote plaque formation, directly and indirectly, and are thus an upstream AD risk factor. Improving oligodendrocyte health and myelin integrity could be a promising target to delay AD.g
Degrading intestinal DAF-2 nearly doubles Caenorhabditis elegans lifespan without affecting development or reproduction
Authors: Zhang Yan-Ping , Zhang Wen-Hong , Zhang Pan , Li Qi , Sun Yue , Wang Jia-Wen , Zhang Shao-Bing O. , Cai Tao , Zhan Cheng , Dong Meng-Qiu
Published: August 2021

Twenty-eight years following the breakthrough discovery that a single-gene mutation of daf-2 can double the lifespan of Caenorhabditis elegans, it remains unclear where this gene, which encodes an insulin/IGF-1 receptor, is expressed and where it acts to regulate aging. Here, by inserting DNA sequences of fluorescent tags into the genomic locus of daf-2 and that of its downstream transcription factor daf-16, we determined that both genes are expressed in most or all tissues from embryos through adulthood, in line with their diverse functions. Using tissue-specific auxin-induced protein degradation, we determined that both DAF-2 and DAF-16 act in the intestine to regulate organismal aging. Strikingly, loss of DAF-2 in the intestine nearly doubled C. elegans lifespan but did not produce the adverse developmental or reproductive phenotypes associated with genetic daf-2 mutants. These findings unify the mechanism of lifespan regulation by genes and that by dietary restriction, and begin to focus anti-aging research on nutrient supply.

Highlights

daf-2 and daf-16 are expressed in most or all cells of C. elegans using genome editing.

DAF-2 and DAF-16 both regulate lifespan from the intestine as determined using auxin-induced protein degradation.

Reduced insulin signaling in the intestine nearly doubles C. elegans lifespan without adverse effects on development or reproduction.

Lifespan regulation by genes and dietary restriction are unified by intestinal supply of nutrients and metabolism.
Protein language model embeddings for fast, accurate, alignment-free protein structure prediction
Authors: Weissenow Konstantin , Heinzinger Michael , Rost Burkhard
Published: August 2021

All state-of-the-art (SOTA) protein structure predictions rely on evolutionary information captured in multiple sequence alignments (MSAs), primarily on evolutionary couplings (co-evolution). Such information is not available for all proteins and is computationally expensive to generate. Prediction models based on Artificial Intelligence (AI) using only single sequences as input are easier and cheaper but perform so poorly that speed becomes irrelevant. Here, we described the first competitive AI solution exclusively inputting embeddings extracted from pre-trained protein Language Models (pLMs), namely from the transformer pLM ProtT5, from single sequences into a relatively shallow (few free parameters) convolutional neural network (CNN) trained on inter-residue distances, i.e. protein structure in 2D. The major advance originated from processing the attention heads learned by ProtT5. Although these models required at no point any MSA, they matched the performance of methods relying on co-evolution. Although not reaching the very top, our lean approach came close at substantially lower costs thereby speeding up development and each future prediction. By generating protein-specific rather than family-averaged predictions, these new solutions could distinguish between structural features differentiating members of the same family of proteins with similar structure predicted alike by all other top methods.
Environmental enrichment mitigates the long-lasting sequelae of perinatal fentanyl exposure
Authors: Alipio Jason Bondoc , Riggs Lace Marie , Plank Madeline , Keller Asaf
Published: August 2021

The opioid epidemic is a rapidly evolving societal issue driven, in part, by a surge in synthetic opioid use. A rise in fentanyl use among pregnant women has led to a 40-fold increase in the number of perinatally-exposed infants in the past decade. These children are more likely to develop mood- and somatosensory-related conditions later in life, suggesting that fentanyl may permanently alter neural development. Here, we examined the behavioral and synaptic consequences of perinatal fentanyl exposure in adolescent male and female C57BL/6J mice and assessed the therapeutic potential of environmental enrichment to mitigate these effects. Dams were givenad libitumaccess to fentanyl (10 µg/mL,per os) across pregnancy and until weaning (PD 21). Perinatally-exposed adolescent mice displayed hyperactivity (PD 45), enhanced sensitivity to anxiogenic environments (PD 46), and sensory maladaptation (PD 47) – sustained behavioral effects that were completely normalized by environmental enrichment (PD 21-45). Additionally, environmental enrichment normalized the fentanyl-induced changes in the frequency of miniature excitatory postsynaptic currents of layer 2/3 neurons in the primary somatosensory cortex (S1). We also demonstrate that fentanyl impairs short- and long-term potentiation in S1 layer 2/3 neurons which, instead, exhibit a sustained depression of synaptic transmission that is restored by environmental enrichment. On its own, environmental enrichment suppressed long-term depression of control S1 neurons from vehicle-treated mice subjected to standard housing conditions. These results demonstrate that the lasting effects of fentanyl can be ameliorated with a non-invasive intervention introduced during early development.

Significance Statement

Illicit use of fentanyl accounts for a large proportion of opioid-related overdose deaths. Children exposed to opioids during development have a higher risk of developing neuropsychiatric disorders later in life. Here, we employ a preclinical model of perinatal fentanyl exposure that recapitulates these long-term impairments and show, for the first time, that environmental enrichment can reverse deficits in somatosensory circuit function and behavior. These findings have the potential to directly inform and guide ongoing efforts to mitigate the consequences of perinatal opioid exposure.
Fillable and Unfillable Gaps in Rice Transcriptome under Field and Controlled Environments
Authors: Hashida Yoichi , Tezuka Ayumi , Nomura Yasuyuki , Kamitani Mari , Kashima Makoto , Kurita Yuko , Nagano Atsushi J.
Published: August 2021

The differences between plants grown in field and controlled environments have long been recognised; however, few studies have addressed the underlying molecular mechanisms. Here, we show fillable and unfillable gaps in the transcriptomes of rice grown in field and controlled environments by utilising SmartGC, a high-performance growth chamber that reproduces the fluctuating irradiance, temperature, and humidity of field environments. Rice transcriptome dynamics in SmartGC mimicked those in the field, particularly during the morning and evening; those in conventional growth chamber conditions did not. Further analysis revealed that fluctuation of irradiance affects transcriptome dynamics in the morning and evening, while fluctuation of temperature only affects transcriptome dynamics in the morning. We found upregulation of genes related to biotic and abiotic stress, whose expression was affected by environmental factors that cannot be mimicked by SmartGC. Our results accelerate the understanding of plant responses to field environments for both field and laboratory studies.
Interaction between Discs large and GPSM2: A Comparison Across Species
Authors: Schiller Emily , Bergstralh Dan T.
Published: August 2021

The orientation of the mitotic spindle determines the direction of cell division, and therefore contributes to tissue shape and cell fate. Interaction between the multifunctional scaffolding protein Discs large (Dlg) and the canonical spindle orienting factor GPSM2 (also called Pins in Drosophila and LGN in vertebrates) has been established in bilaterian models, but its function remains unclear. We used a phylogenetic approach to test whether the interaction is obligate in animals, and in particular whether GPSM2 evolved in multicellular organisms as a Dlg-binding protein. We show that Dlg diverged in C. elegans and the syncytial sponge O. minuta and propose that this divergence may correspond to differences in spindle orientation requirements between these organisms and the canonical pathways described in bilaterians. We also demonstrate that GPSM2 is present in basal animals, but the established Dlg-interaction site cannot be found in either Placozoa or Porifera. Our results suggest that the interaction between GPSM2 and Dlg appeared in Cnidaria, and we therefore speculate that it may have evolved to promote accurate division orientation in the nervous system. This work reveals the evolutionary history of the GPSM2/Dlg interaction and suggests new possibilities for its importance in spindle orientation during epithelial and neural tissue development.
Molecular Dynamics Simulation of a Model Brain Membrane with and without a 14-3-3 tau Protein
Authors: Arvayo-Zatarain Jorge A. , Favela-Rosales Fernando , Figueroa Angel D. Reyes , Castro-Villarreal Pavel , Contreras-Aburto Claudio
Published: August 2021

An unbalanced composition of lipids and proteins in brain membranes is related to the appearance neurodegenrative diseases and recent investigations show that the 14-3-3 tau protein might relate to some of these diseases. This article reports results from a coarse-grained model brain membrane with and without a 14-3-3 τ/θ protein inside the membrane. We investigated the symmetrized partial density, thickness, diffusion coefficients, and deuterium order parameters of the membrane with and without protein. We observe a slight increase in heads and linkers in the symmetrized partial density of the membrane with the protein inserted and higher values of the deuterium order parameters for the brain model membrane with protein. We observe a reduction in the diffusion coefficient of the fluid membrane in the presence of the transmembrane tau protein. Our findings show that the protein can modify the structural and dynamical properties of the membrane. This work will serve as a guide for future investigations on the interactions of tau proteins with brain membrane models and their relation to neurodegenerative diseases.
ALLSorts: a RNA-Seq classifier for B-Cell Acute Lymphoblastic Leukemia
Authors: Schmidt Breon , Brown Lauren M. , Ryland Georgina L. , Lonsdale Andrew , Kosasih Hansen J. , Ludlow Louise E. , Majewski Ian J. , Blombery Piers , Ekert Paul G. , Davidson Nadia M. , Oshlack Alicia
Published: August 2021

B-cell acute lymphoblastic leukemia (B-ALL) is the most common childhood cancer. Subtypes within B-ALL are distinguished by characteristic structural variants and mutations, which in some instances strongly correlate with responses to treatment. The World Health Organisation (WHO) recognises seven distinct classifications, or subtypes, as of 2016. However, recent studies have demonstrated that B-ALL can be segmented into 23 subtypes based on a combination of genomic features and gene expression profiles. A method to identify a patient’s subtype would have clear clinical utility. Despite this, no publically available classification methods using RNA-Seq exist for this purpose.

Here we present ALLSorts: a publicly available method that uses RNA-Seq data to classify B-ALL samples to 18 known subtypes and five meta-subtypes. ALLSorts is the result of a hierarchical supervised machine learning algorithm applied to a training set of 1223 B-ALL samples aggregated from multiple cohorts. Validation revealed that ALLSorts can accurately attribute samples to subtypes and can attribute multiple subtypes to a sample. Furthermore, when applied to both paediatric and adult cohorts, ALLSorts was able to classify previously undefined samples into subtypes.

ALLSorts is available and documented on GitHub (https://github.com/Oshlack/AllSorts/).

Key Points

ALLSorts is a gene expression classifier for B-cell acute lymphoblastic leukemia, which predicts 18 distinct genomic subtypes - including those designated by the World Health Organisation (WHO) and provisional entities.

Trained and validated on over 2300 B-ALL samples, representing each subtype and a variety of clinical features.

Correctly identified subtypes in 91% of cases in a held-out dataset and between 82-93% across a newly combined cohort of paediatric and adult samples.

ALLSorts assigned subtypes to samples with previously unknown driver events.

ALLsorts is an accurate, comprehensive and freely available classification tool that distinguishes subtypes of B-cell acute lymphoblastic leukemia from RNA-sequencing.
On the discovery of ADRAM, an experience-dependent long noncoding RNA that drives fear extinction through a direct interaction with the chaperone protein 14-3-3
Authors: Li Xiang , Zhao Qiongyi , Wang Ziqi , Liau Wei-Siang , Basic Dean , Ren Haobin , Marshall Paul R. , Zajaczkowski Esmi L. , Leighton Laura J. , Madugalle Sachithrani U. , Musgrove Mason , Periyakaruppiah Ambika , Shi Jichun , Zhang Jianjian , Mattick John S. , Mercer Timothy R. , Wei Wei , Bredy Timothy W.
Published: August 2021

Long-noncoding RNA (lncRNA) comprise a new class of genes that have been assigned key roles in development and disease. Many lncRNAs are specifically transcribed in the brain where they regulate the expression of protein-coding genes that underpin neuronal function; however, their role in learning and memory remains largely unexplored. We used RNA Capture-Seq to identify a large population of lncRNAs that are expressed in the infralimbic cortex of adult male mice in response to fear-related learning, with 14.5% of these annotated in the GENCODE database as lncRNAs with no known function. We combined these data with cell-type-specific ATAC-seq on neurons that had been selectively activated by fear-extinction learning, and revealed 434 lncRNAs derived from enhancer regions in the vicinity of protein-coding genes. In particular, we discovered an experience-induced lncRNA called ADRAM that acts as both a scaffold and a combinatorial guide to recruit the brain-enriched chaperone protein 14-3-3 to the promoter of the memory-associated immediate early gene Nr4a2. This leads to the expulsion of histone deactylases 3 and 4, and the recruitment of the histone acetyltransferase creb binding protein, which drives learning-induced Nr4a2 expression. Knockdown of ADRAM disrupts this interaction, blocks the expression of Nr4a2, and ultimately impairs the formation of fear-extinction memory. This study expands the lexicon of experience-dependent lncRNA activity in the brain, highlights enhancer-derived RNAs (eRNAs) as key players in the epigenetic regulation of gene expression associated with fear extinction, and suggests eRNAs, such as ADRAM, may constitute viable targets in developing novel treatments for fear-related anxiety disorders.
In vitro evolution reveals primordial RNA-protein interaction mediated by metal cations
Authors: Giacobelli Valerio G. , Fujishima Kosuke , Lepšík Martin , Tretyachenko Vyacheslav , Kadavá Tereza , Bednárová Lucie , Novák Petr , Hlouchová Klára
Published: August 2021

RNA-peptide/protein interactions have been of utmost importance to life since its earliest forms, reaching even before the last universal common ancestor (LUCA). However, the ancient molecular mechanisms behind this key biological interaction remain enigmatic because extant RNA-protein interactions rely heavily on positively charged and aromatic amino acids that were absent (or heavily under-represented) in the early pre-LUCA evolutionary period. Here, an RNA-binding variant of the ribosomal L11 C-terminal domain was selected from a ∼1010 library of partially randomized sequences, all composed of 10 prebiotically plausible canonical amino acids. The selected variant binds to the cognate RNA with a similar overall affinity although it is less structured in the unbound form than the wild-type protein domain. The variant complex association and dissociation are both slower than for the wild-type, implying different mechanistic processes involved. The profile of the wild-type and mutant complex stabilities along with MD simulations uncover qualitative differences in the interaction modes. In the absence of positively charged and aromatic residues, the mutant L11 domain uses bridging ion (K+/Mg2+) interactions between the RNA sugar-phosphate backbone and glutamic acid residues as an alternative source of stabilization. This study presents experimental support to provide a new perspective on how early protein-RNA interactions evolved, where the lack of aromatic/basic residues was compensated by acidic residues plus metal ions.
A recombinant baculovirus TnGV in Trichoplusia ni larvae using the PIG bombardment method and the CRISPR/Cas9 system
Authors: Ortiz-Arrazola Oscar J. , Del Rincón-Castro Ma. Cristina
Published: August 2021

Baculoviruses have been used for the expression of heterologous proteins of biotechnological interest. However, most of these proteins are obtained by homologous co-transfection recombination in cell lines, limiting their use. Recently, the CRISPR/Cas9 system has excelled in its high efficiency in editing specific sequences without the need for insect cell lines. In this work, the CRISPR/Cas9 system was used to edit the genome of Trichopusia ni granulovirus (TnGV) and transformation of insects by the PIG bombardment method. A homologous repair vector (pTnGV101) was designed with regions orf5 and orf7, as well as sgRNA flanking TnGV P10 of this virus. The bombardment transformation was carried out at 175 psi with 40% of infected T. ni larvae, of which 38% expressed the reporter protein EGFP. These results demonstrate that the CRISPR/Cas9 system and PIG bombardment can be used for genetic modification of baculovirus in vivo.
Microbial transformation of traditional fermented fertilizer bokashi alters chemical composition and improves plant growth
Authors: Abo-Sido Nisreen , Goss John W , Griffith Alden , Klepac-Ceraj Vanja
Published: August 2021

Bokashi is an organic soil amendment that makes use of microbial processes to break down agricultural waste and create a nutrient-rich fertilizer. The benefits of various types of bokashi on soil fertility and plant growth are well documented, however the changes in microbial community composition and nutrients during bokashi maturation remain poorly characterized. Here, we aimed to identify potential differences in the quality of bokashi made using different ingredients and to investigate the biochemical transformation and microbial community succession of bokashi throughout the maturation process. We compared the effects of these different types of bokashi on the growth of cucumber (Cucumis sativus) and kale (Brassica napus subsp. pabularia) seedlings, measured concentrations of NH4+ and PO43-, and characterized the bokashi bacterial and fungal communities over a 12-day maturation period. We found that cucumber and kale plants growing in all types of bokashi-amended soils exhibited increased chlorophyll levels and dry biomass. During bokashi maturation, we observed a decrease in available PO43-, and an increase in NH4+. There also appeared to be an increase in relative abundances of decomposers and beneficial microbes and a decrease in putative plant pathogens. Regardless of starting bokashi ingredients and differences in microbial composition and nutrient trends, all types of bokashi similarly improve plant growth and contain beneficial microbes.
High-fidelity, high-spatial-resolution diffusion MRI of the ex-vivo whole human brain on the 3T Connectom scanner using structured low-rank EPI ghost correction
Authors: Ramos-Llordén Gabriel , Lobos Rodrigo A. , Kim Tae Hyung , Tian Qiyuan , Witzel Thomas , Lee Hong-Hsi , Scholz Alina , Keil Boris , Yendiki Anastasia , Bilgiç Berkin , Haldar Justin P. , Huang Susie Y.
Published: August 2021

Diffusion MRI (dMRI) of whole, intact, fixed postmortem human brain at high spatial resolution serves as key bridging technology for 3D mapping of structural connectivity and tissue microstructure at the mesoscopic scale. Ex vivo dMRI offers superior spatial resolution compared to in vivo dMRI but comes with its own technical challenges due to the significantly reduced T2 relaxation times and decreased diffusivity incurred by tissue fixation. The altered physical properties of fixed tissue necessitate the use of alternative acquisition strategies to preserve SNR and achieve sufficient diffusion weighting. Multi-shot or segmented 3D echo planar imaging (EPI) sequences have been used to shorten echo times (TEs) with reduced distortions from field inhomogeneity and eddy currents on small-bore MR scanners and have been adopted for high b-value dMRI of ex vivo whole human brain specimens.

The advent of stronger gradients on human MRI scanners has led to improved image quality and a wider range of diffusion-encoding parameters for dMRI but at the cost of more severe eddy currents that result in spatial and temporal variations in the background magnetic field, which cannot be corrected for using standard vendor-provided ghost correction solutions. In this work, we show that conventional ghost correction techniques based on navigators and linear phase correction may be insufficient for EPI sequences using strong diffusion-sensitizing gradients in ex vivo dMRI experiments, resulting in orientationally biased dMRI estimates. This previously unreported problem is a critical roadblock in any effort to leverage scanners with ultra-high gradients for high-precision mapping of human neuroanatomy at the mesoscopic scale. We propose an advanced reconstruction method based on structured low-rank matrix modeling that reduces the ghosting substantially. We show that this method leads to more accurate and reliable dMRI metrics, as exemplified by diffusion tensor imaging and high angular diffusion imaging analyses in distributed neuroanatomical areas of fixed whole human brain specimens. Our findings advocate for the use of advanced reconstruction techniques for recovering unbiased metrics from ex vivo dMRI acquisitions and represent a crucial step toward making full use of strong diffusion-encoding gradients for neuroscientific studies seeking to study brain structure at multiple spatial scales.
Mixed Effects Machine Learning Models for Colon Cancer Metastasis Prediction using Spatially Localized Immuno-Oncology Markers
Authors: Levy Joshua J. , Bobak Carly A. , Nasir-Moin Mustafa , Veziroglu Eren M. , Palisoul Scott M. , Barney Rachael E. , Salas Lucas A. , Christensen Brock C. , Tsongalis Gregory J. , Vaickus Louis J.
Published: August 2021

Spatially resolved characterization of the transcriptome and proteome promises to provide further clarity on cancer pathogenesis and etiology, which may inform future clinical practice through classifier development for clinical outcomes. However, batch effects may potentially obscure the ability of machine learning methods to derive complex associations within spatial omics data. Profiling thirty-five stage three colon cancer patients using the GeoMX Digital Spatial Profiler, we found that mixed-effects machine learning (MEML) methods† may provide utility for overcoming significant batch effects to communicate key and complex disease associations from spatial information. These results point to further exploration and application of MEML methods within the spatial omics algorithm development life cycle for clinical deployment.
Ectopic cervical thymi and no thymic involution until midlife in naked mole-rats
Authors: Emmrich Stephan , Zakusilo Frances Tolibzoda , Trapp Alexandre , Zhou Xuming , Zhang Quanwei , Irving Ellen M. , Drage Michael G. , Zhang Zhengdong , Gladyshev Vadim N. , Seluanov Andrei , Gorbunova Vera
Published: August 2021

Immunosenescence is a hallmark of aging and manifests as increased susceptibility to infection, autoimmunity, and cancer in the elderly. One component of immunosenescence is thymic involution, age-associated shrinkage of the thymus, observed in all vertebrates studied to date. The naked mole-rat (Heterocephalus glaber) has become an attractive animal model in aging research due to its extreme longevity and resistance to disease. Here we show that naked mole rats display no thymic involution up to 11 years of age. Furthermore, we found large ectopic cervical thymi in addition to the canonical thoracic thymus, both being identical in their cell composition. The developmental landscape in naked mole-rat thymi revealed overt differences from the murine T cell compartment, most notably a decrease of CD4+/CD8+ double-positive cells and lower abundance of cytotoxic effector T cells. Our observations suggest that naked mole rats display a delayed immunosenescence. Therapeutic interventions aimed at reversing thymic aging remain limited, underscoring the importance of understanding the cellular and molecular mechanisms behind a sustained immune function in the naked mole rat.
Prediction of Plastic Degrading Microbes
Authors: Hemalatha N , Wilson Akhil , Akhil T
Published: August 2021

Plastic pollution is one of the challenging problems in the environment. But a life without plastic we cannot imagine. This paper deals with the prediction of plastic degrading microbes using Machine Learning. Here we have used Decision Tree, Random Forest, Support vector Machine and K Nearest Neighbor algorithms in order to predict the plastic degrading microbes. Among the four classifiers, Random Forest model gave the best accuracy of 99.1%.