bluuebunny/crossref_metadata_2025 huggingface dataset:
Deep Stroop: Using eye tracking and speech processing to characterize people with neurodegenerative disorders while performing the Stroop Test
Authors: Meyer Trevor , Favaro Anna , Cao Tianyu , Butala Ankur , Oh Esther , Motley Chelsie , Irazoqui Pedro , Dehak Najim , Moro-Velázquez Laureano
Published: June 2023

Although many neurodegenerative diseases affect different neural circuits, they often express complex and overlapping symptom profiles making them difficult to differentiate precisely. Current methods of analyzing patients are limited to bedside examination, patient self-rating scales, semiquantitative clinician-rating scales, and other observational evidence, which are often non-specific, resulting in open multiple interpretations and ambiguity in diagnosis and treatment plans. We present a method to analyze patient symptom profiles using multimodal analysis of subjects performing the Stroop Test. We use high-sample-rate eye tracking and speech recording tools to record subject behavior while completing the Stroop Test and simultaneously analyze multiple traits of their interaction with the test. We compare the performance of healthy controls to patients with Parkinson’s Disease, Alzheimer’s Disease, and other neurodegenerative diseases with clinical parkinsonism. We automatically extract metrics based on eye motor behavior, gaze characteristic uttered responses, and the temporal relationship between gaze and uttered responses. We identify many that have clinical relevance through high correlations with existing MoCA and MDS-UPDRS, many of which have significantly different distributions between groups. We present here our analysis approach, provide freely available source code to replicate it and demonstrate the potential of multi-modal recording and analysis of patients throughout their execution of neuro-psychological tests like the Stroop Test.
An explanation for SARS-CoV-2 rebound after Paxlovid treatment
Authors: Perelson Alan S. , Ribeiro Ruy M. , Phan Tin
Published: June 2023

In a fraction of SARS-CoV-2 infected individuals treated with the oral antiviral Paxlovid, the virus rebounds following treatment. The mechanism driving rebound is not understood. Here, we show that viral dynamic models based on the hypothesis that Paxlovid treatment near the time of symptom onset halts the depletion of target cells, but may not fully eliminate the virus, which can lead to viral rebound. We also show that the occurrence of viral rebound is sensitive to model parameters, and the time treatment is initiated, which may explain why only a fraction of individuals develop viral rebound. Finally, the models are used to test the therapeutic effects of two alternative treatment schemes. These findings also provide a possible explanation for rebounds following other antiviral treatments for SARS-CoV-2.

Significance

Paxlovid is an effective treatment for SARS-CoV-2. In some patients treated with Paxlovid, the initial reduction in viral load is followed by a rebound once treatment is stopped. Understanding the mechanisms of the rebound may help us develop better treatment strategies to minimize this possibility. We hypothesize that early treatment with Paxlovid stops viral growth, but may not fully clear the virus, thus preserving host resources that would have otherwise been used by the virus. Once treatment ends, the remaining viruses can utilize the available resources to grow, leading to the observed transient viral rebound. We built standard viral dynamic models based on this hypothesis and fit the models to data to show its feasibility. We further examined the effect of two alternative treatment schemes.
Comparison of caffeine consumption behavior with plasma caffeine levels as exposures in drug-target Mendelian randomization and implications for interpreting effects on obesity
Authors: Woolf Benjamin , Cronjé Héléne T. , Zagkos Loukas , Larsson Susanna C. , Gill Dipender , Burgess Steve
Published: June 2023

Drug-target Mendelian randomization (MR) is a popular approach for exploring the effects of pharmacological targets.Cis-MR designs select variants within the gene region that code for a protein of interest to mimic pharmacological perturbation. An alternative uses variants associated with behavioral proxies of target perturbation, such as drug usage. Both have been employed to investigate the effects of caffeine but have drawn different conclusions. We use the effects of caffeine on body mass index (BMI) as a case study to highlight two potential flaws of the latter strategy in drug-target MR: misidentifying the exposure and using invalid instruments. Some variants associate with caffeine consumption because of their role in caffeine metabolism. Since people with these variants require less caffeine for the same physiological effect, the direction of the caffeine-BMI association is flipped depending on whether estimates are scaled by caffeine consumption or plasma caffeine levels. Other variants seem to associate with caffeine consumption via behavioral pathways. Using multivariable-MR, we demonstrate that caffeine consumption behavior influences BMI independently of plasma caffeine. This implies the existence of behaviorally mediated exclusion restriction violations. Our results support the superiority ofcis-MR study designs in pharmacoepidemiology over the use of behavioral proxies of drug targets.
Opposing implications of co-evolutionary lineages and traits of gut microbiome on human health status
Authors: Li Hao , He Junliang , Liang Jieping , Liang Yiting , Zheng Wei , Qu Qingming , Guo Feng
Published: June 2023

Little is known about the co-evolutionary history of the human gut microbe and its relevance to host physiology. Here, we constructed a gut prokaryotic genomic database of wild primates (pSGBs) and compared it with the human gut prokaryotic database (hSGBs) to define shared co-evolutionary clusters (SCEC-hSGBs) and co-evolutionary traits of hSGBs. We analyzed the evolutionary trends of specific functions like carbohydrate-active enzymes and antibiotic resistance in hSGBs and uncovered host-jumping events and genome reduction tendencies in SCEC-hSGBs. Intriguingly, the SCEC-hSGBs and the super enrichers of the traits (SUEN-hSGBs), which are putatively partially derived from carnivores, showed opposite implications for host health status. Specifically, SUEN-hSGBs are enriched in various diseases, showing a negative correlation with gut biodiversity and disproportionate contributions to the known health-negative marker taxa and metabolite. Our study provides insight into the origin and adaptability of human gut microbes and references for developing probiotics and microbiome-based host health prediction.
Modulation of antigen discrimination by duration of immune contacts in a kinetic proofreading model of T cell activation with extreme statistics
Authors: Morgan Jonathan , Lindsay Alan E.
Published: June 2023

T cells form transient cell-to-cell contacts with antigen presenting cells (APCs) to facilitate surface interrogation by membrane bound T cell receptors (TCRs). Upon recognition of molecular signatures (antigen) of pathogen, T cells may initiate an adaptive immune response. The duration of the T cell/APC contact is observed to vary widely, yet it is unclear what constructive role, if any, such variations might play in immune signaling. Modeling efforts describing antigen discrimination often focus on steady-state approximations and do not account for the transient nature of cellular contacts. Within the framework of a kinetic proofreading (KP) mechanism, we develop a stochasticFirst Receptor Activation Model(FRAM) describing the likelihood that a productive immune signal is produced before the expiry of the contact. Through the use of extreme statistics, we characterize the probability that the first TCR triggering is induced by a rare agonist antigen and not by that of an abundant self-antigen. We show that defining positive immune outcomes as resilience to extreme statistics and sensitivity to rare events mitigates classic tradeoffs associated with KP. By choosing a sufficient number of KP steps, our model is able to yield single agonist sensitivity whilst remaining non-reactive to large populations of self antigen, even when self and agonist antigen are similar in dissociation rate to the TCR but differ largely in expression. Additionally, our model achieves high levels of accuracy even when agonist positive APCs encounters are rare. Finally, we discuss potential biological costs associated with high classification accuracy, particularly in challenging T cell environments.

Author summary

Physical contact between the T cell and antigen presenting cell (APC) is essential for productive immune signaling. Wide variations in this contact time have been observed yet little is known of mechanisms controlling this crucial timescale, nor how its duration may impact antigen discrimination. We develop and analyze a probabilistic mathematical model of T cell activation which combines kinetic proofreading (KP) with a finite contact duration. Our model is capable of suppressing large populations of self ligands while remaining sensitive to only a single agonist in T cell/APC cellular contacts. Additionally, we explored two challenging cases, one in which self and agonist antigen are similar and one in which agonist positive APCs are rare. We found that our model could overcome these environmental challenges by increasing the number of kinetic proofreading steps. Finally, we discuss the potential biological costs of achieving such accuracy. Our work demonstrates the extreme effectiveness of kinetic proofreading in a temporal context while also demonstrating the possible challenges in biological implementation of such a model.
P-DOR, an easy-to-use pipeline to reconstruct outbreaks using pathogen genomics
Authors: Batisti Biffignandi Gherard , Bellinzona Greta , Petazzoni Greta , Sassera Davide , Zuccotti Gian Vincenzo , Bandi Claudio , Baldanti Fausto , Comandatore Francesco , Gaiarsa Stefano
Published: June 2023

Bacterial Healthcare Associated Infections (HAIs) are a major threat worldwide, which can be counteracted by establishing effective infection control measures, guided by constant surveillance and timely epidemiological investigations. Genomics is crucial in modern epidemiology but lacks standard methods and user-friendly software, accessible to users without a strong bioinformatics proficiency. To overcome these issues we developed P-DOR, a novel tool for rapid bacterial outbreak characterization. P-DOR accepts genome assemblies as input, it automatically selects a background of publicly available genomes using k-mer distances and adds it to the analysis dataset before inferring a SNP-based phylogeny. Epidemiological clusters are identified considering the phylogenetic tree topology and SNP distances. By analyzing the SNP-distance distribution, the user can gauge the correct threshold. Patient metadata can be inputted as well, to provide a spatio-temporal representation of the outbreak. The entire pipeline is fast and scalable and can be also run on low-end computers.

Availability and implementation

P-DOR is implemented in Python3 and R and can be installed using conda environments. It is available from GitHubhttps://github.com/SteMIDIfactory/P-DORunder the GPL-3.0 license.
The road to restoration: Identifying and conserving the adaptive legacy of American chestnut
Authors: Sandercock Alexander M , Westbrook Jared W , Zhang Qian , Holliday Jason A
Published: June 2023

The American chestnut (Castanea dentata) is a functionally extinct tree species that was decimated by an invasive fungal pathogen in the early 20thcentury. Disease resistant chestnuts have been developed through hybridization and genetic modification, but these populations may lack the adaptive genomic diversity necessary to restore the species across its climatically diverse historical range. An understanding of the genomic architecture of local adaptation in wild American chestnut and identification of seed zones for germplasm conservation are necessary in order to deploy locally adapted, disease-resistant American chestnut populations. Here, we characterize the genomic basis of climate adaptation in remnant wild American chestnut, define seed zones based on climate envelopes and adaptive diversity, and make sampling recommendations for germplasm conservation. Whole genome re-sequencing of 384 trees coupled with genotype-environment association methods suggest the species range can be most parsimoniously subdivided into three seed zones characterized by relatively homogeneous allele frequencies relative to rangewide adaptive diversity. Using these data, we developed a method to estimate the number of samples required from each seed zone to recapitulate standing adaptive diversity in each seed zone, and found that on average, 21-29 trees will need to be conserved to capture 95% of the wild adaptive diversity. Taken together, these results will inform the development of anex situgermplasm conservation and breeding plan to develop locally adapted blight-resistant American chestnut populations, and provide a blueprint for developing restoration plans for other imperiled tree species.
Multi-target genome editing reduces polyphenol oxidase activity in wheat (Triticum aestivumL.) grains
Authors: Wold-McGimsey Forrest , Krosch Caitlynd , Reverte Rocío Alarcón , Ravet Karl , Katz Andrew , Stromberger John , Mason Richard Esten , Pearce Stephen
Published: June 2023

Polyphenol oxidases (PPO) are dual activity metalloenzymes that catalyse the production of quinones. In plants, PPO activity may contribute to biotic stress resistance and secondary metabolism but is undesirable for food producers because it causes the discolouration and changes in flavour profiles of products during post-harvest processing. In wheat (Triticum aestivumL.), PPO released from the aleurone layer of the grain during milling results in the discolouration of flour, dough, and end-use products, reducing their value.

Loss-of-function mutations in thePPO1andPPO2paralogous genes on homoeologous group 2 chromosomes confer reduced PPO activity in the wheat grain but limited natural variation and small intergenic distances between these genes complicates the selection of extremely low-PPO wheat varieties by recombination.

In the current study, a CRISPR/Cas9 construct with one single guide RNA (sgRNA) targeting a conserved copper binding domain was used to edit all sevenPPO1andPPO2genes in the spring wheat cultivar ‘Fielder’. Five of the seven edited T1lines exhibited significant reductions in PPO activity, and T2lines had PPO activity up to 86.7% lower than wild-type controls. In the elite winter wheat cultivars ‘Guardian’ and ‘Steamboat’, which have fivePPO1andPPO2genes, PPO activity was reduced by >90% in both T1and T2lines. This study demonstrates that multi-target editing at late stages of variety development could complement selection for beneficial alleles in crop breeding programmes by inducing novel variation in loci inaccessible to recombination.
Colonial ground nesting byArchaeopteryxsuggests wing evolution in primal association with nesting and the ground up evolution of flight
Authors: Guimarães M. Jorge
Published: June 2023

Following an investigation into the hypothesis that the iconic Berlin specimen ofArchaeopteryxfossilized in nesting position, which led to the discovery not only of its association with soft eggs and several hatchlings, but also similar findings in a secondArchaeopteryxspecimen, an attempt to characterize the entire Berlin specimen nest and estimate its number of eggs is reported here.

The Berlin specimen arranged and brooded its eggs on the ground. Its clutch size appears to have exceeded one hundred eggs. Egg littering found not only in its fossil bed but also in the sediment layer immediately above it, inclusively with evidence that a subsequent generation nested over the specimen, is consistent with repeated usage of a ground nesting site.

AllArchaeopteryxspecimens fossilized in different views of a similar pose that is compatible with a nesting posture, and evidence of eggs of consistent size with the 2D outlines of 3D flattened eggs is present not only in the Berlin, Teylers, Thermopolis and Maxberg specimens, but also in the isolatedArchaeopteryxfeather fossil.

In addition, egg and hatchling littering are present in the Berlin, Teylers and isolatedArchaeopteryxfeather fossils.

Taken together, these findings are indicative of colonial ground nesting behavior byArchaeopteryxin Solnhofen.

Egg littering, eggs dorsal to the Berlin specimen torso and limb rotations in the London and ThermopolisArchaeopteryxspecimens can all be explained by nesting in reentrances located at the margins or in sand banks of marine lagoons in Solnhofen, which would have been flooded, causing the subsequent collapse of the nest and the still-life preservation of its content.

The discovery of colonial ground nesting in a winged Jurassic bird relative favors the evolution of birds from the ground up and suggests that wings and their elongated feathers were primarily associated with ground nest protection and only secondarily with flight.
Yeast Ixr1 mediates the DNA replication stress response through it HMGB DNA binding domains and interaction with checkpoint Mrc1
Authors: Teng Siying , wang Yi , Jiang Jingyuan , Li Mengyuan , Liu Yingxin , Guan Yangying , Wei Anhui , Cong Zhongyi , Zhang Xinmin
Published: June 2023

Background

High mobility group box (HMGB) family protein Ixr1 has been shown to be involved in DNA damage repair, however, its role and mechanism remain largely unclear.

Methods

Genes ofS. cerevisiaewere deleted or tagged with myc, GFP, or mcherry using the lithium acetate method. Sensitivity of strains to hydroxyurea (HU), methyl methanesulfonate (MMS), camptothe-cin (CPT), 4-nitroquinoline N-oxide (4-NQ), or Zeocin was tested. Distribution of GFP or mcherry fusion proteins was visualized with laser scanning confocal microscopy. RNA-seq was used to determine differential gene expression between mutant and control strains.

Results

Ixr1 deletion (ixr1Δ) mutant strain was sensitive to HU. Additionally, phosphorylation of effector of DNA damage checkpoint kinase Rad53 was lower in ixr1Δ than WT. Deletion of DNA damage checkpoint mediators ixr1Δ Rad9Δ was more sensitive to HU than ixr1Δ or Rad9Δ, and ixr1Δ mrc1Δ had similar sensitivity to HU as mrc1Δ but stronger than ixr1Δ. Deletion of ribonucleotide reductase inhibitors sml1Δ or crt10Δ didn’t reduce the sensitivity of ixr1Δ induced by HU. Repli-cation fork nuclease exo1Δ ixr1Δ or helicase sgs1Δ ixr1Δ double deletions were more sensitive to HU than single deletion. In addition, laser scanning confocal microscopy imaging indicated that in response to HU, Ixr1 may be in the same pathway as Mrc1, possibly downstream. Gene Ontol-ogy enrichment analysis of differentially expressed genes (DEGs) between ixr1Δ and wildtype, untreated and treated with HU, confirmed that Ixr1 plays an important role in regulating the transcription of genes related to DNA replication or DNA damage repair. We also found that, re-gardless of HU exposure, Ixr1 localized to the nucleus and may bind DNA through its two HMG-boxes.

Conclusion

Ixr1 participates in the DNA replication stress response through a DNA damage checkpoint pathway mediated by Mrc1, and regulates expression of genes related to DNA damage repair.
PERK-mediated antioxidant response is key for pathogen persistence in ticks
Authors: Rosche Kristin L. , Hurtado Joanna , Fisk Elis A. , Vosbigian Kaylee A. , Warren Ashley L. , Sidak-Loftis Lindsay C. , Wright Sarah J. , Ramirez-Zepp Elisabeth , Park Jason M. , Shaw Dana K.
Published: June 2023

A crucial phase in the lifecycle of tick-borne pathogens is the time spent colonizing and persisting within the arthropod. Tick immunity is emerging as a key force shaping how transmissible pathogens interact with the vector. How pathogens remain in the tick despite immunological pressure remains unknown. In persistently infectedIxodes scapularis, we found thatBorrelia burgdorferi(Lyme disease) andAnaplasma phagocytophilum(granulocytic anaplasmosis) activate a cellular stress pathway mediated by the endoplasmic reticulum receptor PERK and the central regulatory molecule, eIF2α. Disabling the PERK pathway through pharmacological inhibition and RNAi significantly decreased microbial numbers.In vivoRNA interference of the PERK pathway not only reduced the number ofA. phagocytophilumandB. burgdorfericolonizing larvae after a bloodmeal, but also significantly reduced the number of bacteria that survive the molt. An investigation into PERK pathway-regulated targets revealed thatA. phagocytophilumandB. burgdorferiinduce activity of the antioxidant response regulator, Nrf2. Tick cells deficient fornrf2expression or PERK signaling showed accumulation of reactive oxygen and nitrogen species in addition to reduced microbial survival. Supplementation with antioxidants rescued the microbicidal phenotype caused by blocking the PERK pathway. Altogether, our study demonstrates that theIxodesPERK pathway is activated by transmissible microbes and facilitates persistence in the arthropod by potentiating an Nrf2-regulated antioxidant environment.
Culturable approach to rice-root associated bacteria in Burkina Faso: diversity, plant growth-promoting rhizobacteria properties and cross-comparison with metabarcoding data
Authors: Sondo Moussa , Wonni Issa , Koïta Kadidia , Rimbault Isabelle , Barro Mariam , Tollenaere Charlotte , Moulin Lionel , Klonowska Agnieszka
Published: June 2023

Plant-associated bacteria are essential partners in plant health and development. In addition to taking advantage of the rapid advances recently achieved in high-throughput sequencing approaches, studies on plant-microbiome interactions require experiments with culturable bacteria. A study on the rice root microbiome was recently initiated in Burkina Faso. As a follow up, the aim of the present study was to develop a collection of corresponding rice root-associated bacteria covering maximum diversity so as, to be able to assess the diversity of the collection based on the culture medium used, and to describe the taxonomy, phenotype and abundance of selected isolates in the rice microbiome. More than 3,000 isolates were obtained using five culture media (TSA, NGN, NFb, PCAT, Baz). The 16S rRNA fragment sequencing of 1,013 selected working collection isolates showed that our working collection covered four bacterial phyla (Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes) and represented 33% of the previously described diversity of the rice root microbiome at the order level. Phenotypicin vitroanalysis of the plant growth promoting capacity of the isolates revealed an overall ammonium production and auxin biosynthesis capacity, while siderophore production and phosphate solubilisation were enriched inBurkholderia,Ralstonia,AcinetobacterandPseudomonasspecies. Of 45 representative isolates screened for growth promotion on seedlings of two rice cultivars, five showed an ability to improve the growth of both cultivars, while five others were effective on only one cultivar. The best results were obtained withPseudomonas taiwanensisABIP 2315 andAzorhizobium caulinodansABIP 1219, which increased seedling growth by 158% and 47%, respectively. Among the 14 best performing isolates, eight appeared to be abundant in the rice root microbiome dataset from previous study. The findings of this research contribute to the functional description of rice root-associated bacteria and their potential importance for plants by providing, for the first time, insight into their prevalence in the rice root microbiome.
Single cell-guided prenatal derivation of primary epithelial organoids from the human amniotic and tracheal fluids
Authors: Gerli Mattia Francesco Maria , Calà Giuseppe , Beesley Max Arran , Sina Beatrice , Tullie Lucinda , Panariello Francesco , Michielin Federica , Yunyan Kylin Sun , Davidson Joseph R , Russo Francesca Maria , Jones Brendan C , Lee Dani , Savvidis Savvas , Xenakis Theodoros , Simcock Ian , Straatman-Iwanowska Anna A , Hirst Robert A , David Anna L , O’Callaghan Christopher , Olivo Alessandro , Eaton Simon , Loukogeorgakis Stavros P , Cacchiarelli Davide , Deprest Jan , Li Vivian SW , Giobbe Giovanni Giuseppe , Coppi Paolo De
Published: June 2023

Despite advances in prenatal diagnosis, it is still difficult to predict severity and outcomes of many congenital malformations. New patient-specific prenatal disease modelling may optimise personalised prediction. We and others have described the presence of mesenchymal stem cells in amniotic fluid (AFSC) that can generate induced pluripotent stem cells (iPSCs). The lengthy reprogramming processes, however, limits the ability to define individual phenotypes or plan prenatal treatment. Therefore, it would be advantageous if fetal stem cells could be obtained during pregnancy and expanded without reprogramming. Using single cell analysis, we characterised the cellular identities in amniotic fluid (AF) and identified viable epithelial stem/progenitor cells of fetal intestinal, renal and pulmonary origin. With relevance for prenatal disease modelling, these cells could be cultured to form clonal epithelial organoids manifesting small intestine, kidney and lung identity. To confirm this, we derived lung organoids from AF and tracheal fluid (TF) cells of Congenital Diaphragmatic Hernia (CDH) fetuses and found that they show differences to non-CDH controls and can recapitulate some pathological features of the disease. Amniotic Fluid Organoids (AFO) allow investigation of fetal epithelial tissues at clinically relevant developmental stages and may enable the development of therapeutic tools tailored to the fetus, as well as to predicting the effects of such therapies.
Genomic diversity of wild and cultured Yesso scallopMizuhopecten yessoensisfrom Japan and Canada
Authors: Sutherland Ben J. G. , Itoh Naoki , Gilchrist Korrina , Boyle Brian , Roth Myron , Green Timothy J.
Published: June 2023

The Yesso scallopMizuhopecten yessoensisis an important aquaculture species that was introduced to Western Canada from Japan to establish an economically viable scallop farming industry. This highly fecund species has been propagated in Canadian aquaculture hatcheries for the past 40 years, raising questions about genetic diversity and genetic differences among hatchery stocks. In this study, we compare cultured Canadian and wild Japanese populations of Yesso scallop using double-digest restriction site-associated DNA (ddRAD)-sequencing to genotype 21,048 variants in 71 wild-caught scallops from Japan, 65 scallops from the Vancouver Island University breeding population, and 37 scallops obtained from a commercial farm off Vancouver Island, British Columbia. The wild scallops are largely comprised of equally unrelated individuals, whereas cultured scallops are comprised of multiple families of related individuals. The polymorphism rate estimated in wild scallops was 1.7%, whereas in the cultured strains it ranged between 1.35% and 1.07%. Interestingly, heterozygosity rates were highest in the cultured populations, which is likely due to shellfish hatchery practices of crossing divergent strains to gain benefits of heterosis and to avoid inbreeding. Evidence of founder effects and drift were observed in the cultured strains, including high genetic differentiation between cultured populations and between cultured populations and the wild population. Cultured populations had effective population sizes ranging from 9-26 individuals whereas the wild population was estimated at 25-50K individuals. Further, a depletion of low frequency variants was observed in the cultured populations. These results indicate significant genetic diversity losses in cultured scallops in Canadian breeding programs.

Article Summary

Yesso scallop was introduced to breeding programs in Canada around 40 years ago and has become a valuable aquaculture species in the country with little information regarding its genetic diversity. This work genotypes over 20K genetic variants in wild Yesso scallops from Japan and compares to a major broodstock collection in British Columbia, Canada, as well as a commercial farm in the same region. Reduced polymorphism but elevated heterozygosity indicates value of using genetic information to guide breeding programs.
Detection and characterization of novel luchacoviruses, genusAlphacoronavirus, shed in saliva and feces of meso-carnivores in the northeastern United States
Authors: Olarte-Castillo Ximena A. , Plimpton Laura , McQueary Holly , Sun Yining , Yu Y. Tina , Cover Sarah , Richardson Amy N. , Jin Yuhan , Grenier Jennifer K. , Cummings Kevin J. , Bunting Elizabeth , Diuk-Wasser Maria , Needle David , Schuler Krysten , Stanhope Michael J. , Whittaker Gary , Goodman Laura B.
Published: June 2023

Small to mid-sized carnivores, or meso-carnivores, comprise a group of diverse mammals, many of which can adapt to anthropogenically disturbed environments. Wild meso-carnivores living in urban areas may get exposed to or spread pathogens to other species, including stray/feral domestic animals. Several coronaviruses (CoVs) have been detected in domesticated and farmed meso-carnivores, but knowledge of CoVs circulating in free-ranging wild meso-carnivores remains limited. In this study, we analyzed 321 samples collected between 2016 and 2022 from 9 species of free-ranging wild meso-carnivores and stray/feral domestic cats in the northeastern United States. Using a pan-CoV PCR, we screened tissues, feces, and saliva, nasal, and rectal swabs. We detected CoV RNA in fecal and saliva samples of animals in four species: fisher (Pekania pennanti), bobcat (Lynx rufus), red fox (Vulpes vulpes), and domestic cat(Felis catus). Next-generation sequencing revealed that all these viruses belonged to theLuchacovirussubgenus (Alphacoronavirusgenus), previously reported only in rodents and lagomorphs (i.e., rabbits). Genetic comparison of the 3’-end of the genome (∼12,000bp) revealed that although the viruses detected group with, and have a genetic organization similar to other luchacoviruses, they are genetically distinct from those from rodents and lagomorphs. Genetic characterization of the spike protein revealed that the meso-carnivore luchacoviruses do not have an S1/S2 cleavage motif but do have highly variable structural loops containing cleavage motifs similar to those identified in certain pathogenic CoVs. This study highlights the importance of characterizing the spike protein of CoVs in wild species for further targeted epidemiologic monitoring.

Importance

Several coronaviruses (CoVs) have been detected in domesticated, farmed, and wild meso-carnivores, causing a wide range of diseases, and infecting diverse species, highlighting their important but understudied role in the epidemiology of these viruses. Assessing the viral diversity hosted in wildlife species is essential to understand their significance in the cross-species transmission of CoVs. Our focus here was on CoV discovery in meso-carnivores in the Northeast USA as a potential “hotspot” area with high density of humans and urban wildlife. This study identifies novel alphacoronaviruses circulating in multiple free-ranging wild and domestic species in this area and explores their potential epidemiological importance based on regions of the Spike gene that are relevant for virus-host interactions.
Contributions of early and mid-level visual cortex to high-level object categorization
Authors: Kramer Lily E. , Chen Yi-Chia , Long Bria , Konkle Talia , Cohen Marlene R.
Published: June 2023

The complexity of visual features for which neurons are tuned increases from early to late stages of the ventral visual stream. Thus, the standard hypothesis is that high-level functions like object categorization are primarily mediated by higher visual areas because they require more complex image formats that are not evident in early visual processing stages. However, human observers can categorize images as objects or animals or as big or small even when the images preserve only some low- and mid-level features but are rendered unidentifiable (‘texforms’, Long et al., 2018). This observation suggests that even the early visual cortex, in which neurons respond to simple stimulus features, may already encode signals about these more abstract high-level categorical distinctions. We tested this hypothesis by recording from populations of neurons in early and mid-level visual cortical areas while rhesus monkeys viewed texforms and their unaltered source stimuli (simultaneous recordings from areas V1 and V4 in one animal and separate recordings from V1 and V4 in two others). Using recordings from a few dozen neurons, we could decode the real-world size and animacy of both unaltered images and texforms. Furthermore, this neural decoding accuracy across stimuli was related to the ability of human observers to categorize texforms by real-world size and animacy. Our results demonstrate that neuronal populations early in the visual hierarchy contain signals useful for higher-level object perception and suggest that the responses of early visual areas to simple stimulus features display preliminary untangling of higher-level distinctions.
genomicBERT and data-free deep-learning model evaluation
Authors: Chen Tyrone , Tyagi Navya , Chauhan Sarthak , Peleg Anton Y. , Tyagi Sonika
Published: June 2023

The emerging field of Genome-NLP (Natural Language Processing) aims to analyse biological sequence data using machine learning (ML), offering significant advancements in data-driven diagnostics. Three key challenges exist in Genome-NLP. First, long biomolecular sequences require “tokenisation” into smaller subunits, which is non-trivial since many biological “words” remain unknown. Second, ML methods are highly nuanced, reducing interoperability and usability. Third, comparing models and reproducing results are difficult due to the large volume and poor quality of biological data.

To tackle these challenges, we developed the first automated Genome-NLP workflow that integrates feature engineering and ML techniques. The workflow is designed to be species and sequence agnostic. In this workflow: a) We introduce a new transformer-based model for genomes calledgenomicBERT, which empirically tokenises sequences while retaining biological context. This approach minimises manual preprocessing, reduces vocabulary sizes, and effectively handles out-of-vocabulary “words”. (b) We enable the comparison of ML model performance even in the absence of raw data.

To facilitate widespread adoption and collaboration, we have madegenomicBERTavailable as part of the publicly accessible conda package calledgenomeNLP. We have successfully demonstrated the application ofgenomeNLPon multiple case studies, showcasing its effectiveness in the field of Genome-NLP.

Highlights

We provide a comprehensive classification of genomic data tokenisation and representation approaches for ML applications along with their pros and cons.

We infer k-mers directly from the data and handle out-of-vocabulary words. At the same time, we achieve a significantly reduced vocabulary size compared to the conventional k-mer approach reducing the computational complexity drastically.

Our method is agnostic to species or biomolecule type as it is data-driven.

We enable comparison of trained model performance without requiring original input data, metadata or hyperparameter settings.

We present the first publicly available, high-level toolkit that infers the grammar of genomic data directly through artificial neural networks.

Preprocessing, hyperparameter sweeps, cross validations, metrics and interactive visualisations are automated but can be adjusted by the user as needed.
Single-cell type analysis of wing premotor circuits in the ventral nerve cord ofDrosophila melanogaster
Authors: Ehrhardt Erica , Whitehead Samuel C , Namiki Shigehiro , Minegishi Ryo , Siwanowicz Igor , Feng Kai , Otsuna Hideo ,   FlyLight Project Team, Meissner Geoffrey W , Stern David , Truman Jim , Shepherd David , Dickinson Michael H , Ito Kei , Dickson Barry J , Cohen Itai , Card Gwyneth M , Korff Wyatt
Published: June 2023

To perform most behaviors, animals must send commands from higher-order processing centers in the brain to premotor circuits that reside in ganglia distinct from the brain, such as the mammalian spinal cord or insect ventral nerve cord. How these circuits are functionally organized to generate the great diversity of animal behavior remains unclear. An important first step in unraveling the organization of premotor circuits is to identify their constituent cell types and create tools to monitor and manipulate these with high specificity to assess their function. This is possible in the tractable ventral nerve cord of the fly. To generate such a toolkit, we used a combinatorial genetic technique (split-GAL4) to create 195 sparse driver lines targeting 196 individual cell types in the ventral nerve cord. These included wing and haltere motoneurons, modulatory neurons, and interneurons. Using a combination of behavioral, developmental, and anatomical analyses, we systematically characterized the cell types targeted in our collection. In addition, we identified correspondences between the cells in this collection and a recent connectomic data set of the ventral nerve cord. Taken together, the resources and results presented here form a powerful toolkit for future investigations of neural circuits and connectivity of premotor circuits while linking them to behavioral outputs.
BrainAGE as a measure of maturation during early adolescence
Authors: Whitmore Lucy B. , Weston Sara J. , Mills Kathryn L.
Published: June 2023

The Brain-Age Gap Estimation (BrainAGE) is an important new tool that purports to evaluate brain maturity when used in adolescent populations. However, it is unclear whether BrainAGE tracks with other maturational metrics in adolescence. In the current study, we related BrainAGE to metrics of pubertal and cognitive development using both a previously validated model and a novel model trained specifically on an early adolescent population. The previously validated model was used to predict BrainAGE in two age bands, 9-11 and 10-13 years old, while the novel model was used with 9-11 year olds only. Across both models and age bands, an older BrainAGE was related to more advanced pubertal development. The relationship between BrainAGE and cognition was less clear, with conflicting relationships across the two models. Additionally, longitudinal analysis revealed moderate to high stability in BrainAGE across early adolescence. The results of the current study provide initial evidence that BrainAGE tracks with some metrics of maturation, including pubertal development. However, the conflicting results between BrainAGE and cognition lead us to question the utility of these models for non-biological processes.
Wolbachia-induced inhibition of O’nyong nyong virus inAnophelesmosquitoes is mediated by Toll signaling and modulated by cholesterol
Authors: Pujhari Sujit , Hughes Grant L , Pakpour Nazzy , Suzuki Yasutsugu , Rasgon Jason L
Published: June 2023

Enhanced host immunity and competition for metabolic resources are two main competing hypotheses for the mechanism ofWolbachia-mediated pathogen inhibition in arthropods. Using anAnophelesmosquito – somaticWolbachiainfection – O’nyong nyong virus (ONNV) model, we demonstrate that the mechanism underpinningWolbachia-mediated virus inhibition is up-regulation of the Toll innate immune pathway. However, the viral inhibitory properties ofWolbachiawere abolished by cholesterol supplementation. This result was due toWolbachia-dependent cholesterol-mediated suppression of Toll signaling rather than competition for cholesterol betweenWolbachiaand virus. The inhibitory effect of cholesterol was specific toWolbachia-infectedAnophelesmosquitoes and cells. These data indicate that bothWolbachiaand cholesterol influence Toll immune signaling inAnophelesmosquitoes in a complex manner and provide a functional link between the host immunity and metabolic competition hypotheses for explainingWolbachia-mediated pathogen interference in mosquitoes. In addition, these results provide a mechanistic understanding of the mode of action ofWolbachia-induced pathogen blocking in Anophelines, which is critical to evaluate the long-term efficacy of control strategies for malaria andAnopheles-transmitted arboviruses.

HIGHLIGHTS

Wolbachiainhibits O’nyong nyong virus (ONNV) inAnophelesmosquitoes.

Enhanced Toll signaling is responsible forWolbachia-induced interference of ONNV.

Cholesterol suppresses Toll signaling to modulateWolbachia-induced ONNV interference.
Functional Genomics of GastrointestinalEscherichia coliIsolated from Patients with Cancer and Diarrhea
Authors: Carter Hannah , Clark Justin , Carlin Lily G. , Vaughan Ellen , Rajan Anubama , Olvera Adilene , Yu Xiaomin , Zeng Xi-Lei , Kambal Amal , Holder Michael , Qin Xiang , Gibbs Richard A. , Petrosino Joseph F. , Muzny Donna M. , Doddapaneni Harsha , Menon Vipin K. , Hoffman Kristi L. , Meng Qingchang , Ross Matthew C. , Javornik Cregeen Sara J. , Metcalf Ginger , Jenq Robert , Blutt Sarah , Estes Mary K. ,   TMC-GCID team, Maresso Anthony , Okhuysen Pablo C.
Published: June 2023

We describe the epidemiology and clinical characteristics of 29 patients with cancer and diarrhea in whom EnteroaggregativeEscherichia coli(EAEC) was initially identified by GI BioFire panel multiplex.E. colistrains were successfully isolated from fecal cultures in 14 of 29 patients. Six of the 14 strains were identified as EAEC and 8 belonged to other diverseE. coligroups of unknown pathogenesis. We investigated these strains by their adherence to human intestinal organoids, cytotoxic responses, antibiotic resistance profile, full sequencing of their genomes, and annotation of their functional virulome. Interestingly, we discovered novel and enhanced adherence and aggregative patterns for several diarrheagenic pathotypes that were not previously seen when co-cultured with immortalized cell lines. EAEC isolates displayed exceptional adherence and aggregation to human colonoids compared not only to diverse GIE. coli, but also compared to prototype strains of other diarrheagenicE. coli. Some of the diverseE. colistrains that could not be classified as a conventional pathotype also showed an enhanced aggregative and cytotoxic response. Notably, we found a high carriage rate of antibiotic resistance genes in both EAEC strains and diverse GIE. coliisolates and observed a positive correlation between adherence to colonoids and the number of metal acquisition genes carried in both EAEC and the diverseE. colistrains. This work indicates thatE. colifrom cancer patients constitute strains of remarkable pathotypic and genomic divergence, including strains of unknown disease etiology with unique virulomes. Future studies will allow for the opportunity to re-defineE. colipathotypes with greater diagnostic accuracy and into more clinically relevant groupings.
Ribosomal protein control of hematopoietic stem cell transformation through direct, non-canonical regulation of metabolism
Authors: Harris Bryan , Singh Dinesh K. , Verma Monika , Fahl Shawn P. , Rhodes Michele , Sprinkle Shanna R. , Wang Minshi , Zhang Yong , Perrigoue Jaqueline , Kessel Rachel , Peri Suraj , West Joshua , Giricz Orsi , Boultwood Jacqueline , Pellagatti Andrea , Ramesh KH , Montagna Cristina , Pradhan Kith , Tyner Jeffrey W. , Kennedy Brian K. , Holinstat Michael , Steidl Ulrich , Sykes Stephen , Verma Amit , Wiest David L.
Published: June 2023

We report here that expression of the ribosomal protein, RPL22, is frequently reduced in human myelodysplastic syndrome (MDS) and acute myelogenous leukemia (AML); reduced RPL22 expression is associated with worse outcomes. Mice null for Rpl22 display characteristics of an MDS-like syndrome and develop leukemia at an accelerated rate. Rpl22-deficient mice also display enhanced hematopoietic stem cell (HSC) self-renewal and obstructed differentiation potential, which arises not from reduced protein synthesis but from increased expression of the Rpl22 target, ALOX12, an upstream regulator of fatty acid oxidation (FAO). The increased FAO mediated by Rpl22-deficiency also persists in leukemia cells and promotes their survival. Altogether, these findings reveal that Rpl22 insufficiency enhances the leukemia potential of HSC via non-canonical de-repression of its target, ALOX12, which enhances FAO, a process that may serve as a therapeutic vulnerability of Rpl22 low MDS and AML leukemia cells.

Highlights

RPL22 insufficiency is observed in MDS/AML and is associated with reduced survival

Rpl22-deficiency produces an MDS-like syndrome and facilitates leukemogenesis

Rpl22-deficiency does not impair global protein synthesis by HSC

Rpl22 controls leukemia cell survival by non-canonical regulation of lipid oxidation

eTOC:Rpl22 controls the function and transformation potential of hematopoietic stem cells through effects on ALOX12 expression, a regulator of fatty acid oxidation.
Progress toward the development of an effective vaccine for Extraintestinal pathogenicE. coli(ExPEC): The application of the multiple-protein subunits vaccine in different murine models
Authors: Xing Yikun , Clark Justin R. , Chang James D. , Zulk Jacob J. , Chirman Dylan M. , Piedra Felipe-Andres , Patras Kathryn A. , Maresso Anthony W.
Published: June 2023

Extraintestinal pathogenicE. coli(ExPEC) is the primary Gram-negative bacterial pathogen, and the leading cause of life-threatening sepsis and urinary tract infections (UTI) in adults. The emergence and increasing prevalence of multidrug-resistance (MDR) ExPEC strains have led to considerable treatment failures, increased hospitalization rates, morbidity, and mortality. A prophylactic vaccine against ExPEC has the potential to reduce severe infection-related morbidity and mortality, helping to address the escalating antimicrobial resistance (AMR) crisis worldwide. The α-hemolysin (HlyA) is a critical, frequently detected secreted cytotoxic virulence factor in ExPEC, with HlyA-expressing ExPEC strains correlating with increased severity and infection dissemination in clinical levels. In this study, we assessed the protective efficacy of pro-HlyA (the inactive and immature precursor of HlyA) and Dual-Hit (a combination of pro-HlyA and SinH-3, the previously reported immunoglobulin-like domain-3 of the invasin-like autotransporter protein SinH), as ExPEC vaccine candidates. We demonstrated that immunizing mice with pro-HlyA or Dual-Hit significantly reduced bacterial burden and increased survival rates against pandemic ExPEC sequence type strains, ST73 (CFT073) and ST95 (UTI89), in the model of bacteremia and mortality. Both pro-HlyA or Dual-Hit immunizations also provided significant protection against UTI89 colonization in the bladder in the murine UTI model. Furthermore, vaccination with Dual-Hit provided enduring and robust protection against a mixture of ten typical high-virulent sequence types of ExPEC strains, resulting in a promising broad-spectrum vaccine candidate. These findings suggest that pro-HlyA and Dual-Hit might serve as highly effective vaccine targets and highlight the potential of these vaccine candidates for further development and evaluation.