bluuebunny/crossref_metadata_2025 huggingface dataset:
VabHLH137 promotes proanthocyanidin and anthocyanin biosynthesis and enhances resistance to Colletotrichum gloeosporioides in grapevine
Authors: Yu Dan , Wei Wei , Fan Zhongqi , Chen Jianye , You Yilin , Huang Weidong , Zhan Jicheng
Published: December 2022

Proanthocyanidins (PAs) and anthocyanins are involved in the response of plants to various environmental stresses. However, the mechanism behind defense-induced PA biosynthetic regulation is still not completely elucidated, also in grapevine. This study performed a transcriptome sequencing analysis of grape berries infected with Colletotrichum gloeosporioides to highlight the induction of the VabHLH137 factor from the basic helix–loop–helix (bHLH) XII subfamily by the fungus, which appeared to be significantly co-expressed with PA-related genes. The functional analysis of VabHLH137 overexpression and knockdown in transgenic grape calli showed that it positively regulated PA and anthocyanin biosynthesis. Moreover, VabHLH137 overexpression in the grape calli significantly increased resistance to C. gloeosporioides. A yeast one-hybrid and electrophoretic mobility shift assay revealed that VabHLH137 directly bound to the VaLAR2 promoter, enhancing its activity and interacting with VaMYBPAR, a transcriptional activator of PA biosynthesis. Furthermore, transient experiments showed that although the VabHLH137 + VaMYBPAR complex activated VaLAR2 expression, it failed to further enhance VaLAR2 expression compared to VaMYBPAR alone. The findings indicated that VabHLH137 enhanced PA biosynthesis by activating of VaLAR2 expression, providing new insight into the transcriptional regulation of defense-induced PA biosynthesis in grapevine.
Genome-wide association study of 23 flowering phenology traits and 4 floral agronomic traits in tree peony (Paeonia section Moutan DC.) reveals five genes known to regulate flowering time
Authors: Li Yuying , Guo Lili , Wang Zhanying , Zhao Dehui , Guo Dalong , Carlson John E. , Yin Weilun , Hou Xiaogai
Published: December 2022

Tree peony is a unique traditional flower in China, with large, fragrant, and colorful flowers. However, a relatively short and concentrated flowering period limits the applications and production of tree peony. A genome-wide association study (GWAS) was conducted to accelerate molecular breeding for the improvement of flowering phenology traits and ornamental phenotypes in tree peony. A diverse panel of 451 tree peony accessions was phenotyped for 23 flowering phenology traits and 4 floral agronomic traits over 3 years. Genotyping by sequencing (GBS) was used to obtain a large number of genome-wide single-nucleotide polymorphisms (SNPs) (107 050) for the panel genotypes, and 1047 candidate genes were identified by association mapping. Eighty-two related genes were observed during at least 2 years for flowering, and seven SNPs repeatedly identified for multiple flowering phenology traits over multiple years were highly significantly associated with five genes known to regulate flowering time. We validated the temporal expression profiles of these candidate genes and highlighted their possible roles in the regulation of flower bud differentiation and flowering time in tree peony. This study shows that GWAS based on GBS can be used to identify the genetic determinants of complex traits in tree peony. The results expand our understanding of flowering time control in perennial woody plants. Identification of markers closely related to these flowering phenology traits can be used in tree peony breeding programs for important agronomic traits.
Theanine, a tea-plant-specific non-proteinogenic amino acid, is involved in the regulation of lateral root development in response to nitrogen status
Authors: Chen Tingting , Lin Shijia , Chen Ziping , Yang Tianyuan , Zhang Shupei , Zhang Jinsong , Xu Guohua , Wan Xiaochun , Zhang Zhaoliang
Published: December 2022

Glutamine synthetase type I (GSI)-like proteins are proposed to mediate nitrogen signaling and developmental fate by synthesizing yet unidentified metabolites. Theanine, the most abundant non-proteinogenic amino acid in tea plants, is the first identified metabolite synthesized by a GSI-like protein (CsTSI) in a living system. However, the roles of theanine in nitrogen signaling and development are little understood. In this study we found that nitrogen deficiency significantly reduced theanine accumulation and increased lateral root development in tea plant seedlings. Exogenous theanine feeding significantly repressed lateral root development of seedlings of tea plants and the model plant Arabidopsis. The transcriptomic analysis revealed that the differentially expressed genes in the roots under theanine feeding were enriched in the apoplastic pathway and H2O2 metabolism. Consistently, theanine feeding reduced H2O2 levels in the roots. Importantly, when co-treated with H2O2, theanine abolished the promoting effect of H2O2 on lateral root development in both tea plant and Arabidopsis seedlings. The results of histochemical assays confirmed that theanine inhibited reactive oxygen species accumulation in the roots. Further transcriptomic analyses suggested the expression of genes encoding enzymes involved in H2O2 generation and scavenging was down- and upregulated by theanine, respectively. Moreover, the expression of genes involved in auxin metabolism and signaling, cell division, and cell expansion was also regulated by theanine. Collectively, these results suggested that CsTSI-synthesized theanine is likely involved in the regulation of lateral root development, via modulating H2O2 accumulation, in response to nitrogen levels in tea plants. This study also implied that the module consisting of GSI-like protein and theanine-like metabolite is probably conserved in regulating development in response to nitrogen status in plant species.
Haem Oxygenase 1 is a potential target for creating etiolated/albino tea plants (Camellia sinensis) with high theanine accumulation
Authors: Chen Ziping , Lin Shijia , Chen Tingting , Han Mengxue , Yang Tianyuan , Wang Yan , Bao Shilai , Shen Zhougao , Wan Xiaochun , Zhang Zhaoliang
Published: December 2022

Theanine content is highly correlated with sensory quality and health benefits of tea infusion. The tender shoots of etiolated and albino tea plants contain higher theanine than the normal green tea plants and are valuable materials for high quality green tea processing. However, why these etiolated or albino tea plants can highly accumulate theanine is largely unknown. In this study, we observed an Arabidopsis etiolated mutant hy1–100 (mutation in Haem Oxygenase 1, HO1) that accumulated higher levels of glutamine (an analog of theanine). We therefore identified CsHO1 in tea plants and found CsHO1 is conserved in amino acid sequences and subcellular localization with its homologs in other plants. Importantly, CsHO1 expression in the new shoots was much lower in an etiolated tea plants ‘Huangkui’ and an albino tea plant ‘Huangshan Baicha’ than that in normal green tea plants. The expression levels of CsHO1 were negatively correlated with theanine contents in these green, etiolated and albino shoots. Moreover, CsHO1 expression levels in various organs and different time points were also negatively correlated with theanine accumulation. The hy1–100 was hypersensitive to high levels of theanine and accumulated more theanine under theanine feeding, and these phenotypes were rescued by the expression of CsHO1 in this mutant. Transient knockdown CsHO1 expression in the new shoots of tea plant using antisense oligonucleotides (asODN) increased theanine accumulation. Collectively, these results demonstrated CsHO1 negatively regulates theanine accumulation in tea plants, and that low expression CsHO1 likely contributes to the theanine accumulation in etiolated/albino tea plants.
What every neuropathologist needs to know: condensed protocol work-up for clinical dementia syndromes
Authors: Multz Rachel A , Spencer Callen , Matos Arleen , Ajroud Kaouther , Zamudio Carlos , Bigio Eileen , Mao Qinwen , Medeiros Rose A , Ahrendsen Jared T , Castellani Rudolph J , Flanagan Margaret E
Published: December 2022

Concerns about the costs associated with autopsy assessment of Alzheimer disease and related dementias according to 2012 NIA-AA Guidelines have been expressed since the publication of those guidelines. For this reason, we designed and validated a Condensed Protocol for the neuropathologic diagnoses of Alzheimer disease neuropathologic change, Lewy Body disease neuropathologic change, as well as chronic microvascular lesions, hippocampal sclerosis of aging, and cerebral amyloid angiopathy. In this study, the Condensed Protocol is updated to include frontotemporal lobar degeneration [FTLD] tau (corticobasal degeneration, progressive supranuclear palsy, and Pick disease), FTLD-TDP, and limbic-predominant, age-related TDP-43 encephalopathy. The same 20 brain regions are sampled and processed in 5 tissue cassettes, which reduces reagent costs by approximately 65%. Three board-certified neuropathologists were blinded to the original Northwestern University Alzheimer’s Disease Research Center Original Protocol neuropathological diagnoses and all clinical history information. The results yielded near uniform agreement with the original comprehensive Alzheimer’s Disease Research Center neuropathologic assessments. Diagnostic sensitivity was not impacted. In summary, our recent results show that our updated Condensed Protocol is also an accurate and less expensive alternative to the comprehensive protocols for the additional neuropathologic diagnoses of FTLD Tau and TDP43 proteinopathies.
Firm Finances and the Spread of COVID-19: Evidence from Nursing Homes
Authors: Begley Taylor A , Weagley Daniel
Published: December 2022

We find that firms’ financial resources play an important role in mitigating the spread of COVID-19. We study nursing homes—whose residents account for over one-third of all U.S. COVID-19 deaths—at a time when investment in risk mitigation was costly and critical. Facilities with less liquidity and those experiencing more severe cash flow shocks had more cases of COVID-19. The importance of cash flow is further supported by tests exploiting state-level variation in Medicaid reimbursement expansion. Evidence on personal protective equipment supplies suggests a lack of financial resources leads to lower investment in risk mitigation. (JEL G30, G32, I10)

Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online.
Impact on Dental Utilization of the Integration of Oral Health in Pediatric Primary Care Through Quality Improvement
Authors: Danesh David O. , Peng Jin , Hammersmith Kimberly J. , Gowda Charitha , Maciejewski Heather , Amini Homa , Wapner Andrew W. , Meyer Beau D.
Published: December 2022

Objectives:

To evaluate child-level dental utilization and expenditure outcomes based on if and where children received fluoride varnish (FV) at quality improvement (QI) medical practices, at non-QI medical practices, at dental practices, or those who never received FV from any practice.

Design:

Retrospective claims-based analysis cohort study.

Setting:

Children with Medicaid insurance through an Ohio pediatric accountable care organization.

Participants:

Children aged 1 to 5 years with 1 or more well-child visits between 2015 and 2017.

Intervention:

FV receipt versus no FV. Among children who received FV, categorized if FV delivered by a QI-participating medical provider, a non-QI-participating medical provider, and a dental provider.

Main Outcome Measure:

Dental claims from 2014 to 2019 were collected for preventive dental visits, caries-related treatment visits, dental general anesthesia (GA) visit, and emergency department visit for a dental problem to examine utilization patterns, expenditures, and dental outcomes.

Results:

The QI group had a significantly higher incidence of preventive dental visits than the dental (incidence rate ratio [IRR] = 0.93; 95% confidence interval [CI], 0.91-0.96) or non-QI groups (IRR = 0.86; 95% CI, 0.84-0.88). Compared with the QI group, the non-QI (adjusted odds ratio [aOR] = 2.6; 95% CI, 2.4-2.9) and dental (aOR = 2.9; 95% CI, 2.6-3.3) groups were significantly more likely to have caries-related treatment visits. The dental group children were significantly more likely to have dental treatment under GA than the QI group (aOR = 5.3; 95% CI, 2.0-14.4).

Conclusions:

Children seen at QI practices appear to have an increased uptake of preventive dental services, which may explain the lower incidence of dental caries visits and GA treatment.
ICTV Virus Taxonomy Profile: Secoviridae 2022
Authors: Fuchs Marc , Hily Jean-Michel , Petrzik Karel , Sanfaçon Hélène , Thompson Jeremy R. , van der Vlugt René , Wetzel Thierry ,   ICTV Report Consortium
Published: December 2022

Members of the family Secoviridae are non-enveloped plant viruses with mono- or bipartite linear positive-sense ssRNA genomes with a combined genome of 9 to 13.7 kb and icosahedral particles 25–30 nm in diameter. They are related to picornaviruses and are members of the order Picornavirales. Genera in the family are distinguished by the host range, vector, genomic features and phylogeny of the member viruses. Most members infect dicotyledonous plants, and many cause serious disease epidemics. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) report on the family Secoviridae, which is available at ictv.global/report/secoviridae.
Deep EEG Source Localization via EMD-based fMRI High Spatial Frequency
Authors: Moradi Narges , Goodyear Bradley G. , Sotero Roberto C.
Published: December 2022

Brain imaging with a high-spatiotemporal resolution is crucial for accurate brain-function mapping. Electroencephalography (EEG) and functional Magnetic Resonance Imaging (fMRI) are two popular neuroimaging modalities with complementary features that record brain function with high temporal and spatial resolution, respectively. One popular non-invasive way to obtain data with both high spatial and temporal resolutions is to combine the fMRI activation map and EEG data to improve the spatial resolution of the EEG source localization. However, using the whole fMRI map may cause spurious results for the EEG source localization, especially for deep brain regions. Considering the head’s conductivity, deep regions’ sources with low activity are unlikely to be detected by the EEG electrodes at the scalp. In this study, we use fMRI’s high spatial-frequency component to identify the local high-intensity activations that are most likely to be captured by the EEG. The 3D Empirical Mode Decomposition (3D-EMD), a data-driven method, is used to decompose the fMRI map into its spatial-frequency components. Different validation measurements for EEG source localization show improved performance for the EEG inverse-modeling informed by the fMRI’s high-frequency spatial component compared to the fMRI-informed EEG source-localization methods. The level of improvement varies depending on the voxels’ intensity and their distribution. Our experimental results also support this conclusion.
Automated head-fixation training system with high levels of animal participation in psychoacoustic tasks
Authors: Liu Ji , Maximov Kate , Kanold Patrick O.
Published: December 2022

Many animal training paradigms rely on head-fixation. Head-fixation training is typically laborious and can benefit from automation to relieve the workload as well as to reduce the variability in the training outcome. Several groups have reported successful implementations of such systems, but throughput varied greatly across groups. In addition, most studies relied on brief periods head-fixation sessions (≤ 1 minute) to reduce the potential stress on the animal. Here, we report the design of a new system that could achieve head-fixation sessions on the order of minutes with high participation rate from the animal (100%). Throughout the training period, each mouse performed a total of close to 40 minutes of head-fixation training on average on each day and learned common psychoacoustic tasks, i.e., tone detection and tone discrimination. Our system can achieve highly efficient training with minimum idling time, providing an opportunity for combinations with high-end neural recording equipment to achieve maximum training and data collection efficiency.
Dual functions oflabialresolve the Hox logic of chelicerate head segments
Authors: Gainett Guilherme , Klementz Benjamin C. , Blaszczyk Pola O. , Bruce Heather , Patel Nipam , Sharma Prashant P.
Published: December 2022

Despite an abundance of gene expression surveys, comparatively little is known about Hox gene function in Chelicerata, with emphasis on the Hox logic of the anterior prosomal segments, which bear the mouthparts. Previous investigations of individual paralogs oflabial(lab) andDeformed(Dfd) in the spiderParasteatoda tepidariorumhave shown that these play a role in tissue maintenance of the pedipalpal segment (labial-1) and in patterning the first walking leg identity (Deformed-1), respectively. However, broader extrapolations of these data points across chelicerates are hindered by the existence of duplicated copies of Hox genes in arachnopulmonates (e.g., spiders and scorpions), which have resulted from an ancient whole genome duplication event. Here, we investigated the function of single-copy orthologs oflabin the harvestmanPhalangium opilio, an exemplar of a lineage that was not subject of this whole genome duplication. Embryonic RNAi againstlabresulted in homeotic transformations of pedipalps to chelicerae, as well as reduction and fusion of the pedipalpal segment with adjacent segments. To test for combinatorial function, we performed double knockdown oflabandDfd, which results in homeotic transformation of both pedipalps and first walking legs into cheliceral identity, whereas the second walking leg is transformed into a pedipalpal identity. Taken together, these results elucidate a model for the Hox logic of head segments in Chelicerata. To substantiate the validity of this model, we additionally performed expression surveys for duplicated copies oflabandDfdin scorpions and horseshoe crabs, toward understanding the genetic basis of a heteronomous prosoma. We show that repetition of morphologically similar appendages is correlated with uniform expression levels of the Hox geneslabandDfd, irrespective of the number of gene copies.
Improving Protein Subcellular Localization Prediction with Structural Prediction & Graph Neural Networks
Authors: Dubourg-Felonneau Geoffroy , Abbasi Arash , Akiva Eyal , Lee Lawrence
Published: December 2022

The majority of biological functions are carried out by proteins. Proteins perform their roles only upon arrival to their target location in the cell, hence elucidating protein subcellular localization is essential for better understanding their function. The exponential growth in genomic information and the high cost of experimental validation of protein localization call for the development of predictive methods. We present a method that improves subcellular localization prediction for proteins based on their sequence by leveraging structure prediction and Graph Neural Networks. We demonstrate how Language Models, trained on protein sequences, and Graph Neural Networks, trained on protein’s 3D structures, are both efficient approaches for this task. They both learn meaningful, yet different representations of proteins; hence, ensembling them outperforms the reigning state of the art method. Our architecture improves the localization prediction performance while being lighter and more cost-effective.
Validation of six commercial antibodies for detection of heterologous and endogenous TRPM8 ion channel expression
Authors: Hernández-Ortego Pablo , Torres-Montero Remedios , de la Peña Elvira , Viana Félix , Fernández-Trillo Jorge
Published: December 2022

TRPM8 is a non-selective cation channel expressed in primary sensory neurons and other tissues, including prostate and urothelium. Its participation in different physiological and pathological processes such as thermoregulation, pain, itch, inflammation and cancer has been widely described, making it a promising target for therapeutic approaches. The detection and quantification of TRPM8 seems crucial for advancing in the knowledge of the mechanisms under-lying its role in these pathophysiological conditions. Antibody-based techniques are commonly used for protein detection and quantification, although their performance with many ion channels, including TRPM8, is suboptimal. Thus, the search for reliable antibodies is of utmost importance. In this study, we characterized the performance of six TRPM8 commercial antibodies in three immunodetection techniques: western blot, immunocytochemistry and immunohistochemistry. Different outcomes were obtained for the tested antibodies; two of them proved to be successful detecting TRPM8 in the three approaches while, in the conditions tested, the other four were acceptable only for specific techniques. Considering our results, we offer some insight into the usefulness of these antibodies for detection of TRMP8 depending on the methodology of choice.
FBXO42activity is required to prevent mitotic arrest, spindle assembly checkpoint activation, and lethality in glioblastoma and other cancers
Authors: Hoellerbauer Pia , Kufeld Megan , Arora Sonali , Girard Emily J. , Herman Jacob A. , Olson James M. , Paddison Patrick J.
Published: December 2022

Glioblastoma (GBM) is the most common and aggressive brain tumor in adults. To identify genes differentially required for the viability of GBM stem-like cells (GSCs), we performed functional genomic lethality screens comparing GSCs and control human neural stem cells. Among top scoring hits in a subset of GBM cells was the F-box-containing geneFBXO42, which was also essential in ∼15% of cell lines derived from a broad range of cancers. Mechanistic studies revealed that, in sensitive cells,FBXO42activity prevents chromosome alignment defects, mitotic cell cycle arrest, and cell death. The cell cycle arrest, but not the cell death, triggered byFBXO42inactivation could be suppressed by brief exposure to a chemical inhibitor of Mps1, a key spindle assembly checkpoint (SAC) kinase.FBXO42’s cancer-essential function requires its F-box and Kelch domains, which are necessary for FBXO42’s substrate recognition and targeting by SCF ubiquitin ligase complex. However, none of FBXO42’s previously proposed targets, including ING4, p53, and RBPJ, were responsible for the observed phenotypes. Instead, our results suggest thatFBOX42activity suppresses the accumulation of one or more proteins that perturb chromosome-microtubule dynamics in cancer cells, which, in turn, leads to induction of the SAC and cell death.
Hippocampal engram networks for fear memory recruit new synapses and modify pre-existing synapsesin vivo
Authors: Lee Chaery , Lee Byung Hun , Jung Hyunsu , Lee Chiwoo , Sung Yongmin , Kim Hyopil , Kim Jooyoung , Shim Jae Youn , Kim Ji-il , Choi Dong Il , Park Hye Yoon , Kaang Bong-Kiun
Published: December 2022

As basic units of neural networks, ensembles of synapses underlie cognitive functions like learning and memory. These synaptic engrams show elevated synaptic density among engram cells following contextual fear memory formation. Subsequent analysis of the CA3-CA1 engram synapse revealed larger spine sizes, as the synaptic connectivity correlated to the memory strength. Here, we elucidate the synapse dynamics between CA3 and CA1 by tracking identical synapses at multiple time points by adapting two-photon microscopy and dual-eGRASP techniquein vivo. After memory formation, synaptic connections between engram populations are enhanced in conjunction with synaptogenesis within the hippocampal network. However, extinction learning specifically correlated with the disappearance of CA3 engram to CA1 engram (E-E) synapses. We observed “newly formed” synapses near pre-existing synapses, which clustered CA3-CA1 engram synapses after fear memory formation. Overall, we conclude that dynamics at CA3 to CA1 E-E synapses are key sites for modification during fear memory states.

Highlights

We adapted four-color two-photon microscopy with dual-eGRASP for a longitudinal observation of synaptic connections between CA3 and CA1.

Synaptogenesis according to fear memory formation was specifically observed in E-E synapses.

Extinction learning significantly correlated with the disappearance of E-E synapses.

Particular distribution pattern of newly formed E-E synapses was observed after memory formation.
Drug Resistance Mutations In Transplant Recipients With Suspected Resistance
Authors: González Irene , Tarragó David
Published: December 2022

Resistant CMV infections are challenging complications after SOT and HSCT. Prompt recognition of ARMs is imperative for appropriate therapy. 108 plasma samples from 96 CMV+ transplant recipients with suspected resistance were analysed in CNM in a retrospective nationwide study from January 2018 to July 2022 for resistance genotyping. ARMs in UL97 and UL54 were found in 26.87 % (18/67) and 10.60 % (7/66) of patients, respectively. Patients’ ARM distribution in UL97 was as follows: L595S n=3; L595S/M460I n=1; L595S/N510S n=1; L595W n=1; C603W n=4; A594V n=3; A594E n=1; C607Y n=1; L397R/T409M/H411L/M460I n=1; L397I n=1; H520Q n=1; four patients showed ARMs in UL54 as well (F412C n=1; T503I n=2; P522S n=1), whereas three patients exhibited ARMs in UL54 only (L501I/T503I/L516R/A834P n=1; A987G n=2). L516R in UL54 and L397R/I and H411L in UL97 have been found for the first time in a clinical sample. L595S/W was the most prevalent ARM found to lend resistance to GCV. In UL54 all ARMs lent resistance to GCV and CDV. In addition, A834P, found in one patient, also lent resistance to FOS. CMV load did not differ significantly in patients with or without ARMs, and no differences were found either between patients with ARMs in UL97 or in UL97 and UL54. Despite extensive use of classical antivirals for the treatment of CMV infection after HSCT and SOT, ARMs occurred mainly in viral UL97 kinase, which suggests that CDV and mostly FOS continue to be useful alternatives to nucleoside analogues after genotypic detection of ARMs.
Modeling the Sequence Dependence of Differential Antibody Binding in the Immune Response to Infectious Disease
Authors: Chowdhury Robayet , Taguchi Alexander T. , Kelbauskas Laimonas , Stafford Philip , Diehnelt Chris , Zhao Zhan-Gong , Williamson Phillip C. , Green Valerie , Woodbury Neal W.
Published: December 2022

Past studies have shown that incubation of human serum samples on high density peptide arrays followed by measurement of total antibody bound to each peptide sequence allows detection and discrimination of humoral immune responses to a wide variety of infectious disease agents. This is true even though these arrays consist of peptides with near-random amino acid sequences that were not designed to mimic biological antigens. Previously, this immune profiling approach or “immunosignature” has been implemented using a purely statistical evaluation of pattern binding, with no regard for information contained in the amino acid sequences themselves. Here, a neural network is trained on immunoglobulin G binding to 122,926 amino acid sequences selected quasi-randomly to represent a sparse sample of the entire combinatorial binding space in a peptide array using human serum samples from uninfected controls and 5 different infectious disease cohorts infected by either dengue virus, West Nile virus, hepatitis C virus, hepatitis B virus orTrypanosoma cruzi. This results in a sequence-binding relationship for each sample that contains the differential disease information. Processing array data using the neural network effectively aggregates the sequence-binding information, removing sequence-independent noise and improving the accuracy of array-based classification of disease compared to the raw binding data. Because the neural network model is trained on all samples simultaneously, the information common to all samples resides in the hidden layers of the model and the differential information between samples resides in the output layer of the model, one column of a few hundred values per sample. These column vectors themselves can be used to represent each sample for classification or unsupervised clustering applications such as human disease surveillance.

Author Summary

Previous work from Stephen Johnston’s lab has shown that it is possible to use high density arrays of near-random peptide sequences as a general, disease agnostic approach to diagnosis by analyzing the pattern of antibody binding in serum to the array. The current approach replaces the purely statistical pattern recognition approach with a machine learning-based approach that substantially enhances the diagnostic power of these peptide array-based antibody profiles by incorporating the sequence information from each peptide with the measured antibody binding, in this case with regard to infectious diseases. This makes the array analysis much more robust to noise and provides a means of condensing the disease differentiating information from the array into a compact form that can be readily used for disease classification or population health monitoring.
Synthetic extremophiles: Species-specific formulations for microbial therapeutics and beyond
Authors: Jimenez Miguel , L’Heureux Johanna , Kolaya Emily , Martin Kyle B. , Villaverde Zachary , Khazi-Syed Afeefah , Cao Qinhao , Muller Benjamin , Byrne James D. , Traverso Giovanni
Published: December 2022

Microorganisms have been used for millennia to produce food and medicine and are now being developed as products themselves to treat disease and boost crop production. However, as required for these new applications, maintaining high viability throughout manufacturing, transportation and use remains a significant challenge requiring sophisticated cold-chains and packaging. In fact, we found that commercial microbial products (probiotics) provide a poor solution to this challenge, in particular for key industrial organisms likeE. coli. To overcome this technological gap, we report the development of synthetic extremophiles of industrially important gram-negative bacteria (E. coliNissle 1917,Ensifer meliloti), gram positive bacteria (Lactobacillusplantarum) and yeast (Saccharomyces boulardii). Specifically, we developed a high throughput pipeline to define species-specific materials that allow these organisms to survive drying, elevated temperatures, organic solvents and even ionizing radiation. We enhanced the stability ofE.coliNissle 1917 by >4 orders of magnitude over commercial formulations and demonstrate the capacity to remain viable while undergoing tableting and pharmaceutical methodologies involving organic solvents. The development of synthetic materials-based enhanced stabilization stands to transform our capacity to apply micro-organisms in extreme environments including those found on Earth as well as in space.

One-Sentence Summary

Fragile therapeutic bacteria can be made to survive the manufacturing extremes normally reserved for small molecule drugs.
A high-cholesterol diet leads to faster induction of general anesthesia in two model animals:D. magna and C. elegans
Authors: Robledo-Sánchez K. Carlo Martín , Ruiz-Suárez J. C.
Published: December 2022

General anesthesia (GA) has been under scientific scrutiny since its discovery more than a century ago, resulting in conceptually different proposed mechanisms to explain its origin and operation. Two mechanisms stand out: the lipid and the protein hypothesis. The Meyer-Overton rule (the more anesthetics dissolve in octanol, the greater their action) backups the first hypothesis, while the ligand-receptor interaction, specifically on ion channels, sustains the second. A recent study onDrosophila melanogasterdraws attention to the possibility that both paradigms come together to explain GA synergistically, with the important caveat that this hybrid mechanism lies in the existence of lipid rafts in which cholesterol plays an essential role. Using two model organisms, the water flea (D. magna) and the nematodeC. elegans, we give a further step to clarify this puzzle by carrying out anesthetic experiments with xenon and nitrous oxide. First, the obtained dose-response curves are very steep, implying that Hill coefficients greater than one are needed to describe them correctly, supporting an unspecific action mechanism. Second, we show that the animals’ response to both gases is influenced by a cholesterol diet modification, thus proving that this lipid promotes anesthetic induction. Our findings reenforce the idea that GA is driven by an allosteric induction rather than selective actions on single-target receptors.
Analysis of prokaryotic genes in an impaired Great Lakes harbour reveals seasonal metabolic shifts and a previously undetected cyanobacterium
Authors: Palermo Christine N. , Fulthorpe Roberta R. , Saati Rosemary , Short Steven M.
Published: December 2022

As primary drivers of organic matter re-mineralization and trophic carbon transfer, bacteria promote biogeochemical cycling and shape ecosystems globally. We studied bacterial communities spatially and seasonally in an impaired harbour of Lake Ontario by extracting and sequencing community DNA from water samples collected biweekly from different sites. Assembled contigs were annotated at the phylum level, and Cyanobacteria were further characterized at order and species levels. Actinobacteria were most abundant in early summer, while Cyanobacteria were dominant in mid-summer.Microcystis aeruginosaandLimnoraphis robustawere most abundant throughout the sampling period, expanding the documented diversity of Cyanobacteria in Hamilton Harbour. Functional annotations were performed using the MG-RAST pipeline and SEED database, revealing that genes for photosynthesis, nitrogen metabolism and aromatic compound metabolism varied in relative abundances over the season, while phosphorus metabolism remained consistent, suggesting that these genes remain essential despite fluctuating environmental conditions and community succession. We observed seasonal shifts from anoxygenic to oxygenic phototrophy, and from ammonia assimilation to nitrogen fixation, coupled with decreasing heterotrophic bacteria and increasing cyanobacteria relative abundances. Our data contribute important insights into bacterial taxa and functional potentials in Hamilton Harbour, revealing seasonal and spatial dynamics that can be used to inform ongoing remediation efforts.
Hepatocyte Growth Factor and β1-integrin signalling axis drives tunneling nanotube formation in A549 lung adenocarcinoma cells
Authors: Awanis Griselda , Raveenthiraraj Sathuwarman , Johnson Robert , Gavrilovic Jelena , Warren Derek , Sobolewski Anastasia
Published: December 2022

Tunneling nanotubes (TNTs) are thin cytoplasmic protrusions involved in long-distance cellular communication. The presence of TNTs has been foundin vivoandin vitrostudies in non-small cell lung cancer (NSCLC). Cancer cells transport a range of organelles and signalling molecules along TNTs, to confer a survival phenotype for the recipient cell, contributing toward chemoresistance and malignancy. Despite its important role in cancer progression, the molecular mechanisms underlying TNT formation is not well defined. Within the tumour microenvironment (TME) of NSCLC, hepatocyte growth factor (HGF) and its receptor, c-Met, are mutationally upregulated causing growth, and invasion. In this study, we report a novel crosstalk between HGF/c-Met and β1-integrin involved in the formation of functional TNTs in A549 cells. Through pharmacological inhibitor studies, we discovered Arp2/3 complex, MAPK and PI3K pathways were activated downstream of this crosstalk signalling axis. Furthermore, paxillin was recruited during this key process, localising at the protrusion site of HGF-induced TNTs, and therefore serving as the central link between the upstream and downstream regulators involved. Overall, these results demonstrate a novel strategy to inhibit TNT formation in NSCLC through targeting the HGF/c-Met and β1-integrin signalling axis, thus highlighting the importance of personalised multi-drug targeting in NSCLC.
Mannose-coupled AAV2: a second generation AAV vector for increased retinal gene therapy efficiency
Authors: Mével Mathieu , Pichard Virginie , Bouzelha Mohammed , Alvarez-Dorta Dimitri , Lalys Pierre-Alban , Provost Nathalie , Allais Marine , Mendes Alexandra , Landagaray Elodie , Ducloyer Jean-Baptiste , Galy Anne , Brument Nicole , Lefevre Gaëlle M. , Gouin Sébastien G. , Isiegas Carolina , Le Meur Guylène , Cronin Thérèse , Le Guiner Caroline , Weber Michel , Moullier Philippe , Ayuso Eduard , Deniaud David , Adjali Oumeya
Published: December 2022

Inherited retinal diseases are a leading and untreatable cause of blindness and are therefore candidate diseases for gene therapy. Recombinant vectors derived from adeno-associated virus (rAAV) are currently the most promising vehicles forin vivotherapeutic gene delivery to the retina. However, there is a need for novel AAV-based vectors with greater efficacy for ophthalmic applications, as underscored by recent reports of dose-related inflammatory responses in clinical trials of rAAV-based ocular gene therapies. Improved therapeutic efficacy of vectors would allow for decreases in the dose delivered, with consequent reductions in immune reactions. Here, we describe the development of new rAAV vectors using bioconjugation chemistry to modify the rAAV capsid, thereby improving the therapeutic index. Covalent coupling of a mannose ligand,viathe formation of a thiourea bond, to the amino groups of the rAAV capsid significantly increases vector transduction efficiency of both rat and nonhuman primate retinas. These optimized rAAV vectors have important implications for the treatment of a wide range of retinal diseases.
Identification of combinatorial colistin resistance mutations inShewanella algae
Authors: Huang Yao-Ting , Mao Yan-Chiao , Tseng Chien-Hao , Liu Chia-Wei , Liu Po-Yu
Published: December 2022

Background

Colistin is one of the last-line antimicrobial agents against drug-resistant gram-negative bacteria. Currently, little is known about the genetic mechanisms underlying colistin resistance inShewanella algae, partly due to complex epistatic interactions among multiple genes.

Methodology/Principal Findings

This study sequenced, assembled, and compared the genomes of 23 mcr-negative colistin-resistantShewanella algaefrom marine, clam, oyster, and human. Comparative genomics and computational approach were applied to find combinatorial mutations. A combination of three mutations (PmrB451, PmrE168, PmrH292) was found to be strongly associated with colistin resistance inShewanella algae.

Conclusions/Significance

This study demonstrates a computational approach for identifying epistatic-interacted mutations.

Author summary

Shewanella algaeis an emerging pathogen related to Neglected Tropical Diseases (NTDs), including cobra-bite wound infections, marine injuries or ingestion of contaminated seafood.Shewanella algaeis intrinsic resistant to various classes of β-lactams. Additionally, growing resistance to colistin inmcr-negativeShewanella algaefurther limits therapeutic options, especially in resource-limited regions. Currently, little is known about the genetic mechanisms underlying colistin resistance inShewanella algae, partly due to complex epistatic interactions among multiple genes. We conduct comparative genomics to identify combinatorial colistin resistance mutations inmcr-negative colistin-resistantShewanella algaeand a combination of three mutations (PmrB451, PmrE168, PmrH292) is strongly associated with colistin-resistance.
Competition between myosin II and βH-Spectrin regulates cytoskeletal tension
Authors: Ibar Consuelo , Chinthalapudi Krishna , Heissler Sarah M. , Irvine Kenneth D.
Published: December 2022

Spectrins are membrane cytoskeletal proteins generally thought to function as heterotetramers comprising two ⍺-spectrins and two β-spectrins. They influence cell shape and Hippo signaling, but the mechanism by which they influence Hippo signaling has remained unclear. We have investigated the role and regulation of theDrosophilaβ-heavy Spectrin (βH-Spectrin, encoded by thekarstgene) in wing imaginal discs. Our results establish that βH-Spectrin regulates Hippo signaling through the Jub biomechanical pathway due to its influence on cytoskeletal tension. While we find that ⍺-Spectrin also regulates Hippo signaling through Jub, unexpectedly, we find that βH-Spectrin localizes and functions independently of ⍺-Spectrin. Instead, βH-Spectrin co-localizes with and reciprocally regulates and is regulated by myosin. In vivo and in vitro experiments support a model in which βH-Spectrin and myosin directly compete for binding to apical F-actin. This competition can explain the influence of βH-Spectrin on cytoskeletal tension and myosin accumulation. It also provides new insight into how βH-Spectrin participates in ratcheting mechanisms associated with cell shape change.
Quantification of the diversity sampling bias resulting from rice root bacterial isolation on popular and nitrogen-free culture media, using 16S amplicon barcoding
Authors: Sondo Moussa , Wonni Issa , Klonowska Agnieszka , Koïta Kadidia , Moulin Lionel
Published: December 2022

Culturing bacteria from plant material is well known to introduce a strong bias compared to the real diversity present in the original samples. This bias is related to cultivability of bacteria, the chemical composition of media and culture conditions. The bias of recovery is often observed but was never quantified on different media using an amplicon barcoding approach comparing plant microbiota DNA extractions versus DNA extracted from serial dilutions of the same plant tissues grown on bacterial culture media. In this study, we i) quantified the culturing diversity bias using 16S amplicon barcode sequencing by comparing a culture-dependent approach (CDA) on rice roots on four popular bacterial media (Tryptone Soybean Agar-TSA-at two concentrations, 10% and 50%; a plant-based media with rice flour; Norris Glucose Nitrogen Free Medium-NGN; and Nitrogen Free -NFb) versus a culture-independent approach (CIA) assessed from DNA extracted directly on root and rhizosphere samples; ii) assessed enriched and missing taxa detected on the different media; iii) use biostatistics functional predictions to predict which metabolic profiles are enriched in the CDA and CIA. A comparative analysis of the two approaches revealed that among the 22 phyla present in the microbiota of the studied rice root samples, only five were present on the culture media approach (Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Verrucomicrobia). TheProteobacteriaphylum was the most abundant in all cultured media samples, showing a high enrichment of gamma-Proteobacteria. The diversity of the combined culture media represented about 1/3 of the diversity of the total microbiota, and its genus diversity and frequency was documented. The functional prediction tool (PiCrust2) detected an enrichment of nitrogenase enzyme in bacterial taxa sampled from Nitrogen-free media, validating its predictive capacity. Further functional predictions also showed that the CDA missed mostly anaerobic, methylotrophic, methanotrophic and photosynthetic bacteria compared to the culture independent approach, delivering valuable insights to design ad-hoc culture media and conditions to increase cultivability of the rice-associated microbiota.
Memory out of context: Spacing effects and decontextualization in a computational model of the medial temporal lobe
Authors: Antony James , Liu Xiaonan L. , Zheng Yicong , Ranganath Charan , O’Reilly Randall C.
Published: December 2022

Some neural representations change across multiple timescales. Here we argue that modeling this “drift” could help explain the spacing effect (the long-term benefit of distributed learning), whereby differences between stored and current temporal context activity patterns produce greater error-driven learning. We trained a neurobiologically realistic model of the entorhinal cortex and hippocampus to learn paired associates alongside temporal context vectors that drifted between learning episodes and/or before final retention intervals. In line with spacing effects, greater drift led to better model recall after longer retention intervals. Dissecting model mechanisms revealed that greater drift increased error-driven learning, strengthened weights in slower-drifting temporal context neurons (temporal abstraction), and improved direct cue-target associations (decontextualization). Intriguingly, these results suggest that decontextualization — generally ascribed only to the neocortex — can occur within the hippocampus itself. Altogether, our findings provide a mechanistic formalization for established learning concepts such as spacing effects and errors during learning.
Visiomode: an open-source platform for building rodent touchscreen-based behavioral assays
Authors: Eleftheriou Constantinos , Clarke Thomas , Poon Victoriana , Zechner Marie , Duguid Ian
Published: December 2022

Background

Touchscreen-based behavioral assays provide a robust method for assessing cognitive behavior in rodents, offering great flexibility and translational potential. The development of touchscreen assays presents a significant programming and mechanical engineering challenge, where commercial solutions can be prohibitively expensive and open-source solutions are underdeveloped, with limited adaptability.

New method

Here, we present Visiomode (www.visiomode.org), an open-source platform for building rodent touchscreen-based behavioral tasks. Visiomode leverages the inherent flexibility of touchscreens to offer a simple yet adaptable software and hardware platform. The platform is built on the Raspberry Pi computer combining a web-based interface and powerful plug-in system with an operant chamber that can be adapted to generate a wide range of behavioral tasks.

Results

As a proof of concept, we use Visiomode to build both simple stimulus-response and more complex visual discrimination tasks, showing that mice display rapid sensorimotor learning including switching between different motor responses (i.e., nose poke versus reaching).

Comparison with existing methods

Commercial solutions are the ‘go to’ for rodent touchscreen behaviors, but the associated costs can be prohibitive, limiting their uptake by the wider neuroscience community. While several open-source solutions have been developed, efforts so far have focused on reducing the cost, rather than promoting ease of use and adaptability. Visiomode addresses these unmet needs providing a low-cost, extensible platform for creating touchscreen tasks.

Conclusions

Developing an open-source, rapidly scalable and low-cost platform for building touchscreen-based behavioral assays should increase uptake across the science community and accelerate the investigation of cognition, decision-making and sensorimotor behaviors both in health and disease.
Hormonal gatekeeping via the blood brain barrier governs behavior
Authors: Ju Linyang , Glastad Karl M. , Sheng Lihong , Gospocic Janko , Kingwell Callum J. , Davidson Shawn M. , Kocher Sarah D. , Bonasio Roberto , Berger Shelley L.
Published: December 2022

Here we reveal an unanticipated role of the blood-brain-barrier (BBB) in regulating complex social behavior in ants. Using scRNA-seq we find localization in the BBB of a key hormone-degrading enzyme called Juvenile hormone esterase (Jhe), and we show that this localization governs the level of Juvenile Hormone (JH3) entering the brain. Manipulation of the Jhe level reprograms the brain transcriptome between ant castes. While ant Jhe is retained and functions intracellularly within the BBB, we show thatDrosophilaJhe is naturally extracellular. Heterologous expression of ant Jhe into theDrosophilaBBB alters behavior in fly to mimic what is seen in ant. Most strikingly, manipulation of Jhe levels in ant reprograms complex behavior between worker castes. Our study thus uncovers a novel, potentially conserved role of the BBB serving as a molecular gatekeeper for a neurohormonal pathway that regulates social behavior.