bluuebunny/crossref_metadata_2025 huggingface dataset:
Use of Neuronavigation in Suturectomy for Craniosynostosis
Authors: Claypool Megan , Muh Carrie R. , Zellner Elizabeth , Pisapia Jared
Published: March 2023

Smaller operative exposures associated with suturectomy for craniosynostosis may result in difficulties visualizing the prematurely fused suture during surgery. The authors report cases of suturectomy for lambdoid and metopic craniosynostosis in which neuronavigation or frameless stereotaxy was used to assist with incision planning and intraoperative localization of the fused suture. In both cases, neuronavigation integrated easily and safely into established workflows and was associated with complete suture release. To our knowledge, this is the first report of applying this noninvasive technology, which does not require cranial pinning or rigid fixation, to suturectomy, and the authors demonstrate its use as an adjunct, especially for surgeons beginning in practice. Larger studies are needed to determine if neuronavigation in suturectomy is associated with a clinically significant reduction in blood loss or operative time or an increase in the rate of complete suturectomy.
A Modified of Bilateral Sagittal Split Osteotomy: Technical Note and Proposal of a Nomenclature on the Osteotomy Lines
Authors: Santagata Mario , D’Amato Salvatore , Ferrieri Ivo , Pollice Annalisa , Verolino Pasquale , Emiliano Boschetti Ciro , Tartaro Gianpaolo
Published: March 2023

Bilateral sagittal split osteotomy for orthognathic surgery is the most used technique for mandible advancement or setback and has been well documented and modified over the years since Trauner and Obwegeser described it. The improvement brought by each technique allowed the surgeons to perform safer osteotomies, shorten the operative time, and increased the flexibility of the programmed mandibular movements. The authors present a modification of the bilateral sagittal osteotomy technique with the aim of making the technique easier to perform and more comfortable for the surgeon for the purpose of positioning the osteosynthesis plates and screws. Finally, the authors describe a nomenclature on the osteotomy lines of the bilateral sagittal split osteotomy.
Robot-Assisted Nasal Reconstruction: A Cadaveric Study
Authors: Smith Corey , Fowler James , Ferreira Louis , Moore Corey
Published: March 2023

Objective:

Manual contouring of cartilage for nasal reconstruction is tedious and time-consuming. The use of a robot could improve the speed and precision of the contouring process. This cadaveric study evaluates the efficiency and accuracy of a robot methodology for contouring the lower lateral cartilage of the nasal tip.

Methods:

An augmented robot with a spherical burring tool attached was utilized to carve 11 cadaveric rib cartilage specimens. In phase 1, the right lower lateral cartilage was harvested from a cadaveric specimen and used to define a carving path for each rib specimen. In phase 2, the cartilage remained in situ during the scanning and 3-dimensional modeling. The final carved specimens were compared with the preoperative plans through topographical accuracy analysis. The contouring times of the specimens were compared with 14 retrospectively reviewed cases (2017–2020) by an experienced surgeon.

Results:

Phase 1 root mean square error of 0.40±0.15 mm and mean absolute deviation of 0.33±0.13 mm. Phase 2 root mean square error of 0.43 mm and mean absolute deviation of 0.28 mm. The average carving time for the robot specimens was 14±3 minutes and 16 minutes for Phase 1 and Phase 2, respectively. The average manual carving by an experienced surgeon was 22±4 minutes.

Conclusions:

Robot-assisted nasal reconstruction is very precise and more efficient than manual contouring. This technique represents an exciting and innovative alternative for complex nasal reconstruction.
Inferring functional organization of posterior parietal cortex circuitry based on information flow
Authors: Kang Jung Uk , Mooshagian Eric , Snyder Lawrence H.
Published: March 2023

Many studies infer the role of neurons by asking what information can be decoded from their activity or by observing the consequences of perturbing their activity. An alternative approach is to consider information flow between neurons. We applied this approach to the Parietal Reach Region (PRR) and the Lateral Intraparietal area (LIP) in posterior parietal cortex. Two complementary methods show that, across a range of reaching tasks, information flows primarily from PRR to LIP but not vice versa. This suggests that PRR determines the spatial goals of coordinated eye and arm movements and instructs LIP of those goals. Based on these findings, we conclude that PRR and LIP operate in a parallel rather than hierarchical manner to plan arm and eye movements, respectively. Similar methodology can be applied to other areas to infer their relative relationships.
Discrepancies in patient and caregiver ratings of personality change in Alzheimer’s disease and related dementias
Authors: Rhodes Emma , Mechanic-Hamilton Dawn , Phillips Jeffrey S. , McMillan Corey , Bahena Alejandra , Vitali Nykko , Hlava Quinn , Cook Philip , Gee James , Grossman Murray , Massimo Lauren
Published: March 2023

Background

Assessment of personality change in Alzheimer’s disease and related dementias (ADRD) is clinically meaningful but complicated by patient (i.e., reduced insight) and informant (i.e., caregiver burden) factors that confound accurate reporting of personality traits. This study assessed the impact of caregiver burden on informant report of Big Five personality traits (Extraversion, Agreeableness, Conscientiousness, Neuroticism, and Openness) and investigated regional cortical volumes associated with larger discrepancies in patient and informant report of Big Five personality traits.

Methods

Sixty-four ADRD participants with heterogeneous neurodegenerative clinical phenotypes and their informants completed the Big Five Inventory (BFI). Caregiver burden was measured using the Zarit Burden Interview (ZBI). Discrepancy scores were computed as the absolute value of the difference between patient and informant ratings for all BFI trait scores and summed to create a global score. Regional grey matter volumes from T1-weighted 3T MRI were normalized to intracranial volume and related to global Big Five discrepancy scores using linear regression.

Results

Higher levels of caregiver burden were associated with higher informant ratings of patient Neuroticism (ß =0.27, p =.016) and lower informant ratings of patient Agreeableness (ß =-0.32, p =.002), Conscientiousness (ß =-0.3, p =.002), and Openness (ß =-0.34, p =.003) independent of disease severity. Patients with greater Big Five discrepancy scores showed smaller cortical volumes in right medial PFC (β = -0.00015,p= .002), right superior temporal gyrus (β = -0.00028,p= .025), and left inferior frontal gyrus (β = -0.00006p= .013).

Conclusions

Informant ratings of personality traits in ADRD can be confounded by caregiver burden, highlighting the need for more objective measures of personality and behavior in dementia samples. Discrepancies between informant and patient ratings of personality may additionally reflect loss of insight secondary to cortical atrophy in frontal and temporal structures.
Constraint-based modeling predicts metabolic signatures of low- and high-grade serous ovarian cancer
Authors: Meeson Kate E. , Schwartz Jean-Marc
Published: March 2023

Ovarian cancer is an aggressive, heterogeneous disease, burdened with late diagnosis and resistance to chemotherapy. Clinical features of ovarian cancer could be explained by investigating its metabolism, and how the regulation of specific pathways link to individual phenotypes. Ovarian cancer is of particular interest for metabolic research due to its heterogeneous nature, with five distinct subtypes having been identified, each of which may display a unique metabolic signature. To elucidate metabolic differences, constraint-based modeling (CBM) represents a powerful technology, inviting the integration of ‘omics’ data, such as transcriptomics. However, many CBM methods have not prioritised accurate growth rate predictions, and there are very few ovarian cancer genome-scale studies, thus highlighting a niche in disease research. Here, a novel method for constraint-based modeling has been developed, employing the genome-scale model Human1 and flux balance analysis (FBA), enabling the integration ofin vitrogrowth rates, transcriptomics data and media conditions to predict the metabolic behaviour of cells. Using low- and high-grade ovarian cancer as a case study, subtype-specific metabolic differences have been predicted, which have been supported with CRISPR-Cas9 data and an extensive literature review. Metabolic drivers of aggressive phenotypes, as well as pathways responsible for increased proliferation and chemoresistance in low-grade cell lines have been suggested. Experimental gene dependency data has been used to validate fatty acid biosynthesis and the pentose phosphate pathway as essential for low-grade cellular growth, highlighting potential vulnerabilities for this ovarian cancer subtype.
Knockout of αβ but not γδ T cells in chickens is associated with high cytotoxicity and deficiency of regulatory and helper T cells
Authors: von Heyl Theresa , Klinger Romina , Aumann Dorothea , Zenner Christian , Alhussien Mohanned , Schlickenrieder Antonina , Lengyel Kamila , Vikkula Hanna-Kaisa , Mittermair Teresa , Sid Hicham , Schusser Benjamin
Published: March 2023

The availability of genetically modified mice has facilitated the study of mammalian T cells. No model has yet been developed to study these cells in chicken, an important livestock species with a high availability of γδ T cells. To investigate the role of γδ and αβ T cell populations in birds, we generated chickens lacking these T cell populations. This was achieved by genomic deletion of the constant region of the T cell receptor γ or αβ chain, leading to a complete loss of either γδ or αβ T cells. Our results show that a deletion of αβ T cells but not γδ T cells resulted in a severe phenotype in knockout chickens. The αβ T cell knockout chickens exhibited granulomas associated with inflammation of the spleen and the proventriculus. Immunophenotyping of αβ T cell knockout chickens revealed a significant increase in monocytes and the absence of CD4+T cells and FoxP3+regulatory T cells compared to wild type chickens. In addition, we observed a significant decrease in immunoglobulins, B lymphocytes, and changes in the bursa morphology. Our data reveal the consequences of T cell knockouts in chickens and provide new insights into their function in vertebrates.

Significance statement

The lack of genetically modified chickens has severely limited research in avian immunology compared to other animal models. Here, we report the generation of two T cell knockout chicken lines that will contribute significantly to the understanding of T cell biology as a very important research model as well as an important livestock species. The generated animals reveal the function of different T cell populations in chickens and will help to better understand the role of these cells during the interaction with various pathogens in birds.
MetaGut: Insights into gut microbiomes in stem cell transplantation by comprehensive shotgun long-read sequencing
Authors: Spohr Philipp , Scharf Sebastian , Rommerskirchen Anna , Henrich Birgit , Jäger Paul , Klau Gunnar W. , Haas Rainer , Dilthey Alexander , Pfeffer Klaus
Published: March 2023

The gut microbiome is a diverse ecosystem, dominated by bacteria; however, fungi, phages/viruses, archaea, and protozoa are also important members of the gut microbiota. Up to recently, exploration of taxonomic compositions beyond bacteria as well as an understanding of the interaction between the bacteriome with the other members was limited due to 16S rDNA sequencing. Here, we developed MetaGut, a method enabling the simultaneous interrogation of the gut microbiome (bacteriome, mycobiome, archaeome, eukaryome, DNA virome) and of antibiotic resistance genes based on optimized long-read shotgun metagenomics protocols and custom bioinformatics. Using MetaGut we investigated the longitudinal composition of the gut microbiome in an exploratory clinical study in patients undergoing allogeneic hematopoietic stem cell transplantation (alloHSCT; n = 31). Pre-transplantation microbiomes exhibited a 3-cluster structure, associated withBacteroides/Phocaeicola, mixed composition andEnterococcusabundances. MetaGut revealed substantial inter-individual and temporal variabilities of microbial domain compositions, human DNA, and antibiotic resistance genes during the course of alloHSCT. Interestingly, viruses and fungi accounted for substantial proportions of microbiome content in individual samples (up to >50% and >20%, respectively). After leukopenia, strains were stable or newly acquired. Our results demonstrate the disruptive effect of alloHSCT on the gut microbiome and pave the way for future studies based on long-read metagenomics.
Signature reversion of three disease-associated gene signatures prioritizes cancer drug repurposing candidates
Authors: Fisher Jennifer L. , Wilk Elizabeth J. , Oza Vishal H. , Howton Timothy C. , Flanary Victoria , Clark Amanda D. , Hjelmeland Anita B. , Lasseigne Brittany N.
Published: March 2023

Drug repurposing is promising because approving a drug for a new indication requires fewer resources than approving a new drug. Signature reversion detects drug perturbations most inversely related to the disease-associated gene signature to identify drugs that may reverse that signature. We assessed the performance and biological relevance of three approaches for constructing disease-associated gene signatures (i.e, limma, DESeq2, and MultiPLIER) and prioritized the resulting drug repurposing candidates for four low-survival human cancers. Our results were enriched for candidates that had been used in clinical trials or performed well in the PRISM drug screen. Additionally, we found that pamidronate and nimodipine, drugs predicted to be efficacious against the brain tumor glioblastoma (GBM), inhibited the growth of a GBM cell line and cells isolated from a patient derived xenograft (PDX). Our results demonstrate that by applying multiple disease-associated gene signature methods, we prioritized several drug repurposing candidates for low-survival cancers.

Graphical Abstract
Leukemic stem cells hijack lineage inappropriate signalling pathways to promote their growth
Authors: Kellaway Sophie G , Potluri Sandeep , Keane Peter , Blair Helen J. , Chin Paulynn S , Ptasinska Anetta , Worker Alice , Ames Luke , Adamo Assunta , Coleman Daniel JL , Khan Naeem , Assi Salam A. , Krippner-Heidenreich Anja , Raghavan Manoj , Cockerill Peter N , Heidenreich Olaf , Bonifer Constanze
Published: March 2023

Acute Myeloid Leukemia (AML) is caused by multiple mutations which dysregulate growth and differentiation of myeloid cells. Cells adopt different gene regulatory networks specific to individual mutations, maintaining a rapidly proliferating blast cell population with fatal consequences for the patient if not treated. The most common treatment option is still chemotherapy which targets such cells. However, patients harbour a population of quiescent leukemic stem cells (LSCs) which can emerge from quiescence to trigger relapse after therapy. The processes that allow such cells to re- grow remain unknown. Here, we examined the well characterised t(8;21) AML sub-type as a model to address this question. Using a novel t(8;21) patient-derived xenograft model, we show that t(8;21) LSCs aberrantly activate the VEGF and IL-5 signalling pathways. Both pathways operate within a regulatory circuit consisting of the driver oncoprotein RUNX1::ETO and an AP-1/GATA2 axis allowing LSCs to re-enter the cell cycle while preserving self-renewal capacity.
Loss of daylength sensitivity by splice site mutation in Cannabis
Authors: Leckie Keegan M. , Sawler Jason , Kapos Paul , Mackenzie John O. , Giles Ingrid , Baynes Katherine , Lo Jessica , Celedon Jose M , Baute Gregory J.
Published: March 2023

Adaptations to high latitude photoperiods have been under positive selection during the domestication of many short-day (SD) flowering crops. Photoperiod insensitivity (auto-flowering) in drug-typeCannabis sativacircumvents the need for SD flowering requirements making outdoor cultivation in high latitudes possible. However, the benefits of photoperiod insensitivity are counterbalanced by low cannabinoid contents and poor flower quality in auto-flowering genotypes. Despite recent legalization in some countries, a mechanistic understanding of photoperiod insensitivity in cannabis is still lacking. Herein, we identify a splice site mutation withinPSEUDO-RESPONSE REGULATOR 37 (CsPRR37) in auto-flowering cannabis that causes photoperiod insensitivity. Using a combination of GWAS, fine mapping, and gene expression analyses, our results strongly indicateCsPRR37as the most likely candidate for causing photoperiod insensitivity. Research into the pervasiveness of this mutation and others effecting flowering time will help elucidate its domestication history and advance cannabis breeding towards a more sustainable outdoor cultivation system.
Geographic distribution of feather δ34S in Europe
Authors: Brlik Vojtech , Prochazka Petr , Bontempo Luana , Camin Federica , Jiguet Frederic , Osvath Gergely , Wunder Michael B , Powell Rebecca L
Published: March 2023

Geographic distribution models of environmental stable isotopes (so called "isoscapes") are widely employed in animal ecology, wildlife forensics and conservation. However, the application of isoscapes is limited to elements and regions for which the spatial patterns have been estimated. Here, we focused on the ubiquitous yet less commonly used stable sulfur isotopes (δ34S). To predict the European δ34S isoscape, we used 242 feather samples from Eurasian Reed Warbler (Acrocephalus scirpaceus) formed at 69 European wetland sites. We quantified the relationships between sample δ34S and environmental covariates using a random forest regression model and applied the model to predict the geographic distribution of δ34S. We also quantified within-site variation in δ34S and complementarity with other isotopes on both individual and isoscape levels. The predicted feather δ34S isoscape shows only slight differences between the central and southern parts of Europe while the coastal regions were most enriched in 34S. The most important covariates of δ34S were distance to coastline, surface elevation and atmospheric concentrations of SO2 gases. The absence of a systematic spatial pattern impedes the application of the δ34S isoscape but high complementarity with other isoscapes advocates the combination of multiple isoscapes to increase precision of animal tracing. Feather δ34S compositions showed considerable within-site variation with highest values in inland parts of Europe, likely attributed to wetland anaerobic conditions and redox sensitivity of sulfur. The complex European geography and topography as well as using δ34S samples from wetlands may contribute to the absence of a systematic spatial gradient of δ34S values in Europe. We thus encourage future studies to focus on the geographic distribution of δ34S using tissues from diverse taxa collected in various habitats over large land masses in the world (i.e., Africa, South America or East Asia).
Compartmentalisation proteomics revealed endolysosomal protein network changes in a goat model of atrial fibrillation
Authors: Ayagama Thamali , Charles Philip D , Bose Samuel J , Boland Barry , Priestman David A , Aston Daniel , Berridge Georgina , Fisher Roman , Cribbs Adam P , Song Qianqian , Mirams Gary R , Heather Lisa , Galione Antony , Herring Neil , Schotten Ulrich , Capel Rebecca A , Platt Frances M , Platt Frances M , Krame Holger , Verheule Sander , Burton Rebecca AB
Published: March 2023

Endolysosomes (EL) are known for their role in regulating both intracellular trafficking and proteostasis. EL help facilitate elimination of damaged membrane and cytosolic proteins, protein aggregates, membranous organelles and also play an important role in calcium signalling. Despite the importance of EL, their specific role in cardiovascular disease is not well understood. In particular, it’s unclear how EL contribute to atrial pathology over longer time frames. To shed light on this question, we conducted a comprehensive analysis that involved proteomics, transcriptomics, integrated analysis, electron tomography, western blotting, and enzyme assays. To identify the role of EL in atrial fibrillation (AF), we applied a recently published organelle protein isolation method. We used this method to study biopsies from AF goat model and analyse the EL-specific proteins and pathways involved in this condition. Our results revealed the upregulation of the AMPK pathway and the expression of EL-specific proteins that were not found in whole tissue lysates (TL), including GAA, DYNLRB1, CLTB, SIRT3, CCT2, and muscle-specific HSPB2. We also observed structural anomalies, such as autophago-vacuole formation, irregularly shaped mitochondria, and glycogen deposition, which provide insights into the EL’s contribution to AF and related pathways and molecular mechanisms. Overall, our findings suggest that EL play an important role in the development of AF over longer time frames, and provide a more detailed understanding of the underlying molecular processes involved.
Addressing Erroneous Scale Assumptions in Microbe and Gene Set Enrichment Analysis
Authors: McGovern Kyle C. , Nixon Michelle Pistner , Silverman Justin D.
Published: March 2023

By applying Differential Set Analysis (DSA) to sequence count data, researchers can determine whether groups of microbes or genes are differentially enriched. Yet these data lack information about the scale (i.e., size) of the biological system under study, leading some authors to call these data compositional (i.e., proportional). In this article we show that commonly used DSA methods make strong, implicit assumptions about the unmeasured system scale. We show that even small errors in these assumptions can lead to false positive rates as high as 70%. To mitigate this problem, we introduce a sensitivity analysis framework to identify when modeling results are robust to such errors and when they are suspect. Unlike standard benchmarking studies, our methods do not require ground-truth knowledge and can therefore be applied to both simulated and real data.
Patterns of Neural Activation During an Initial Social Stress Encounter are Predictive of Future Susceptibility or Resilience: A FosTRAP2 Study
Authors: Murra Dalia , Hilde Kathryn L. , Khalil Huzefa , Watson Stanley J. , Akil Huda
Published: March 2023

Repeated social stress is a significant factor in triggering depression in vulnerable individuals, and genetic and environmental factors interact to contribute to this vulnerability. Interestingly, the role of experience in shaping vulnerability is not well studied. To what extent does an individual’s initial reaction to a given stressor influence their response to similar stressors in the future? And how is this initial response encoded at the neural level to bias towards future susceptibility or resilience?

The Chronic Social Defeat Stress (CSDS) mouse model offers an ideal opportunity to address these questions. Following 10 days of repeated social defeat, mice diverge into two distinct populations of social reactivity: resilient (interactive) and susceptible (avoidant). It is notable that the CSDS paradigm traditionally uses genetically inbred mice, indicating that this divergence is not genetically determined. Furthermore, the emergence of the two phenotypes only occurs following several days of exposure to stress, suggesting that the repeated experience of social defeat influences future susceptibility or resilience.

In this study, we asked whether specific patterns of neural activation during the initial exposure to the social defeat stress can predict whether an individual will eventually emerge as resilient or susceptible. To address this question, we used Fos-TRAP2 mouse technology to capture brain-wide neural activation patterns elicited during the initial stress exposure, while allowing the mice to go on to experience the full course of CSDS and diverge into resilient and susceptible populations. Using a high-throughput brain-wide cell counting approach, we identified the bed nucleus of the stria terminalis and lateral septal nucleus as key hubs for encoding social defeat. We also identified the basomedial amygdala as a hub for encoding future susceptibility, and the hippocampal CA1 area and medial habenula for encoding future resilience.

Our findings demonstrate that the initial experience with social stress induces a distinct brain-wide pattern of neural activation associated with defeat, as well as unique activation patterns that appear to set the stage for future resilience or susceptibility. This highly orchestrated response to defeat is seen especially in animals that emerge as resilient compared to susceptible. Overall, our work represents a critical starting place for elucidating mechanisms whereby early experiences can shape vulnerability to affective disorders.
Distinct Th17 effector cytokines differentially promote microglial and blood-brain barrier inflammatory responses during post-infectious encephalitis
Authors: Wayne Charlotte R. , Bremner Luca , Faust Travis E. , Durán-Laforet Violeta , Ampatey Nicole , Ho Sarah J. , Feinberg Philip A. , Arvanitis Panos , Ciric Bogoljub , Ruan Chunsheng , Elyaman Wassim , Delaney Shannon L. , Vargas Wendy S. , Swedo Susan , Menon Vilas , Schafer Dorothy P. , Cutforth Tyler , Agalliu Dritan
Published: March 2023

Group AStreptococcus(GAS) infections can cause neuropsychiatric sequelae in children due to post-infectious encephalitis. Multiple GAS infections induce migration of Th17 lymphocytes from the nose into the brain, which are critical for microglial activation, blood-brain barrier (BBB) and neural circuit impairment in a mouse disease model. How endothelial cells (ECs) and microglia respond to GAS infections, and which Th17-derived cytokines are essential for these responses are unknown. Using single-cell RNA sequencing and spatial transcriptomics, we found that ECs downregulate BBB genes and microglia upregulate interferon-response, chemokine and antigen-presentation genes after GAS infections. Several microglial-derived chemokines were elevated in patient sera. Administration of a neutralizing antibody against interleukin-17A (IL-17A), but not ablation of granulocyte-macrophage colony-stimulating factor (GM-CSF) in T cells, partially rescued BBB dysfunction and microglial expression of chemokine genes. Thus, IL-17A is critical for neuropsychiatric sequelae of GAS infections and may be targeted to treat these disorders.
CRISPR based programmable RNA editing in primary neurons
Authors: Ravichandran Karthick , Khargonkar Tulika , Samaddar Sarbani , Banerjee Sourav
Published: March 2023

Investigating the RNA regulation landscape primarily relies on our understanding of how RNA-protein interactions are governed in various cell types, including neurons. Analysis of RNA-protein interactions in physiological environments warrants the development of new tools that rely on RNA manipulation. Recently, A CRISPR-based RNA-editing tool (dCas13b-ADAR2DD) was developed to mitigate disease associated point mutations in cell lines. Here, we have explored the targeted sequence editing potential of the tool (dCas13b-ADAR2DDsystem) by adapting it to manipulate RNA function with an aim to visualize RNA editing in primary hippocampal neurons. This is a two-component system that includes a programmable guide RNA (gRNA) complementary to the target RNA, and a catalytically dead version of the Cas13b enzyme fused to ADAR. The RNA editing protocol outlined in this manuscript relies on using the gRNA-dependent targeting of dCas13b-ADAR fusion protein to the mutant form of mDendra transcript. We first abrogated the fluorescence of Dendra2 by introducing a nonsense mutation that precludes the formation of the functional protein. To visualize the efficacy of the RNA editing in neurons, we used the dCas13b-ADAR2DDsystem to edit specific nucleotides within the Dendra2 mRNA to restore the amino acid codes critical for Dendra2 fluorescence. This method therefore lays the foundation to future studies on the dynamicity of activity-induced RNA-protein interactions in neurons and can be extended to manipulate the endogenous RNome in diverse neuronal subtypes. Furthermore, this methodology will enable investigators to visualize the spatial and temporal resolution of RNA-protein interactions without altering the genomesviaconventional methods.

Highlights

CRISPR-Cas13 based application that enables site specific A-to-I in target RNAs directed by gRNA; optimized in neurons.

Enables the temporal mapping of developmentally relevant RNAs and their cis-interacting RNA binding proteins.
Parallel and divergent morphological adaptations underlying the evolution of jumping ability in ants
Authors: Aibekova Lazzat , Keller Roberto A. , Katzke Julian , Allman Daniel M , Garcia Francisco Hita , Labonte David , Narendra Ajay , Economo Evan P.
Published: March 2023

Jumping is a rapid locomotory mode widespread in terrestrial organisms. However, it is a rare specialization in ants. Forward jumping has been reported within four distantly related ant genera:Gigantiops,Harpegnathos,Myrmecia, andOdontomachus. The temporal engagement of legs/body parts during jump, however, varies across these genera. It is unknown what morphological adaptations underlie such behaviors, and whether jumping in ants is solely driven directly by muscle contraction or additionally relies on elastic recoil mechanism. We investigate the morphological adaptations for jumping behavior by comparing differences in the locomotory musculature between jumping and non-jumping relatives using x-ray micro- CT and 3D morphometrics. We found that the size-specific volumes of the trochanter depressor muscle (scm6) of the middle and hind legs are 3-5 times larger in jumping ants, and that one coxal remotor muscle (scm2) is reduced in volume in the middle and/or hind legs. Notably, the enlargement in the volume of other muscle groups is directly linked to the legs or body parts engaged during the jump. Furthermore, a direct comparison of the muscle architecture revealed two significant differences between in jumping versus non-jumping ants: First, the relative Physiological Cross-Sectional Area (PCSA) of the trochanter depressor muscles of all three legs were larger in jumping ants, except in the front legs ofO. rixosusandM. nigrocincta; second, the relative muscle fiber length was shorter in jumping ants compared to non-jumping counterparts, except in the front legs ofO. rixosusandM. nigrocincta. This suggests that the difference in relative muscle volume in jumping ants is largely invested in the area (PCSA), and not in fiber length. There was no clear difference in the pennation angle between jumping and non-jumping ants. However, the length of hind legs relative to body length was longer in jumping ants. Based on direct comparison of the observed vs. possible work and power output during jumps, we surmise that direct muscle contractions suffice to explain jumping performance, in two species, but elastic recoil is likely important in one. We suggest that increased investment in jumping-relevant musculature is a primary morphological adaptation that separates jumping from non-jumping ants. These results elucidate the common and idiosyncratic morphological changes underlying this rare adaptation in ants.
Machine Learning to Identify Molecular Markers for Metabolic Disease Development Using Mouse Models
Authors: Yang Guiyan , Liu Rex , Rezaei Shahbaz , Liu Xin , Wan Yu-Jui Yvonne
Published: March 2023

Background

Aging, Western diet (WD) intake, and bile acid (BA) receptor farnesoid X receptor (FXR) inactivation are risk factors for metabolic disease development including nonalcoholic fatty liver disease (NAFLD) and chronic inflammation-related health issues such as dementia. The progression of the metabolic disease can be escalated when those risks are combined. Inactivation of FXR is cancer prone in both humans and mice. The current study used omics data generated within the gut-liver axis to classify those risks using bioinformatics and machine learning approaches.

Methods

Different ages (5, 10, and 15 months) of wild-type (WT) and FXR knockout (KO) male mice were fed with either a healthy control diet (CD) or a WD since weaning. Hepatic transcripts, liver, serum, and urine metabolites, hepatic bile acids (BAs), as well as gut microbiota were used for risk prediction. A linear support vector machine withK-fold cross-validation was used for classification and feature selection.

Results

Increased urine sucrose alone achieved 91% accuracy in predicting WD intake. Hepatic lithocholic acid (LCA) and serum pyruvate had 100% and 95% accuracy, respectively to classify age. Association analyses showed hepatic LCA was positively associated with serum concentrations of acetone, a ketone body, and 1,3-dihydroxyacetone (DHA), but negatively correlated with serum pyruvate. Urine metabolites (decreased creatinine and taurine as well as increased succinate) or gut microbiota (increasedDorea, Dehalobacterium, andOscillospira) could predict FXR functional status with greater than 90% accuracy. Integrated pathway analyses revealed that the predictors for diet and FXR expression were implicated in the central carbon metabolism in cancer. To assess the translational relevance, mouse hepatic transcripts were crosschecked with human NAFLD and hepatocellular carcinoma (HCC) datasets. WD-affected hepaticCyp39a1andGramd1bexpression were associated with human HCC and NAFLD, respectively. The metabolites and diseases interaction analyses uncovered that the identified features are implicated in human metabolic diseases, mental disorders, and cancer.

Conclusion

The risk prediction using mouse models contributes to the identification of noninvasive biomarkers for early diagnosis of metabolic disease development.
Whitefly effector G4 interacts with tomato proteins of which MIPDB141 affects whitefly performance
Authors: Naalden Diana , Dermauw Wannes , Ilias Aris , Baggerman Geert , Mastop Marieke , Dangol Sarmina , Gaertner Nicolas , Roseboom Winfried , Kwaaitaal Mark , Kramer Gertjan , van den Burg Harrold A. , Vontas John , Van Leeuwen Thomas , Kant Merijn R. , Schuurink Robert C.
Published: March 2023

The phloem-feeding insectBemisia tabaciis an important pest, responsible for the transmission of several crop-threatening virus species. While feeding, the insect secretes a cocktail of effectors to modulate defense responses. Here, we present a set of proteins that was identified in artificial diet on whichB. tabaciwas salivating. We studied whether these candidate effectors can play a role in plant immune suppression. Effector G4 was the most robust suppressor of the flg22-induced ROS response when transiently expressed inNicotiana benthamiana. In addition, G4 was able to supress ROS inSolanum lycopersicum(tomato) andCapsicum annuum(pepper). Fused to a fluorescence tag, G4 localized in the cytoplasm inN. benthamiana. A yeast two-hybrid screen combined with a luciferase bimolecular complementation and co-localization assays resulted in the identification of two target proteins in tomato: REF-like stress related protein 1 (RSP1) and meloidogyne-induced giant cell protein DB141 (MIPDB141). Silencing ofMIPDB141in tomato, using virus-induced gene silencing, reduced whitefly fecundity up to 40% demonstrating that the protein is involved in susceptibility toB. tabaci. Together our data demonstrate that effector G4 impairs tomato immunity to whiteflies by interfering with the ROS production and via a direct interaction with tomato susceptibility protein MIPDB141.
Unraveling dynamically-encoded latent transcriptomic patterns in pancreatic cancer cells by topic modelling
Authors: Zhang Yichen , Khalilitousi Mohammadali (Sam) , Park Yongjin P
Published: March 2023

Building a comprehensive topic model has become an important research tool in single-cell genomics. With a topic model, we can decompose and ascertain distinctive cell topics shared across multiple cells, and the gene programs implicated by each topic can later serve as a predictive model in translational studies. Here, we present a Bayesian topic model that can uncover short-term RNA velocity patterns from a plethora of spliced and unspliced single-cell RNA-seq counts. We showed that modelling both types of RNA counts can improve robustness in statistical estimation and reveal new aspects of dynamic changes that can be missed in static analysis. We showcase that our modelling framework can be used to identify statistically-significant dynamic gene programs in pancreatic cancer data. Our results discovered that seven dynamic gene programs (topics) are highly correlated with cancer prognosis and generally enrich immune cell types and pathways.
PHR1 and PHL1 mediate rapid high-light responses and acclimation to triose phosphate oversupply
Authors: Ackermann Lukas , Müller Monika , Hieber Alina Johanna , Klecker Maria
Published: March 2023

Fluctuations in light intensity require immediate metabolic adjustment which includes reprogramming of both plastidial and nuclear gene expression, but the signaling pathways behind such responses are not fully understood. Here we report the identification of an early high-light responsive pathway inArabidopsis thalianathat depends on PHOSPHATE STARVATION RESPONSE 1 (PHR1) and PHR1-LIKE 1 (PHL1) transcription factors involved in low phosphate (Pi) signaling. High-light treatment rapidly induced the accumulation of PHR1-responsive transcripts in wildtype plants grown under nutrient-sufficient conditions, but not inphr1 phl1double knockout plants. Differences in starch accumulation and ATP levels were detected between wildtype andphr1 phl1mutants subjected to high light, suggesting a link between Pisignaling, carbohydrate partitioning, and energy status during stress. In line with a function of PHR1/PHL1 upon triose phosphate accumulation, we observed that blocking starch biosynthesis in thephr1 phl1double mutant, by introducing theagd1-1allele, causes a severe growth defect. Phenotypes of theadg1 phr1 phl1triple mutant such as high-light sensitivity and growth restriction in the absence of exogenously supplied sucrose resemble the previously described double mutantadg1 tpt-2, lacking a functional copy of the TRIOSE PHOSPHATE/PHOSPHATE TRANSLOCATOR (TPT), and we show that Piresponses are disturbed inadg1 tpt-2. We propose that Pisequestration by photosynthesis and import of Piinto the chloroplast transiently depletes cytosolic Pireserves upon sudden increases in light intensity. The low-Pisensing machinery in the nucleus consequently implements early high-light transcriptional responses, qualifying Pias a new operational retrograde signal.
Development of monoclonal antibody-based blocking ELISA for detecting SARS-CoV-2 exposure in animals
Authors: Yuan Fangfeng , Chen Chi , Covaleda Lina M. , Martins Mathias , Reinhart Jennifer M. , Sullivan Drew R. , Diel Diego G. , Fang Ying
Published: March 2023

The global pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a significant threat to public health. Besides humans, SARS-CoV-2 can infect several animal species. Highly sensitive and specific diagnostic reagents and assays are urgently needed for rapid detection and implementation of strategies for prevention and control of the infection in animals. In this study, we initially developed a panel of monoclonal antibodies (mAbs) against SARS-CoV-2 nucleocapsid (N) protein. To detect SARS-CoV-2 antibodies in a broad spectrum of animal species, a mAb-based bELISA was developed. Test validation using a set of animal serum samples with known infection status obtained an optimal percentage of inhibition (PI) cut-off value of 17.6% with diagnostic sensitivity of 97.8% and diagnostic specificity of 98.9%. The assay demonstrates high repeatability as determined by a low coefficient of variation (7.23%, 6.95%, and 5.15%) between-runs, within-run, and within-plate, respectively. Testing of samples collected over time from experimentally infected cats showed that the bELISA was able to detect seroconversion as early as 7 days post-infection. Subsequently, the bELISA was applied for testing pet animals with COVID-19-like symptoms and specific antibody responses were detected in two dogs. The panel of mAbs generated in this study provides a valuable tool for SARS-CoV-2 diagnostics and research. The mAb-based bELISA provides a serological test in aid of COVID-19 surveillance in animals.

IMPORTANCE

Antibody tests are commonly used as a diagnostic tool for detecting host immune response following infection. Serology (antibody) tests complement nucleic acid assays by providing a history of virus exposure, no matter symptoms developed from infection or the infection was asymptomatic. Serology tests for COVID-19 are in high demand, especially when the vaccines become available. They are important to determine the prevalence of the viral infection in a population and identify individuals who have been infected or vaccinated. ELISA is a simple and practically reliable serological test, which allows high-throughput implementation in surveillance studies. Several COVID-19 ELISA kits are available. However, they are mostly designed for human samples and species-specific secondary antibody is required for indirect ELISA format. This paper describes the development of an all species applicable monoclonal antibody (mAb)-based blocking ELISA to facilitate the detection and surveillance of COVID-19 in animals.
Connectome-constrained deep mechanistic networks predict neural responses across the fly visual system at single-neuron resolution
Authors: Lappalainen Janne K. , Tschopp Fabian D. , Prakhya Sridhama , McGill Mason , Nern Aljoscha , Shinomiya Kazunori , Takemura Shin-ya , Gruntman Eyal , Macke Jakob H. , Turaga Srinivas C.
Published: March 2023

We can now measure the connectivity of every neuron in a neural circuit, but we are still blind to other biological details, including the dynamical characteristics of each neuron. The degree to which connectivity measurements alone can inform understanding of neural computation is an open question. Here we show that with only measurements of the connectivity of a biological neural network, we can predict the neural activity underlying neural computation. We constructed a model neural network with the experimentally determined connectivity for 64 cell types in the motion pathways of the fruit fly optic lobe but with unknown parameters for the single neuron and single synapse properties. We then optimized the values of these unknown parameters using techniques from deep learning, to allow the model network to detect visual motion. Our mechanistic model makes detailed experimentally testable predictions for each neuron in the connectome. We found that model predictions agreed with experimental measurements of neural activity across 24 studies. Our work demonstrates a strategy for generating detailed hypotheses about the mechanisms of neural circuit function from connectivity measurements. We show that this strategy is more likely to be successful when neurons are sparsely connected—a universally observed feature of biological neural networks across species and brain regions.
Design of a holder for the improved maneuvering of the concurrent TMS-MRI setup
Authors: Lee Hsin-Ju , Woudsma KJ , Ishraq Moh , Lin Fa-Hsuan
Published: March 2023

Background

Concurrent transcranial magnetic stimulation (TMS) and magnetic resonance imaging (MRI) is time-consuming because of the limited space in the MRI bore and the sophisticated placement and orientation of the TMS coil to elicit the desired brain activities and behaviors.

Objective

We developed a TMS coil holder capable of quick adjustment of the TMS coil position and orientation. The holder can also hold an MRI receiver coil array.

Methods

A holder with one controlling knob, two omni-direction rotation joints, and two in-plane rotation joints was developed.

Results

Different TMS coil positions and orientations can be arranged and fixed in seconds. The holder can also accommodate two TMS coils to allow for multi-coil TMS-MRI.

Conclusion

Our development significantly improves the workflow of the concurrent TMS-MRI in new neuroscience studies and clinical applications.
Odor-evoked transcriptomics ofAedes aegyptimosquitoes
Authors: Mappin Fredis , Bellantuono Anthony J. , Ebrahimi Babak , DeGennaro Matthew
Published: March 2023

Modulation of odorant receptors mRNA induced by prolonged odor exposure is highly correlated with ligand-receptor interactions inDrosophilaas well as mammals of the Muridae family. If this response feature is conserved in other organisms, this presents a potentially potent initial screening tool when searching for novel receptor-ligand interactions in species with predominantly orphan olfactory receptors. We demonstrate that mRNA modulation in response to 1-octen-3-ol odor exposure occurs in a time- and concentration-dependent manner inAedes aegyptimosquitoes. To investigate gene expression patterns at a global level, we generated an odor-evoked transcriptome associated with 1-octen-3-ol odor exposure. Transcriptomic data revealed that ORs and OBPs were transcriptionally responsive whereas other chemosensory gene families showed little to no differential expression. Alongside chemosensory gene expression changes, transcriptomic analysis found that prolonged exposure to 1-octen-3-ol modulated xenobiotic response genes, primarily members of the cytochrome P450, insect cuticle proteins, and glucuronosyltransferases families. Together, these findings suggest that mRNA transcriptional modulation caused by prolonged odor exposure is pervasive across taxa and accompanied by the activation of xenobiotic responses. Furthermore, odor-evoked transcriptomics create a potential screening tool for filtering and identification of chemosensory and xenobiotic targets of interest.
Crystal structure of mRNA cap (guanine-N7) methyltransferase E12 subunit from monkeypox virus and discovery of its inhibitors
Authors: Wang De-Ping , Zhao Rong , Wang Hao-Feng , Wang Mei-Yue , Hu Wen-Shu , Lin Meng-Meng , Shu Wen , Cao Ji-Min , Cui Wen , Zhou Xin
Published: March 2023

In July 2022, the World Health Organization announced monkeypox as a public health emergency of international concern (PHEIC), over 85,000 global cases have been reported currently. However, preventive and therapeutic treatments are very limited. The monkeypox virus (MPXV) E12, an mRNA capping enzyme small subunit, is essential for the methyltransferase activity of RNA capping enzymes of MPXV. Here, we solved a 2.16 Å crystal structure of E12. We also docked the D1 subunit c-terminal domain (D1CTD) of vaccinia virus (VACV) with E12 to analyze the critical residues of interface between them. These residues are used for drug screening. The top six compounds are Rutin, Quercitrin, Epigallocatechin, Rosuvastatin, 5-hydroxy-L-Tryptophan, and Deferasirox. These findings may provide insights into the development of anti-MPXV drugs.