bluuebunny/crossref_metadata_2025 huggingface dataset:
First concrete documentation for presence ofAedes (Stegomyia) albopictusin Bolivia: Dispelling previous anecdotes
Authors: Lardeux Frédéric , Boussès Philippe , Tejerina-Lardeux Rosenka , Berger Audric , Barnabé Christian , Garcia Lineth
Published: March 2024

Background

The presence ofAedes albopictusin Bolivia has been a subject of controversy, lacking concrete documentation until now.

Objectives

This study aimed to furnish evidence ofAe. albopictuspresence in Bolivia.

Methods

Larval breeding sites were sampled in two northern Bolivian localities, Rosario del Yata and San Agustin, both situated in the Beni department within the Vaca Diez province and Guayaramerin Municipio, approximately 10 km apart. Mosquito larvae collected underwent rearing to L4 and adult stages for morphological identification, with some specimens sequenced for confirmation.

Findings

Ae. albopictuswas identified in multiple breeding sites in both localities, confirming its establishment in the area. This marks the first concrete documentation of the species in Bolivia. The collections (larvae and adults) have been deposited in the Medical Entomology Laboratory of the Universidad Mayor de San Simón in Cochabamba, Bolivia, and the Laboratory of Entomology of the Instituto Nacional de Laboratorios de Salud of the Ministry of Health in La Paz, Bolivia.

Main conclusion

Acknowledging its role as a vector for arboviruses like dengue and Chikungunya,Ae. albopictusshould be incorporated into the Bolivian National Program of Vector Control for monitoring.
Graphical pangenomics-enabled characterisation of structural variant impact on gene expression in Brassica napus
Authors: Golicz Agnieszka A. , Yildiz Gözde , Weber Sven , Kox Tobias , Abbadi Amine , Snowdon Rod J. , Zanini Silvia F.
Published: March 2024

Structural variants (SVs, eg. insertions and deletions) are genomic variations > 50 bp that are known to be associated with a range of crop traits, from yield to flowering behaviour and stress responses. Recently, pangenome graphs have emerged as a powerful framework for analysing genomic data by encoding population- or species-level diversity in one data structure. Pangenome graphs have the potential to serve as unbiased references for downstream applications, including SV genotyping and pan-transcriptomic analyses.

In this work, we hypothesized that extensive variation affects transcript quantification and expression quantitative trait locus (eQTL) analysis when relying on a single reference, and that using pangenome graphs can mitigate reference sequence bias.

We combined long and short read whole genome sequencing data with expression profiling ofBrassica napus(oilseed rape) to assess the impact of SVs on gene expression regulation and explored the utility of pangenome graphs for eQTL analysis. We demonstrate that pangenome graphs provides a superior framework for eQTL analysis by eliminating single reference bias in gene expression quantification. Combined with the graph-based genotyping of SVs, we identified 240 eQTL-SVs found in close proximity of target loci. These SVs affect expression of genes related to important traits, are often not in linkage with SNPs and represent diversity unaccounted for in classical SNP-based analyses.

This study highlights the multiple advantages of graph-based approaches in population-scale studies and provides novel insight into gene expression regulation in an important crop.
The Hitchhiker’s Guide to Sequencing Data Types and Volumes for Population-Scale Pangenome Construction
Authors: Sarashetti Prasad , Lipovac Josipa , Tomas Filip , Šikic Mile , Liu Jianjun
Published: March 2024

Long-read (LR) technologies from Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have transformed genomics research by providing diverse data types like HiFi, Duplex, and ultra-long ONT (ULONT). Despite recent strides in achieving haplotype-phased gapless genome assemblies using long-read technologies, concerns persist regarding the representation of genetic diversity, prompting the development of pangenome references. However, pangenome studies face challenges related to data types, volumes, and cost considerations for each assembled genome, while striving to maintain sensitivity. The absence of comprehensive guidance on optimal data selection exacerbates these challenges. To fill this gap, our study evaluates available data types, their significance, and the required volumes for robust de novo assembly in population-level pangenome projects. The results show that achieving chromosome-level haplotype-resolved assembly requires 20x high-quality long reads (HQLR) such as PacBio HiFi or ONT duplex, combined with 15-20x of ULONT per haplotype and 30x of long-range data such as Omni-C. High-quality long reads from both platforms yield assemblies with comparable contiguity, with HiFi excelling in NG50 and phasing accuracies, while usage of duplex generates more T2T contigs. As Long-Read Technologies advance, our study reevaluates recommended data types and volumes, providing practical guidelines for selecting sequencing platforms and coverage. These insights aim to be vital to the pangenome research community, contributing to their efforts and pushing genomic studies with broader impacts.
In Situ-Crosslinked Zippersomes Enhance Cardiac Repair by Increasing Accumulation and Retention
Authors: Jasiewicz Natalie E. , Mei Kuo-Ching , Oh Hannah M. , Bonacquisti Emily E. , Chaudhari Ameya , Byrum Camryn , Jensen Brian C. , Nguyen Juliane
Published: March 2024

Mesenchymal stem cell (MSC)-derived extracellular vesicles (EVs) are a promising treatment for myocardial infarction, but their therapeutic efficacy is limited by inefficient accumulation at the target site. A non-invasive MSC EV therapy that enhances EV accumulation at the disease site and extends EV retention could significantly improve post-infarct cardiac regeneration. Here we show that EVs decorated with the next-generation of high-affinity heterodimerizing leucine zippers, termed high-affinity (HiA) Zippersomes, amplify targetable surface areas through in situ crosslinking and exhibited ∼7-fold enhanced accumulation within the infarcted myocardium in mice after three days and continued to be retained up to day 21, surpassing the performance of unmodified EVs. After myocardial infarction in mice, high-affinity Zippersomes increase the ejection fraction by 53% and 100% compared with unmodified EVs and PBS, respectively. This notable improvement in cardiac function played a crucial role in restoring healthy heart performance. High-affinity Zippersomes also robustly decrease infarct size by 52% and 60% compared with unmodified EVs and PBS, respectively, thus representing a promising platform for non-invasive vesicle delivery to the infarcted heart.

Translational Impact Statement

Therapeutic delivery to the heart remains inefficient and poses a bottleneck in modern drug delivery. Surgical application and intramyocardial injection of therapeutics carry high risks for most heart attack patients. To address these limitations, we have developed a non-invasive strategy for efficient cardiac accumulation of therapeutics using in situ crosslinking. Our approach achieves high cardiac deposition of therapeutics without invasive intramyocardial injections. Patients admitted with myocardial infarction typically receive intravenous access, which would allow painless administration of Zippersomes alongside standard of care.
Modeling interpretable correspondence between cell state and perturbation response with CellCap
Authors: Xu Yang , Fleming Stephen , Tegtmeyer Matthew , McCarroll Steven A. , Babadi Mehrtash
Published: March 2024

Single-cell transcriptomics, in conjunction with genetic and compound perturbations, offers a robust approach for exploring cellular behaviors in diverse contexts. Such experiments allow un-covering cell-state-specific responses to perturbations, a crucial aspect in unraveling the intricate molecular mechanisms governing cellular behavior and potentially discovering novel regulatory pathways and therapeutic targets. However, prevailing computational methods predominantly focus on predicting average cellular responses, disregarding the inherent response heterogeneity associated with cell state diversity. In this study, we present CellCap, a deep generative model designed for the end-to-end analysis of single-cell perturbation experiments. CellCap employs sparse dictionary learning in a latent space to deconstruct cell-state-specific perturbation responses into a set of transcriptional response programs. These programs are then utilized by each perturbation condition and each cell at varying degrees. The incorporation of specific model design choices, such as dot-product cross-attention between cell states and response programs, along with a linearly-decoded latent space, underlay the interpretation power of CellCap. We evaluate CellCap’s model interpretability through multiple simulated scenarios and apply it to two real single-cell perturbation datasets. These datasets feature either heterogeneous cellular populations or a complex experimental setup. Our results demonstrate that CellCap successfully uncovers the relationship between cell state and perturbation response, unveiling novel insights overlooked in previous analyses. The model’s interpretability, coupled with its effectiveness in capturing heterogeneous responses, positions CellCap as a valuable tool for advancing our understanding of cellular behaviors in the context of perturbation experiments.
Mapping the Cellular Biogeography of Human Bone Marrow Niches Using Single-Cell Transcriptomics and Proteomic Imaging
Authors: Bandyopadhyay Shovik , Duffy Michael , Ahn Kyung Jin , Pang Minxing , Smith David , Duncan Gwendolyn , Sussman Jonathan , Zhang Iris , Huang Jeffrey , Lin Yulieh , Xiong Barbara , Imtiaz Tamjid , Chen Chia-Hui , Thadi Anusha , Chen Changya , Xu Jason , Reichart Melissa , Pillai Vinodh , Snaith Oraine , Oldridge Derek , Bhattacharyya Siddharth , Maillard Ivan , Carroll Martin , Nelson Charles , Qin Ling , Tan Kai
Published: March 2024

The bone marrow is the organ responsible for blood production. Diverse non-hematopoietic cells contribute essentially to hematopoiesis. However, these cells and their spatial organization remain largely uncharacterized as they have been technically challenging to study in humans. Here, we used fresh femoral head samples and performed single-cell RNA sequencing (scRNA-Seq) to profile 29,325 enriched non-hematopoietic bone marrow cells and discover nine transcriptionally distinct subtypes. We next employed CO-detection by inDEXing (CODEX) multiplexed imaging of 18 individuals, including both healthy and acute myeloid leukemia (AML) samples, to spatially profile over one million single cells with a novel 53-antibody panel. We discovered a relatively hyperoxygenated arterio-endosteal niche for early myelopoiesis, and an adipocytic, but not endosteal or perivascular, niche for early hematopoietic stem and progenitor cells. We used our atlas to predict cell type labels in new bone marrow images and used these predictions to uncover mesenchymal stromal cell (MSC) expansion and leukemic blast/MSC-enriched spatial neighborhoods in AML patient samples. Our work represents the first comprehensive, spatially-resolved multiomic atlas of human bone marrow and will serve as a reference for future investigation of cellular interactions that drive hematopoiesis.
Neural correlates in the time course of inferences: costs and benefits for less-skilled readers at the university level
Authors: Urrutia Mabel , Pino Esteban J. , Troncoso-Seguel María , Bustos Claudio , Guevara Pamela , Torres-Ocampo Karina , Mariángel Sandra , Fu Yang , Marrero Hipólito
Published: March 2024

Inferences are an indicator of a greater reading comprehension, as they imply a combination of implicit and explicit information that usually combines a textual representation with background knowledge of the reader. The aim of this study is to explore the costs and benefits of the time course of inferences in university students with reading comprehension difficulties at 3 stages during a narration. The method used was the event-related potential (ERP) technique in order to register the brain activity of 63 teaching program students while they read familiar, less-familiar and neutral stories. Results show a slow negativity potential component with greater negativity in words coming from familiar contexts when compared to less familiar and neutral ones in the first locus; an N400 component and a Post-N400 component in the second locus, reflecting greater negativity in familiar contexts when compared to less-familiar ones; and, lastly, through the use of a lexical decision task, FN400 and N400 components were found in the third locus, especially for pseudowords. These results are interpreted as a preferably bottom-up processing, which is characterized by lexical access difficulties in less-skilled readers.
Multisystemic inflammatory disease in Pheasantshell (Unionidae,Actinonaias pectorosa) associated withYokenella regensburgeiinfection at sites experiencing seasonal mass mortality events
Authors: Da Silva Neto Jeronimo G. , Hardman Rebecca H. , Engman Augustin C. , Dinkins Gerald R. , Lane Timothy W. , Fry Michael M. , Rines Christian , Bisenieks Amber , Rajeev Sree , Dennis Michelle M.
Published: March 2024

Freshwater mussels are integral components of riverine ecosystems, influencing water quality, nutrient cycling, and habitat characteristics. Enigmatic freshwater mussel declines, often characterized by sudden mass mortality events, pose significant challenges to conservation efforts. The Clinch River, a freshwater biodiversity hotspot, has experienced several enigmatic mass mortality events since 2016. Studies have reported bacteria associated with moribund Pheasantshell (Actinonaias pectorosa) during mortality events in the Clinch River, specificallyYokenella regensburgei. Despite reports of bacterial infection, little is known about their role as pathogens. Through a multiyear case-control study, combining in-situ experiments, field surveys, histology, bacterial isolation, and high-throughput sequencing, we assessed the role of bacteria in Pheasantshell (Actinonais pectorosa) mortality at two sites in the Clinch River. Between May 2021 and December 2023, we collected 29 wild moribund free-livingA. pectorosaand 68 hatchery-rearedA. pectorosamaintained in silos at the same sites and investigated differences in pathology and microbiology between groups. No silo mussels presented clinical signs of disease, or gross or microscopic lesions associated with pathological conditions leading to mortality. Our findings reveal a significant association betweenYokenella regensburgeiand severe multisystemic and multifocal infiltrative hemocytosis with necrosis, consistent with sepsis. Lesions associated with yokenellosis were of sufficient severity and physiological significance to explain mortality in infected hosts. Although our study does not explain the cause of these infections, it confirms that mussels at our study sites are ultimately dying from an infectious disease and thatY. regensburgeican be pathogenic in free-living mussels. Our results underscore the importance of considering bacterial diseases in wild mussel populations and emphasize the need for further research to elucidate the epidemiology and pathogenicity ofY. regensburgei. Overall, our study highlights the importance of integrated approaches combining pathology, microbiology, and epidemiology in freshwater mussel conservation efforts.
Postembryonic developmental roles of the ArabidopsisKEULEgene
Authors: Ruiz-Bayón Alejandro , Cara-Rodríguez Carolina , Sarmiento-Mañús Raquel , Muñoz-Viana Rafael , Lozano Francisca M. , Ponce María Rosa , Micol José Luis
Published: March 2024

Cytokinesis in plant cells begins with the fusion of vesicles that transport cell wall materials at the center of the cell division plane, where the cell plate forms and expands radially until it fuses with the parental cell wall at the preprophase band. Vesicle fusion is facilitated bytrans-SNARE complexes, with assistance from Sec1/Munc18 (SM) proteins. The SNARE protein KNOLLE and the SM protein KEULE are required for membrane fusion at the cell plate. Due to the crucial function of KEULE, all Arabidopsis (Arabidopsis thaliana)keulemutants identified to date are seedling lethal. Here, we identified the Arabidopsisserrata4-1(sea4-1) andsea4-2mutants, which carry recessive, hypomorphic alleles ofKEULE. Homozygoussea4-1andsea4-2plants are viable and fertile but exhibit smaller rosettes and fewer leaves at bolting than the wild type. Their leaves are serrated, small, and undulated, with a complex venation pattern, develop necrotic patches, and undergo premature senescence. We established a likely relationship between these phenotypes and their defects in cytokinesis through reduced cell wall integrity and increased unfolded protein response. These findings shed light on the roles of KEULE in postembryonic development, particularly in the patterning of rosette leaves and leaf margins.
Subtle Visual Latency Can Profoundly Impair Implicit Sensorimotor Learning
Authors: Hadjiosif Alkis M. , Abraham George , Ranjan Tanvi , Smith Maurice A.
Published: March 2024

Short sub-100ms visual feedback latencies are common in many types of human-computer interactions yet are known to markedly reduce performance in a wide variety of motor tasks from simple pointing to operating surgical robotics. These latencies are also present in the computer-based experiments used to study the sensorimotor learning that underlies the acquisition of motor performance. Inspired by neurophysiological findings showing that cerebellar LTD and cortical LTP would both be disrupted by sub-100ms latencies, we hypothesized that implicit sensorimotor learning may be particularly sensitive to these short latencies. Remarkably, we find that improving latency by just 60ms, from 85 to 25ms in latency-optimized experiments, increases implicit learning by 50% and proportionally decreases explicit learning, resulting in a dramatic reorganization of sensorimotor memory. We go on to show that implicit sensorimotor learning is considerably more sensitive to latencies in the sub-100ms range than at higher latencies, in line with the latency-specific neural plasticity that has been observed. This suggests a clear benefit for latency reduction in computer-based training that involves implicit sensorimotor learning and that across-study differences in implicit motor learning might often be explained by disparities in feedback latency.
MetaDIA: A Novel Database Reduction Strategy for DIA Human Gut Metaproteomics
Authors: Duan Haonan , Ning Zhibin , Sun Zhongzhi , Guo Tiannan , Sun Yingying , Figeys Daniel
Published: March 2024

Background

Microbiomes, especially within the gut, are complex and may comprise hundreds of species. The identification of peptides in metaproteomics presents a significant challenge, as it involves matching peptides to mass spectra within an enormous search space for complex and unknown samples. This poses difficulties for both the accuracy and the speed of identification. Specifically, analysis of data-independent acquisition (DIA) datasets has relied on libraries constructed from prior data-dependent acquisition (DDA) results. This approach requires running the samples in DDA mode to construct a library from the identified results, which can then be used for the DIA data. However, this method is resource-intensive, consumes samples, and limits identification to peptides previously identified by DDA. These limitations restrict the application of DIA in metaproteomics research.

Results

We introduced a novel strategy to reduce the search space by utilizing species abundance and functional abundance information from the microbiome to score each peptide and prioritize those most likely to be detected. Employing this strategy, we have developed and optimized a workflow called MetaDIA for analysis of microbiome DIA data, which operates independently of DDA assistance. Our method demonstrated strong consistency with the traditional DDA-based library approach at both protein and functional levels.

Conclusion

Our approach successfully created a smaller, yet sufficient database for DIA data search requirements in metaproteomics, showing high consistency with results from the conventional DDA-based library. We believe this method can facilitate the application of DIA in metaproteomics.
Microglia contact cerebral vasculature through gaps between astrocyte endfeet
Authors: Morris Gary P. , Foster Catherine G. , Sutherland Brad A. , Grubb Søren
Published: March 2024

The close spatial relationship between microglia and cerebral blood vessels implicates microglia in vascular development, homeostasis and disease. In this study we used the publicly available Cortical MM^3 electron microscopy dataset to systematically investigate microglial interactions with the vasculature. Our analysis revealed that approximately 20% of microglia formed direct contacts with blood vessels through gaps between adjacent astrocyte endfeet. We termed these contact points “plugs”. Plug-forming microglia exhibited closer proximity to blood vessels than non-plug forming microglia and formed multiple plugs, predominantly near the soma, ranging in surface area from ∼0.01 μm2to ∼15 μm2. Plugs were enriched at the venule end of the vascular tree and displayed a preference for contacting endothelial cells over pericytes at a ratio of 3:1. In summary, we provide novel insights into the ultrastructural relationship between microglia and the vasculature, laying a foundation for understanding how these contacts contribute to the functional cross-talk between microglia and cells of the vasculature in health and disease.
A Novel ex-vivo platform for personalized treatment in metastatic ovarian cancer
Authors: Valdivia Alain , Adefolaju Adebimpe , Thang Morrent , Cuaboy Luz Andrea , John Catherine , Mann Breanna , Satterlee Andrew , Bae-Jump Victoria L , Hingtgen Shawn
Published: March 2024

The lack of functional precision models that recapitulate the pathology and structure/function relationship of advanced ovarian cancer (OC) within an appropriate anatomic setting constitutes a hurdle on the path to developing more reliable therapies and matching those therapies with the right patients. Here, we developed and characterized an Organotypic Mesentery Membrane Culture (OMMC) model as a novel ex-vivo platform where freshly resected human patient OC tumor tissue or established cell lines are seeded directly atop living intact rat mesenteric membranes, rapidly engraft, and enable functional assessment of treatment response to FDA-approved standard care of treatment as single and combination drug therapies within just five days. This study showed successful survival of dissected mesentery tissue, survival and engraftment of tumor cells and patient tumor tissue seeded on OMMCs, mesentery-tumor cell interaction, and quantification of tumor response to treatment and off-target toxicity. Summarized “drug sensitivity scores”, using a multi-parametric algorithm, were also calculated for each patient’s treatment response, enabling us to suggest the most effective therapeutic option. Finally, we compared drug sensitivity results from patient tumor tissue on OMMCs to matched outcomes of individual patients in the clinic and identified positive correlations in drug sensitivity, beginning to validate the functionality of OMMCs as a functional predictor of treatment response.

Summary sentence

We have successfully developed and characterized a novel ex-vivo platform for personalized treatment of metastatic ovarian cancer.
Cancer Stemness Online: A resource for investigating cancer stemness and associations with immune response
Authors: Zhou Weiwei , Su Minghai , Jiang Tiantongfei , Xie Yunjin , Shi Jingyi , Ma Yingying , Xu Kang , Xu Gang , Li Yongsheng , Xu Juan
Published: March 2024

Cancer progression involves the gradual loss of a differentiated phenotype and acquisition of progenitor and stem-cell-like features, which are potential culprit in immunotherapy resistance. Although the state-of-art predictive computational methods have facilitated predicting the cancer stemness, currently there is no efficient resource that can meet various requirements of usage. Here, we presented the Cancer Stemness Online, an integrated resource for efficiently scoring cancer stemness potential at bulk and single-cell level. The resource integrates 8 robust predictive algorithms as well as 27 signature gene sets associated with cancer stemness for predicting the stemness scores. Downstream analyses were performed from five different aspects, including identifying the signature genes of cancer stemness, exploring the association with cancer hallmarks, cellular states, immune response and communication with immune cells, investigating the contributions for patient survival and the robustness analysis of cancer stemness among different methods. Moreover, the pre-calculated cancer stemness atlas for more than 40 cancer types can be accessed by users. Both the tables and diverse visualization for the analytical results are available for download. Together, Cancer Stemness Online is a powerful resource for scoring cancer stemness and going deeper and wider in the downstream functional interpretation, including immune response as well as cancer hallmark. Cancer Stemness Online is freely accessible athttp://bio-bigdata.hrbmu.edu.cn/CancerStemnessOnline.
BayesianSSA: a Bayesian statistical model based on structural sensitivity analysis for predicting responses to enzyme perturbations in metabolic networks
Authors: Hosoda Shion , Iwata Hisashi , Miura Takuya , Tanabe Maiko , Okada Takashi , Mochizuki Atsushi , Sato Miwa
Published: March 2024

Background

Chemical bioproduction has attracted attention as a key technology in a decarbonized society. In computational design for chemical bioproduction, it is necessary to predict changes in metabolic fluxes when up-/down-regulating enzymatic reactions, that is, responses of the system to enzyme perturbations. Structural sensitivity analysis (SSA) was previously developed as a method to predict qualitative responses to enzyme perturbations on the basis of the structural information of the reaction network. However, the network structural information can sometimes be insufficient to predict qualitative responses unambiguously, which is a practical issue in bioproduction applications. To address this, in this study, we propose BayesianSSA, a Bayesian statistical model based on SSA. BayesianSSA extracts environmental information from perturbation datasets collected in environments of interest and integrates it into SSA predictions.

Results

We applied BayesianSSA to synthetic and real datasets of the central metabolic pathway ofEscherichia coli. Our result demonstrates that BayesianSSA can successfully integrate environmental information extracted from perturbation data into SSA predictions. In addition, the posterior distribution estimated by BayesianSSA can be associated with the known pathway reported to enhance succinate export flux in previous studies.

Conclusions

We believe that BayesianSSA will accelerate the chemical bioproduction process and contribute to advancements in the field.
High-fidelity enhanced AsCas12a knock-in mice for efficient multiplexed gene editing, disease modeling and orthogonal immunogenetics
Authors: Tang Kaiyuan , Zhou Xiaoyu , Fang Shao-Yu , Vandenbulcke Erica , Du Andrew , Shen Johanna , Cao Hanbing , Zhou Jerry , Chen Krista , Xin Shan , Zhou Liqun , Lin Shawn H. , Majety Medha , Ling Xingyu , Lam Stanley Z. , Chow Ryan , Bai Suxia , Nottoli Timothy , Booth Carmen , Liu Chen , Dong Matthew B. , Chen Sidi
Published: March 2024

The advancement of CRISPR gene editing technology, especially the development of Cas9 knock-in mice, has significantly boosted the functional discovery of various genetics factors in diverse fields including genetics, genomics, immunology, and the biology of cancer. However, the pleiotropic effects on human disease and the complex nature of gene interaction networks require a knock-in mouse model capable of simultaneous multiplexed gene perturbation. Here, we present the generation and applications of Cre-dependent conditional and constitutive high-fidelity, enhanced AsCas12a (enAsCas12a-HF1) Rosa26-knock-in mice in the C57BL/6 background. With these mouse strains, we demonstrate highly efficient and multiplexedin vivoandex vivogenome engineering as applied to lipid nanoparticle (LNP)-RNA-based liver protein targeting, AAV-based tumor modeling, and retrovirus-based immune cell engineering. By integrating with a dCas9-SPH CRISPR activation transgenic strain, we establish a simultaneous dual gene activation and knockout (DAKO) system that showcases the modular potential of these enAsCas12a-HF1 mice. Importantly, constitutive expression of enAsCas12a-HF1 does not lead to any discernable pathological differences as compared to the C57BL/6 background strain. These knock-in mice and the accompanying delivery methods would empower the deconvolution of complex gene interaction networks in broad areas of research.
Thoracic epidural blockade after myocardial infarction benefits from anti-arrhythmic pathways mediated in part by parasympathetic modulation
Authors: Hoang Jonathan D , van Weperen Valerie YH , Kang Ki-Woon , Jani Neil R , Swid Mohammed A , Chan Christopher A , Lokhandwala Zulfiqar Ali , Lux Robert L , Vaseghi Marmar
Published: March 2024

Background

Thoracic epidural anesthesia (TEA) has been shown to reduce the burden of ventricular tachyarrhythmias (VT) in small case-series of patients with refractory VT and cardiomyopathy. However, its electrophysiological and autonomic effects in diseased hearts remain unclear and its use after myocardial infarction (MI) is limited by concerns for potential RV dysfunction.

Methods

MI was created in Yorkshire pigs (N=22) by LAD occlusion. Six weeks post-MI, an epidural catheter was placed at the C7-T1 vertebral level for injection of 2% lidocaine. RV and LV hemodynamics were recorded using Millar pressure-conductance catheters, and ventricular activation-recovery intervals (ARIs), a surrogate of action potential durations, by a 56-electrode sock and 64-electrode basket catheter. Hemodynamics and ARIs, baroreflex sensitivity (BRS) and intrinsic cardiac neural activity, and ventricular effective refractory periods (ERP) and slope of restitution (Smax) were assessed before and after TEA. VT/VF inducibility was assessed by programmed electrical stimulation.

Results

TEA reduced inducibility of VT/VF by 70%. TEA did not affect RV-systolic pressure or contractility, although LV-systolic pressure and contractility decreased modestly. Global and regional ventricular ARIs increased, including in scar and border zone regions post-TEA. TEA reduced ARI dispersion specifically in border zone regions. Ventricular ERPs prolonged significantly at critical sites of arrhythmogenesis, and Smaxwas reduced. Interestingly, TEA significantly improved cardiac vagal function, as measured by both BRS and intrinsic cardiac neural activity.

Conclusion

TEA does not compromise RV function in infarcted hearts. Its anti-arrhythmic mechanisms are mediated by increases in ventricular ERP and ARIs, decreases in Smax, and reductions in border zone heterogeneity. TEA improves parasympathetic function, which may independently underlie some of its observed anti-arrhythmic mechanisms. This study provides novel insights into the anti-arrhythmic mechanisms of TEA, while highlighting its applicability to the clinical setting.

Abstract Illustration

Myocardial infarction is known to cause cardiac autonomic dysfunction characterized by sympathoexcitation coupled with reduced vagal tone. This pathological remodeling collectively predisposes to ventricular arrhythmia. Thoracic epidural anesthesia not only blocks central efferent sympathetic outflow, but by also blocking ascending projections of sympathetic afferents, relieving central inhibition of vagal function. These complementary autonomic effects of thoracic epidural anesthesia may thus restore autonomic balance, thereby improving ventricular electrical stability and suppressing arrhythmogenesis. DRG=dorsal root ganglion, SG=stellate ganglion.
Helical Twists and β-Turns in Structures at Serine–Proline Sequences: Stabilization of cis-Proline and type VI β-turns via C–H/O interactions
Authors: Oven Harrison C. , Yap Glenn P. A. , Zondlo Neal J.
Published: March 2024

Structures at serine-proline sites in proteins were analyzed using a combination of peptide synthesis with structural methods and bioinformatics analysis of the PDB. Dipeptides were synthesized with the proline derivative (2S,4S)-(4-iodophenyl)hydroxyproline [hyp(4-I-Ph)]. The crystal structure of Boc-Ser-hyp(4-I-Ph)-OMe had two molecules in the unit cell. One molecule exhibitedcis-proline and a type VIa2 β-turn (BcisD). Thecis-proline conformation was stabilized by a C–H/O interaction between Pro C–Hαand the Ser side-chain oxygen. NMR data were consistent with stabilization ofcis-proline by a C–H/O interaction in solution. The other crystallographically observed molecule hadtrans-Pro and both residues in the PPII conformation. Two conformations were observed in the crystal structure of Ac-Ser-hyp(4-I-Ph)-OMe, with Ser adopting PPII in one and the β conformation in the other, each with Pro in the δ conformation andtrans-Pro. Structures at Ser-Pro sequences were further examined via bioinformatics analysis of the PDB and via DFT calculations. Ser–ProversusAla-Pro sequences were compared to identify bases for Ser stabilization of local structures. C–H/O interactions between the Ser side-chain Oγand Pro C–Hαwere observed in 45% of structures with Ser-cis- Pro in the PDB, with nearly all Ser-cis-Pro structures adopting a type VI β-turn. 53% of Ser-trans-Pro sequences exhibited main-chain C=Oi•••H–Ni+3or C=Oi•••H–Ni+4hydrogen bonds, with Ser as theiresidue and Pro as thei+1 residue. These structures were overwhelmingly either type I β-turns or N-terminal capping motifs on α-helices or a 310-helices. These results indicate that Ser-Pro sequences are particularly potent in favoring these structures. In each, Ser is in either the PPII or β conformation, with the Ser Oγcapable of engaging in a hydrogen bond with the amide N–H of thei+2 (type I β-turn or 3 -helix; Serχ1t) ori+3 (α-helix; Serχ1g+) residue. Non-prolinecisamide bonds can also be stabilized by C–H/O interactions.

Abstract Figure

Graphical Table of Contents
DNA barcoding and species delimitation based on four Chloroplast loci to identify species within the Elaeocarpaceae family
Authors: Khushwaha Jyotsana , Joshi Alpana , Das Subrata K.
Published: March 2024

Abstract

DNA barcoding is an indispensable taxonomic tool for plant species identification. The present research successfully amplified the four coding regions of plastid namely;matK,rpoB,ndhJ, andaccD, sequenced, and submitted it to NCBI Genbank after verification. This study evaluated the significance of single (matK,rpoB,ndhJ, andaccD) and two-locus plastid loci (rpoB+matK,ndhJ+matK,accD+matK) and examined their abilities for species identification and phylogenetic construction of Elaeocarpaceae plants. The average aligned length formatK,rpoB,ndhJ,accD,ndhJ+matK,rpoB+matK, andaccD+matKwas 395 bp, 538 bp, 477 bp, 254 bp, 872 bp, 937 bp, and 649 bp, respectively. The highest substitution rate was recorded in therpoB(18.47%), followed byndhJ(17.38%),accD(14.00%), andmatK(11.23%). The number of variable sites, segregating sites (S), nucleotide diversity (Pi), and mutations (Eta) were observed to be highest in thematKregion. Evolutionary relationship based on the Neighbor-joining method demonstrated that candidate barcode sequences were competent for identifyingCrinodendron,Elaeocarpus,Sloanea, andValleaspecies. A significant barcoding gap was identified in two barcoding regions (matKandndhJ+matK). The species-specific barcodes for the genusElaeocarpuswere generated based on Single Nucleotide Polymorphism (SNP) analysis. This study offers novel strategies for effectively identifying species within Elaeocarpaceae and lays the foundation for germplasm conservation and utilization.
Non-endoscopic screening for Barrett’s esophagus and Esophageal Adenocarcinoma in at risk Veterans
Authors: Greer Katarina B. , Blum Andrew E. , Faulx Ashley L. , Deming Erica M. , Hricik Lauren L. , Siddiqui Hinnah , Wilson Brigid M. , Chak Amitabh
Published: March 2024

Background

While rates of Esophageal Adenocarcinoma (EAC) in the US continue to rise, many patients at risk of disease are not screened. EsoCheck (EC), a non-endoscopic esophageal balloon sampling device coupled with EsoGuard (EG), a DNA based screening assay, is an FDA-approved minimally invasive alternative to the traditional screening method of upper endoscopy.

Aim

Aim To prospectively determine the diagnostic accuracy, tolerance, and acceptability of the EC/EG test in a screening population.

Methods

We recruited Veterans who met the American College of Gastroenterology (ACG) Guideline criteria for endoscopic Barrett’s Esophagus (BE) and EAC screening at Louis Stokes Cleveland Veteran Affairs Medical Center. All study participants completed unsedated EC guided distal esophageal sampling followed by a sedated esophagogastroduodenoscopy (EGD). Diagnostic yield of the EG assay and EGD was recorded and used in calculation of sensitivity and specificity of EC/EG in prospective screening. The abbreviated Spielberger State-Trait Anxiety Inventory (STAI-6) questionnaire was administered before and after completion of EC. Overall tolerance of EC sampling was evaluated on a 10-point Likert scale.

Results

Results Esophageal cancer screening was accepted by 130/782 (16.6%) eligible veterans and we analyzed results of those who completed both screening tests (N = 124). Prevalence of BE/EAC among studied veterans was 12.9% (16/124), based on EGD. Sensitivity and specificity of EC/EG for EGD-detected BE/EAC were 92.9% (95% CI 66.1, 99.8) and 72.2% (95% CI 62.1, 80.8), respectively. Positive and negative predictive values were 32.5% (95% CI 18.6, 49.1) and 98.6% (95% CI 92.4, 100), respectively. Baseline STAI-6 scores were reflective of notable levels of anxiety among veterans in the peri-procedural setting. Mean post-procedure acceptability score for Esocheck test was 7.23 (SD 2.45).

Conclusions

Conclusions Our data suggest excellent sensitivity and negative predictive value of EC/EG in a screening population of veterans, making this modality a powerful screening tool for BE and EAC.
Retention and the Intersection of Structural Inequities in a Breastfeeding Intervention Study
Authors: LaPlant Helen Wilde , Francis-Edoziuno Confidence , Guan Zhe , Aderibigbe Tumilara , Chang Xiaolin , Alhabodal Ashwag Saad , Delaney Kristen , Scott Dana , Marshall-Crim Mary , Freytes Idelisa , Henderson Wendy A. , Walsh Stephen , Lucas Ruth F.
Published: March 2024

Introduction

Women below the poverty threshold have lower representation and retention in breastfeeding studies.

Methods

A secondary analysis of a longitudinal randomized controlled self-management for breast and nipple pain during breastfeeding study. Participants completed online surveys at discharge, weeks 1, 2, 3, 6, 9, 12, 18, and 24, with face-to-face interviews at 6 and 24 weeks. Text messages were sent to participants when modules and surveys were due. Retention was assessed in R with descriptive statistics, Mann-Whitney, Pearson’s chi-square, and Cox Proportional Hazard Regression.

Results

Two hundred and forty-four women (89 ≤$50,000 and 155 >$50,000) were recruited. Retention rates at 1 (93%), 2 (87%), 6 (82%), 9 (77%) and 24 (72%) weeks. For women of low income compared to those of high income there was a hazard ratio (HR) of 2.5 (p=0.0001) for retention. For non-Hispanic Black and Hispanic women compared to the combined non-Hispanic White and Other group, HRs for retention were 3.3 and 2.6 respectively (p=0.0001). Adjustment for age in the final hazard regression model of income, age, race and ethnicity decreased the HR for women of low income to 1.6 and HRs for non-Hispanic Black and Hispanic women to 2.1 and 1.9, respectively (p=.0001). However, none of the individual factors in the model achieved statistical significance.

Discussion

Retention in breastfeeding studies impacts breastfeeding duration, a key lifelong preventative health behavior. Despite accessible study design, retention of women desiring to breastfeed was adversely affected by the intersection of income, race and ethnicity, and age.
Molecular dissection of HERV-W dependent microglial- and astroglial cell polarization
Authors: Gruchot Joel , Reiche Laura , Werner Luisa , Herrero Felisa , Schira Jessica , Meyer Urs , Küry Patrick
Published: March 2024

Abstract/Subject

The endogenous retrovirus type W (HERV-W) is a human-specific entity, which was initially discovered in multiple sclerosis (MS) patient derived cells. We initially found that the HERV-W envelope (ENV) protein negatively affects oligodendrogenesis and controls microglial cell polarization towards a myelinated axon associated and damaging phenotype. Such first functional assessments were conductedex vivo, given the human-specific origin of HERV-W. Recent experimental evidence gathered on a novel transgenic mouse model, mimicking activation and expression of the HERV-W ENV protein, revealed that all glial cell types are impacted and that cellular fates, differentiation, and functions were changed. In order to identify HERV-W-specific signatures in glial cells, the current study analyzed the transcriptome of ENV protein stimulated microglial- and astroglial cells and compared the transcriptomic signatures to lipopolysaccharide (LPS) stimulated cells, owing to the fact that both ligands can activate toll-like receptor-4 (TLR-4). Additionally, a comparison between published disease associated glial signatures and the transcriptome of HERV-W ENV stimulated glial cells was conducted. We, therefore, provide here for the first time a detailed molecular description of specific HERV-W ENV evoked effects on those glial cell populations that are involved in smoldering neuroinflammatory processes relevant for progression of neurodegenerative diseases.
Dendritic Cell – Fibroblast Crosstalk via TLR9 and AHR Signaling Drives Lung Fibrogenesis
Authors: Carter Hannah , Costa Rita Medina , Adams Taylor S. , Gilchrist Talon , Emch Claire E. , Bame Monica , Oldham Justin M. , Linderholm Angela L. , Noth Imre , Kaminski Naftali , Moore Bethany B. , Gurczynski Stephen J.
Published: March 2024

Idiopathic pulmonary fibrosis (IPF) is characterized by progressive scarring and loss of lung function. With limited treatment options, patients succumb to the disease within 2-5 years. The molecular pathogenesis of IPF regarding the immunologic changes that occur is poorly understood. We characterize a role for non-canonical aryl-hydrocarbon receptor signaling (ncAHR) in dendritic cells (DCs) that leads to production of IL-6 and IL-17, promoting fibrosis. TLR9 signaling in myofibroblasts is shown to regulate production of TDO2 which converts tryptophan into the endogenous AHR ligand kynurenine. Mice with augmented ncAHR signaling were created by crossing floxed AHR exon-2 deletion mice (AHRΔex2) with mice harboring a CD11c-Cre. Bleomycin was used to study fibrotic pathogenesis. Isolated CD11c+ cells and primary fibroblasts were treated ex-vivo with relevant TLR agonists and AHR modulating compounds to study how AHR signaling influenced inflammatory cytokine production. Human datasets were also interrogated. Inhibition of all AHR signaling rescued fibrosis, however, AHRΔex2mice treated with bleomycin developed more fibrosis and DCs from these mice were hyperinflammatory and profibrotic upon adoptive transfer. Treatment of fibrotic fibroblasts with TLR9 agonist increased expression of TDO2. Study of human samples corroborate the relevance of these findings in IPF patients. We also, for the first time, identify that AHR exon-2 floxed mice retain capacity for ncAHR signaling.
Synchrony between midbrain gene transcription and dopamine terminal regulation is modulated by chronic alcohol drinking
Authors: Farahbakhsh Zahra Z. , Holleran Katherine M. , Sens Jonathon P. , Fordahl Steve C. , Mauterer Madelyn I. , López Alberto J. , Cuzon Carlson Verginia C. , Kiraly Drew D. , Grant Kathleen A. , Jones Sara R. , Siciliano Cody A.
Published: March 2024

Alcohol use disorder is marked by disrupted behavioral and emotional states which persist into abstinence. The enduring synaptic alterations that remain despite the absence of alcohol are of interest for interventions to prevent relapse. Here, 28 male rhesus macaques underwent over 20 months of alcohol drinking interspersed with three 30-day forced abstinence periods. After the last abstinence period, we paired direct sub-second dopamine monitoring viaex vivovoltammetry in nucleus accumbens slices with RNA-sequencing of the ventral tegmental area. We found persistent augmentation of dopamine transporter function, kappa opioid receptor sensitivity, and dynorphin release – all inhibitory regulators which act to decrease extracellular dopamine. Surprisingly, though transcript expression was not altered, the relationship between gene expression and functional readouts of these encoded proteins was highly dynamic and altered by drinking history. These results outline the long-lasting synaptic impact of alcohol use and suggest that assessment of transcript-function relationships is critical for the rational design of precision therapeutics.
A matter of food and substrain: obesogenic diets induce differential severity of cardiac remodeling and diastolic dysfunction in C57Bl/6J and C57Bl/6N substrains
Authors: Cascarano Lorena , Esfahani Hrag , Michel Pierre , Bouzin Caroline , Dessy Chantal , Balligand Jean-Luc , Michel Lauriane Y.M.
Published: March 2024

The prevalence of metabolic syndrome in cardiac diseases such as heart failure with preserved ejection fraction (HFpEF) prompts the scientific community to investigate its adverse effects on cardiac function and remodeling and its associated mechanisms. However, the choice of a preclinical model of obesity-induced cardiac remodeling has proven more challenging with inconsistencies often found in very similar mouse models. Here, we invesgated the implication of both genetic background of mouse substrains as well as diet composition to identify a suitable model of diet-induced cardiac alterations. C57Bl/6J and C57Bl/6N male mice were subjected to distinct obesogenic diets consisting of high-fat and moderate-sucrose content (HF-S) or High-Sucrose and moderate lipid content (F-HS) versus matching control diets. 5-month dietary intervention with obesogenic diets induced weight gain, adipocyte hypertrophy and increased visceral and subcutaneous fat mass in both substrains. Obese mice showed similar impairment of glucose disposition and insulin tolerance among genotypes, both strains developing insulin resistance within two months. However, echocardiographic follow-up and histological analysis confirmed that HF-S diet increases cardiac hypertrophy, interstitial fibrosis as well as le atrial area in the C57Bl/6J strain only. On the contrary C57Bl/6N exhibit cardiac eccentric remodeling under control diets, possibly owing to a genetic mutation in the myosin light chain kinase 3 (Mylk3)gene, specific to this substrain, which was not further enhanced under obesogenic diets. Altogether, the present results highlight the importance of carefully selecting the suitable mouse strain and diets to model diet-induced cardiac remodeling. In this regard, C57Bl/6J mice develop significant cardiac remodeling in response to HF-S, and seem a suitable model for cardiometabolic disease.