bluuebunny/crossref_metadata_2025 huggingface dataset:
Temporal and spatial analysis of Plasmodium falciparum genomics reveals patterns of connectivity in a low-transmission district in Southern Province, Zambia
Authors: Moser Kara A. , Aydemir Ozkan , Hennelly Chris , Kobayashi Tamaki , Shields Timothy , Hamapumbu Harry , Musonda Michael , Katowa Ben , Matoba Japhet , Stevenson Jennifer C. , Norris Douglas E. , Thuma Philip E. , Wesolowski Amy , Moss William J. , Bailey Jeffrey A. , Juliano Jonathan J.
Published: October 2021

Understanding temporal and spatial dynamics of ongoing malaria transmission will be critical to inform effective interventions and elimination strategies in low transmission regions approaching elimination. Parasite genomics are being used as a tool to monitor epidemiologic trends, including assessing residual transmission across seasons or importation of malaria into these regions. Southern Province, Zambia is a low-transmission setting with seasonal malaria. We genotyped 441 Plasmodium falciparum samples using molecular inversion probes at 1,832 positions across the genome, using dried blood spots collected from 2012-2018 from 8 health centers in the catchment area of Macha Hospital in Choma District. We show that highly related parasites persist across multiple seasons, suggesting that the persistence of malaria is at least in part fueled by parasites “seeding” across the dry season. In addition, we identify clusters of clonal parasites that are dissimilar to the general population, suggesting that introduction of parasites from elsewhere may contribute to the continued malaria burden. We identified signals of population size fluctuation over the course of individual transmission seasons, suggesting a ramp-up of malaria transmission from a season’s beginning. Despite the small spatial scale of the study (2,000 sq km), we identified an inverse relationship between genetic relatedness of parasite pairs and distance between health centers, as well as increased relatedness between specific health centers. These results, leveraging both genomic and epidemiological data, provide a comprehensive picture of fluctuations in parasite populations in this pre-elimination setting of southern Zambia.
Using random forests to understand unrecognized progression to late-stage CKD, a case-control study
Authors: Hane Christopher , Dunning Stephan , McPheeters Jeff , Mosely David , Clair Russell Jennifer St. , Spencer Donna
Published: October 2021

Background and objectives

Patients with undiagnosed CKD are at increased risk of suboptimal dialysis initiation and therefore reduced access to home dialysis and transplantation as well as poor outcomes. Improved understanding of how patients remain undiagnosed is important to determine better intervention strategies.

Design, setting, participants, and measurements

A retrospective, matched, case-control analysis of 1,535,053 patients was performed to identify factors differentiating 4 patient types: unrecognized late-stage CKD, recognized late-stage CKD, early-stage CKD and a control group without CKD. The sample included patients with commercial insurance, Medicare Advantage, and Medicare fee-for service coverage. Patient demographics, comorbidities, health care utilization, and prescription use were analyzed using random forests to determine the most salient features discriminating the types. Models were built using all four types, as well as pairwise for each type versus the unrecognized late-stage type.

Results

Area under the curve for the three pairwise models (unrecognized late-stage vs recognized late-stage; unrecognized late-stage vs early-stage; unrecognized late-stage vs no CKD) were 82%, 68% and 82%.

Conclusions

The lower performance of the unrecognized late-stage vs early-stage model indicates a greater similarity of these two patient groups. The unrecognized late-stage CKD group is not simply avoiding or unable to get care in a manner distinguishable from the early-stage group. New outreach for CKD to undiagnosed or undetected, insured patients should look more closely at patient sets that are like diagnosed early-stage CKD patients.
Peripheral optical coherence tomography assisted by scleral depression in retinopathy of prematurity
Authors: Scruggs Brittni A. , Ni Shuibin , Nguyen Thanh-Tin P. , Ostmo Susan , Chiang Michael F. , Jia Yali , Huang David , Jian Yifan , Campbell J. Peter
Published: October 2021

Objective

To determine whether handheld widefield optical coherence tomography (OCT) can be used to document retinopathy of prematurity (ROP) stage while using scleral depression to improve peripheral views.

Design

Prospective observational study

Participants

Consecutive neonates admitted to the neonatal intensive care unit (NICU) in a single academic medical center who also met criteria for ROP screening and consented for research imaging.

Methods

Scleral depression was combined with widefield OCT using an investigational 400-kHz, 55-degree field of view handheld OCT during ROP screening from October 28, 2020 to March 03, 2021.

Main Outcome Measures

Acquisition of en face and B-scan imaging of the peripheral retina to objectively assess early vitreoretinal pathology, including the demarcation between vascularized and anterior avascular retina, the presence of early ridge formation, and small neovascular tufts.

Results

Various stages of ROP were detected using a rapid acquisition OCT system. In one neonate, serial OCT imaging over a five-week period demonstrated accumulation of neovascular tufts with progression to stage 3 ROP with extraretinal fibrovascular proliferation along the ridge. Videography of this technique is included in this report for instructional purposes.

Conclusions

Serial examinations using widefield OCT and scleral depression may improve detection and documentation of ROP disease progression. Earlier detection of ROP-related proliferation may prevent vitreoretinal traction, retinal detachment, and blindness.
Long-term evolution of antibiotic persistence in P. aeruginosa lung infections
Authors: Ghoul Melanie , Andersen Sandra B. , Johansen Helle Krogh , Jelsbak Lars , Molin Søren , Perron Gabriel , Griffin Ashleigh S.
Published: October 2021

Pathogenic bacteria respond to antibiotic pressure with the evolution of resistance but survival can also depend on their ability to tolerate antibiotic treatment, known as persistence. While a variety of resistance mechanisms and underlying genetics are well characterised in vitro and in vivo, the evolution of persistence, and how it interacts with resistance in situ is less well understood. We assayed for persistence and resistance with three clinically relevant antibiotics: meropenem, ciprofloxacin and tobramycin, in isolates of Pseudomonas aeruginosa from chronic cystic fibrosis lung infections spanning up to forty years of evolution. We find evidence that persistence is under positive selection in the lung and that it can particularly act as an evolutionary stepping stone to resistance. However, this pattern is not universal and depends on the bacterial clone type and antibiotic used, indicating an important role for antibiotic mode of action.
Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches
Authors: Guilliams Martin , Bonnardel Johnny , Haest Birthe , Vanderborght Bart , Bujko Anna , Martens Liesbet , Thoné Tinne , Browaeys Robin , De Ponti Federico F. , Remmerie Anneleen , Wagner Camille , Vanneste Bavo , Zwicker Christian , Vanhalewyn Tineke , Gonçalves Amanda , Lippens Saskia , Devriendt Bert , Cox Eric , Ferrero Giuliano , Wittamer Valerie , Willaert Andy , Kaptein Suzanne J.F. , Neyts Johan , Dallmeier Kai , Geldhof Peter , Casaert Stijn , Deplancke Bart , ten Dijke Peter , Hoorens Anne , Vanlander Aude , Berrevoet Frederik , Van Nieuwenhove Yves , Saeys Yvan , Saelens Wouter , Van Vlierberghe Hans , Devisscher Lindsey , Scott Charlotte L.
Published: October 2021

The liver is the largest solid organ in the body, yet it remains incompletely characterized. Here, we present a spatial proteogenomic atlas of the healthy human and murine liver combining single-cell CITE-seq, single-nuclei sequencing, spatial transcriptomics and spatial proteomics. By integrating these multi-omic datasets, we provide validated strategies to reliably discriminate and localize all hepatic cells. We then align this atlas across seven species, revealing the conserved program of bona fide Kupffer cells and bile-duct macrophages. We also uncover the respective spatially-resolved cellular niches of these macrophages and the microenvironmental circuits driving their unique transcriptomic identities. We demonstrate that bile-duct macrophages are induced by local lipid exposure, while Kupffer cells crucially depend on their crosstalk with hepatic stellate cells via the evolutionarily-conserved ALK1-BMP9/10 axis.
Identification of binding interaction between Curcumin derivative and PERK13 Proline rich receptor like protein kinase protein using In silico docking techniques – to help plants tackle salt water
Authors: Vaithyanathan Prakash
Published: October 2021

Introduction

Arabidopsis thaliana, mouse ear cress or thale cress are small flowering plants included in the cruciferae family. They comprise of various characteristics such as diploid genetics, small genome size, rapid growth cycle, and relatively low repetitive DNA content, making it a perfect model for plant genome projects.

Objective

The aim of this present Insilico research study is to carry out molecular drug docking studies between PERK13-Proline rich receptor like protein kinase and De O Acetylated Curcumin Di Galactose or di–galactosylated curcumin, a derivative of curcumin. PERK13 protein is considered to play a significant role in helping plants tackle salinity levels in water.

Methods

In this study, protein modelling tools and servers are used to model the 3D structure and the same is validated using Protein structure validation tools. Automated drug docking servers were used to dock the modelled protein with the chemical compound to analyse the electrostatic (H bond) interaction between PERK13 and De O Acetylated Curcumin Di Galactose, a better water-soluble compound than curcumin. The docked structure was visualized using an advanced molecular visualization tool.

Results and Discussion

The overall results obtained from this study on De O Acetylated Curcumin Di Galactose and PERK13 protein shows that De O Acetylated Curcumin Di Galactose, directly binds with the active site and other potentially binding regions of PERK13. Hence, it is concluded that De O Acetylated Curcumin Di Galactose could potentially play a vital role in future research related to the problem of helping the plants tackle increased saline levels in water.
Blood flow synchronization in renal microcirculation - a high-resolution imaging study
Authors: Postnov Dmitry D. , Marsh Donald J. , Cupples Will A. , Holstein-Rathlou Niels-Henrik , Sosnovtseva Olga
Published: October 2021

Aims

Internephron signalling and interaction are fundamental for kidney function. Earlier studies have shown that nephrons signal to each other over short distances and adjust their activity accordingly. Micropuncture experiments revealed synchronous clusters of 2-3 nephrons formed from such interactions, while imaging and modelling results suggested the possibility of larger clusters. Such clusters are expected to play an important role in renal autoregulation, but their presence has not been confirmed and their size has not been estimated. In this study, we present methodology for high resolution renal blood flow imaging and apply it to estimate frequency and phase angle differences in kidney blood vessels under normal conditions and after administration of the vasoactive agents angiotensin II and acetylcholine.

Methods and results

To resolve signals from separate arterioles in a sufficiently large field of view, we developed a method for renal laser speckle contrast imaging. Our setup provides imaging of blood flow in the kidney cortex with a limit of image resolution at 0.8μm per pixel and imaging frequency of 160Hz. We used the method to record from 1.5×1.5 mm2 sections of the renal surface in anaesthetised Sprague-Dawley rats in unstimulated conditions and during IV infusion of the vasoconstrictor angiotensin II or the vasodilator acetylcholine. In each section, we resolved and segmented 94.8±15.66 individual arterioles and venules, and analyzed blood flow using wavelet spectral analysis to identify clusters of synchronized blood vessels.

Conclusions

We observed spatial and temporal evolution of blood vessel clusters of various sizes, including the formation of large (>90 vessels) long-lived clusters (>10 periods) locked at the frequency of the tubular glomerular feedback (TGF) mechanism. The analysis showed that synchronization patterns and thus the co-operative dynamics of nephrons change significantly when either of the vasoactive agents is administered. On average, synchronization was stronger (larger clusters, longer duration) with angiotensin II administration than in the unstimulated state or with acetyl choline. While it weakens with distance, increased synchronization duration spanned the whole field of view, and likely, beyond it. Neighbouring vessels tend to demonstrate in-phase synchronization, especially in the vasoconstricted condition, which is expected to cause locally increased pressure variation. Our results confirm both the presence of the local synchronization in the renal microcirculatory blood flow and the fact that it changes depending on the condition of the vascular network and the blood pressure, which might have further implications for the role of such synchronization in pathologies development.
Amoeboid-like neuronal migration ensures correct horizontal cell layer formation in the developing vertebrate retina
Authors: Amini Rana , Schlüßler Raimund , Möllmert Stephanie , Bhatnagar Archit , Guck Jochen , Norden Caren
Published: October 2021

As neurons are often born at positions different than where they ultimately function, neuronal migration is key to ensure successful nervous system development. Radial migration during which neurons featuring unipolar and bipolar morphology, employ pre-existing processes or underlying cells for directional guidance, is the most well explored neuronal migration mode. However, how neurons that display multipolar morphology, without such processes, move through highly crowded tissue environments towards their final positions remains elusive. To understand this, we here investigated multipolar migration of horizontal cells in the zebrafish retina. We found that horizontal cells tailor their movements to the environmental spatial constraints of the crowded retina, by featuring several characteristics of amoeboid migration. These include cell and nucleus shape changes, and persistent rearward polarization of stable F-actin, which enable horizontal cells to successfully move through the crowded retina. Interference with the organization of the developing retina by changing nuclear properties or overall tissue architecture, hampers efficient horizontal cell migration and layer formation. Thus, cell-tissue interplay is crucial for efficient migration of horizontal cells in the retina. In view of high proportion of multipolar neurons, the here uncovered ameboid-like neuronal migration mode might also be crucial in other areas of the developing brain.
Effects of dual deletion ofglnRandmtrAon expression of nitrogen metabolism genes inStreptomyces venezuelae
Authors: Zhu Yanping , Wang Jiao , Su Wenya , Lu Ting , Li Aiying , Pang Xiuhua
Published: October 2021

GlnR activates nitrogen metabolism genes under nitrogen-limited conditions whereas MtrA represses these genes under nutrient-rich conditions inStreptomyces. In this study, we compared the transcription patterns of nitrogen metabolism genes in a double deletion mutant (ΔmtrA-glnR) lacking bothmtrAandglnRand in mutants lacking eithermtrA(ΔmtrA) orglnR(ΔglnR). The nitrogen metabolism genes were expressed similarly in ΔmtrA-glnRand ΔglnRunder both nitrogen-limited and nutrient-rich conditions, with patterns distinctly different from that of ΔmtrA, suggesting a decisive role for GlnR in the control of nitrogen metabolism genes and further suggesting that regulation of these genes by MtrA is GlnR-dependent. MtrA and GlnR utilize the same binding sites upstream of nitrogen metabolism genes, and we showed strongerin vivobinding of MtrA to these sites under nutrient-rich conditions and of GlnR under nitrogen-limited conditions, consistent with the higher levels of MtrA or GlnR under those respective conditions. In addition, we showed that bothmtrAandglnRare auto-regulatory. Our study provides new insights into the regulation of nitrogen metabolism genes inStreptomyces.
Airpart: Interpretable statistical models for analyzing allelic imbalance in single-cell datasets
Authors: Mu Wancen , Sarkar Hirak , Srivastava Avi , Choi Kwangbom , Patro Rob , Love Michael I.
Published: October 2021

Motivation

Allelic expression analysis aids in detection of cis-regulatory mechanisms of genetic variation which produce allelic imbalance (AI) in heterozygotes. Measuring AI in bulk data lacking time or spatial resolution has the limitation that cell-type-specific (CTS), spatial-, or time-dependent AI signals may be dampened or not detected.

Results

We introduce a statistical method airpart for identifying differential CTS AI from single-cell RNA-sequencing (scRNA-seq) data, or other spatially- or time-resolved datasets. airpart outputs discrete partitions of data, pointing to groups of genes and cells under common mechanisms of cis-genetic regulation. In order to account for low counts in single-cell data, our method uses a Generalized Fused Lasso with Binomial likelihood for partitioning groups of cells by AI signal, and a hierarchical Bayesian model for AI statistical inference. In simulation, airpart accurately detected partitions of cell types by their AI and had lower RMSE of allelic ratio estimates than existing methods. In real data, airpart identified differential AI patterns across cell states and could be used to define trends of AI signal over spatial or time axes.

Availability

The airpart package is available as an R/Bioconductor package at https://bioconductor.org/packages/airpart.
Multiplexed ultrasound imaging using clustered gas vesicles and spectral imaging
Authors: Kim Sangnam , Zhang Siyuan , Yoon Sangpil
Published: October 2021

Current advances in ultrasound imaging techniques including super-resolution ultrasound imaging allows us to visualize microvasculature in biological specimens using microbubbles. However, microbubbles diffuse in blood stream limiting imaging acquisition and frame subtraction scheme of super-resolution ultrasound imaging cannot improve spatial resolution without moving microbubbles. Fluorescent proteins revolutionized to understand molecular and cellular functions in biological systems. Here, we devised a panel of gas vesicles to realize multiplexed ultrasound imaging to uniquely visualize locations of different species of gas vesicles. Mid-band fit spectral imaging technique demonstrated that stationary gas vesicles were efficiently localized in gel phantom and murine liver specimens by visualizing three-dimensional vessel structures. Clustered and unclustered gas vesicles were phagocytosed by murine macrophages to serve as carriers and beacons for the proposed multiplexed and single cell level imaging technique. The spatial distribution of macrophages containing clustered and unclustered gas vesicles were reconstructed by mid-band fit spectral imaging with pseudo-coloring scheme.
Recurrent Independent Pseudogenization Events of the Sperm Fertilization Gene ZP3r in Apes and Monkeys
Authors: Carlisle J.A. , Gurbuz D.H. , Swanson W. J.
Published: October 2021

In mice, ZP3r/sp56 is a binding partner to the egg coat protein ZP3 and may mediate induction of the acrosome reaction. ZP3r, as a member of the RCA cluster, is surrounded by paralogs, some of which have been shown to be evolving under positive selection. Sequence divergence paired with paralogous relationships with neighboring genes, has complicated the accurate identification of the human ZP3r ortholog. Here, we phylogenetically and syntenically resolve that the human ortholog of ZP3r is the pseudogene C4BPAP1. We investigate the evolution of this gene within primates. We observe independent pseudogenization events of ZP3r in all Apes with the exception of Orangutans, and many monkey species. ZP3r in both primates that retain ZP3r and rodents contains positively selected sites. We hypothesize that redundant mechanisms mediate ZP3 recognition in mammals and ZP3r’s relative importance to ZP recognition varies across species.
Interactive 3D visualization and post-processing analysis of vertex-based unstructured polyhedral meshes with ParaView
Authors: Sanematsu Paula C.
Published: October 2021

The development of physics-based 3D models that investigate the behavior of biological tissues requires effective and efficient visualization tools. The open-source software ParaView has such capabilities, but often impose a steep learning curve due to the use of the Visualization Toolkit (VTK) data structures. To overcome this, I show how to setup the components of 3D vertex-like models, i.e., vertices, faces, and polyhedra, into the VTK data format and then output as ParaView unstructured grid files. I present a few relevant tools to visualize and analyze the files in ParaView. All sample codes are available in the Github repository vis3Dvertex.
Anti-TRAP/SSP2 monoclonal antibodies can inhibit sporozoite infection and enhance protection of anti-CSP monoclonal antibodies
Authors: Wilder Brandon K. , Vigdorovich Vladimir , Carbonetti Sara , Minkah Nana , Hertoghs Nina , Raappana Andrew , Cardamone Hayley , Oliver Brian G. , Trakhimets Olesya , Kumar Sudhir , Dambrauskas Nicholas , Arredondo Silvia A. , Camargo Nelly , Kappe Stefan H.I. , Sather D. Noah
Published: October 2021

Vaccine-induced sterilizing protection from infection by Plasmodium parasites, the pathogens that cause malaria, will be essential in the fight against malaria as it would prevent both malaria-related disease and transmission. Stopping the relatively small number of parasites injected by the mosquito before they can migrate from the skin to the liver is an attractive means to this goal. Antibody-eliciting vaccines have been used to pursue this objective by targeting the major parasite surface protein present during this stage, the circumsporozoite protein (CSP). While CSP-based vaccines have recently had encouraging success in disease reduction, this was only achieved with extremely high antibody titers and appeared less effective for a complete block of infection (i.e. sterile protection). While such disease reduction is important, these and other results indicate that strategies focusing on CSP alone may not achieve the high levels of sterile protection needed for malaria eradication. Here, we show that monoclonal antibodies (mAbs) recognizing another sporozoite protein, TRAP/SSP2, exhibit a range of inhibitory activity and that these mAbs can augment CSP-based protection despite conferring no sterile protection on their own. Therefore, pursuing a multivalent subunit vaccine immunization is a promising strategy for improving infection-blocking malaria vaccines.
Evolutionary epidemiology of a zoonosis
Authors: Corsi Giulia I. , Tichkule Swapnil , Sannella Anna Rosa , Vatta Paolo , Asnicar Francesco , Segata Nicola , Jex Aaron R. , Oosterhout Cock van , Cacciò Simone M.
Published: October 2021

Cryptosporidium parvum is a global zoonoses and a major cause of diarrhoea in humans and ruminants. The parasite’s life cycle comprises an obligatory sexual phase, during which genetic exchanges can occur between previously isolated lineages. Here, we compare 32 whole genome sequences from human- and ruminant-derived parasite isolates collected across Europe, Egypt and China. We identify three strongly supported clusters that comprise a mix of isolates from different host species, geographic origins, and subtypes. We show that: (1) recombination occurs between ruminant isolates into human isolates; (2) these recombinant regions can be passed on to other human subtypes through gene flow and population admixture; (3) there have been multiple genetic exchanges, and all are likely recent; (4) putative virulence genes are significantly enriched within these genetic exchanges, and (5) this results in an increase in their nucleotide diversity. We carefully dissect the phylogenetic sequence of two genetic exchanges, illustrating the long-term evolutionary consequences of these events. Our results suggest that increased globalisation and close human-animal contacts increase the opportunity for genetic exchanges between previously isolated parasite lineages, resulting in spillover and spillback events. We discuss how this can provide a novel substrate for natural selection at genes involved in host-parasite interactions, thereby potentially altering the dynamic coevolutionary equilibrium in the Red Queens arms race.

Data Summary

All raw and processed sequencing data generated and analysed during the current study have been submitted to the NCBI Sequence Read Archive (https://www.ncbi.nlm.nih.gov/bioproject/), under BioProjects PRJNA634014 and PRJNA633764.
Genomic insights into the population history and biological adaptation of Southwestern Chinese Hmong-Mien people
Authors: Liu Yan , Xie Jie , Wang Mengge , Liu Changhui , Zhu Jingrong , Zou Xing , Li Wenshan , Wang Lin , Leng Cuo , Xu Quyi , Yeh Hui-Yuan , Wang Chuan-Chao , Wen Xiaohong , Liu Chao , He Guanglin
Published: October 2021

Hmong-Mien-speaking (HM) populations, widely distributed in South China, North of Thailand, Laos and Vietnam, have experienced different settlement environments, dietary habits and pathogen exposure. However, their specific biological adaptation also remained largely uncharacterized, which is important in the population evolutionary genetics and Trans-Omics for regional Precision Medicine. Besides, the origin and genetic diversity of HM people and their phylogenetic relationship with surrounding modern and ancient populations are unknown. Here, we reported genome-wide SNPs in 52 representative Miao people and combined them with 144 HM people from 13 geographically representative populations to characterize the full genetic admixture and adaptive landscape of HM speakers. We found that obvious genetic substructures existed in geographically different HM populations and also identified one new ancestral lineage specifically exited in HM people, which spatially distributed from Sichuan and Guizhou in the North to Thailand in the South and temporally dated to at least 500 years. The sharing patterns of the newly-identified homogeneous ancestry component combined the estimated admixture times via the decay of Linkage Disequilibrium and haplotype sharing in GLOBETROTTER suggested that the modern HM-speaking populations originated from Southwest China and migrated southward recently, which is consistent with the reconstructed phenomena of linguistic and archeological documents. Additionally, we identified specific adaptive signatures associated with several important human nervous system biological functions. Our pilot work emphasized the importance of anthropologically-informed sampling and deeply genetic structure reconstruction via whole-genome sequencing in the next step in the deep Chinese population genomic diversity project (CPGDP), especially in the ethnolinguistic regions.
In vivo adenine base editing corrects newborn murine model of Hurler syndrome
Authors: Su Jing , Jin Xiu , She Kaiqin , Liu Yi , Zhong Xiaomei , Zhao Qinyu , Xiao Jianlu , Li Ruiting , Deng Hongxin , Yang Yang
Published: October 2021

Mucopolysaccharidosis type I (MPS I) is a severe disease caused by loss-of-function mutations variants in the α-L-iduronidase (IDUA) gene. In vivo genome editing represents a promising strategy to correct IDUA mutations, and has the potential to permanently restore IDUA function over the lifespan of the patients. Here, we used adenine base editing to directly convert A>G (TAG>TGG) in newborn murine model harboring Idua-W392X mutation, which recapitulates the human condition and is analogous to the highly prevalent human W402X mutation. We engineered a split-intein dual-adeno-associated virus (AAV) 9 in vivo adenine base editor to circumvent the package size limit of AAV vectors. Intravenous injection of AAV9-base editor system into MPS I newborn mice led to sustained enzyme expression sufficient for correction of metabolic disease (GAGs substrate accumulation) and prevention of neurobehavioral deficits. We observed a reversion of the W392X mutation in 22.46±6.74% of hepatocytes, 11.18±5.25% of heart and 0.34±0.12% of brain, along with decreased GAGs storage in peripheral organs (liver, spleen, lung and kidney). Collectively, these data showed the promise of a base editing approach to precisely correct a common genetic cause of MPS I in vivo and could be broadly applicable to the treatment of a wide array of monogenic diseases.
Amyloid-beta and tau pathologies are both necessary to induce novel stage-specific microglia subtypes during Alzheimer’s disease progression
Authors: Kim Dong Won , Tu Kevin , Wei Alice , Lau Ashley , Gonzalez-Gil Anabel , Cao Tianyu , Braunstein Kerstin , Ling Jonathan P. , Troncoso Juan C. , Wong Philip C. , Blackshaw Seth , Schnaar Ronald L. , Li Tong
Published: October 2021

It is unknown whether specific microglia are selectively induced by amyloid-β (Aβ), tau pathologies, or both in combination. To address this, we use single-cell RNA-sequencing to profile mice bearing both Aβ and tau pathologies during Alzheimer’s disease (AD) progression. We identify novel microglia subtypes induced in a disease stage-specific manner. We show that during early-stage disease, interferon signaling induces a subtype of microglia termed EADAM. During late-stage disease, a second microglia subtype termed LADAM is detected. While EADAM and LADAM-like microglia are observed in other neurodegenerative models, the magnitude and composition of subtype markers are distinct from microglia observed with AD-like pathology. The pattern of EADAM- and LADAM-associated gene expression is observed in microglia from human AD, during the early and late stages of disease, respectively. Furthermore, we observe that several siglec genes are selectively expressed in either EADAM or LADAM.Siglecgis expressed in white-matter-associated LADAM, and expression of the human orthologue ofSiglecgis progressively elevated in AD-stage-dependent manner but not shown in non-AD tauopathy. Our findings imply that both Aβ and tau pathologies are required for disease stage-specific induction of EADAM and LADAM.
Oxidative stress induces inflammation of lens cells and triggers immune surveillance of ocular tissues
Authors: Thompson Brian , Davidson Emily A. , Chen Ying , Orlicky David J. , Thompson David C. , Vasiliou Vasilis
Published: October 2021

Recent reports have challenged the notion that the lens is immune-privileged. However, these studies have not fully identified the molecular mechanism(s) that promote immune surveillance of the lens. Using a mouse model of targeted glutathione (GSH) deficiency in ocular surface tissues, we have investigated the role of oxidative stress in upregulating cytokine expression and promoting immune surveillance of the eye. RNA-sequencing of lenses from postnatal day (P) 1- agedGclcf/f;Le-CreTg/−(KO) andGclcf/f;Le-Cre−/−control (CON) mice revealed upregulation of many cytokines (e.g., CCL4, GDF15, CSF1) and immune response genes in the lenses of KO mice. The eyes of KO mice had a greater number of cells in the aqueous and vitreous humors at P1, P20 and P50 than age-matched CON andGclcw/w;Le-CreTg/−(CRE) mice. Histological analyses revealed the presence of innate immune cells (i.e., macrophages, leukocytes) in ocular structures of the KO mice. At P20, the expression of cytokines and ROS content was higher in the lenses of KO mice than in those from age-matched CRE and CON mice, suggesting that oxidative stress may induce cytokine expression.In vitroadministration of the oxidant, hydrogen peroxide, and the depletion of GSH (using buthionine sulfoximine (BSO)) in 21EM15 lens epithelial cells induced cytokine expression, an effect that was prevented by co-treatment of the cells withN-acetyl-L-cysteine (NAC), a antioxidant. Thein vivoandex vivoinduction of cytokine expression by oxidative stress was associated with the expression of markers of epithelial-to-mesenchymal transition (EMT), α-SMA, in lens cells. Given that EMT of lens epithelial cells causes posterior capsule opacification (PCO), we propose that oxidative stress induces cytokine expression, EMT and the development of PCO in a positive feedback loop. Collectively these data indicate that oxidative stress induces inflammation of lens cells which promotes immune surveillance of ocular structures.

Highlights

Immune surveillance of ocular structures occurs in mouse eyes deficient in glutathione.

Oxidative stress upregulates the expression of pro-inflammatory cytokines (e.g., GDF15, CSF1) in lens cellsin vitroandin vivo.

The upregulation of cytokines in lens cells is associated with markers of an epithelial-to-mesenchymal transition phenotype.

Oxidative stress-induced inflammation and associated epithelial-to-mesenchymal transition may play a role in the development of posterior capsule opacification.
Cortical Spheroid Model for Studying the Effects of Ischemic Brain Injury
Authors: McLaughlin Rachel M. , Laguna Amanda , Top Ilayda , Hernandez Christien , Livi Liane L. , Kramer Liana , Zambuto Samantha , Hoffman-Kim Diane
Published: October 2021

Stroke is a devastating neurological disorder and a leading cause of death and long-term disability. Despite many decades of research, there are still very few therapeutic options for patients suffering from stroke or its consequences. This is partially due to the limitations of current research models, including traditional in vitro models which lack the three-dimensional (3D) architecture and cellular make-up of the in vivo brain. 3D spheroids derived from primary postnatal rat cortex provide an in vivo-relevant model containing a similar cellular composition to the native cortex and a cell-synthesized extracellular matrix. These spheroids are costeffective, highly reproducible, and can be produced in a high-throughput manner, making this model an ideal candidate for screening potential therapeutics. To study the cellular and molecular mechanisms of stroke in this model, spheroids were deprived of glucose, oxygen, or both oxygen and glucose for 24 hours. Both oxygen and oxygen-glucose deprived spheroids demonstrated many of the hallmarks of stroke, including a decrease in metabolism, an increase in neural dysfunction, and an increase in reactive astrocytes. Pretreatment of spheroids with the antioxidant agent N-acetylcysteine (NAC) mitigated the decrease in ATP seen after 24 hours of oxygen-glucose deprivation. Together, these results show the utility of our 3D cortical spheroid model for studying ischemic injury and its potential for screening stroke therapeutics.

Significance Statement

Those who survive after suffering a stroke often have long-term cognitive or physical disabilities. There is currently only one available therapeutic, tissue plasminogen activator (tPA), and it must be administered within a few hours after the onset of stroke. As stroke prevalence increases with our aging population, there is a growing need for therapies to mitigate or reverse the resulting brain damage. Three-dimensional (3D) culture systems have the potential to screen novel therapeutics more reliably than traditional in vitro models. Here we present a novel 3D cortical spheroid ischemia model which replicates many of the characteristics of stroke and has the potential to be an effective tool in therapeutic development.
Immunogenic potential of neopeptides depends on parent protein subcellular location
Authors: Castro Andrea , Kaabinejadian Saghar , Hildebrand William , Zanetti Maurizio , Carter Hannah
Published: October 2021

Antigen presentation via the major histocompatibility complex (MHC) is essential for anti-tumor immunity, however the rules that determine what tumor-derived peptides will be immunogenic are still incompletely understood. Here we investigate whether protein subcellular location driven constraints on accessibility of peptides to the MHC associate with potential for peptide immunogenicity. Analyzing over 380,000 peptides from studies of MHC presentation and peptide immunogenicity, we find clear spatial biases in both eluted and immunogenic peptides. We find that including parent protein location improves prediction of peptide immunogenicity in multiple datasets. In human immunotherapy cohorts, location was associated with response to a neoantigen vaccine, and immune checkpoint blockade responders generally had a higher burden of neopeptides from accessible locations. We conclude that protein subcellular location adds important information for optimizing immunotherapies.

Highlights

Peptides eluted from class I and II MHC reflect biases in the subcellular location of the parent proteins

An embedding-based indicator of parent protein location improves prediction of neoepitope immunogenicity and immunotherapy response

Neoepitope location improves estimation of effective neoantigen burden and stratification of potential for immunotherapy response
SPOT-1D-LM: Reaching Alignment-profile-based Accuracy in Predicting Protein Secondary and Tertiary Structural Properties without Alignment
Authors: Singh Jaspreet , Paliwal Kuldip , Singh Jaswinder , Zhou Yaoqi
Published: October 2021

Protein language models have emerged as an alternative to multiple sequence alignment for enriching sequence information and improving downstream prediction tasks such as biophysical, structural, and functional properties. Here we show that a combination of traditional one-hot encoding with the embeddings from two different language models (ProtTrans and ESM-1b) allows a leap in accuracy over single-sequence based techniques in predicting protein 1D secondary and tertiary structural properties, including backbone torsion angles, solvent accessibility and contact numbers. This large improvement leads to an accuracy comparable to or better than the current state-of-the-art techniques for predicting these 1D structural properties based on sequence profiles generated from multiple sequence alignments. The high-accuracy prediction in both secondary and tertiary structural properties indicates that it is possible to make highly accurate prediction of protein structures without homologous sequences, the remaining obstacle in the post AlphaFold2 era.
Identification of electroporation sites in the complex lipid organization of the plasma membrane
Authors: Rems Lea , Tang Xinru , Zhao Fangwei , Pérez-Conesa Sergio , Testa Ilaria , Delemotte Lucie
Published: October 2021

The plasma membrane of a biological cell is a complex assembly of lipids and membrane proteins, which tightly regulate transmembrane transport. When a cell is exposed to a strong electric field, the membrane integrity becomes transiently disrupted by formation of transmembrane pores. This phenomenon, termed electroporation, is already utilized in many rapidly developing applications in medicine including gene therapy, cancer treatment, and treatment of cardiac arrythmias. However, the molecular mechanisms of electroporation are not yet sufficiently well understood; in particular, it is unclear where exactly pores form in the complex organization of the plasma membrane. In this study we combine coarse-grained molecular dynamics simulations, machine learning methods, and Bayesian survival analysis to identify how formation of pores depends on the local lipid organization. We show that pores do not form homogeneously across the membrane, but colocalize with domains that have specific features, the most important being high density of polyunsaturated lipids. We further show that knowing the lipid organization is sufficient to reliably predict poration sites with machine learning. However, by analysing poration kinetics with Bayesian survival analysis we then show that poration does not depend solely on local lipid arrangement, but also on membrane mechanical properties and the polarity of the electric field. Finally, we discuss how the combination of atomistic and coarse-grained molecular dynamics simulations, machine learning methods, and Bayesian survival analysis can guide the design of future experiments and help us to develop an accurate description of plasma membrane electroporation on the whole-cell level. Achieving this will allow us to shift the optimization of electroporation applications from blind trial-and-error approaches to mechanistic-driven design.
Single-cell transcriptomics unveils xylem cell development and evolution
Authors: Tung Chia-Chun , Kuo Shang-Che , Yang Chia-Ling , Huang Chia-En , Yu Jhong-He , Sun Ying-Hsuan , Shuai Peng , Su Jung-Chen , Ku Chuan , Lin Ying-Chung Jimmy
Published: October 2021

As the most abundant tissue on Earth1, xylem is responsible for lateral growth in plants. Typical xylem has a radial system composed of ray parenchyma cells and an axial system of fusiform cells2. In most angiosperms, fusiform cells are a combination of vessel elements for water transportation and libriform fibers for mechanical support, while both functions are performed together by tracheids in other vascular plants2. However, little is known about the developmental programs and evolutionary relationships of these xylem cell types. Through both single-cell and laser-capture microdissection transcriptomic profiling, here we demonstrate the developmental lineages of ray and fusiform cells in stem-differentiating xylem across four divergent woody angiosperms. Cross-species analyses of single-cell trajectories reveal highly conserved ray, yet variable fusiform, lineages across angiosperms. Core eudicots Populus trichocarpa and Eucalyptus grandis share nearly identical fusiform lineages. The tracheids in the basal eudicot Trochodendron aralioides, an evolutionarily reversed character3, 4, exhibit strong transcriptomic similarity to vessel elements but not libriform fibers, suggesting that water transportation, instead of mechanical support, is the major feature. We also found that the more basal angiosperm Liriodendron chinense has a fusiform lineage distinct from that in core eudicots. This evo-developmental framework provides a comprehensive understanding of the formation of xylem cell lineages across multiple plant species spanning over a hundred million years of evolutionary history5.
Nanopore microscope identifies RNA isoforms with structural colors
Authors: Bošković Filip , Keyser Ulrich Felix
Published: October 2021

Identifying RNA transcript isoforms requires intricate protocols that suffer from various enzymatic biases. Here we design three-dimensional molecular constructs that enable identification of transcript isoforms at the single-molecule level using solid-state nanopore microscopy. We refold target RNA into RNA identifiers (IDs) with designed sets of complementary DNA strands. Each reshaped molecule carries a unique sequence of structural (pseudo)colors. Structural colors consist of DNA structures, protein labels, native RNA structures, or a combination of all three. The sequence of structural colors of RNA IDs enables simultaneous identification and relative quantification of multiple RNA targets without prior amplification. Our Amplification-free RNA TargEt Multiplex Isoform Sensing (ARTEMIS) reveals structural arrangements in native transcripts in agreement with published variants. ARTEMIS discriminates circular and linear transcript isoforms in a one step, enzyme-free reaction in a complex human transcriptome using single-molecule readout.

One sentence summary

Here we show enzyme-free identification and relative quantification of RNA isoforms using a nanopore microscope and structural colors.
Automatic identification and annotation of MYB gene family members in plants
Authors: Pucker Boas
Published: October 2021

Background

MYBs are among the largest transcription factor families in plants. Consequently, members of this family are involved in a plethora of processes including development and specialized metabolism. The MYB families of many plant species were investigated in the last two decades since the first investigation looked at Arabidopsis thaliana. This body of knowledge and characterized sequences provide the basis for the identification, classification, and functional annotation of candidate sequences in new genome and transcriptome assemblies.

Results

A pipeline for the automatic identification and functional annotation of MYBs in a given sequence data set was implemented in Python. MYB candidates are identified, screened for the presence of a MYB domain and other motifs, and finally placed in a phylogenetic context with well characterized sequences. In addition to technical benchmarking based on existing annotation, the transcriptome assembly of Croton tiglium and the annotated genome sequence of Castanea crenata were screened for MYBs. Results of both analyses are presented in this study to illustrate the potential of this application. The analysis of one species takes only a few minutes depending on the number of predicted sequences and the size of the MYB gene family. This pipeline, the required bait sequences, and reference sequences for a classification are freely available on github: https://github.com/bpucker/MYB_annotator.

Conclusions

This automatic annotation of the MYB gene family in novel assemblies makes genome-wide investigations consistent and paves the way for comparative studies in the future. Candidate genes for in-depth analyses are presented based on their orthology to previously characterized sequences which allows the functional annotation of the newly identified MYBs with high confidence. The identification of orthologs can also be harnessed to detect duplication and deletion events.
iHypoxia: an integrative database of the expression dynamics of proteins in response to hypoxia in animals
Authors: Liu Ze-Xian , Wang Panqin , Zhang Qingfeng , Li Shihua , Zhang Yuxin , Guo Yutong , Jia Chongchong , Shao Tian , Li Lin , Cheng Han , Wang Zhenlong
Published: October 2021

Decreased oxygen concentrations (hypoxia) outside of the physiological range may severely subvert cell, tissue, and organism survival. Mammals have evolved mechanisms to sense hypoxia and induce a series of hypoxic responses. In recent years, high-throughput techniques have greatly promoted global perturbation studies of protein expression during hypoxia, and these studies have contributed to the understanding of the complex regulatory networks of hypoxia. In this study, we developed an integrated resource for the expression dynamics of proteins in response to hypoxia (iHypoxia), which contains 1,629 expression events of 1,215 proteins identified by low-throughput experiments (LTEs) and 154,953 quantitative expression events of 36,194 proteins identified by high-throughput experiments (HTEs) from five mammals that exhibit a response to hypoxia. Various experimental details such as the hypoxic experimental conditions, expression patterns, and samples were carefully collected and integrated. In addition, we conducted an orthologous search and identified 581,763 proteins that may respond to hypoxia among 50 animals. An enrichment analysis of human proteins identified from LTEs showed that these proteins were enriched in certain drug targets and cancer genes. The annotation of known posttranslational modification (PTM) sites to proteins identified by LTEs revealed that these proteins underwent extensive PTMs, particularly phosphorylation, ubiquitination and acetylation. Based on the results, iHypoxia provides a convenient and user-friendly method for users to obtain hypoxia-related information of interest. We anticipate that iHypoxia, which is freely accessible at http://ihypoxia.omicsbio.info, will advance the understanding of hypoxia and serve as a valuable data resource.