bluuebunny/crossref_metadata_2025 huggingface dataset:
Signaling specificity and kinetics of the human metabotropic glutamate receptors
Authors: McCullock Tyler W. , Cardani Loren P. , Kammermeier Paul J.
Published: July 2023

Metabotropic glutamate receptors (mGluRs) are obligate dimer G protein coupled receptors that can all function as homodimers. Here, each mGluR homodimer was examined for its G protein coupling profile using a BRET based assay that detects the interaction between a split YFP-tagged Gβ1γ2and a Nanoluc tagged free Gβγsensor, MAS-GRK3-ct-NLuc with 14 specific G⍺ proteins heterologously expressed, representing each family. Canonically, the group II and III mGluRs (2&3, and 4, 6, 7&8, respectively) are thought to couple to Gi/oexclusively. In addition, the group I mGluRs (1&5) are known to couple to the Gq/11family, and generally thought to also couple to the PTX-sensitive Gi/ofamily; some reports have suggested Gscoupling is possible as cAMP elevations have been noted. In this study, coupling was observed with all 8 mGluRs through the Gi/oproteins, and only mGluR1&5 through Gq/11, and perhaps surprisingly, not G14. None activated any Gsprotein. Interestingly, coupling was seen with the group I and II, but not the group III mGluRs to G16. Slow but significant coupling to Gzwas also seen with the group II receptors.
The brain hierarchically represents the past and future during multistep anticipation
Authors: Tarder-Stoll Hannah , Baldassano Christopher , Aly Mariam
Published: July 2023

Memory for temporal structure enables both planning of future events and retrospection of past events. We investigated how the brain flexibly represents extended temporal sequences into the past and future during anticipation. Participants learned sequences of environments in immersive virtual reality. Pairs of sequences had the same environments in a different order, enabling context-specific learning. During fMRI, participants anticipated upcoming environments multiple steps into the future in a given sequence. Temporal structure was represented in the hippocampus and across higher-order visual regions (1) bidirectionally, with graded representations into the past and future and (2) hierarchically, with further events into the past and future represented in successively more anterior brain regions. In hippocampus, these bidirectional representations were context-specific, and suppression of far-away environments predicted response time costs in anticipation. Together, this work sheds light on how we flexibly represent sequential structure to enable planning over multiple timescales.
Temporal sensitivity for achromatic and chromatic flicker across the visual cortex
Authors: Gentile Carlyn Patterson , Spitschan Manuel , Taskin Huseyin O. , Bock Andrew S. , Aguirre Geoffrey K.
Published: July 2023

The retinal ganglion cells (RGCs) receive different combinations of L, M, and S cone inputs and give rise to one achromatic and two chromatic post-receptoral channels. Beyond the retina, RGC outputs are subject to filtering and normalization along the geniculo-striate pathway, ultimately producing the properties of human vision. The goal of the current study was to determine temporal sensitivity across the three post-receptoral channels in subcortical and cortical regions involved in vision. We measured functional magnetic resonance imaging (MRI) responses at 7 Tesla from three participants (two males, one female) viewing a high-contrast, flickering, spatially-uniform wide field (~140°). Stimulus flicker frequency varied logarithmically between 2 and 64 Hz and targeted the L+M+S, L–M, and S–[L+M] cone combinations. These measurements were used to create temporal sensitivity functions of primary visual cortex (V1) across eccentricity, and spatially averaged responses from lateral geniculate nucleus (LGN), V2/V3, hV4, and V3A/B. Functional MRI responses reflected known properties of the visual system, including higher peak temporal sensitivity to achromatic vs. chromatic stimuli, and low-pass filtering between the LGN and V1. Peak temporal sensitivity increased across levels of the cortical visual hierarchy. Unexpectedly, peak temporal sensitivity varied little across eccentricity within area V1. Measures of adaptation and distributed pattern activity revealed a subtle influence of 64 Hz achromatic flicker in area V1, despite this stimulus evoking only a minimal overall response. Comparison of measured cortical responses to a model of integrated retinal output to our stimuli demonstrates that extensive filtering and amplification is applied to post-retinal signals.

Significance Statement

We report the temporal sensitivity of human visual cortex across the three canonical post-receptoral channels from central vision to the far periphery. Functional MRI measurements of responses from the LGN, V1, and higher visual cortical areas demonstrate modification of temporal sensitivity across the visual hierarchy. This includes amplification of chromatic signals between the LGN and V1, and an increase in peak temporal sensitivity in visual areas beyond V1. Within V1, we find a surprising stability of peak temporal sensitivity in the periphery for all three post-receptoral directions. Comparison of our results to a model of retinal output demonstrates the presence of substantial post-retinal filtering, yielding greater uniformity of responses across area V1 than would be predicted from unmodified retinal signals.
The mouse dorsal peduncular cortex encodes fear memory
Authors: Cardoso Rodrigo Campos , Desa Zephyr R. , Fitzgerald Brianna L. , Moore Alana , Duhon Jace , Landar Victoria A. , Clem Roger L. , Cummings Kirstie A.
Published: July 2023

The rodent medial prefrontal cortex (mPFC) is a locus for both the promotion and suppression (e.g. extinction) of fear and is composed of four anatomically distinct subregions, including anterior cingulate 1 (Cg1), prelimbic (PL), infralimbic (IL), and the dorsal peduncular (DP) cortex. A vast majority of studies have focused on Cg1, PL, and IL. The Cg1 and PL have been implicated in the promotion of fear, while the IL has been linked to a role in the suppression, or extinction, of fear. Due to its anatomical location ventral to IL, the DP has been hypothesized to function as a fear-suppressing brain region however, no studies have explicitly tested its role in this function or in the regulation of memory generally. Moreover, some studies have pointed towards a dichotomous role for ventral mPFC in the dual suppression and promotion of fear, but the mechanisms underlying these opposing observations remains unclear. Here, we provide evidence that the DP paradoxically functions as a cued fear-encoding brain region and plays little to no role in fear memory extinction. By using a combination of cFos immunohistochemistry, whole-cell brain slice electrophysiology, fiber photometry, and activity-dependent neural tagging, we demonstrate that DP neurons exhibit learning-related plasticity, acquire cue-associated activity across learning and memory retrieval, and that DP neurons activated by learning are preferentially reactivated upon fear memory retrieval. Further, optogenetic activation and silencing of fear learning-related DP neural ensembles drives the promotion and suppression of freezing, respectively. Overall, these data suggest that the DP plays an unexpected role in fear memory encoding. More broadly, our results reveal new principles of organization across the dorsoventral axis of the mPFC.
Activation of the Aryl Hydrocarbon Receptor in Endothelial Cells Impairs Ischemic Angiogenesis in Chronic Kidney Disease
Authors: Palzkill Victoria R. , Tan Jianna , Yang Qingping , Morcos Juliana , Laitano Orlando , Ryan Terence E.
Published: July 2023

Rationale

Chronic kidney disease (CKD) is a strong risk factor for peripheral artery disease (PAD) that is associated with worsened clinical outcomes. CKD leads to accumulation of tryptophan metabolites that associate with adverse limb events in PAD and are ligands of the aryl hydrocarbon receptor (AHR) which may regulate ischemic angiogenesis.

Objectives

To test if endothelial cell-specific deletion of the AHR (AHRecKO) alters ischemic angiogenesis and limb function in mice with CKD subjected to femoral artery ligation.

Findings

Male AHRecKOmice with CKD displayed better limb perfusion recovery and enhanced ischemic angiogenesis compared to wildtype mice with CKD. However, the improved limb perfusion did not result in better muscle performance. In contrast to male mice, deletion of the AHR in female mice with CKD had no impact on perfusion recovery or angiogenesis. Using primary endothelial cells from male and female mice, treatment with indoxyl sulfate uncovered sex-dependent differences in AHR activating potential and RNA sequencing revealed wide ranging sex-differences in angiogenic signaling pathways.

Conclusion

Endothelium-specific deletion of the AHR improved ischemic angiogenesis in male, but not female, mice with CKD. There are sex- dependent differences inAhractivating potential within endothelial cells that are independent of sex hormones.
YAP-Driven Oral Epithelial Stem Cell Malignant Reprogramming at Single Cell Resolution
Authors: Faraji Farhoud , Ramirez Sydney I , Clubb Lauren , Sato Kuniaki , Burghi Valeria , Hoang Thomas S , Officer Adam , Anguiano Quiroz Paola Y , Galloway William MG , Mikulski Zbigniew , Medetgul-Ernar Kate , Marangoni Pauline , Jones Kyle B , Molinolo Alfredo A , Kim Kenneth , Sakaguchi Kanako , Califano Joseph A , Smith Quinton , Goren Alon , Klein Ophir D , Tamayo Pablo , Gutkind J Silvio
Published: July 2023

Tumor initiation represents the first step in tumorigenesis during which normal progenitor cells undergo cell fate transition to cancer. Capturing this process as it occurs in vivo, however, remains elusive. Here we employ spatiotemporally controlled oncogene activation and tumor suppressor inhibition together with multiomics to unveil the processes underlying oral epithelial progenitor cell reprogramming into tumor initiating cells (TIC) at single cell resolution. TIC displayed a distinct stem-like state, defined by aberrant proliferative, hypoxic, squamous differentiation, and partial epithelial to mesenchymal (pEMT) invasive gene programs. YAP-mediated TIC programs included the activation of oncogenic transcriptional networks and mTOR signaling, and the recruitment of myeloid cells to the invasive front contributing to tumor infiltration. TIC transcriptional programs are conserved in human head and neck cancer and associated with poor patient survival. These findings illuminate processes underlying cancer initiation at single cell resolution, and identify candidate targets for early cancer detection and prevention.
SharePro: an accurate and efficient genetic colocalization method accounting for multiple causal signals
Authors: Zhang Wenmin , Lu Tianyuan , Sladek Robert , Li Yue , Najafabadi Hamed S. , Dupuis Josée
Published: July 2023

Motivation

Colocalization analysis is commonly used to assess whether two or more traits share the same genetic signals identified in genome-wide association studies (GWAS), and is important for prioritizing targets for functional follow-up of GWAS results. Existing colocalization methods can have suboptimal performance when there are multiple causal variants in one genomic locus.

Results

We propose SharePro to extend the COLOC framework for colocalization analysis. Share-Pro integrates linkage disequilibrium (LD) modelling and colocalization assessment by grouping correlated variants into effect groups. With an efficient variational inference algorithm, posterior colocalization probabilities can be accurately estimated. In simulation studies, SharePro demonstrated increased power with a well-controlled false positive rate at a low computational cost. Through a challenging case of the colocalization analysis of the circulating abundance of R-spondin 3 (RSPO3) GWAS and estimated bone mineral density GWAS, we demonstrated the utility of SharePro in identifying biologically plausible colocalized signals.

Availability and Implementation

The SharePro software for colocalization analysis is openly available athttps://github.com/zhwm/SharePro_colocand the analysis conducted in this study is available athttps://github.com/zhwm/SharePro_coloc_analysis.
Dietary n-3 PUFA enhances DMI in transition cows by regulating taste transduction gene expression in liver associated with rumen microbial alteration
Authors: Sun Xiaoge , Guo Cheng , Wang Qianqian , Zhang Yan , Wang Zhonghan , Cao Zhijun , Wang Wei , Li Shengli
Published: July 2023

We hypothesised that the addition of n-3 polyunsaturated fatty acids (PUFAs) in the diet could affect gene expression in the liver and have beneficial effects on the recovery of cows in the transition phase. A total of 30 multiparous non-lactating Holstein dairy cows (35 days before expected calving) were randomly fed a diet with either 1% dry matter (DM) of hydrogenated fatty acid (C16:00 enriched; CON) or 3.5% DM of extruding flaxseed (n-3 enriched; HN3). Parity, body weight (BW), body condition score (BCS) and milk yield were 2.6 ± 1.2, 757.5 ± 65.8 kg, 3.3 ± 0.2 and 10,286.5 ± 1464.8 kg/d (mean ± SD), respectively, at the beginning of the experiment. The relative abundance ofBacteroidota(P= 0.047) andSpirochaetota(P= 0.091) was higher and that ofPatescibacteria(P= 0.076) was lower in the HN3 group than in the CON group on prepartum day 4. The DMI of cows was positively correlated with the abundance of bacteria in the rumen (Spirochaetota: r = 0.871,P< 0.001;Bacteroidota: r = 0.896,P< 0.001) and the differential expression of genes involved in taste transduction (ACSL1: r = 0.673,P< 0.001; PLIN4: r = 0.632,P< 0.01; CPT1A: r = 0.694,P< 0.001). These results suggest that dietary n-3 PUFA at an appropriate concentration can promote DMI recovery by upregulating the expression of these genes and maintaining the balance of the rumen microbiota.
Microstructure-Based Nuclear Lamina Constitutive Model
Authors: Mostafazadeh Nima , Peng Zhangli
Published: July 2023

The nuclear lamina is widely recognized as the most crucial component in providing mechanical stability to the nucleus. However, it is still a significant challenge to model the mechanics of this multilayered protein network. We developed a constitutive model of the nuclear lamina network based on its microstructure, which accounts for the deformation phases at the dimer level, as well as the orientational arrangement and density of lamin filaments. Instead of relying on homology modeling in the previous studies, we conducted molecular simulations to predict the force-extension response of a highly accurate lamin dimer structure obtained through X-ray diffraction crystallography experimentation. Furthermore, we devised a semi-flexible worm-like chain extension-force model of lamin dimer as a substitute, incorporating phases of initial stretching, uncoiling of the dimer coiled-coil, and transition of secondary structures. Subsequently, we developed a 2D network continuum model for the nuclear lamina by using our extension-force lamin dimer model and derived stress resultants. By comparing with experimentally measured lamina modulus, we found that the lamina network has sharp initial strain-hardening behavior. This also enabled us to carry out finite element simulations of the entire nucleus with an accurate microstructure-based nuclear lamina model. Finally, we conducted simulations of transendothelial transmigration of a nucleus and investigated the impact of varying network density and uncoiling constants on the critical force required for successful transmigration. The model allows us to incorporate the microstructure characteristics of the nuclear lamina into the nucleus model, thereby gaining insights into how laminopathies and mutations affect nuclear mechanics.
HLA-DR4Pred2: an improved method for predicting HLA-DRB1*04:01 binders
Authors: Patiyal Sumeet , Dhall Anjali , Kumar Nishant , Raghava Gajendra P. S.
Published: July 2023

HLA-DRB1*04:01 is associated with many disease that include sclerosis, arthritis, diabetes and Covid19. Thus, it is important to scan binders of HLA-DRB1*04:01 in an antigen to develop immunotherapy, vaccine and protection against these diseases. One of the major limitations of existing methods for predicting with HLA-DRB1*04:01 binders is that these methods trained on small datasets. This study present a method HLA-DR4Pred2 developed on a large dataset contain 12676 binders and equal number of non-binders. It is an improved version of HLA-DR4Pred, which was trained on a small dataset contain only 576 binders and equal number of binders. All models in this study were trained, optimized and tested on 80% of data called training datasets using five-fold cross-validation; final models were evaluated on 20% of data called validation/independent dataset. A wide range of machine learning techniques have been employed to develop prediction models and achieved maximum AUC of 0.90 and 0.87 on validation dataset using composition and binary profile features respectively. The performance of our composition based model increased from 0.90 to 0.93 when combined with BLAST search. In addition, we also developed our models on alternate or realistic dataset that contain 12676 binders and 86300 non-binders and achieved maximum AUC 0.99. Our method perform better than existing methods when we compare the performance of our best model with performance of existing methods on validation dataset. Finally, we developed standalone and online version of HLA-DR4Pred2 for predicting, designing and virtual scanning of HLA- DRB1*04:01(https://webs.iiitd.edu.in/raghava/hladr4pred2/;https://github.com/raghavagps/hladr4pred2).

Key Points

HLADR4Pred2.0 is an update of HLADR4Pred

Predict the binding or non-binding peptides for MHC-Class II allele HLA- DRB1*04:01

Used alignment free and alignment based hybrid approach

Motifs which are highly specific to HLA-DRB1*04:01 binders

Benchmark the performance of the other existing methods with HLADR4Pred2.0

Author’s Biography

Sumeet Patiyal is currently working as Ph.D. in Computational biology from Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India

Anjali Dhall is currently working as Ph.D. in Computational Biology from Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India.

Nishant Kumar is currently working as Ph.D. in Computational biology from Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India

Gajendra P. S. Raghava is currently working as Professor and Head of Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India.
Continuous respiratory rate monitoring using photoplethysmography technology in patients with Obstructive Sleep Apnea
Authors: Gehring J.M. , Niel L.C. Saeijs-van , ten Bosch-Paniagua L.P , Frank M.H.
Published: July 2023

Purpose

Respiratory rate is an important physiological parameter whose abnormality could be, in the presence of other suggestive symptoms, supportive of a diagnose of various serious illnesses. Photoplethysmography (PPG) in wearable sensors potentially plays an important role in early disease detection by making respiratory rate measurements more accessible. We investigated the accuracy of a new non-invasive, continuous, wrist-worn and wireless monitoring PPG device (Corsano CardioWatch 287) in measuring respiratory rate (RR) and heart rate (HR) at rest.

Methods

Subjects with and without diagnosed Obstructive Sleep Apnea (OSA) underwent simultaneous, continuous PPG and home sleep apnea testing (HSAT) for one night. We assessed the PPG sensor’s measurement accuracy by calculating root-mean-square accuracy (Arms) and by performing Bland Altman and correlation analysis. Subgroups were defined based on skin type, hair density, age, BMI, gender and OSA severity.

Results

In 26 participants a total of 31083 RR and 38693 HR measurement pairs were obtained. For RR measurements, Armswas 0.60 breaths per minute (brpm). Correlation was high (r = 0.964 (95%CI 0.963 - 0.965)) and 95% Limits of Agreement (LoA) were −1.28 to 1.71 brpm (mean bias −0.14 brpm). For HR measurements, Armswas 0.95 beats per minute (bpm). Correlation was similarly high (r = 0.996 (95%CI 0.996 - 0.996) and 95% LoA were – 2.09 to 1.17 bpm (mean bias −0.46 bpm). Results were comparable across all subgroups, without significant difference in RR accuracy between subjects with and without diagnosed OSA. In free-living conditions, Armswas 2.43 brpm and 95% LoA were −5.00 to 4.47 brpm (mean bias −0.27 brpm).

Conclusion

We showed that the Corsano Cardiowatch 287 using PPG technology can monitor continuous RR and HR with high accuracy in healthy subjects as well as in patients diagnosed with OSA. We conclude that wearable devices like these enable new and more accessible ways to measure health, ultimately improving healthcare delivery. The trial was registered in the ISCRTN registry under referenceISRCTN13965929.
Plasma proteomic signatures of adiposity are associated with cardiovascular risk factors and type 2 diabetes risk in a multi-ethnic Asian population
Authors: Lim Charlie G.Y. , Ozkan Bige , Liang Yujian , Yao Jiali , Khaing Nang Ei Ei , Rooney Mary R. , Ndumele Chiadi E. , Tai E Shyong , Coresh Josef , Sim Xueling , van Dam Rob M.
Published: July 2023

The molecular mechanisms connecting obesity and cardiometabolic diseases are not fully understood. We evaluated the associations between body mass index (BMI), waist circumference (WC), and ∼5,000 plasma proteins in the Singapore Multi-Ethnic Cohort (MEC1). Among 410 BMI-associated and 385 WC-associated proteins, we identified protein signatures of BMI and WC and validated them in an independent dataset across two timepoints and externally in the Atherosclerosis Risk in Communities (ARIC) study. The BMI- and WC-protein signatures were highly correlated with total and visceral body fat, respectively. Furthermore, the protein signatures were significantly associated with cardiometabolic risk factors and were able to differentiate between metabolically healthy and unhealthy obesity. In prospective analyses, the protein signatures were strongly associated with type 2 diabetes risk in MEC1 (odds ratio per SD increment in WC-protein signature = 2.84, 95% CI 2.47 to 3.25) and ARIC (hazard ratio = 1.97, 95% CI 1.87 to 2.07). Pathways related to cell signaling, systemic inflammation, and glucose and fat metabolism were overrepresented in the BMI- and WC-protein signatures. Our protein signatures have potential uses for the monitoring of metabolically unhealthy obesity.

Article Highlights

We evaluated the associations between ∼5000 plasma proteins and BMI and WC in a multi-ethnic Asian population.

We identified 410 proteins associated with BMI and 385 proteins associated with WC and derived protein signatures of BMI and WC, which we validated externally in a US cohort.

Both the BMI- and WC-protein signatures were strongly associated with cardiometabolic risk factors and the risk of type 2 diabetes and were enriched in pathways relating to cell signaling, systemic inflammation, and glucose and fat metabolism.

Our protein signatures have potential uses for monitoring metabolically unhealthy obesity.
On the detectability and accuracy of computational measurements of enlarged perivascular spaces from magnetic resonance images
Authors: Coello Roberto Duarte , Valdés Hernández Maria del C. , Zwanenburg Jaco J.M. , van der Velden Moniek , Kuijf Hugo J. , De Luca Alberto , Moyano José Bernal , Ballerini Lucia , Chappell Francesca M. , Brown Rosalind , Biessels Geert Jan , Wardlaw Joanna M.
Published: July 2023

Magnetic Resonance Imaging (MRI) visible perivascular spaces (PVS) have been associated with age, decline in cognitive abilities, interrupted sleep, and markers of small vessel disease. Therefore, several computational methods have been developed for their assessment from brain MRI. But the limits of validity of these methods under various spatial resolutions, and the accuracy in detecting and measuring the dimensions of these structures have not been established. We use a digital reference object (DRO) previously developed for this purpose, to construct anin-silicophantom for answering these questions; and validate it using a physical phantom. Ourin-silicoand physical phantoms use cylinders of different sizes as models for PVS. Using both phantoms, we also evaluate the influence of the “PVS” orientation on the accuracy of the diameter measured, different sets of parameters for two vesselness filters that have been used for enhancing tubular structures, namely Frangi and RORPO filters, and the influence of the vesselness filterper-sein the accuracy of the measurements. Our experiments indicate that PVS measurements in MRI are only a proxy of their true dimensions, as the boundaries of their representation are consistently overestimated. The success in the use of the Frangi filter for this task relies on a careful tuning of several parameters. The combination of parameters α=0.5, β=0.5 and c=500 proved to yield the best results. RORPO, on the contrary, does not have these requirements, and allows detecting smaller cylinders in their entirety more consistently in the ideal scenarios tested. The segmentation of the cylinders using the Frangi filter seems to be best suited for voxel sizes equal or larger than 0.4 mm-isotropic and cylinders larger than 1 mm diameter and 2 mm length. “PVS” orientation did not influence their measures for image data with isotropic voxel size. Further evaluation of the emerging deep-learning methods is still required, and these results should be tested in “real” world data across several diseases.
KCL TEST: an open-source inspired asymptomatic SARS-CoV-2 surveillance programme in an academic institution
Authors: Reis de Andrade J. , Scourfield E. , Peswani-Sajnani S. , Poulton K. , Ap Rees T. , Khooshemehri P. , Doherty G. , Ong S. , Ivan I. , Goudarzi N. , Gardiner I. , Caine E. , Maguire T. , Leightley D. , Torrico L. , Gasulla A. , Menendez-Vazquez A. , Ortega Prieto Ana Maria , Pickering Suzanne , Guardeño Jose Jimenez , Batra Rahul , Tan A.V.F. , Griffin A. , Papaioannou S. , Trouillet C. , Mischo H. , Giralt V. , Wilson S. , Kirk M. , Neil Stuart , Ribeiro Galao Rui Pedro , Martindale J. , Curtis C. , Zuckerman M. , Razavi R. , Malim M.H. , Martinez-Nunez R.T.
Published: July 2023

Testing was paramount in the management of the COVID-19 pandemic. Our university established KCL TEST: a SARS-CoV-2 asymptomatic testing programme that enabled sensitive and accessible PCR testing of SARS-CoV-2 RNA in saliva. We performed 158,277 PCRs for our staff, students, and their household contacts, free of charge. Our average turnaround time was 16h and 37 mins from user registration to result delivery. KCL TEST combined open-source automation and in house non-commercial reagents, which allows for rapid deployment. Here we provide our blueprint, recently recommended for ISO15189 accreditation, and results to enable the rapid launch of diagnostic laboratories where and when needed, particularly in low-resource settings. Our data span over 18 months and parallels that of the UK Office for National Statistics, with a lower positive rate and virtually no delta wave. Our observations strongly support regular asymptomatic community testing to decrease outbreaks and provide safe working spaces. Universities can therefore provide agile, resilient, and accurate testing that reflects the infection rate and trend of the general population. We call for the integration of academic institutions in pandemic preparedness, with capabilities to rapidly deploy highly skilled staff, as well as develop, test and accommodate efficient low-cost pipelines.
Highly resolved genome assembly and comparative transcriptome profiling reveal genes related to developmental stages of tapewormLigula intestinalis
Authors: Nazarizadeh Masoud , Nováková Milena , Drábková Marie , Catchen Julian , Olson Peter D. , Štefka Jan
Published: July 2023

Ligula intestinalis(Cestoda: Diphyllobothriidae) is an emerging model organism for studies on parasite population biology and host-parasite interactions. However, a well resolved genome and catalogue of its gene content has not been previously developed. Here, we present the first genome assembly ofL. intestinalis, based on Oxford Nanopore Technologies, Illumina and Omni-C sequencing methodologies. We use transcriptome profiling to compare plerocercoid larvae and adult worms and identify differentially expressed genes associated with these life stages. The genome assembly is 775.5 Mbp in size, with scaffold N50 value of 118 Mbp and encodes 27,256 predicted protein-coding sequences. Over 60% of the genome consists of repetitive sequences. Synteny analyses showed that the 10 largest scaffolds representing 75% of the genome display high correspondence to full chromosomes of cyclophyllidean tapeworms. Mapping RNA-seq data to the new reference genome we identified 3,922 differentially expressed genes in adults compared to plerocercoids. Gene Ontology analyses revealed overrepresented genes involved in reproductive development of the adult stage (e.g. sperm production) and significantly enriched DEGs associated with immune evasion of plerocercoids in their fish host. This study provides the first insights into the molecular biology ofL. intestinalisand provides the most highly contiguous assembly to date of a diphyllobothriid tapeworm useful for population and comparative genomic investigations of parasitic flatworms.
Non-neutralizing SARS-CoV-2 N-terminal domain antibodies protect mice against severe disease using Fc-mediated effector functions
Authors: Pierre Camille N. , Adams Lily E. , Anasti Kara , Goodman Derrick , Stanfield-Oakley Sherry , Powers John M. , Li Dapeng , Rountree Wes , Wang Yunfei , Edwards Robert J. , Alam S. Munir , Ferrari Guido , Tomaras Georgia D. , Haynes Barton F. , Baric Ralph S. , Saunders Kevin O.
Published: July 2023

Antibodies perform both neutralizing and non-neutralizing effector functions that protect against certain pathogen-induced diseases. A human antibody directed at the SARS-CoV-2 Spike N-terminal domain (NTD), DH1052, was recently shown to be non-neutralizing yet it protected mice and cynomolgus macaques from severe disease. The mechanisms of this non-neutralizing antibody-mediated protection are unknown. Here we show that Fc effector functions mediate non-neutralizing antibody (non-nAb) protection against SARS-CoV-2 MA10 viral challenge in mice. Though non-nAb infusion did not suppress infectious viral titers in the lung as potently as NTD neutralizing antibody (nAb) infusion, disease markers including gross lung discoloration were similar in nAb and non-nAb groups. Fc functional knockout substitutions abolished non-nAb protection and increased viral titers in the nAb group. Finally, Fc enhancement increased non-nAb protection relative to WT, supporting a positive association between Fc functionality and degree of protection in SARS-CoV-2 infection. This study demonstrates that non-nAbs can utilize Fc-mediated mechanisms to lower viral load and prevent lung damage due to coronavirus infection.

AUTHOR SUMMARY

COVID-19 has claimed over 6.8 million lives worldwide and caused economic and social disruption globally. Preventing more deaths from COVID-19 is a principal goal of antibody biologic and vaccine developers. To guide design of such countermeasures, an understanding of how the immune system prevents severe COVID-19 disease is needed. We demonstrate here that antibody functions other than neutralization can contribute to protection from severe disease. Specifically, the functions of antibodies that rely on its Fc portion were shown to confer antibody-mediated protection of mice challenged with a mouse adapted version of SARS-CoV-2. Mice given an antibody that could not neutralize SARS-CoV-2 still showed a decrease in the amount of infectious virus in the lungs and less lung damage than mice given an irrelevant antibody. The decrease in infectious virus in the lungs was even larger when the non-neutralizing antibody was engineered to mediate non-neutralizing effector functions such as antibody-dependent cellular cytotoxicity more potently. Thus, in the absence of neutralization activity, non-neutralizing binding antibodies can contribute to the overall defense against SARS-CoV-2 infection and COVID-19 disease progression.
The p53 Protein is a Suppressor of Atox1 Copper Chaperon in Tumor Cells Under Genotoxic Effects
Authors: Tsymbal Sergey A. , Refeld Alexander G. , Zatsepin Viktor V. , Kuchur Oleg A.
Published: July 2023

The p53 protein is crucial for regulating cell survival and apoptosis in response to DNA damage. However, its influence on therapy effectiveness is controversial: when DNA damage is high p53 directs cells toward apoptosis, while under moderate genotoxic stress it saves the cells from death and promote DNA repair. Furthermore, these processes are influenced by the metabolism of transition metals, particularly copper since they serve as cofactors for critical enzymes. The metallochaperone Atox1 is under intensive study in this context because it serves as transcription factor allegedly mediating described effects of copper. Investigating the interaction between p53 and Atox1 could provide insights into tumor cell survival and potential therapeutic applications in oncology. This study explores the relationship between p53 and Atox1 in HCT116 and A549 cell lines with wild type and knockout TP53. The study found an inverse correlation between Atox1 and p53 at the transcriptional and translational levels in response to genotoxic stress. Atox1 expression decreased with increased p53 activity, while cells with inactive p53 had significantly higher levels of Atox1. Suppression of both genes increased apoptosis, while suppression of the ATOX1 gene prevented apoptosis even under the treatment with chemotherapeutic drugs. The findings suggest that Atox1 may act as one of key elements in promotion of cell cycle under DNA-damaging conditions, while p53 works as an antagonist by inhibiting Atox1. Understanding of this relationship could help identify potential targets in cell signaling pathways to enhance the effectiveness of antitumor therapy, especially in tumors with mutant or inactive p53.
The Vk*MYC Mouse Model recapitulates human multiple myeloma evolution and genomic diversity
Authors: Maura Francesco , Coffey David G. , Stein Caleb K , Braggio Esteban , Ziccheddu Bachisio , Sharik Meaghen E , Du Megan , Alvarado Yuliza Tofaya , Shi Chang-Xin , Zhu Yuan Xiao , Meermeier Erin W. , Morgan Gareth J. , Landgren Ola , Leif Bergsagel P. , Chesi Marta
Published: July 2023

Despite advancements in profiling multiple myeloma (MM) and its precursor conditions, there is limited information on mechanisms underlying disease progression. Clincal efforts designed to deconvolute such mechanisms are challenged by the long lead time between monoclonal gammopathy and its transformation to MM. MM mouse models represent an opportunity to overcome this temporal limitation. Here, we profile the genomic landscape of 118 genetically engineered Vk*MYC MM and reveal that it recapitulates the genomic heterogenenity and life history of human MM. We observed recurrent copy number alterations, structural variations, chromothripsis, driver mutations, APOBEC mutational activity, and a progressive decrease in immunoglobulin transcription that inversely correlates with proliferation. Moreover, we identified frequent insertional mutagenesis by endogenous retro-elements as a murine specific mechanism to activate NF-kB and IL6 signaling pathways shared with human MM. Despite the increased genomic complexity associated with progression, advanced tumors remain dependent onMYCexpression, that drives the progression of monoclonal gammopathy to MM.
Benchmarking DNA Isolation Methods for Marine Metagenomics Studies
Authors: Demkina Alina , Slonova Darya , Mamontov Viktor , Konovalova Olga , Yurikova Daria , Rogozhin Vladimir , Belova Vera , Korostin Dmitriy , Sutormin Dmitry , Severinov Konstantin , Isaev Artem
Published: July 2023

Metagenomics is a powerful tool to study marine microbial communities. However, obtaining high-quality environmental DNA suitable for downstream sequencing applications is a challenging task. The quality and quantity of isolated DNA heavily depend on the choice of purification procedure and the type of sample. Selection of an appropriate DNA isolation method for a new type of material often entails a lengthy trial and error process. Further, each DNA purification approach introduces biases and thus affects the composition of the studied community. To account for these problems and biases, we systematically investigated efficiency of DNA purification from three types of samples (water, sea sediment, and digestive tract of a model invertebrateMagallana gigas) with eight commercially available microbial DNA isolation kits. For each kit-sample combination we measured the quantity of purified DNA, extent of DNA fragmentation, the presence of PCR-inhibiting contaminants, admixture of eukaryotic DNA, alpha-diversity, and reproducibility of the resulting community composition based on 16S rRNA amplicons sequencing. Additionally, we determined a “kitome”, e.g., a set of contaminating taxa inherent for each type of purification kit used. The resulting matrix of evaluated parameters allows one to select the best DNA purification procedure for a given type of sample.
cloudrnaSPAdes: Isoform assembly using bulk barcoded RNA sequencing data
Authors: Meleshko Dmitry , Prjbelski Andrey D. , Raiko Mikhail , Tomescu Alexandru I. , Tilgner Hagen , Hajirasouliha Iman
Published: July 2023

Motivation

Recent advancements in long-read RNA sequencing have enabled the examination of full-length isoforms, previously uncaptured by short-read sequencing methods. An alternative powerful method for studying isoforms is through the use of barcoded short-read RNA reads, for which a barcode indicates whether two short-reads arise from the same molecule or not. Such techniques included the 10x Genomics linked-read based SParse Isoform Sequencing (SPIso-seq), as well as Loop-Seq, or Tell-Seq. Some applications, such as novel-isoform discovery, require very high coverage. Obtaining high coverage using long reads can be difficult, making barcoded RNA-seq data a valuable alternative for this task. However, most annotation pipelines are not able to work with a set of short reads instead of a single transcript, also not able to work with coverage gaps within a molecule if any. In order to overcome this challenge, we present an RNA-seq assembler allowing the determination of the expressed isoform per barcode.

Results

In this paper, we present cloudrnaSPAdes, a tool for assembling full-length isoforms from barcoded RNA-seq linked-read data in a reference-free fashion. Evaluating it on simulated and real human data, we found that cloudrnaSPAdes accurately assembles isoforms, even for genes with high isoform diversity.

Availability

cloudrnaSPAdes is a feature release of a SPAdes assembler and available athttps://cab.spbu.ru/software/cloudrnaspades/.

Contact

dmm2017@med.cornell.edu
“You can change your life through sports”: Physical activity interventions to improve the health and wellbeing of adults experiencing homelessness: a mixed methods systematic review
Authors: Dawes Jo , Rogans-Watson Raphael , Broderick Julie
Published: July 2023

Objectives

Systematically synthesise evidence of physical activity interventions for people experiencing homelessness (PEH).

Design

Mixed-methods systematic review.

Data sources

EMBASE, Web of Science, CINAHL, PubMed (MEDLINE), PsycINFO, SPORTDiscus, and Cochrane Library, searched from inception to October 2022.

Eligibility Criteria

PICO framework: Population (quantitative and qualitative studies of PEH from high-income countries); Intervention (physical activity, any setting); Comparison (with/ without comparator); Outcome (any health/wellbeing-related outcome).

Results

3,614 records screened, generating 17 reports [16 studies, 11 qualitative and 5 quantitative (1 RCT, 3 quasi-experimental, 1 analytical cross-sectional)] from UK, USA, Denmark and Australia, including 539 participants (501 PEH, 38 staff). Interventions: soccer (n= 6), group exercise [indoor (n=3), outdoor (n=5)] and individual activities (n=2). Risk of bias assessed using JBI critical appraisal tools. Mixed methods synthesis identified physical and mental health benefits. Qualitative evidence highlighted benefits carried into wider life, challenges participating and positive impact on addiction. Qualitative and quantitative evidence was aligned for the mental health benefits of outdoor exercise and increase in physical activity from indoor group exercise. Quantitative evidence suggested improved bone health and blood lipid markers.

Conclusion

Diverse interventions were identified with soccer predominating. Qualitative evidence suggested physical activity can benefit health and wellbeing with positive translation to wider daily life. There was some positive quantitative evidence, although most was inconclusive. Evidence suggests a tentative recommendation for physical activity interventions for PEH, however a limitation is that results may not be transferable outside high-income countries. More high-quality research is required to determine effectiveness and optimal programme design.

What is already known?

People experiencing homelessness suffer a disproportionally higher burden of physical and mental health conditions than housed populations.

Regular physical activity can address many health conditions prevalent amongst people experiencing homelessness.

What are the new findings?

There is evidence of a variety of physical activity interventions that have been designed and provided to engage people experiencing homelessness (for example: soccer, outdoor and indoor group activities, and individual activities).

The synthesis of qualitative and quantitative evidence suggests that physical activity can benefit the mental and physical health of people experiencing homelessness with positive translation of benefits to wider life.
Rapid disassembly and Piwi-independent reassembly ofDrosophilapiRNA cluster heterochromatin following acute heat shock
Authors: Rice Nicholas , Ho Samantha , Weng Zhiping , Theurkauf William E.
Published: July 2023

Environmental stress activates transposons and is proposed to generate genetic diversity that facilitates adaptive evolution. piRNAs guide germline transposon silencing, but the impact of stress on the piRNA pathway is not well understood. InDrosophila,the Rhino-Deadlock-Cuff complex (RDC) drives transcription of clusters composed of nested transposon fragments, generating precursors that are processed into mature piRNAs in the cytoplasm. We show that acute heat shock triggers rapid, reversable, loss of RDC localization and cluster transcript expression with coordinate changes in the cytoplasmic processing machinery. Maternal piRNAs bound to Piwi are proposed to guide Rhino localization to clusters during early embryogenesis. However, RDC re-localization after heat shock is accelerated inpiwimutants and delayed inthoc7mutants, which disrupt piRNA precursor binding to THO complex, and we show that maternally deposited piRNAs are dispensable for RDC localization to the major 42AB cluster. Cluster specification is reconsidered in light of these findings.
TheAcinetobacter baumanniivirulence factor Omp33 is important for tolerance to benzalkonium chloride
Authors: Naidu Varsha , Shah Bhumika S. , Hassan Karl A. , Paulsen Ian T.
Published: July 2023

Benzalkonium chloride (BAC) is widely used in many disinfectant solutions in clinical settings to eradicate potential bacterial pathogens, such asAcinetobacter baumannii. We sought to investigate the transcriptomic response of a drug resistantA. baumanniiisolate, AB5075-UW, on exposure to a sub-inhibitory concentration of BAC. Our transcriptomic analysis found that BAC caused an increase in the expression of genes associated with protein synthesis, such as translation initiation factors, ribosomal proteins and tRNA synthetases. It also induced the expression of genes associated with energy production and central carbon metabolism. We also observed increased expression of peptidoglycan and rod shape determining genes, which may provide increased mechanical strength to withstand osmotic challenges posed by compounds such as BAC. The most highly expressed genes under BAC stress include those that encode the RND efflux pump AdeABC and theA. baumanniiporin Omp33. Mutants ofadeABCand its regulator genesadeRShad a higher susceptibility to BAC. Disruption of the gene encoding Omp33 also resulted in higher susceptibility to BAC, and complementation of the mutant withomp33together with a 450bp upstream region restored tolerance to BAC to parental strain levels (AB5075-UW). Site directed mutagenesis of amino acids associated with Omp33 periplasmic turn (T1), which folds into the lumen of the porin and blocks the channel, suggests that Omp33 may act to prevent entry of BAC into the cell. In previous studies, Omp33 has been described as an important virulence factor inA. baumannii.The results presented in this study describe a novel role for Omp33 in BAC tolerance and reveal thatA. baumanniitolerates BAC stress through a combination of mechanisms.
Apical annuli are specialised sites of post-invasion secretion of dense granules inToxoplasma
Authors: Chelaghma Sara , Ke Huiling , Barylyuk Konstantin , Krueger Thomas , Koreny Ludek , Waller Ross F.
Published: July 2023

Apicomplexans are ubiquitous intracellular parasites of animals. These parasites use a programmed sequence of secretory events to find, invade, and then reengineer their host cells to enable parasite growth and proliferation. The secretory organelles micronemes and rhoptries mediate the first steps of invasion. Both secrete their contents through the apical complex which provides an apical opening in the parasite’s elaborate inner membrane complex (IMC) — an extensive subpellicular system of flattened membrane cisternae and proteinaceous meshwork that otherwise limits access of the cytoplasm to the plasma membrane for material exchange with the cell exterior. After invasion, a second secretion programme drives host cell remodelling and occurs from dense granules. The site(s) of dense granule exocytosis, however, has been unknown. InToxoplasma gondii, small subapical annular structures that are embedded in the IMC have been observed, but the role or significance of these apical annuli to plasma membrane function has also been unknown. Here, we determined that integral membrane proteins of the plasma membrane occur specifically at these apical annular sites, that these proteins include SNARE proteins, and that the apical annuli are sites of vesicle fusion and exocytosis. Specifically, we show that dense granules require these structures for the secretion of their cargo proteins. When secretion is perturbed at the apical annuli, parasite growth is strongly impaired. The apical annuli, therefore, represent a second type of IMC-embedded structure to the apical complex that is specialised for protein secretion, and reveal that inToxoplasmathere is a physical separation of the processes of pre- and post-invasion secretion that mediate host-parasite interactions.