bluuebunny/crossref_metadata_2025 huggingface dataset:
Rho GTPase Activating Protein 15 (ARHGAP15) increases cancer risk in patients with diverticular disease
Authors: Lehrer Steven , Rheinstein Peter H.
Published: November 2022

Introduction

Patients with diverticular disease who have colorectal histopathology, normal or abnormal, have increased risk of overall incident cancer. To determine whether the cancer risk might have a genetic basis, we performed a Genome Wide Association Study (GWAS) with data from UK Biobank.

Methods

We used PLINK 2, a whole-genome association analysis toolset, to analyze the UKB chromosome files. To identify cases, we used ICD10 code K57.3, diverticular disease of large intestine without perforation or abscess. We selected subjects younger than 45, since genetic forms of disease tend to manifest in younger patients.

Results

GWAS summary (Manhattan) plot of the meta-analysis association statistics, highlighting one susceptibility locus, Rho GTPase Activating Protein 15 (ARHGAP15), with genome wide significance for diverticulosis.

Conclusion

We conclude that ARHGAP15 could be responsible for the association of diverticular disease and cancer.
Study the combination of brain MRI imaging and other datatypes to improve Alzheimer’s disease diagnosis
Authors: Stubblefield Jonathan , Kronberger Alan , Causey Jason , Qualls Jake , Fowler Jennifer , Zeng Kaiman , Walker Karl , Huang Xiuzhen ,   the Alzheimer’s Disease Neuroimaging Initiative
Published: November 2022

Alzheimer’s Disease (AD) is a degenerative brain disease and is the most common cause of dementia. Despite being a common disease, AD is poorly understood. Current medical treatments for AD are aimed at slowing the progression of the disease. So early detection of AD is important to intervene at an early stage of the disease. In recent years, by using machine learning predictive algorithms, assisted clinic diagnosis has received great attention due to its success of machine learning advances in the domains of computer vision. In this study, we have combined brain MRI imaging features and the features of other datatypes, and adopted various models, including XGBoost, logistic regression, and k-Nearest Neighbors, to improve AD diagnosis. We evaluated the models on the benchmark dataset of Alzheimer’s Disease Neuroimaging Initiative. Experiment results show that the logistic regression model is the top performer in terms of evaluation metrics of precision, recall, and F1-score. The prediction of the models could provide valuable information for diagnosis and prognosis of patients with suspected Alzheimer’s disease. The XGBoost model achieves a comparable performance and has the potential to serve as a valuable diagnostic tool for patients with suspected AD with its self-validation by rediscovering previously known associations with AD.
Between-Occupation Differences in Work-Related COVID-19 Mitigation Strategies over Time: Analysis of the Virus Watch Cohort in England and Wales
Authors: Beale Sarah , Yavlinsky Alexei , Hoskins Susan , Nguyen Vincent , Byrne Thomas , Fong Wing Lam Erica , Kovar Jana , Van Tongeren Martie , Aldridge Robert W , Hayward Andrew
Published: November 2022

Background

COVID-19 pandemic mitigations have had a profound impact on workplaces, however, multisectoral comparison of how work-related mitigations were applied across different phases of the pandemic are limited. This study aimed to investigate occupational differences in the usage of key work-related mitigations over time, and to investigate workers’ perceptions of these mitigations.

Methods

A survey covering the periods of late December 2020–February 2022 was developed and disseminated online to employed or self-employed participants in the Virus Watch study (n=6,279 respondents). Logistic regression was used to investigate occupation- and time-related differences in the usage of work-related mitigation methods. Responses regarding workers’ perceptions of mitigation methods were investigated descriptively using proportions.

Findings

Usage of work-related mitigation methods differed between occupations and over time, likely reflecting variation in job roles, workplace environments, legislation and guidance. Healthcare workers had the highest predicted probabilities for several mitigations, including frequent hand and surface hygiene (up to 0.61 [0.56, 0.66]), wearing face coverings (up to 0.80 [0.76, 0.84]), and employers providing face coverings for workers (0.96 [0.94, 0.98]) and other people on worksites (0.90 [0.87, 0.93]). There was a cross-occupational trend towards reduced mitigations during periods of less stringent national restrictions. The majority of workers across occupations (55-88%) agreed that most mitigations were reasonable and worthwhile; agreement was lower for physical distancing (39-44%).

Interpretation

While usage of work-related mitigations appeared to vary alongside stringency of national restrictions, agreement that most mitigations were reasonable and worthwhile remained substantial. Further investigation into the factors underlying between-occupational differences could assist pandemic planning and prevention of workplace COVID-19 transmission.
MACE prediction using high-dimensional machine learning and mechanistic interpretation: A longitudinal cohort study in US veterans
Authors: Dhaubhadel Sayera , Kolade Beauty , Ribeiro Ruy M. , Ganguly Kumkum , Hengartner Nicolas W. , Bhattacharya Tanmoy , Cohn Judith D. , Agarwal Khushbu , Cho Kelly , Costa Lauren , Ho Yuk-Lam , Murata Allison E. , Murata Glen H. , Vassy Jason L. , Posner Daniel C. , Gaziano J. Michael , Sun Yan V. , Wilson Peter W. , Madduri Ravi , Justice Amy C. , Tsao Phil , O’Donnell Christopher J. , Damrauer Scott , McMahon Benjamin H.
Published: November 2022

High dimensional predictive models of Major Adverse Cardiac Events (MACE), which includes heart attack (AMI), stroke, and death caused by cardiovascular disease (CVD), were built using four longitudinal cohorts of Veterans Administration (VA) patients created from VA medical records. We considered 247 variables / risk factors measured across 7.5 years for millions of patients in order to compare predictions for the first reported MACE event using six distinct modelling methodologies. The best-performing methodology varied across the four cohorts. Model coefficients related to disease pathophysiology and treatment were relatively constant across cohorts, while coefficients dependent upon the confounding variables of age and healthcare utilization varied considerably across cohorts. In particular, models trained on a retrospective case-control (Rcc) cohort (where controls are matched to cases by date of birth cohort and overall level of healthcare utilization) emphasize variables describing pathophysiology and treatment, while predictions based on the cohort of all active patients at the start of 2017 (C-17) rely much more on age and variables reflecting healthcare utilization. In consequence, directly using an Rcc-trained model to evaluate the C-17 cohort resulted in poor performance (C-statistic = 0.65). However, a simple reoptimization of model dependence on age, demographics, and five other variables improved the C-statistic to 0.74, nearly matching the 0.76 obtained on C-17 by a C-17-trained model. Dependence of MACE risk on biomarkers for hypertension, cholesterol, diabetes, body mass index, and renal function in our models was consistent with the literature. At the same time, including medications and procedures provided important indications of both disease severity and the level of treatment. More detailed study designs will be required to disentangle these effects.
Single-nucleus RNA velocity reveals synaptic and cell-cycle dysregulations missed by gene expression in neuropathologic Alzheimer disease
Authors: Adewale Quadri , Khan Ahmed F , Bennett David A , Iturria-Medina Yasser
Published: November 2022

To characterize the dynamic genetic and cellular differences in AD neuropathology, we apply the novel concept of RNA velocity to the study of single-nucleus RNA from the cortex of 60 subjects with varied levels of AD pathology. RNA velocity captures the rate of change of gene expression by comparing intronic and exonic sequence counts. We performed differential analyses to find the significant genes driving both cell-specific RNA velocity and expression differences in AD, extensively compared these two transcriptomic metrics, and clarified their associations with multiple neuropathologic traits. The results were cross-validated in an independent dataset.
Automated analysis of PD1 and PDL1 in lymph nodes and the microenvironment of transmissible tumors in Tasmanian devils
Authors: Russell Grace G , Palmieri Chiara , Darby Jocelyn , Morris Gary P. , Fountain-Jones Nicholas M. , Pye Ruth J. , Flies Andrew S.
Published: November 2022

The wild Tasmanian devil (Sarchophilus harrisii) population has suffered a devastating decline due to two clonal transmissible cancers. Devil facial tumor 1 (DFT1) was first observed in 1996, followed by a second genetically distinct transmissible tumor, devil facial tumor 2 (DFT2), in 2014. DFT1/2 frequently metastasize, with lymph nodes being common metastatic sites. Downregulation of MHC-I by DFT1 cells is a primary means of evading allograft immunity aimed at polymorphic MHC-I proteins. DFT2 cells constitutively express MHC-I, and MHC-I is upregulated on DFT1/2 cells by interferon gamma, suggesting other immune evasion mechanisms may contribute to overcoming allograft and anti-tumor immunity. Human clinical trials have demonstrated PD1/PDL1 blockade effectively treats patients showing increased expression of PD1 in tumor draining lymph nodes, and PDL1 on peritumoral immune cells and tumor cells. The effects of DFT1/2 on systemic immunity remain largely uncharacterized. This study applied the open-access software QuPath to develop a semiautomated pipeline for whole slide analysis of stained tissue sections to quantify PD1/PDL1 expression in devil lymph nodes. The QuPath protocol provided strong correlations to manual counting. PD-1 expression was approximately 10-fold higher than PD-L1 expression in lymph nodes and was primarily expressed in germinal centers, whereas PD-L1 expression was more widely distributed throughout the lymph nodes. The density of PD1 positive cells was increased in lymph nodes containing DFT2 metastases, compared to DFT1. This suggests PD1/PDL1 exploitation may contribute to the poorly immunogenic nature of transmissible tumors in some devils and could be targeted in therapeutic or prophylactic treatments.
Kinetic Model With Feedback Cycle for Age-Dependent Beta Amyloid Accumulation in Mice
Authors: Tyng Vivian , Kellman Michael E.
Published: November 2022

Amyloid beta (Aβ) is believed to play a key role in Alzheimer’s disease (AD), whose causes, progression, diagnosis, and treatment nonetheless remain poorly understood despite decades of research. Recent studies suggest that Aβ in its various forms participates in multiple mutual feedback loops (“vicious cycles”) including tauopathy, oxidative stress, inflammation, calcium dysregulation, excitotoxicity, and probably many others, eventually leading to neurodegeneration and cognitive decline. Here, we explore a simple kinetic model of a coupled feedback vicious cycle for Aβ buildup based on literature data for Tg2576 mice. The model is used to examine the efficacy of various hypothetical therapeutic approaches, either singly or in combination, to mitigate Aβ buildup. While our computational results support the possible efficacy of combination interventions, they also suggest caution, inasmuch as clear synergy is not found. This kinetic approach highlights the essential importance of a vicious cycle of positive feedbacks in a quantitative model.
Network analysis uncovers associations in the turnover of C1 molecules in a winter lake
Authors: Mondav Rhiannon , Martin Gaëtan , Peura Sari , Garcia Sarahi L
Published: November 2022

The generation and consumption of single carbon molecules (CO2and CH4) by aquatic microbial communities is an essential aspect of the global carbon budget. Organic carbon flow (warm sunlit regimes) is depicted as beginning at the surface with autochthonous fixation followed by biomass settling to sediments, CO2 respiration to the atmosphere, and outflow. We sought to broaden understanding of C1 cycling and consortia by examining the microbial community of a below-ice lake water column in which both input and output are likely disrupted due to ice cover. By analysing the microbial community composition and co-occurrence network of an ice-covered lake timeseries, we were able to identify potential consortia involved in C1 cycling. The network confirmed known associations supporting the efficacy of such analyses but also pointed to previously unknown potential associations. Further and contrary to typical organic carbon flow under warm sunlit regimes, we found support for upward flow of recently fixed carbon in cold low-light conditions under-ice in winter.
Targeting AAV vectors to the CNS viade novoengineered capsid-receptor interactions
Authors: Huang Qin , Chen Albert T. , Chan Ken Y. , Sorensen Hikari , Barry Andrew J. , Azari Bahar , Beddow Thomas , Zheng Qingxia , Zhao Binhui , Tobey Isabelle G. , Eid Fatma-Elzahraa , Chan Yujia A. , Deverman Benjamin E.
Published: November 2022

Viruses have evolved the ability to bind and enter cells through interactions with a wide variety of host cell macromolecules. Here, we screened for AAV capsids that bind two host cell proteins expressed on the mouse blood-brain barrier, LY6A or the related protein LY6C1. Introducing interactions with either protein target generated hundreds of capsids with dramatically enhanced central nervous system (CNS) tropisms. In contrast to the AAV-PHP.B capsid family, which interacts with LY6A and only exhibits its enhanced CNS tropism in a subset of mouse strains, the capsids that engage LY6C1 maintain their CNS tropism in BALB/cJ mice. Compared to conventionalin vivoscreens for CNS cell transducing capsids, a single round of protein target binding screening recovered significantly more capsids with enhanced performance that were validated in subsequentin vivoscreens. Moreover, the initial screening round generated reproducible and quantitative target binding data that enabled the efficient machine learning-guided generation of more diverse targetspecific capsids. This work demonstrates that AAV capsids can be directly targeted to specific proteins to generate potent gene delivery vectors with known mechanisms of action and predictable tropisms.
Polyploidy impacts population growth and competition with diploids: multigenerational experiments reveal key life history tradeoffs
Authors: Anneberg Thomas J. , O’Neill Elizabeth M. , Ashman Tia-Lynn , Turcotte Martin M.
Published: November 2022

Ecological theory predicts that early generation polyploids (“neopolyploids”) should quickly go extinct owing to the disadvantages of rarity and competition with their diploid progenitors. However, polyploids persist in natural habitats globally. This paradox has been addressed theoretically by recognizing that reproductive assurance of neopolyploids and niche differentiation can promote establishment. Despite this, the direct effects of polyploidy at the population level remain largely untested even though establishment is an intrinsically population-level process.

We conducted population-level experiments where investment in current and future growth was tracked in four lineage pairs of diploids and synthetic neopolyploids of the aquatic plantSpirodela polyrhiza. Population growth was evaluated with and without competition between diploids and neopolyploids across a range of nutrient treatments.

Although neopolyploid populations produce more biomass, they reach lower population sizes, and have reduced carrying capacities when growing alone or in competition across all nutrient treatments. Thus, contrary to individual-level studies, our population-level data suggest that neopolyploids are competitively inferior to diploids. Conversely, neopolyploid populations have greater investment in dormant propagule production than diploids.

Our results show that neopolyploid populations should not persist based on current growth dynamics, but high potential future growth may allow polyploids to establish in subsequent growing seasons.
Hereditary Fusion Genes Are Associated with the Inheritance of Acute Myeloid Leukemia
Authors: Ling Fei , Zhuo Degen
Published: November 2022

Fusion genes are thought to be somatic and cause cancer, including acute myeloid leukemia (AML). Validating highly-recurrent fusion genes in healthy samples compelled us to systematically study hereditary fusion genes (HFGs). Here, we used curated HFGs to analyze AML fusion genes, and we identified 243 HFGs associated with AML inheritance from 926 potential HFGs. Many HFGs were one-to-many and many-to-one fusions that augmented signals from environmental and genomic alterations and seemed to support the “two-hit” hypothesis. The most highly-recurrent HFGs were also observed in multiple myeloma and monozygotic twin datasets, suggesting that AML is a complex genetic disease. HFGs, as cancer genetic biomarkers, are the most basic foundations for future genetic and genomic studies.
Receptor Elimination by E3 Ubiquitin Ligase Recruitment (REULR): A Targeted Protein Degradation Toolbox
Authors: Siepe Dirk H. , Picton Lora K. , Garcia K. Christopher
Published: November 2022

In recent years, targeted protein degradation (TPD) of plasma membrane proteins by hijacking the ubiquitin proteasome system (UPS) or the lysosomal pathway have emerged as novel therapeutic avenues in drug development to address and inhibit canonically difficult targets. While TPD strategies have been successful to target cell surface receptors, these approaches are limited by the availability of suitable binders to generate heterobifunctional molecules. Here, we present the development of a nanobody (VHH) based degradation toolbox termed REULR (Receptor Elimination by E3 Ubiquitin Ligase Recruitment). We generated human and mouse cross-reactive nanobodies against 5 transmembrane PA-TM-RING type E3 Ubiquitin Ligases (RNF218, RNF130, RNF167, RNF43, ZNRF3) covering a broad range and selectivity of tissue expression with which we characterized expression in human and mouse cell lines and immune cells (PBMCs). We demonstrate that heterobifunctional REULR molecules can enforce transmembrane E3 ligase interaction with a variety of disease relevant target receptors (EGFR, EPOR, PD-1) by induced proximity resulting in effective membrane clearance of the target receptor at varying levels. In addition, we designed E3 Ligase self-degrading molecules, ‘fratricide’ REULRs (RNF128, RNF130, RENF167, RNF43, ZNRF3), that allow downregulation of one or several E3 Ligases from the cell surface and consequently modulate receptor signaling strength. REULR molecules represent a VHH-based, modular and versatile “mix and match” targeting strategy for facile modulation of cell surface proteins by induced proximity to transmembrane PA-TM-RING E3 ligases.
The evolution of antibiotic resistance is associated with collateral drug phenotypes inMycobacterium tuberculosis
Authors: Waller Natalie J.E. , Cheung Chen-Yi , Cook Gregory M. , McNeil Matthew B.
Published: November 2022

The increasing incidence of drug resistance inMycobacterium tuberculosishas diminished the efficacy of almost all available antibiotics, complicating efforts to combat the spread of this global health burden. Alongside the development of new drugs, optimised drug combinations are needed to improve treatment success and prevent the further spread of antibiotic resistance. Typically, antibiotic resistance leads to reduced sensitivity, yet in some cases the evolution of drug resistance can lead to enhanced sensitivity to unrelated drugs. This phenomenon of collateral sensitivity is largely unexplored inM. tuberculosisbut has the potential to identify alternative therapeutic strategies to combat drug-resistant strains that are unresponsive to current treatments. To investigate the collateral impacts of drug resistance inM. tuberculosis, we generated an isogenic collection of mono-resistant strains in a PC2-approved avirulent background ofM. tuberculosisagainst 23 structurally and functionally diverse antibiotics. Through drug susceptibility profiling, genomics, and evolutionary studies we provide evidence for the existence of collateral drug sensitivity inM. tuberculosis. In proof-of-concept studies, we demonstrate how collateral drug phenotypes can be targeted to select against and prevent the emergence of drug-resistant strains ofM. tuberculosis. This study highlights that the evolution of drug resistance inM. tuberculosisleads to collateral drug responses that can be exploited to design improved drug regimens.
A CRISPRi-based genetic resource to study essentialStaphylococcus aureusgenes
Authors: Reed Patricia , Sorg Moritz , Alwardt Dominik , Serra Lúcia , Veiga Helena , Schäper Simon , Pinho Mariana G.
Published: November 2022

We have optimized a CRISPR interference system to facilitate gene knockdown in the gram-positive bacterial pathogenStaphylococcus aureus.Our approach used a CRISPRi system derived fromStreptococcus pyogenes,which involves the co-expression of thedcas9gene encoding a catalytically inactive Cas9 protein and a customizable single guide RNA (sgRNA). In our system,dcas9is expressed from a single copy in the chromosome of methicillin resistantS. aureus(MRSA) strains COL or JE2, under the control of a tightly regulated promoter, inducible by anhydrotetracycline. The sgRNAs are expressed from a replicative plasmid under the control of a constitutively active promoter. This system enables efficient, inducible, knockdown of both essential and non-essential genes. Using this approach, we constructed the Lisbon CRISPRi Mutant Library (LCML) comprising 261 strains, in the JE2 background, containing sgRNAs targeting 200 essential genes/operons. This library facilitates the study of the function of essentialS. aureusgenes and is complementary to the Nebraska Transposon Mutant Library which consists of nearly 2000 strains, each carrying a transposon insertion within a non-essential gene. The availability of these two libraries will facilitate the study ofS. aureuspathogenesis and biology.

Abstract Importance

Staphylococcus aureusis an important clinical pathogen that causes a high number of antibiotic resistant infections. The study ofS. aureusbiology, and particularly of the function of essential proteins, is of particular importance to develop new approaches to combat this pathogen. We have optimized a CRISPRi system that allows efficient targeting of essentialS. aureusgenes. Furthermore, we have used that system to construct a library of 261 strains which allow the depletion of essential proteins encoded in 200 genes/operons. This library, which we have named Lisbon CRISPRi Mutant Library (LCML), should facilitate the study ofS. aureuspathogenesis and biology.
Identification of the EH CRISPR-Cas9 system on a metagenome and its application to genome engineering
Authors: Esquerra-Ruvira Belen , Baquedano Ignacio , Ruiz Raul , Fernandez Almudena , Montoliu Lluis , Mojica Francisco JM
Published: November 2022

Non-coding RNAs (crRNAs) produced from clustered regularly interspaced short palindromic repeats (CRISPR) loci, and CRISPR associated (Cas) proteins of the prokaryotic CRISPR-Cas systems, form complexes that interfere with the spread of transmissible genetic elements through Cas-catalysed cleavage of foreign genetic material matching the guide crRNA sequences. The easily programmable targeting of nucleic acids enabled by these ribonucleoproteins has facilitated the implementation of CRISPR-based molecular biology tools forin vivoandin vitromodification of DNA and RNA targets. Despite the diversity of DNA-targeting Cas nucleases so far identified, native and engineered derivatives of theStreptococcus pyogenesSpCas9 are the most used for genome engineering, at least in part due to its catalytic robustness and the requirement of an exceptionally short motif (5’-NGG-3’ PAM) flanking the target sequence. However, the large size of the SpCas9 variants impairs the delivery of the tool to eukaryotic cells and smaller alternatives are demanded. Here we identify in a metagenome a new CRISPR-Cas9 system associated with a smaller Cas9 protein (EHCas9) that targets DNA sequences flanked by 5’-NGG-3’ PAMs. We develop a simplified EHCas9 tool that specifically cleaves DNA targets and is functional for genome editing applications in prokaryotes and eukaryotic cells.
Propagation-based phase-contrast breast computed tomography: a visual grading assessment of the performance of photon-counting and flat-panel X-ray detectors
Authors: Giannotti Nicola , Taba Seyedamir Tavakoli , Gureyev Timur , Lewis Sarah , Brombal Luca , Longo Renata , Donato Sandro , Tromba Giuliana , Pena Lucia Arana , Hausermann Daniel , Hall Chris , Maksimenko Anton , Arhatari Benedicta , Nesterets Yakov , Brennan Patrick
Published: November 2022

Rationale and objectives

Breast cancer represents the leading cause of death from cancer in women worldwide. Early detection of breast tumours improves the prognosis and survival rate. Propagation-based phase-contrast computed tomography (PB-CT) is a technique that uses refraction and absorption of the X-ray to produce images for clinical applications. This study compared the performance of photon-counting and flat-panel X-ray detectors in PB-CT breast imaging using synchrotron radiation.

Materials and methods

Mastectomy specimens underwent PB-CT imaging using the Hamamatsu C10900D Flat Panel and PIXIRAD-8 CdTe single-photon-counting detectors. PB-CT images generated at different imaging conditions were compared to absorption-based CT (AB-CT) reference images acquired with the same detectors to investigate the image quality improvement delivered by PB-CT relative to AB-CT. The image quality of the different image sets was assessed by eleven readers in a visual grading characteristics (VGC) study.

Results

The intraclass correlation coefficient showed a moderate/good interobserver agreement for the image set analysed (ICC = 0.626, p = <0.001). The area under the curve showed that the image quality improvement in PB-CT images obtained by the PIXIRAD-8 CdTe single-photon-counting detector were consistently higher than the one for flat-panel Hamamatsu detector. The level of improvement in image quality was more substantial at lower radiation doses.

Conclusion

In this study, the PIXIRAD-8 photon-counting detector was associated with higher image quality scores at all tested radiation dose levels, which was likely a result of the combined effect of the absence of dark current noise and better spatial resolution, compared to the flat-panel detector.
Moderate to Vigorous Intensity Locomotor Training After Stroke: A Systematic Review and Meta-Analysis of Mean Effects and Individual Response Variability
Authors: Boyne Pierce , Miller Allison , Kubalak Owen , Mink Caroline , Reisman Darcy S. , Fulk George
Published: November 2022

Background and Purpose

This meta-analysis quantified mean effects of moderate-to-vigorous intensity locomotor training (LTmv) on walking outcomes in subacute and chronic stroke, and the magnitude of individual variability in LTmvresponse.

Methods

Databases were searched for randomized trials comparing LTmvwith no intervention, non-gait intervention or low-intensity gait training. Comfortable gait speed (CGS), fastest gait speed (FGS), 6-minute walk distance (6MWT), walking activity (steps/day) and adverse effect/event (AE) data were extracted. Pooled estimates were calculated for mean changes within and between groups, the relative risk of different AEs, and the standard deviation of individual response (SDIR) to LTmvversus control groups, stratified by study chronicity where possible.

Results

There were 19 eligible studies (total N=1,096); 14 in chronic stroke (N=839) and 5 in subacute stroke (N=257). Compared with control interventions, LTmvyielded significantly greater increases in CGS, FGS and 6MWT in both subacute and chronic stroke, with subacute studies showing significantly greater effect sizes for CGS, FGS and nearly 6MWT (p=0.054). In 4 studies reporting steps/day data, LTmvwas not significantly different from control interventions. In 14 studies reporting on AEs, there were no treatment-related serious AEs among 398 LTmvparticipants. SDIRestimates indicated significant individual response variability for CGS, nearly FGS (p=0.0501) and 6MWT.

Discussion and Conclusions

LTmvimproves mean walking capacity outcomes in subacute and chronic stroke and does not appear to have high risk of serious harm, but response magnitude varies between chronicity subgroups and individuals, and few studies have tested effects on daily walking activity or non-serious AEs.
Dlg5 and Cadherins are key to peripheral glia integrity
Authors: Mriga Das , Duo Cheng , Till Matzat , Vanessa J. Auld
Published: November 2022

Glial cells in the peripheral nerve wrap axons to insulate them and ensure efficient conduction of neuronal signals. In the myelin sheath, it is proposed that the autotypic tight junctions and adherens junctions form glia-glia complexes that stabilize the glia sheath in myelinating glia. Yet the role of adhesion junctions in non-myelinating glia of vertebrates or invertebrates has not been clearly established. Many components of adhering junctions contain PDZ (PSD-95, Dlg, ZO1) domains or are recruited to these junctions by PDZ binding motifs. To test for the role of PDZ domain proteins in glial sheath formation, we carried out an RNAi screen usingDrosophila melanogasterto knockdown each of the 66 predicted PDZ domain proteins in the peripheral glia. We identified six PDZ genes with potential roles in glial morphology, and further investigated Discs-large 5 (Dlg5), a scaffolding protein with no previously known function in glia. Knockdown of Dlg5 disrupts subperineurial glia (SPG) morphology, including gaps in the membrane that coincide with disruption of septate junction proteins. To further our investigation of Dlg5, we focused on cadherins and found both N-Cadherin and E-Cadherin are expressed throughout peripheral glia. Knockdown of E-Cadherin phenocopied the loss of Dlg5 leading to gaps in the SPG and septate junctions while only simultaneous loss of both N-Cadherins (NCad, and CadN2) had the same effect. The loss of all three Cadherins enhanced these phenotypes as did loss of Dlg5 when paired with cadherin knockdown. This leads to a model where Dlg5 plays a role in conjunction with cadherins in glial membrane stabilization and septate junction formation in the subperineurial glia.
Impaired HIV-specific T-cell responses in HIV andS. mansonicoinfected Ugandans
Authors: Obuku Andrew Ekii , Sharma Ashish , Rukundo Anjellina , Odong Matthew , Auma Betty , Serwanga Jennifer , Nkangi Ronald , Okello Joseph , Nakitto Zahara , Joloba Moses , Pantaleo Giuseppe , Kaleebu Pontiano , Sekaly Rafik
Published: November 2022

Fishing communities surrounding Lake Victoria in Uganda show an HIV-1 prevalence of 28% and incidence rates of 5%. More than 50% of the fishermen on the shores of Lake Victoria are infected withS. mansoni. Fishermen are more likely to die of AIDS related illness than farmers in the Lake Victoria region.

Using polychromatic flow cytometry and mesoscale discovery platform, HIV specific and non-specific responses were measured and compared within individuals when HIV andS. mansonicoinfected and after theS. mansoniwas cleared.

Sixty-two unique clusters of cells in the UMAP space were identified after stimulations with GAG PTE POOL-1 and GAG PTE POOL-2 independently. However, the frequency of only three clusters is significantly higher after S.mansoniclearance. In addition,S. mansoniinfection is associated with higher IL-9 and IL-10 and lower IL-15 in HIV andS. mansonicoinfected individuals. IL-9 concentration at enrolment visit predicts CD4 decline.

S. mansoniinfection negatively affects HIV specific and non-specific immune responses in HIV andS. mansonicoinfected individuals.
Synchro-PASEF allows precursor-specific fragment ion extraction and interference removal in data-independent acquisition
Authors: Skowronek Patricia , Krohs Florian , Lubeck Markus , Wallmann Georg , Itang Ericka , Koval Polina , Wahle Maria , Thielert Marvin , Meier Florian , Willems Sander , Raether Oliver , Mann Matthias
Published: November 2022

Data-independent acquisition (DIA) methods have become increasingly popular in mass spectrometry (MS)-based proteomics because they enable continuous acquisition of fragment spectra for all precursors simultaneously. However, these advantages come with the challenge of correctly reconstructing the precursor-fragment relationships in these highly convoluted spectra for reliable identification and quantification. Here we introduce a scan mode for the combination of trapped ion mobility spectrometry (TIMS) with parallel accumulation – serial fragmentation (PASEF) that seamlessly and continuously follows the natural shape of the ion cloud in ion mobility and peptide precursor mass dimensions. Termed synchro-PASEF, it increases the detected fragment ion current several-fold at sub-second cycle times. Consecutive quadrupole selection windows move synchronously through the mass and ion mobility range, defining precursor-quadrupole relationships. In this process, the quadrupole slices through the peptide precursors, which separates fragment ion signals of each precursor into adjacent synchro-PASEF scans. This precisely defines precursor – fragment relationships in ion mobility and mass dimensions and effectively deconvolutes the DIA fragment space. Importantly, the partitioned parts of the fragment ion transitions provide a further dimension of specificity via a lock and key mechanism. This is also advantageous for quantification, where signals from interfering precursors in the DIA selection window do not affect all partitions of the fragment ion, allowing to retain only the specific parts for quantification. Overall, we establish the defining features of synchro-PASEF and explore its potential for proteomic analyses.
History information emerges in the cortex during learning
Authors: Marmor Odeya , Helmchen Fritjof , Gilad Ariel
Published: November 2022

We learn from our experience but the underlying neuronal mechanisms incorporating past information to facilitate learning is relatively unknown. Specifically, which cortical areas encode history-related information and how is this information modulated across learning? To study the relationship between history and learning, we continuously imaged cortex-wide calcium dynamics as mice learn to use their whiskers to discriminate between two different textures. We mainly focused on comparing the same trial type with different history information, i.e., a different preceding trial. We found history information in barrel cortex (BC) during stimulus presentation. Importantly, history information in BC emerged only as the mouse learned the task. Next, we also found learning-dependent history information in rostrolateral (RL) association cortex that emerges before stimulus presentation, preceding activity in BC. History information was also found in other cortical areas and was not related to differences in body movements. Interestingly, a binary classifier could discriminate history information at the single trial level just as well as current information both in BC and RL. These findings suggest that past experience emerges in the cortex around the time of learning, starting from higher-order association area RL and propagating down (i.e., top-down projection) to lower-order BC where it can be integrated with incoming sensory information. This integration between the past and present may facilitate learning.
Predestined neutrophil heterogeneity in homeostasis varies in transcriptional and phenotypic response toCandida
Authors: Scherer Allison K. , Hopke Alex , Xu Shuying , Viens Adam , Alexander Natalie J. , Timmer Kyle D. , Archambault Dakota , Floyd Daniel , Atallah Natalie J. , Rhee Catherine , Cetinbas Murat , Scadden David T. , Irimia Daniel , Sykes David B. , Sadreyev Ruslan I. , Mansour Michael K.
Published: November 2022

Once perceived to be homogenous effector cells, neutrophils have since been shown to exhibit population heterogeneity. Here, we established an experimental model of clonal neutrophil heterogeneity using conditionally immortalized clonal granulocyte monocyte progenitors (GMPs) and their mature neutrophil progeny. Transcriptional and epigenetic profiling showed conserved genome-wide signatures of transcription and chromatin accessibility that were specific to individual GMP clones and their paired neutrophil progeny, suggesting that clone specificity is established as early as the GMP stage. Clone-specific genes in vital regulatory pathways were pre-programmed and exhibited delayed expression in the mature neutrophil stage. The clone-specific gene expression in the mature neutrophils paired to enhancer activation in their parental GMPs. To determine whether transcriptional heterogeneity predicted the response to fungal pathogens, neutrophil clones were functionally profiled. Clones demonstrated heterogeneous responses to fungal pathogensin vitroand revealed neutrophil subsets with evidence for tailored functional responses toCandida spp. as well as specific transcriptional and epigenetic patterns that may explain these differences. Together, this work establishes that heterogenous GMP and neutrophil compartments exist under homeostatic conditions and that these represent predefined clusters that are uniquely adapted to control invasive fungal pathogens.

Short Summary

Clonal neutrophil progenitors demonstrate heterogeneity in transcription and chromatin accessibility which may inform response to later fungal challenges.
Divergent outcomes of direct conspecific pathogen strain interaction and plant co-infection suggest consequences for disease dynamics
Authors: Bellah Hadjer , Seiler Nicolas F. , Croll Daniel
Published: November 2022

Plant diseases are often caused by co-infections of multiple pathogens with the potential to aggravate disease severity. In genetically diverse pathogen species, co-infections can also be caused by multiple strains of the same species. However, the outcome of such mixed infections by different conspecific genotypes is poorly understood. The interaction among pathogen strains with complex lifestyles outside and inside of the host are likely shaped by diverse traits including metabolic capacity and the ability to overcome host immune responses. To disentangle competitive outcomes among pathogen strains, we investigated the fungal wheat pathogenZymoseptoria tritici. The pathogen infects wheat leaves in complex strain assemblies and highly diverse populations persist between growing seasons. We investigated a set of 14 genetically different strains collected from the same field to assess both competitive outcomes under culture conditions and on the host. Growth kinetics of co-cultured strains significantly deviated from single strain expectations indicating competitive exclusion depending on the strain genotype. We found similarly complex outcomes of lesion development on plant leaves following co-infections by the same pairs of strains. While some pairings suppressed overall damage to the host, other combinations exceeded expectations of lesion development based on single strain outcomes. Strain competition outcomes in absence of the host were poor predictors of outcomes on the host suggesting that the interaction with the plant immune system adds significant complexity. Intraspecific co-infection dynamics likely make important contributions to disease severity and need to be integrated for a more complete understanding of host-pathogen dynamics in the environment.

Importance

Plants are often attacked by a multitude of pathogens simultaneously. Different pathogen species can either facilitate or constrain the colonization by other pathogen species. Hence, natural infections are often the outcome of complex interactions between pathogens. To what extent the simultaneous colonization of genetically different strains of the same pathogen species matters for disease outcomes remains largely unclear though. We assessed the outcome of interactions between strains of the fungal wheat pathogen Zymoseptoria tritici. In absence of the host, strains cultured in pairs were growing differently compared to strains cultured alone. When infecting wheat leaves either with single or pairs of strains, we found also highly variable outcomes. Importantly, interactions between strains outside of the host were only poorly explaining how strains would interact when on the host. This suggests that pathogen strains engage in complex interactions shaped by their environment. Understanding the nature of such interactions within pathogen species will improve our ability to manage crop plant infections in the wild.
Cooperatively Designed Aptamer-PROTACs for Spatioselective Degradation of Nucleocytoplasmic Shuttling Protein for Enhanced Combinational Therapy
Authors: Liu Ran , Liu Zheng , Chen Mohan , Xing Hang , Zhang Jingjing
Published: November 2022

Nucleocytoplasmic shuttling proteins (NSPs) has emerged as a promising class of therapeutic targets for many diseases including cancer. However, most reported NSPs-based therapies largely rely on small molecule inhibitors with limited efficacy and off-target effects. Proteolysis targeting chimera (PROTAC) represents a revolutionary inhibitory modality for targeted protein degradation with many advantages, including substoichiometric catalytic activity, improved selectivity, and high efficacy. However, the majority of reported PROTACs so far are still limited to the degradation of cytoplasmic proteins and lack of tumor-specific targeting. To realize the full potential of the PROTAC technology and broaden its applications for the degradation of NSPs, we herein report a conceptual approach for the design of a new archetype of PROTAC (denoted as PS-ApTCs) by introducing phosphorothioate-modified AS1411 aptamer to a ligand of the CRBN E3 ligase, realizing tumor-targeting and spatioselective degradation with improved efficacy. We have demonstrated that PS-ApTCs is capable of effectively degrading nucleolin in target cell membrane and cytoplasm but not in the nucleus, in a CRBN- and proteasome-dependent manner. In addition, PS-ApTCs exhibits superior antiproliferation, pro-apoptotic, and cell cycle arrest potencies. Importantly, we demonstrate for the first time that combination of PS-ApTCs-mediated nucleolin degradation with aptamer-drug conjugates-based chemotherapy can enable an AND-gated synergistic effect on tumor inhibition. Collectively, our results suggest that PS-ApTCs possess the ability to expand the PROTACs toolbox to even wider range of targets in subcellular localization and accelerate the discovery of new combinational therapeutic approaches.
Neofunctionalized carbonic anhydrases in the biosynthesis of neuroactive plant alkaloids
Authors: Nett Ryan S. , Dho Yaereen , Tsai Chun , Wonderlick Daria , Low Yun-Yee , Sattely Elizabeth S.
Published: November 2022

Plants synthesize numerous alkaloids that mimic animal neurotransmitters. The diversity of alkaloid structures is achieved through the generation and tailoring of unique carbon scaffolds. However, many neuroactive alkaloids belong to a scaffold class for which no biosynthetic route or enzyme catalyst is known. By studying highly coordinated, tissue-specific gene expression in plants that produce neuroactive Lycopodium alkaloids, we identified a new enzyme class for alkaloid biosynthesis: neofunctionalized α-carbonic anhydrases (CAHs). We show that three CAH-like (CAL) enzymes are involved in a cryptic biosynthetic route to a key bicyclic precursor of the Lycopodium alkaloids, and additionally, we describe a series of oxidative tailoring steps that generate the optimized acetylcholinesterase inhibition activity of huperzine A. Our findings suggest a broader involvement of CAL enzymes in specialized metabolism and provide an example for how successive scaffold tailoring steps can drive potency against a natural protein target of interest.
Cholinergic modulation supports dynamic switching of resting state networks through selective DMN suppression
Authors: Sanda Pavel , Hlinka Jaroslav , van den Berg Monica , Skoch Antonin , Bazhenov Maxim , Keliris Georgios A. , Krishnan Giri P.
Published: November 2022

Brain activity during the resting state is widely used to examine brain organization, cognition and alterations in disease states. While it is known that neuromodulation and the state of alertness impact resting-state activity, neural mechanisms behind such modulation of resting-state activity are unknown. In this work, we used a computational model to demonstrate that change in excitability and recurrent connections, due to cholinergic modulation, impacts resting-state activity. The results of such modulation in the model match closely with experimental work on direct cholinergic modulation of Default Mode Network (DMN) in rodents. We further extended our study to the human connectome derived from diffusion-weighted MRI. In human resting-state simulations, an increase in cholinergic input resulted in a brain-wide reduction of functional connectivity. Furthermore, selective cholinergic modulation of DMN closely captured experimentally observed transitions between the baseline resting state and states with suppressed DMN fluctuations associated with attention to external tasks. Our study thus provides insight into potential neural mechanisms for the effects of cholinergic neuromodulation on resting-state activity and its dynamics.
RNA-mediated double-strand break repair in human cells
Authors: Jeon Youngkyu , Ferrari Margherita Maria , Channagiri Tejasvi , Xu Penghao , Balachander Sathya , Park Vivian S. , Marsili Stefania , Pursell Zachary F. , Jonoska Nataša , Storici Francesca
Published: November 2022

Double-strand breaks (DSBs) in DNA are challenging lesions to repair. Human cells employ at least three DSB repair mechanisms, with a preference for non-homologous end joining (NHEJ) over homologous recombination (HR) and microhomology-mediated end joining (MMEJ)1,2. In contrast to HR, NHEJ and MMEJ do not utilize a DNA template molecule to recover damaged and/or lost nucleotides2. NHEJ directly ligates broken DNA ends, while MMEJ exploits the alignment of short microhomologies on the DSB sides and is associated with deletions of the sequence between the microhomologies3,4. It is unknown whether and to what extent a transcript RNA has a direct role in DSB-repair mechanisms in mammalian cells. Here, we show that both coding and non-coding transcript RNA facilitates DSB repair in a sequence-specific manner in human cells. Depending on its sequence complementarity with the broken DNA ends, the transcript RNA could promote the repair of a DSB or gap in its DNA gene via NHEJ or MMEJ, or mediate RNA-templated repair. The transcript RNA influences DSB repair by NHEJ and MMEJ even when the transcription level is low. The results demonstrate an unexpected role of transcript RNA in directing the way DSBs are repaired in human cells and maintaining genome stability.