bluuebunny/crossref_metadata_2025 huggingface dataset:
Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes
Authors: Lim Joe J. , Diener Christian , Wilson James , Valenzuela Jacob J. , Baliga Nitin S. , Gibbons Sean M.
Published: May 2022

Longitudinal sampling of the stool has yielded important insights into the ecological dynamics of the human gut microbiome. However, due to practical limitations, the most densely sampled time series from the human gut are collected at a frequency of about once per day, while the population doubling times for gut commensals are on the order of minutes-to-hours. Despite this, much of the prior work on human gut microbiome time series modeling has, implicitly or explicitly, assumed that day-to-day fluctuations in taxon abundances are related to population growth or death rates, which is likely not the case. Here, we propose an alternative model of the human gut as a flow-through ecosystem at a dynamical steady state, where population dynamics occur internally and the bacterial population sizes measured in a bolus of stool represent an endpoint of these internal dynamics. We formalize this idea as stochastic logistic growth of a population in a system held at a semi-constant flow rate. We show how this model provides a path toward estimating the growth phases of gut bacterial populationsin situ. We validate our model predictions using anin vitro Escherichia coligrowth experiment. Finally, we show how this method can be applied to densely-sampled human stool metagenomic time series data. Consistent with our model, stool donors with slower defecation rates tended to harbor a larger proportion of taxa in later growth phases, while faster defecation rates were associated with more taxa in earlier growth phases. We discuss how these growth phase estimates may be used to better inform metabolic modeling in flow-through ecosystems, like animal guts or industrial bioreactors.
Turnover and replication analysis by isotope labeling (TRAIL) reveals the influence of tissue context on protein and organelle lifetimes
Authors: Hasper John , Welle Kevin , Hryhorenko Jennifer , Ghaemmaghami Sina , Buchwalter Abigail
Published: May 2022

The lifespans of proteins can range from minutes to years within mammalian tissues. Protein lifespan is relevant to organismal aging, as long-lived proteins can accrue damage over time. It is unclear how protein lifetime is shaped by tissue context, where both cell division and proteolytic degradation contribute to protein turnover. Here, we develop turnover and replicationanalysis by15N isotope labeling (TRAIL) to quantify both protein and cell lifetimes with high precision and no toxicity over a 32-day labeling period across 4 mammalian tissues. We report that cell division promotes non-selective protein turnover in proliferative tissues, while physicochemical features such as hydrophobicity, charge, and intrinsic disorder exert a significant influence on protein turnover only in non-proliferative tissues. Protein lifetimes vary non-randomly across tissues after correcting for differences in cell division rate. Multiprotein complexes such as the ribosome have highly consistent lifetimes across tissues, while mitochondria, peroxisomes, and lipid droplets have variable lifetimes. These data indicate that cell turnover, sequence-encoded features, and other environmental factors modulate protein lifespanin vivo. In the future, TRAIL can be used to explore how environment, aging, and disease affect tissue homeostasis.
Mutually exclusive spectral biclustering and its applications in cancer subtyping
Authors: Liu Fengrong , Yang Yaning , Xu Xu Steven , Yuan Min
Published: May 2022

Many soft biclustering algorithms have been developed and applied to various biological and biomedical data analyses. However, until now, few mutually exclusive (hard) biclustering algorithms have been proposed although they can be extremely useful for identify disease or molecular subtypes based on genomic or transcriptomic data. We considered the biclustering problem of expression matrices as a bipartite graph partitioning problem and developed a novel biclustering algorithm, MESBC, based on Dhillon’s spectral method to detect mutually exclusive biclusters. MESBC simultaneously detects relevant features (genes) and corresponding subgroups, and therefore automatically uses the signature features for each subtype to perform the clustering, improving the clustering performance. MESBC could accurately detect the pre-specified biclusters in simulations, and the identified biclusters were highly consistent with the true labels. Particularly, in setting with high noise, MESBC outperformed existing NMF and Dhillon’s method and provided markedly better accuracy. Analysis of two TCGA datasets (LUAD and BRAC cohorts) revealed that MESBC provided similar or more accurate prognostication (i.e., smaller p value) for overall survival in patients with breast and lung cancer, respectively, compared to the existing, gold-standard subtypes for breast (PAM50) and lung cancer (integrative clustering). In the TCGA lung cancer patients, MESBC detected two clinically relevant, rare subtypes that other biclustering or integrative clustering algorithms could not detect. These findings validated our hypothesis that MESBC could improve molecular subtyping in cancer patients and potentially facilitate better individual patient management, risk stratification, patient selection, therapeutic assignments, as well as better understanding gene signatures and molecular pathways for development of novel therapeutic agents.
An evolutionary perspective on the origin, conservation and binding partner acquisition of tankyrases
Authors: Sowa Sven T. , Bosetti Chiara , Galera-Prat Albert , Johnson Mark S. , Lehtiö Lari
Published: May 2022

Tankyrases are poly-ADP-ribosyltransferases that regulate many crucial and diverse cellular processes in humans such as Wnt signaling, telomere homeostasis, mitotic spindle formation and glucose metabolism. While tankyrases are present in most animals, functional differences across species exist. In this work we confirm the widespread distribution of tankyrases throughout the branches of multicellular animal life and identified the single-celled choanoflagellates as earliest origin of tankyrases. We further show that sequence and structural aspects of TNKSs are well conserved even between highly diverged species. We also experimentally characterized an anciently diverged tankyrase homolog from the sponge Amphimedon queenslandica and show that the basic functional aspects, such as poly-ADP-ribosylation activity and interaction with the canonical tankyrase binding peptide motif, are conserved. Conversely, the presence of tankyrase binding motifs in orthologs of confirmed interaction partners vary greatly between species, indicating that tankyrases have different sets of interaction partners depending on the animal lineage. Overall, our analysis suggests a remarkable degree of conservation for tankyrases, although their regulatory functions in cells have likely changed considerably throughout evolution.
Culture Associated DNA Methylation Changes Impact on Cellular Function of Human Intestinal Organoids
Authors: Edgar Rachel D , Perrone Francesca , Foster April R , Payne Felicity , Lewis Sophia , Nayak Komal M , Kraiczy Judith , Cenier Aurélie , Torrente Franco , Salvestrini Camilla , Heuschkel Robert , Hensel Kai O , Harris Rebecca , Jones D. Leanne , Zerbino Daniel R , Zilbauer Matthias
Published: May 2022

Background & Aims

Human intestinal epithelial organoids (IEO) are a powerful tool to model major aspects of intestinal development, health and diseases, as patient derived cultures retain many features found in-vivo. A necessary aspect of the organoid model is the requirement to expand cultures in-vitro through several rounds of passaging. This is of concern, as the passaging of cells has been shown to affect cell morphology, ploidy, and function. In this study, we address concerns around long term passaging of IEO to better characterise and define effects on cell morphology and function.

Methods

Here we have analysed 173 human IEO from two sampling sites, terminal ileum and sigmoid colon and examined the effect of culture duration on DNA methylation (DNAm), gene expression and cellular function including their response to proinflammatory cytokines and in-vitro cell differentiation.

Results

Our analyses revealed a major effect of culture duration on DNAm, leading to significant changes at 61,337 loci representing approximately 8% of all CpGs tested. Although global cellular functions such as gut segment-specific gene expression remained stable, a subset of methylation changes correlated with altered gene expression at baseline as well as in response to inflammatory cytokine exposure and in-vitro differentiation. Importantly, epigenetic changes were found to be enriched in genomic regions associated with colonic cancer and distant to the site of replication indicating similarities to malignant transformation.

Conclusions

Our study reveals culture-associated epigenetic, transcriptomic and functional changes in human mucosa derived IEO and highlights the importance of considering passage number as a potentially confounding factor.

Synopsis

This work describes cell culture induced changes to DNA methylation, gene expression and cellular function in human IEO. Globally organoids lost DNA methylation with time in culture while DNA methylation also became generally more variable. This work suggests a shifted epigenetic profile in organoids cultured long-term.
Molecular Aggregation Induced Photoacoustics for NIR-II in vivo Imaging
Authors: Chang Zong , Liu Liangjian , Liu Chenchen , Zhao Shubi , Chen Jiaqi , Zhang Wenxin , Wang Xiao , Liu Chengbo , Xie Xiaojiang , Sun Qinchao
Published: May 2022

Molecular aggregation induced photo-properties alteration has been found to play a crucial role in the light induced processes, such as aggregation induced emission (AIE) and J aggregation induced dramatic absorption red shift. The light induced acoustic process (photoacoustic) is also considered to be one of the most essential characters of the light absorbing molecules. However, to the best of our knowledge, the molecular aggregation induced photoacoustic effect (MAIPA) has never been reported. Herein, we report the first MAIPA effect for which the PA intensity is dominated by the molecular aggregation, rather than by absorbance as usual concerned. Molecular aggregation induces a strong electronic coupling effect, resulting in significant absorption suppression from the individual state to highly aggregated state (around 5 molecules aggregated). However, the corresponding PA efficiency was found to be about 2-orders of magnitude greater for the latter. A well-behaved linear correlation between the molecular aggregation level and MAIPA effect was observed. The surprisingly significant MAIPA effect was realized via novel NIR-II squaraine-benzothiopyrylium dyes. Excellent photophysical properties of the novel NIR-II dyes were achieved, such as large absorption extinction coefficient and high photostability. Thanks to the relatively narrow FWHM and the high PA efficiency of SQN2@PMAOPEG and ZC825@BSA, in vivo multiplex PA imaging was demonstrated for tumor tissue and macrophage cells, blood and lymphoid vessels.
Highly efficient genome editing in barley using novel LbCas12a variants and impact of sgRNA architecture
Authors: Lawrenson Tom , Hinchliffe Alison , Forner Macarena , Harwood Wendy
Published: May 2022

We report the first successful, high efficiency use of LbCas12a in barley and describe the development and application of two novel Cas12a variants. In total we compared five coding sequence (CDS) variants including the two novel ones and two guide architectures over 5 different target genes using twenty different guides. We found large differences in editing efficiencies between the different CDS versions (0-87%) and guide architectures (0-70%) and show our two novel CDS versions massively outperform the others on test in this species. We show heritability of mutations generated. Our findings highlight the importance of optimising CRISPR systems for individual species and are likely to aid the use of LbCas12a in other monocot species.
Caregivers’ perception of risk for malaria, helminth infection and malaria-helminth co-infection among children living in urban and rural settings of Senegal: a qualitative study
Authors: Afolabi Muhammed O. , Sougou Ndèye Mareme , Diaw Aminata , Sow Doudou , Manga Isaac A. , Mbaye Ibrahima , Greenwood Brian , Ndiaye Jean Louis A.
Published: May 2022

Malaria parasites and worms frequently co-exist in children living in low-and middle-income countries where existing vertical control programmes for the control of these two conditions are not operating at optimal levels. This gap necessitates the development and implementation of strategic interventions to achieve effective control and eventual elimination of these co-infections. Central to the successful implementation of any intervention is its acceptance and uptake by caregivers whose perception about the risk for malaria-helminth co-infection has been little documented. Therefore, we conducted a qualitative study to understand the caregivers’ perspectives about the risk as well as the behavioural and social risk factors promoting malaria-helminth co-infection among pre-school and school-aged children living in endemic rural and urban communities in Senegal. In June and December 2021, we conducted individual and group interviews, and participant observations, among 100 primary caregivers of children recruited from villages in southeast Senegal and among leaders and teachers of Koranic schools in western Senegal. Our findings showed that a majority of the study participants in the two settings demonstrated a high level of perception of risk for malaria and acceptable awareness about handwashing practices, but had misconceptions that malaria-helminth co-infection was due to a combination of excessive consumption of sugary food and mosquito bites. Our observations revealed many factors in the house structures, toilet practices and handwashing with ashes and sands, which the caregivers did not consider as risks for malaria-helminth co-infections. These findings underscore the need to promote caregivers’ awareness about the existence and risk of malaria-helminth co-infection in children. This approach would assist in addressing the caregivers’ misconceptions about the occurrence of the co-infection and could enhance their uptake of the strategic interventions targeted at achieving control and subsequent elimination of malaria and helminth co-infection.
Assessment of oxidative stress markers in elderly patients with SARS-CoV-2 infection and potential prognostic implications. An observational study
Authors: Vazquez-Agra Nestor , Marques-Afonso Ana-Teresa , Cruces-Sande Anton , Novo-Veleiro Ignacio , Pose-Reino Antonio , Mendez-Alvarez Estefania , Soto-Otero Ramon , Hermida-Ameijeiras Alvaro
Published: May 2022

The aim of the study was to evaluate the correlation of plasma levels of thiobarbituric acid reactive substances (TBARS) and reduced thiols with morbidity, mortality and immune response in SARS-CoV-2 infection. This was an observational study that included inpatients with SARS-CoV-2 infection greater than 65 years old. Individuals were followed up until 12 months after hospital discharge. Demographic, clinical and laboratory variables were collected. Plasma levels of TBARS and reduced thiols were quantified as a measure of lipid and protein oxidation, respectively. Events of interest (fatal and non-fatal) were quantified at hospital discharge, third, sixth and twelfth-month post-discharge. The outcomes were differences in oxidative stress markers between groups of interest and time to a negative RT-qPCR and to significant anti-SARS-CoV-2 IgM titers. There were 61 patients (57% women) with a mean age of 83 years old. Patients with higher levels of TBARS and lower levels of reduced thiols had more risk of fatal and non-fatal events between admission and the first 12 months post-discharge. The presence of any event (fatal or non-fatal) at the end of the first 12 months post-discharge was correlated with TBARS levels, anti-SARS-CoV-2 IgM titers, lactate dehydrogenase, platelet count and neutrophil and lymphocyte count. We found a correlation between plasma reduced thiols and time to achieve significant anti-SARS-CoV-2 IgM titers. Assessment of some parameters related to oxidative stress could help to identify groups of patients with a higher risk of morbidity and mortality during and after SARS-CoV-2 infection.
Adherence Monitoring Methods to Measure Virological Failure in People Living with HIV on Long-Term Antiretroviral Therapy in Uganda
Authors: Okoboi Stephen , Musaazi Joseph , King Rachel , Lippman Sheri A. , Kambugu Andrew , Mujugira Andrew , Izudi Jonathan , Parkes-Ratanshi Rosalind , Kiragga Agnes N. , Castelnuovo Barbara
Published: May 2022

Appointment keeping and self-report within 7-day or and 30-days recall periods are non-objective measures of antiretroviral treatment (ART) adherence. We assessed incidence of virological failure (VF), predictive performance and associations of these adherence measures with VF among adults on long-term ART. Data for persons initiated on ART between April 2004 and April 2005, enrolled in a long-term ART cohort at 10-years on ART (baseline) and followed until December 2021 was analyzed. VF was defined as two consecutives viral loads ≥1000 copies/ml at least within 3-months after enhanced adherence counselling. We estimated VF incidence using Kaplan-Meier and Cox-proportional hazards regression for associations between each adherence measure (analyzed as time-dependent annual values) and VF. The predictive performance of appointment keeping and self-reporting for identifying VF was assessed using receiver operating characteristic curves and reported as area under the curve (AUC). We included 900 of 1,000 participants without VF at baseline: median age was 47 years (Interquartile range: 41-51), 60% were women and 88% were virally suppressed. ART adherence was ≥95% for all three adherence measures. Twenty-one VF cases were observed with an incidence rate of 4.37 per 1000 person-years and incidence risk of 2.4% (95% CI: 1.6%-3.7%) over the 5-years of follow-up. Only 30-day self-report measure was associated with lower risk of VF, adjusted hazard ratio (aHR)=0.14, 95% CI:0.05–0.37). Baseline CD4 count ≥200cells/ml was associated with lower VF for all adherence measures. The 30-day self-report measure demonstrated the highest predictive performance for VF (AUC=0.751) compared to appointment keeping (AUC=0.674), and 7-day self-report (AUC=0.687). The incidence of virological failure in this study cohort was low. Whilst 30-day self-report was predictive, appointment keeping and 7-day self-reported adherence measures had low predictive performance in identifying VF. Viral load monitoring remains the gold standard for adherence monitoring and confirming HIV treatment response.
Human Mobility and Infection from Covid-19 in the Osaka Metropolitan Area
Authors: Kato Haruka , Takizawa Atsushi
Published: May 2022

Controlling human mobility is thought to be an effective measure to prevent the spread of the COVID-19 pandemic. This study aims to clarify the human mobility types that impacted the number of COVID-19 cases during the medium-term COVID-19 pandemic in the Osaka metropolitan area. The method used in this study was analysis of the statistical relationship between human mobility changes and the total number of COVID-19 cases after two weeks. In conclusion, the results indicate that it is essential to control the human mobility of groceries/pharmacies to less than 0% and that of parks to more than -20%. The most significant finding for urban sustainability is that urban transit was not found to be a source of infection. Hence governments in cities around the world may be able to encourage communities to return to transit mobility, if they are able to follow the kind of hygiene processes conducted in Osaka.
Beneficial influence of single-stage posterior surgery for the treatment of lumbar brucella spondylitis combined with spondylolisthesis
Authors: Zhang Yao , Zhao Chang-song , Chen Jia-min , Zhang Qiang
Published: May 2022

We aimed to evaluate the clinical efficacy of the single-stage posterior surgical treatment for patients of lumbar brucella spondylitis combined with spondylolisthesis. In this study, we performed a retrospective analysis of 16 patients with lumbar brucellosis spondylitis combined with spondylolisthesis from January 2015 to January 2019. All patients underwent single-stage posterior lumbar debridement, reduction, interbody fusion, and instrumentation. Preoperative and postoperative of the visual analog scale (VAS), the Japanese orthopedic association scores (JOA), the Oswestry disability index (ODI), erythrocyte sedimentation rate (ESR), and C-reactive protein (CRP) were compared. In addition, the spondylolisthesis reduction rate, reduction loss rate, interbody fusion rate, and complication rate were recorded. VAS, JOA, ODI, ESR, and CRP were conducted with repeated analysis of variance data at different follow-ups. The postoperative follow-up was 12 to 36 months, with an average of (25.0±8.1) months. VAS, JOA, ODI, ESR, and CRP were significantly better at two-week and one-year follow-up than preoperative results (P=0.000, respectively). In addition, one year after the operation, VAS, JOA, ODI, ESR, and CRP showed a significant improvement (P=0.000, respectively). The average spondylolisthesis reduction in two weeks after operation was (91.2±6.7) %, and the median reduction loss rate in one year after operation was 8.0 (5.0,9.8) %. At the last follow-up, all patients achieved interbody fusion, no loosening and fracture of instrumentation were found, and no recurrence happened. Single-stage posterior operation for lumbar debridement, reduction, interbody fusion, and instrumentation is beneficial for treating lumbar brucellosis spondylitis combined with spondylolisthesis. Furthermore, the reconstruction of spinal stability may relieve pain, heal lesions, and improve patients’ living.
Modeling ecological communities when composition is manipulated experimentally
Authors: Skwara Abigail , Lemos-Costa Paula , Miller Zachary R. , Allesina Stefano
Published: May 2022

In an experimental setting, the composition of ecological communities can be manipulated directly. Starting from a pool of n species, one can co-culture species in different combinations, spanning mono-cultures, pairs of species, and all the way up to the full pool. Here we advance methods aimed at inferring species interactions from data sets reporting the density attained by species in a variety of sub-communities formed from the same pool.

First, we introduce a fast and robust algorithm to estimate parameters for simple statistical models describing these data, which can be combined with likelihood maximization approaches. Second, we derive from consumer-resource dynamics statistical models with few parameters, which can be applied to study systems where only a small fraction of the potential sub-communities have been observed. Third, we show how a Weighted Least Squares (WLS) framework can be used to account for the fact that species abundances often display a strong relationship between means and variances.

To illustrate our approach, we analyze data sets spanning plants, bacteria, phytoplankton, as well as simulations, recovering a good fit to the data and demonstrating the ability to predict experiments out-of-sample.

We greatly extend the applicability of recently proposed methods, opening the door for the analysis of larger pools of species.
Computationally efficient mechanism discovery for cell invasion with uncertainty quantification
Authors: VandenHeuvel Daniel J. , Drovandi Christopher , Simpson Matthew J.
Published: May 2022

Parameter estimation for mathematical models of biological processes is often difficult and depends significantly on the quality and quantity of available data. We introduce an efficient frame-work using Gaussian processes to discover mechanisms underlying delay, migration, and proliferation in a cell invasion experiment. Gaussian processes are leveraged with bootstrapping to provide uncertainty quantification for the mechanisms that drive the invasion process. Our frame-work is efficient, parallelisable, and can be applied to other biological problems. We illustrate our methods using a canonical scratch assay experiment, demonstrating how simply we can explore different functional forms and develop and test hypotheses about underlying mechanisms, such as whether delay is present. All code and data to reproduce this work are available athttps://github.com/DanielVandH/EquationLearning.jl.

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Author summary

In this work we introduce uncertainty quantification into equation learning methods, such as physics-informed and biologically-informed neural networks. Our framework is computationally efficient and applicable to problems with unknown nonlinear mechanisms that we wish to learn from experiments where only sparse noisy data are available. We demonstrate our methods on a canonical scratch assay experiment from cell biology and show the underlying mechanisms can be learned, providing confidence intervals for functional forms and for solutions to partial differential equation models believed to describe the experiment.
Haploidy-linked cell proliferation defects limit larval growth in Zebrafish
Authors: Yaguchi Kan , Saito Daiki , Menon Triveni , Matsura Akira , Hosono Miyu , Mizutani Takeomi , Kotani Tomoya , Nair Sreelaja , Uehara Ryota
Published: May 2022

Haploid larvae in non-mammalian vertebrates are lethal with characteristic organ growth retardation collectively called “haploid syndrome.” In contrast to mammals whose haploid intolerance is attributed to imprinting misregulation, the cellular principle of haploidy-linked defects in non-mammalian vertebrates remains unknown. Here, we investigated cellular defects that disrupt the ontogeny of gynogenetic haploid zebrafish larvae. Unlike diploid control, haploid larvae manifested unscheduled cell death at the organogenesis stage, attributed to haploidy-linked p53 upregulation. Moreover, we found that haploid larvae specifically suffered the gradual aggravation of mitotic spindle monopolarization during 1-3 days post fertilization, causing spindle assembly checkpoint-mediated mitotic arrest throughout the entire body. High-resolution imaging revealed that this mitotic defect accompanied the haploidy-linked centrosome loss occurring concomitantly with the gradual decrease in larval cell size. Either resolution of mitotic arrest or depletion of p53 partially improved organ growth in haploid larvae. Based on these results, we propose that haploidy-linked mitotic defects and cell death are parts of critical cellular causes shared among vertebrates that limit the larval growth in the haploid state, contributing to an evolutionary constraint on allowable ploidy status in the vertebrate life cycle.
DirectMS1Quant: ultrafast quantitative proteomics with MS/MS-free mass spectrometry
Authors: Ivanov Mark V. , Bubis Julia A. , Gorshkov Vladimir , Tarasova Irina A. , Levitsky Lev I. , Solovyeva Elizaveta M. , Lipatova Anastasiya V. , Kjeldsen Frank , Gorshkov Mikhail V.
Published: May 2022

Recently, we presented the DirectMS1 method of ultrafast proteome-wide analysis based on minute-long LC gradients and MS1-only mass spectra acquisition. Currently, the method provides the depth of human cell proteome coverage of 2500 proteins at 1% false discovery rate (FDR) when using 5-min LC gradients and 7.3 min runtime in total. While the standard MS/MS approaches provide 4000 to 5000 protein identifications within a couple of hours of instrumentation time, we advocate here that the higher number of identified proteins does not always translate into better quantitation quality of the proteome analysis. To further elaborate on this issue we performed one-by-one comparison of quantitation results obtained using DirectMS1 with three popular MS/MS-based quantitation methods: label-free quantification (LFQ), tandem mass tag (TMT), both based on data dependent acquisition (DDA), and data independent acquisition (DIA). For the comparison we performed a series of proteome-wide analysis of well-characterized (ground truth) and biological relevant samples, including a mix of UPS1 proteins spiked at different concentrations into E. coli digest used as a background and a set of glioblastoma cell lines. MS1-only data was analyzed using a novel quantitation workflow called DirectMS1Quant developed in this work. The results obtained in this study demonstrated comparable quantitation efficiency of 5 min DirectMS1 with both TMT and DIA methods utilizing 10 to 20-fold longer instrumentation time.
Miro GTPase domains regulate assembly of the mitochondrial motor-adaptor complex
Authors: Davis Kayla , Basu Himanish , Shurberg Ethan , Schwarz Thomas L.
Published: May 2022

Mitochondrial transport relies on a motor-adaptor complex containing Miro1, a mitochondrial outer membrane protein with two GTPase domains, as well as TRAK1/2, kinesin-1, and dynein. Using a peroxisome-directed Miro1, we quantified the ability of GTPase mutations to influence peroxisomal recruitment of complex components. Miro1 whose N-GTPase is locked in the GDP-state doesn’t recruit TRAK1/2, kinesin or P135 to peroxisomes whereas the GTP-state does. Miro1 C-GTPase mutations have little influence on complex recruitment. Though Miro2 is thought to support mitochondrial motility, peroxisome-directed Miro2 did not recruit the other complex components regardless of the state of its GTPase domains. Neurons expressing peroxisomal Miro1 with the GTP-state form of the N-GTPase had markedly increased peroxisomal transport to growth cones while the GDP-state caused their retention in the soma. Thus, the N-GTPase of Miro1 is critical for regulating Miro1’s interaction with the other components of the motor-adaptor complex and thereby for regulating mitochondrial motility.

A Miro-containing complex mediates mitochondrial motility. Relocalizing Miro1 and 2 to peroxisomes and systematically manipulating each GTPase domain of Miro revealed the importance of the N-terminal GTPase domain of Miro1 for governing interaction with TRAK proteins, motors, and transport.
Changes of oscillatory and aperiodic neuronal activity in working memory following anaesthesia: a prospective observational study
Authors: Lendner Janna D. , Harler Ulrich , Daume Jonathan , Engel Andreas K. , Zöllner Christian , Schneider Till R. , Fischer Marlene
Published: May 2022

Background

Anaesthesia and surgery can lead to cognitive decline, especially in the elderly. However, to date, the neurophysiological underpinnings of perioperative cognitive decline remain unknown.

Methods

We included male patients, who were 60 years or older scheduled for elective radical prostatectomy under general anaesthesia. We obtained neuropsychological (NP) tests as well as a visual match-to-sample working memory (WM) task with concomitant 62-channel scalp electroencephalography (EEG) before and after surgery.

Results

A total number of 26 patients completed neuropsychological assessments and EEG pre- and postoperatively. Behavioural performance declined in the neuropsychological assessment after anaesthesia (total recall; t-tests: t25 = -3.25, Bonferroni-corrected p = 0.015 d = -0.902), while WM performance showed a dissociation between match and mis-match accuracy (rmANOVA: match*session F1,25 = 3.866, p = 0.060). Distinct EEG signatures tracked behavioural performance: Better performance in the NP assessment was correlated with an increase of non-oscillatory (aperiodic) activity, reflecting increased cortical activity (cluster permutation tests: total recall r = 0.66, p = 0.029, learning slope r = 0.66, p = 0.015), while WM accuracy was tracked by distinct temporally-structured oscillatory theta/alpha (7 – 9 Hz), low beta (14 – 18 Hz) and high beta/gamma (34 – 38 Hz) activity (cluster permutation tests: matches: p < 0.001, mis-matches: p = 0.022).

Conclusions

Oscillatory and non-oscillatory (aperiodic) activity in perioperative scalp EEG recordings track distinct features of perioperative cognition. Aperiodic activity provides a novel electrophysiological biomarker to identify patients at risk for developing perioperative neurocognitive decline.
Impact of different mutations on Kelch13 protein levels, ART resistance and fitness cost inPlasmodium falciparumparasites
Authors: Behrens Hannah M. , Schmidt Sabine , Peigney Domitille , Sabitzki Ricarda , Henshall Isabelle , May Jürgen , Maïga-Ascofaré Oumou , Spielmann Tobias
Published: May 2022

Reduced susceptibility to ART, the first-line treatment against malaria, is common in South East Asia (SEA). It is caused by point mutations, mostly inkelch13(k13) but also in other genes, likeupb1. K13 and its compartment neighbors (KICs), including UBP1, are involved in endocytosis of host cell cytosol. We tested 135 mutations in KICs but none conferred ART resistance. Double mutations ofk13C580Y withk13R539T ork13C580Y withubp1R3138H, did also not increase resistance. In contrast,k13C580Y parasites subjected to consecutive RSAs did, but thek13sequence was not altered. Using isogenic parasites with differentk13mutations, we found correlations between K13 protein amount, resistance and fitness cost. Titration of K13 and KIC7 indicated that the cellular levels of these proteins determined resistance through the rate of endocytosis. While fitness cost ofk13mutations correlated with ART resistance,ubp1R3138H caused a disproportionately higher fitness cost.

Significance

ART resistance is only a partial resistance with a proportion of ring stages surviving physiological ART levels. The correlation of resistance with fitness cost in isogenic lines indicates that fitness cost likely prevents resistance levels permitting survival of all ring stages under physiological ART concentrations. We also found no indication that double mutations ink13, including the two most common resistance mutations in SEA, or with non-k13genes, are a threat to lead to higher resistance. However, repeated ART exposure increased resistance by mechanisms not alteringk13gene sequence, indicating changes in the background of these parasites. The disproportionally high fitness cost ofubp1R3138H may explain whykicmutations affecting resistance are rare and highlights the unique property of K13 to influence endocytosis only in ring stages.
Integrating opportunistic and structured non-invasive surveys with spatial capture-recapture models to map connectivity of the Pyrenean brown bear population
Authors: Kervellec Maëlis , Milleret Cyril , Vanpé Cécile , Quenette Pierre-Yves , Sentilles Jérôme , Palazón Santiago , Jordana Ivan Afonso , Jato Ramón , Elósegui Irurtia Miguel Mari , Gimenez Olivier
Published: May 2022

Connectivity, in the sense of the persistence of movements between habitat patches, is key to maintain endangered populations and has to be evaluated in management plans. In practice, connectivity is difficult to quantify especially for rare and elusive species. Here, we use spatial capture-recapture (SCR) models with an ecological detection distance to identify barriers to movement. We focused on the transnational critically endangered Pyrenean brown bear (Ursus arctos) population, which is distributed over Spain, France and Andorra and is divided into two main cores areas following translocations. We integrate structured monitoring from camera traps and hair snags with opportunistic data gathered after depredation events. While structured monitoring focuses on areas of regular bear presence, the integration of opportunistic data allows us to obtain information in a wider range of habitat, which is especially important for ecological inference. By estimating a resistance parameter from encounter data, we show that the road network impedes movements, leading to smaller home ranges with increasing road density. Although the quantitative effect of roads is context-dependent (i.e. varying according to landscape configuration), our model predicts that a brown bear with a home range located in an area with relatively high road density (8.29km/km2) has a home range size reduced by 1.4-fold for males and 1.6-fold for females compared to a brown bear with a home range located in an area with low road density (1.38km/km2). When assessing connectivity, spatial capture-recapture modeling offers an alternative to the use of experts’ opinion when telemetry data are not available.
Single particle tracking with compressive sensing using progressive refinement method on sparse recovery (spt-PRIS)
Authors: Yi Xiyu , Shrestha Rebika , McDonald Torin , Chen De , Bhatia Harsh , Pascucci Valerio , Turbyville Thomas , Bremer Peer-Timo
Published: May 2022

Single particle tracking (SPT) is an indispensable tool for scientific studies. However, SPT for datasets with a high density of particles is still challenging, especially for the study of particle interactions where the point spread functions (PSFs) are overlapping. In this study, we present spt-PRIS, a new SPT solution where we apply compressive sensing to SPT by integrating the progressive refinement method on sparse recovery (PRIS) into the framework of the state-of-the-art SPT algorithm (uTrack). We systematically characterized and validated spt-PRIS performance using simulations, applied it to the experimental data of membrane-bound KRAS4b proteins in either 2-lipid or 8-lipid membrane supported lipid bilayers (SLB), and compared the results to the conventional method (uTrack). Our results show that spt-PRIS is effective for SPT when the data contains overlapping PSFs and provides unprecedented information about KRAS4b subpopulations. spt-PRIS is helpful for a broad range of scientific studies where precise and fast high-density localization is beneficial. spt-PRIS is also flexible for extensions for multi-species, multi-multi-channel, and multi-dimensional SPT methods with the generalization of PRIS reconstruction schemes.
Distinct population and single-neuron selectivity for executive and episodic processing in human dorsal posterior cingulate
Authors: Aponik-Gremillion Lyndsey , Chen Yvonne Y. , Bartoli Eleonora , Koslov Seth R. , Rey Hernan G. , Weiner Kevin S. , Yoshor Daniel , Hayden Benjamin Y. , Sheth Sameer A. , Foster Brett L.
Published: May 2022

Posterior cingulate cortex (PCC) is an enigmatic region implicated in psychiatric and neurological disease, yet its role in cognition remains unclear. Human studies link PCC to episodic memory and default mode network (DMN), while findings from the non-human primate emphasize executive processes more associated with the cognitive control network (CCN) in humans. We hypothesized this difference reflects an important functional division between dorsal (executive) and ventral (episodic) PCC. To test this, we utilized human intracranial recordings of population and single unit activity targeting dorsal PCC during an alternated executive/episodic processing task. Dorsal PCC population responses were significantly enhanced for executive, compared to episodic, task conditions, consistent with the CCN. Single unit recordings, however, revealed four distinct functional types with unique executive (CCN) or episodic (DMN) response profiles. Our findings provide critical electrophysiological data from human PCC, bridging incongruent views within and across species, furthering our understanding of PCC function.
Exogenous DNA upregulates DUOX2 expression and function in human pancreatic cancer cells by activating the cGAS-STING signaling pathway
Authors: Wang Stephen L. , Wu Yongzhong , Konaté Mariam , Lu Jiamo , Antony Smitha , Meitzler Jennifer L. , Jiang Guojian , Dahan Iris , Juhasz Agnes , Diebold Becky , Roy Krishnendu , Doroshow James H.
Published: May 2022

Pro-inflammatory cytokines upregulate the expression of the H2O2-producing NADPH oxidase dual oxidase 2 (DUOX2) which, when elevated, adversely affects survival from pancreatic ductal adenocarcinoma (PDAC). Because the cGAS-STING pathway is known to initiate pro-inflammatory cytokine expression following uptake of exogenous DNA, we examined whether activation of cGAS-STING could play a role in the generation of reactive oxygen species by PDAC cells. Here, we found that a variety of exogenous DNA species markedly increased the production of cGAMP, the phosphorylation of TBK1 and IRF3, and the translocation of phosphorylated IRF3 into the nucleus, leading to a significant, IRF3-dependent enhancement of DUOX2 expression, and a significant flux of H2O2 in PDAC cells. However, unlike the canonical cGAS-STING pathway, DNA-related DUOX2 upregulation was not mediated by NF-κB; and although exogenous IFN-β significantly increased Stat1/2-associated DUOX2 expression, intracellular IFN-β signaling that followed cGAMP or DNA exposure did not itself increase DUOX2 levels. Finally, DUOX2 upregulation subsequent to cGAS-STING activation was accompanied by the enhanced, normoxic expression of HIF-1α as well as DNA double strand cleavage, suggesting that cGAS-STING signaling may support the development of an oxidative, pro-angiogenic microenvironment that could contribute to the inflammation-related genetic instability of pancreatic cancer.
Bioengineering multifunctional extracellular vesicles for targeted delivery of biologics to T cells
Authors: Stranford Devin M. , Simons Lacy M. , Berman Katherine E. , Cheng Luyi , Lucks Julius B. , Hultquist Judd F. , Leonard Joshua N.
Published: May 2022

Genetically modifying T cells can enable applications ranging from cancer immunotherapy to HIV treatment, yet delivery of T cell-targeted therapeutics remains challenging. Extracellular vesicles (EVs) are nanoscale particles secreted by all cells that naturally encapsulate and transfer proteins and nucleic acids, making them an attractive and clinically-relevant platform for engineering biocompatible delivery vehicles. We report a suite of technologies for genetically engineering cells to produce multifunctional EV vehicles—without employing chemical modifications that complicate biomanufacturing. We display high affinity targeting domains on the EV surface to achieve specific, efficient binding to T cells, identify a protein tag to confer active cargo loading into EVs, and display fusogenic glycoproteins to increase EV uptake and fusion with recipient cells. We demonstrate integration of these technologies by delivering Cas9-sgRNA complexes to edit primary human T cells. These approaches could enable targeting vesicles to a range of cells for the efficient delivery of cargo.
The history and organization of the Workshop on Population and Speciation Genomics
Authors: Barth Julia MI , Handley Scott , Kintzl Daniel , Leonard Guy , Malinsky Milan , Matschiner Michael , Meyer Britta S , Salzburger Walter , Stefka Jan , Trucchi Emiliano
Published: May 2022

With the advent of high-throughput genome sequencing, bioinformatics training has become essential for research in evolutionary biology and related fields. However, individual research groups are often not in the position to teach students about the most up-to-date methodology in the field. To fill this gap, extended bioinformatics courses have been developed by various institutions and provide intense training over the course of two or more weeks. Here, we describe our experience with the organization of a course in one of the longest-running extended bioinformatics series of work-shops, the Evomics Workshop on Population and Speciation Genomics that takes place biennially in the UNESCO world heritage town of Český Krumlov, Czech Republic. We list the key ingredients that make this workshop successful in our view, and describe the routine for workshop organization that we have optimized over the years. We report the results of a survey conducted among past workshop participants that quantifies measures of effective teaching and provide examples of how the workshop setting has led to the cross-fertilisation of ideas and ultimately scientific progress. We expect that our account may be useful for other groups aiming to set up their own extended bioinformatics courses.
TGFβ treatment alters the scleral fibroblast migratory response to cyclic strain in an ERK-dependent manner
Authors: Mozzer Ann , Pitha Ian
Published: May 2022

Purpose

Myofibroblasts are associated with scleral remodeling in myopia and glaucoma. We showed reduced myofibroblast alignment with topographic cues in sclera can be modeled by cyclic strain exposure of aligned myofibroblasts in vitro. Here, we characterize the scleral myofibroblast response to cyclic mechanical strain.

Methods

Human peripapillary scleral (PPS) fibroblasts were cultured on topographically aligned grooves to promote cell alignment, exposed to TGFβ (2 ng/ml) in the presence of vehicle or kinase inhibitors, and exposed to uniaxial strain (1 Hz, 5%, 12-24 hours). Alignment with grooves was determined at baseline, immediately following strain, and 24 hours after strain cessation with 0° being completely aligned and 90° being perpendicular to grooves. A wound healing assay was developed to investigate further fibroblast migration across topographic cues. Transcriptional profiling of myofibroblasts with or without strain was performed by RT-PCR and pERK, pSMAD2, and pSMAD3 levels were measured by immunoblot.

Results

Pre-strain alignment (6.2±1.5°) was reduced after strain (21.7±5.3°, p<0.0001) and restored 24 hours after cessation (9.5±2.6°). ERK, FAK, and ALK5 inhibition preserved alignment following strain; however, alignment reduction was not inhibited by ROCK, YAP, or SMAD3 inhibition. TGFβ-induced myofibroblast markers were reduced by strain. While TGFβ-induced phosphorylation of ERK and SMAD2 was unaffected by strain, SMAD3 phosphorylation was reduced (p=0.0004). Wound healing across grooves was enhanced by ROCK and SMAD3 inhibition but not ERK or TGFβR1 inhibition.

Conclusions

Strain-induced myofibroblast migration across topographic confinement is ERK dependent and associated with pSMAD3 inhibition. These results provide insight into potential mechanisms of pathologic scleral remodeling.

Precis

Glaucomatous scleral remodeling is driven by cellular activity. Here we find that scleral myofibroblasts have an exaggerated response to mechanical strain that is ERK dependent, associated with pSMAD3 inhibition and mitigated TGFβ signaling.
Time series transcriptome analysis uncovers regulatory networks and a role for the circadian clock in theDrosophila melanogasterfemale’s response to Sex Peptide
Authors: Delbare Sofie Y.N. , Venkatraman Sara , Scuderi Kate , Wells Martin T. , Wolfner Mariana F. , Basu Sumanta , Clark Andrew G.
Published: May 2022

Sex Peptide, a seminal fluid protein ofD. melanogastermales, has been described as driving a virgin-to-mated switch in females, through eliciting an array of responses, including increased egg laying, activity and food intake and a decreased re-mating rate. While it is known that Sex Peptide achieves this, at least in part, by altering neuronal signaling in females, the identity of key molecular regulators that act downstream of Sex Peptide is not known. Here, we used a high-resolution time series RNA-sequencing dataset of female heads at 10 time points within the first 24 hours after mating to investigate the genetic architecture, at the gene- and exon-level, of the female’s response to Sex Peptide. We find that Sex Peptide is not essential to trigger a virgin-to-mated transcriptional switch, which involves changes in a metabolic gene regulatory network. However, Sex Peptide is needed to maintain and diversify metabolic changes and to trigger changes in a neuronal gene regulatory network. We further find that Sex Peptide might interact with the female’s circadian clock to orchestrate transcriptional changes across different regulatory networks. That a male seminal fluid protein can alter a female’s rhythmic gene expression has implications for our understanding of both reproductive and circadian behaviors.