bluuebunny/crossref_metadata_2025 huggingface dataset:
HAP-multitag, a PET and positive MRI contrast nanotracer for the longitudinal characterization of vascular calcifications in atherosclerosis
Authors: Pellico Juan , Fernández-Barahona Irene , Ruiz-Cabello Jesús , Gutiérrez Lucía , Sánchez-Guisado María J. , Aiestarán-Zelaia Irati , Martínez-Parra Lydia , Rodríguez Ignacio , Bentzon Jacob , Herranz Fernando
Published: October 2020

Vascular microcalcifications are associated with atherosclerosis plaque instability and, therefore, to increased mortality. Because of this key role, several imaging probes have been developed for theirin vivoidentification. Among them [18F]FNa is the gold standard, showing a large uptake in the whole skeleton. Here, we push the field towards the combined anatomical and functional early characterization of atherosclerosis. For that, we have developed HAP-multitag, a bisphosphonate-functionalized68Ga magnetic nanoparticle showing high affinity towards most common calcium salts present in microcalcifications, particularly hydroxyapatite. We characterized this interactionin vitroandin vivo, showing a massive uptake in the atherosclerotic lesion identified by PET and positive contrast MRI. In addition, this accumulation was found to be dependent on the calcification progression, with a maximum uptake in the microcalcification stage. These results confirmed the ability of HAP-multitag to identify vascular calcifications by PET/(T1)MRI during the vulnerable stages of the plaque progression.
TheThermosynechococcusgenus: wide environmental distribution, but a highly conserved genomic core
Authors: Prondzinsky A. Paulina , Berkemer Sarah J. , Ward Lewis M. , McGlynn Shawn E.
Published: October 2020

Cyanobacteria thrive in very diverse environments. However, questions remain about possible growth limitations in ancient environmental conditions. As a single genus, theThermosynechococcusare cosmopolitan and live in chemically diverse habitats. To understand the genetic basis for this, we compared the protein coding component ofThermosynechococcusgenomes. Supplementing the known genetic diversity ofThermosynechococcus, we report draft metagenome-assembled genomes of twoThermosynechococcusrecovered from ferrous carbonate hot springs in Japan. We find that as a genus,Thermosynechococcusis genomically conserved, having a small pan-genome with few accessory genes per individual strain and only 14 putative orthologous protein groups appearing in allThermosynechococcusbut not in any other cyanobacteria in our analysis. Furthermore, by comparing orthologous protein groups, including an analysis of genes encoding proteins with an iron related function (uptake, storage or utilization), no clear differences in genetic content, or adaptive mechanisms could be detected between genus members, despite the range of environments they inhabit. Overall, our results highlight a seemingly innate ability forThermosynechococcusto inhabit diverse habitats without having undergone substantial genomic adaptation to accommodate this. The finding ofThermosynechococcusin both hot and high iron environments without adaptation recognizable from the perspective of the proteome has implications for understanding the basis of thermophily within this clade, and also for understanding the possible genetic basis for high iron tolerance in cyanobacteria on early Earth. The conserved core genome may be indicative of an allopatric lifestyle – or reduced genetic complexity of hot spring habitats relative to other environments.
Self-activation of Wnt signaling in pre-granulosa cells is required for ovarian folliculogenesis
Authors: Habara Okiko , Logan Catriona Y. , Kanai-Azuma Masami , Nusse Roeland , Takase Hinako M.
Published: October 2020

In mammalian ovaries, immature oocytes are reserved in primordial follicles. Precise control of primordial follicle activation (PFA) is a prerequisite for proper reproduction. Although Wnt signaling is thought to be involved in folliculogenesis, the timing and function of Wnt activity remain unclear. Here we show that canonical Wnt signaling is pivotal for the differentiation of pre-granulosa cells (pre-GCs) and subsequent oocyte maturation during PFA. We identified severalWntligands expressed in pre-GCs that cell-autonomously function via canonical Wnt activity. Inhibition of Wnt ligand secretion from pre-GCs/GCs led to infertility due to impaired pre-GC differentiation, whereas constitutive stabilization of β-catenin induced thickening of the pre-GCs. Our data support a two-step model of PFA in which self-activation of Wnt signaling promotes the transition of pre-GCs to GCs, and mature GCs then support oocyte reawakening. We anticipate that application of Wnt inhibitors or activators in vitro will lead to improved fertility treatments.
Inferring spatially transient gene expression pattern from spatial transcriptomic studies
Authors: Kueckelhaus Jan , von Ehr Jasmin , Ravi Vidhya M. , Will Paulina , Joseph Kevin , Beck Juergen , Hofmann Ulrich G. , Delev Daniel , Schnell Oliver , Heiland Dieter Henrik
Published: October 2020

Spatial transcriptomic is a technology to provide deep transcriptomic profiling by preserving the spatial organization. Here, we present a framework for SPAtial Transcriptomic Analysis (SPATA,https://themilolab.github.io/SPATA), to provide a comprehensive characterization of spatially resolved gene expression, regional adaptation of transcriptional programs and transient dynamics along spatial trajectories.
The magnitude of airway remodelling is not altered by distinct allergic inflammatory responses in BALB/c vs C57BL/6 mice but matrix composition differs
Authors: Parkinson James E , Pearson Stella , Rückerl Dominik , Allen Judith E , Sutherland Tara E
Published: October 2020

Allergic airway inflammation is heterogenous with variability in immune phenotypes observed across asthmatic patients. Inflammation has been thought to directly contribute to airway remodelling in asthma, but clinical data suggests that neutralising type 2 cytokines does not necessarily alter disease pathogenesis. Here, we utilised C57BL/6 and BALB/c mice to investigate the development of allergic airway inflammation and remodelling. Exposure to an allergen cocktail for up to 8 weeks led to type 2 and type 17 inflammation, characterized by airway eosinophilia and neutrophilia and increased expression of chitinase-like proteins in both C75BL/6 and BALB/c mice. However, BALB/c mice developed much greater inflammatory responses than C57BL/6 mice, effects possibly explained by a failure to induce pathways that regulate and maintain T cell activation in C57BL/6 mice, as shown by whole lung RNA transcript analysis. Allergen administration resulted in a similar degree of airway remodelling between mouse strains but with differences in collagen subtype composition. Increased collagen III was observed around the airways of C57BL/6 but not BALB/c mice while allergen-induced loss of basement membrane collagen IV was only observed in BALB/c mice. This study highlights a model of type 2/type 17 airway inflammation in mice whereby development of airway remodelling can occur in both BALB/c and C57BL/6 mice despite differences in immune response dynamics between strains. Importantly, compositional changes in the ECM between genetic strains of mice may help us better understand the relationships between lung function, remodelling and airway inflammation.
Experience-dependent alteration of mnemonic representation in early visual cortex and intraparietal sulcus
Authors: Jia Ke , Li Ya , Gong Mengyuan , Huang Hui , Wang Yonghui , Li Sheng
Published: October 2020

The ability to discriminate between stimuli relies on a chain of neural operations associated with perception, memory and decision-making. Accumulating studies show learning-dependent plasticity in perception or decision-making, yet whether perceptual learning modifies mnemonic processing remains unclear. Here, we trained participants on an orientation discrimination task, while using fMRI and TMS to separately examine training-induced changes in working memory (WM) representation. Although fMRI decoding revealed orientation-specific neural patterns during delay period in early visual cortex (V1) before, but not after, training, neurodisruption of V1 during delay period led to behavioral deficit in both phases. In contrast, both fMRI decoding and disruptive effect of TMS showed that intraparietal sulcus (IPS) represent WM content after, but not before, training. These results suggest that sensory engagement for WM is relatively independent of training but the coding format may be altered, whereas the involvement of parietal area in WM depends on training.
DSTG: Deconvoluting Spatial Transcriptomics Data through Graph-based Artificial Intelligence
Authors: Su Jing , Song Qianqian
Published: October 2020

Recent development of spatial transcriptomics (ST) is capable of associating spatial information at different spots in the tissue section with RNA abundance of cells within each spot, which is particularly important to understand tissue cytoarchitectures and functions. However, for such ST data, since a spot is usually larger than an individual cell, gene expressions measured at each spot are from a mixture of cells with heterogenous cell types. Therefore, ST data at each spot needs to be disentangled so as to reveal the cell compositions at that spatial spot. In this study, we propose a novel method, named DSTG, to accurately deconvolute the observed gene expressions at each spot and recover its cell constitutions, thus achieve high-level segmentation and reveal spatial architecture of cellular heterogeneity within tissues. DSTG not only demonstrates superior performance on synthetic spatial data generated from different protocols, but also effectively identifies spatial compositions of cells in mouse cortex layer, hippocampus slice, and pancreatic tumor tissues. In conclusion, DSTG accurately uncovers the cell states and subpopulations based on spatial localization.
Improving power while controlling the false discovery rate when only a subset of peptides are relevant
Authors: Lin Andy , Plubell Deanna L. , Keich Uri , Noble William S.
Published: October 2020

The standard proteomics database search strategy involves searching spectra against a peptide database and estimating the false discovery rate (FDR) of the resulting set of peptide-spectrum matches. One assumption of this protocol is that all the peptides in the database are relevant to the hypothesis being investigated. However, in settings where researchers are interested in a subset of peptides, alternative search and FDR control strategies are needed. Recently, two methods were proposed to address this problem: subset-search and all-sub. We show that both methods fail to control the FDR. For subset-search, this failure is due to the presence of “neighbor” peptides, which are defined as irrelevant peptides with a similar precursor mass and fragmentation spectrum as a relevant peptide. Not considering neighbors compromises the FDR estimate because a spectrum generated by an irrelevant peptide can incorrectly match well to a relevant peptide. Therefore, we have developed a new method, “filter then subsetneighbor search” (FSNS), that accounts for neighbor peptides. We show evidence that FSNS properly controls the FDR when neighbors are present and that FSNS outperforms group-FDR, the only other method able to control the FDR relative to a subset of relevant peptides.
Deep learning model fitting for diffusion-relaxometry: a comparative study
Authors: Grussu Francesco , Battiston Marco , Palombo Marco , Schneider Torben , Gandini Wheeler-Kingshott Claudia A. M. , Alexander Daniel C.
Published: October 2020

Quantitative Magnetic Resonance Imaging (qMRI) signal model fitting is traditionally performed via non-linear least square (NLLS) estimation. NLLS is slow and its performance can be affected by the presence of different local minima in the fitting objective function. Recently, machine learning techniques, including deep neural networks (DNNs), have been proposed as robust alternatives to NLLS. Here we present a deep learning implementation of qMRI model fitting, which uses DNNs to perform the inversion of the forward signal model. We compare two DNN training strategies, based on two alternative definitions of the loss function, since at present it is not known which definition leads to the most accurate, precise and robust parameter estimation. In strategy 1 we define the loss as thel2-norm of tissue parameter prediction errors, while in strategy 2 as thel2-norm of MRI signal prediction errors. We compare the two approaches on synthetic and 3Tin vivosaturation inversion recovery (SIR) diffusion-weighted (DW) MRI data, using a model for joint diffusion-T1 mapping. Strategy 1 leads to lower tissue parameter root mean squared errors (RMSEs) when realistic noise distributions are considered (e.g. Rician vs Gaussian). However, strategy 2 offers lower signal reconstruction RMSE, and allows training to be performed on both synthetic and actualin vivoMRI measurements. In conclusion, both strategies are valid choices for DNN-based fitting. Strategy 2 is more practical, as it does not require pre-computation of reference tissue parameters, but may lead to worse parameter estimation.
Hippocampal replay of experience at real-world speeds
Authors: Denovellis Eric L. , Gillespie Anna K. , Coulter Michael E. , Sosa Marielena , Chung Jason E. , Eden Uri T. , Frank Loren M.
Published: October 2020

Representations related to past experiences play a critical role in memory and decision-making processes. The rat hippocampus expresses these types of representations during sharp-wave ripple (SWR) events, and previous work identified a minority of SWRs that contain “replay” of spatial trajectories at ~20x the movement speed of the animal. Efforts to understand replay typically make multiple assumptions about which events to examine and what sorts of representations constitute replay. We therefore lack a clear understanding of both the prevalence and the range of representational dynamics associated with replay. Here we develop a state space model that uses a combination of movement dynamics of different speeds to capture the spatial content and time evolution of replay during SWRs. Using this model, we find that the large majority of replay events contain spatially coherent, interpretable content. Furthermore, many events progress at real-world, rather than accelerated, movement speeds, consistent with actual experiences.
HOXA9 promotes MYC-mediated leukemogenesis by maintaining gene expression for multiple anti-apoptotic pathways
Authors: Miyamoto Ryo , Kanai Akinori , Okuda Hiroshi , Takahashi Satoshi , Matsui Hirotaka , Inaba Toshiya , Yokoyama Akihiko
Published: October 2020

HOXA9 is often highly expressed in leukemias. However, its precise roles in leukemogenesis remain elusive. Here, we show that HOXA9 maintains gene expression for multiple anti-apoptotic pathways to promote leukemogenesis. InMLL-rearranged leukemia, MLL fusion directly activates the expression of MYC and HOXA9. Combined expression of MYC and HOXA9 induced leukemia, whereas single gene transduction of either did not, indicating a synergy between MYC and HOXA9. HOXA9 sustained expression of the genes implicated to the hematopoietic precursor identity when expressed in hematopoietic precursors, but did not reactivate it once silenced. Among the HOXA9 target genes,BCL2andSOX4synergistically induced leukemia withMYC. Not only BCL2, but also SOX4 suppressed apoptosis, indicating that multiple anti-apoptotic pathways underlie cooperative leukemogenesis by HOXA9 and MYC. These results demonstrate that HOXA9 is a key transcriptional maintenance factor which promotes MYC-mediated leukemogenesis, potentially explaining why HOXA9 is highly expressed in many leukemias.
Girdin regulates dendrite morphogenesis and cilium position in two specialized sensory neuron types inC. elegans
Authors: Nechipurenko Inna , Lavrentyeva Sofia , Sengupta Piali
Published: October 2020

Primary cilia are located at the dendritic tips of sensory neurons and house the molecular machinery necessary for detection and transduction of sensory stimuli. The mechanisms that coordinate dendrite extension with cilium position during sensory neuron development are not well understood. Here, we show that GRDN-1, theCaenorhabditis elegansortholog of the highly conserved scaffold and signaling protein Girdin/GIV, regulates both cilium position and dendrite extension in the postembryonic AQR and PQR gas-sensing neurons. Mutations ingrdn-1disrupt dendrite outgrowth and mislocalize cilia to the soma or proximal axonal segments in AQR, and to a lesser extent, in PQR. GRDN-1 is localized to the basal body and regulates localization of HMR-1/Cadherin to the distal AQR dendrite. However, loss of HMR-1 and/or SAX-7/LICAM, molecules previously implicated in sensory dendrite development inC. elegans, do not alter AQR dendrite morphology or cilium position. We demonstrate that GRDN-1 localization in AQR is regulated by UNC-116/Kinesin-1, and that correspondingly,unc-116mutants exhibit severe AQR dendrite outgrowth and cilium positioning defects. In contrast, GRDN-1 and cilium localization in PQR is modulated by LIN-44/Wnt signaling. Together, these findings identify upstream regulators of GRDN-1, and describe new cellspecific roles for this multifunctional protein in sensory dendrite development.
Multidimensional face representation in deep convolutional neural network reveals the mechanism underlying AI racism
Authors: Tian Jinhua , Xie Hailun , Hu Siyuan , Liu Jia
Published: October 2020

The increasingly popular application of AI runs the risks of amplifying social bias, such as classifying non-white faces to animals. Recent research has attributed the bias largely to data for training. However, the underlying mechanism is little known, and therefore strategies to rectify the bias are unresolved. Here we examined a typical deep convolutional neural network (DCNN), VGG-Face, which was trained with a face dataset consisting of more white faces than black and Asian faces. The transfer learning result showed significantly better performance in identifying white faces, just like the well-known social bias in human, the other-race effect (ORE). To test whether the effect resulted from the imbalance of face images, we retrained the VGG-Face with a dataset containing more Asian faces, and found a reverse ORE that the newly-trained VGG-Face preferred Asian faces over white faces in identification accuracy. In addition, when the number of Asian faces and white faces were matched in the dataset, the DCNN did not show any bias. To further examine how imbalanced image input led to the ORE, we performed the representational similarity analysis on VGG-Face’s activation. We found that when the dataset contained more white faces, the representation of white faces was more distinct, indexed by smaller ingroup similarity and larger representational Euclidean distance. That is, white faces were scattered more sparsely in the representational face space of the VGG-Face than the other faces. Importantly, the distinctiveness of faces was positively correlated with the identification accuracy, which explained the ORE observed in the VGG-Face. In sum, our study revealed the mechanism underlying the ORE in DCNNs, which provides a novel approach of study AI ethics. In addition, the face multidimensional representation theory discovered in human was found also applicable to DCNNs, advocating future studies to apply more cognitive theories to understand DCNN’s behavior.
The collapse of the spindle following ablation in S. pombe is mediated by microtubules and the motor protein dynein
Authors: Zareiesfandabadi Parsa , Elting Mary Williard
Published: October 2020

A microtubule-based machine called the mitotic spindle segregates chromosomes when eukaryotic cells divide. In the fission yeastS. pombe, which undergoes closed mitosis, the spindle forms a single bundle of microtubules inside the nucleus. During elongation, the spindle extends via antiparallel microtubule sliding by molecular motors. These extensile forces from the spindle are thought to resist compressive forces from the nucleus. We probe the mechanism and maintenance of this force balance via laser ablation of spindles at various stages of mitosis. We find that spindle pole bodies collapse toward each other following ablation, but spindle geometry is often rescued, allowing spindles to resume elongation. While this basic behavior has been previously observed, many questions remain about this phenomenon’s dynamics, mechanics, and molecular requirements. In this work, we find that previously hypothesized viscoelastic relaxation of the nucleus cannot fully explain spindle shortening in response to laser ablation. Instead, spindle collapse requires microtubule dynamics and is powered at least partly by the minus-end directed motor protein dynein. These results suggest a role for dynein in redundantly supporting force balance and bipolarity in theS. pombespindle.

STATEMENT OF SIGNIFICANCE

S. pombeserves as an important model organism for understanding cell division. Its structurally simple mitotic spindle is especially suited for mechanical perturbation. SinceS. pombeundergoes a process of closed cell division, without breakdown of the nuclear envelope, force may be exerted between its nuclear envelope and spindle. Here, we mechanically sever spindles via laser ablation to probe this force balance. Following ablation,S. pombespindle fragments collapse toward each other. We find that, contrary to prior expectations, forces from the chromosomes and nuclear envelope are not responsible for this collapse. Instead, it is microtubule-dependent, and is powered at least in part by the minus-end directed microtubule motor protein dynein.
The molecular basis ofAcinetobacter baumanniicadmium toxicity and resistance
Authors: Alquethamy Saleh F. , Adams Felise G. , Maharjan Ram , Delgado Natasha N. , Zang Maoge , Paton James C. , Hassan Karl A. , Paulsen Ian T. , McDevitt Christopher A. , Cain Amy K. , Eijkelkamp Bart A.
Published: October 2020

Acinetobacterspecies are ubiquitous Gram-negative bacteria that can be found in water, soil and as commensals of the human skin. The successful inhabitation ofAcinetobacterspecies in diverse environments is primarily attributable to the expression of an arsenal of stress resistance determinants, which includes an extensive repertoire of metal ion efflux systems. Although metal ion homeostasis in the hospital pathogenAcinetobacter baumanniiis known to contribute to pathogenesis, insights into its metal ion transporters for environmental persistence are lacking. Here, we studied the impact of cadmium stress onA. baumannii. Our functional genomics and independent mutant analyses revealed a primary role for CzcE, a member of the cation diffusion facilitator (CDF) superfamily, in resisting cadmium stress. Further, we show that the CzcCBA heavy metal efflux system also contributes to cadmium efflux. Analysis of theA. baumanniimetallome under cadmium stress showed zinc depletion and copper enrichment, which are likely to influence cellular fitness. Overall, this work expands our understanding of the role of membrane transporters inA. baumanniimetal ion homeostasis.

IMPORTANCE

Cadmium toxicity is a widespread problem, yet the interaction of this heavy metal with biological systems is poorly understood. Some microbes have evolved traits to proactively counteract cadmium toxicity, which includesAcinetobacter baumannii. Here we show thatA. baumanniiutilises a dedicated cadmium efflux protein in concert with a system that is primarily attuned to zinc efflux, to efficiently overcome cadmium stress. The molecular characterization ofA. baumanniiunder cadmium stress revealed how active cadmium efflux plays a key role in preventing the dysregulation of bacterial metal ion homeostasis, which appeared to be the primary means by which cadmium exerts toxicity upon the bacterium.
Identification of Proteinase Activated Receptor (PAR) cleaving enzymes in human osteoarthritis knee joint synovial fluids
Authors: Chandrabalan Arundhasa , Firth Andrew , Litchfield Robert B , Appleton C Thomas , Getgood Alan , Ramachandran Rithwik
Published: October 2020

Objective

Osteoarthritis (OA) is the most prevalent joint disorder with incidence increasing worldwide. Mechanistic insights into OA pathophysiology are still evolving and there are currently no disease-modifying OA drugs available. It is well established that an increase in proteolytic enzyme activity is linked to progressive degradation of the cartilage in OA. Proteolytic enzymes can also trigger inflammation through activation of a family of G-protein coupled receptors (GPCRs) called the Proteinase Activated Receptors (PARs). Here we sought to characterize the PAR activating enzyme repertoire in human OA knee joint fluids.

Methods

Human knee joint synovial fluids derived from twenty-five OA patients and four healthy donors were screened for PAR cleavage activity using novel genetically encoded human PAR biosensor expressing cells. The class or type of enzymes cleaving the PARs was further characterized using enzyme-selective inhibitors and enzyme-specific fluorogenic substrates.

Results

Activity of PAR1, PAR2 and PAR4 activating enzymes were identified at substantially different levels in OA patients relative to healthy knee joint synovial fluids. Using enzyme class or type selective inhibitors and fluorogenic substrates we found that serine proteinases, including thrombin-like enzymes, trypsin-like enzymes, and matrix metalloproteinases are the major PAR activating enzymes present in the OA knee synovial fluids.

Conclusions

Multiple enzymes activating PAR1, PAR2 and PAR4 are present in OA joint fluids. PAR signalling can trigger pro-inflammatory responses and targeting PARs has been proposed as a therapeutic approach in OA. Knowledge of the PAR activators present in the human knee joint will guide study of relevant signaling events and enable future development of novel PAR targeted therapies for OA and other inflammatory joint diseases.
Time-resolved single-cell RNAseq profiling identifies a novelFabp5-expressing subpopulation of inflammatory myeloid cells in chronic spinal cord injury
Authors: Hamel Regan , Peruzzotti-Jametti Luca , Ridley Katherine , Testa Veronica , Yu Bryan , Rowitch David , Marioni John C. , Pluchino Stefano
Published: October 2020

Innate immune responses following spinal cord injury (SCI) participate in early secondary pathogenesis and wound healing events. Here, we used time-resolved scRNAseq to map transcriptional profiles of SC tissue-resident and infiltrating myeloid cells post-SCI.

Our work identifies a novel subpopulation ofFabp5+inflammatory myeloid cells, comprising both resident and infiltrating cells and displaying a delayed cytotoxic profile at the lesion epicentre, which may serve as a target for future therapeutics.
The interaction of physical structure and nutrient loading drives ecosystem change in a large tropical lake over 40 years
Authors: Fadum Jemma M. , Hall Ed K.
Published: October 2020

Many lakes across the world are entering novel states and experiencing altered biogeochemical cycling due to local anthropogenic stressors. In the tropics, understanding the drivers of these changes can be difficult due to a lack of documented historic conditions or an absence of continuous monitoring that can distinguish between intra- and inter-annual variation. Over the last forty years (1980-2020), Lake Yojoa (Honduras) has experienced increased watershed development as well as the introduction of a large net-pen Tilapia farm, resulting in a dramatic reduction in seasonal water clarity, increased trophic state and altered nutrient dynamics, shifting Lake Yojoa from an oligotrophic (low productivity) to mesotrophic (moderate productivity) ecosystem. To assess the changes that have occurred in Lake Yojoa as well as putative drivers for those changes, we compared Secchi depth (water clarity), dissolved inorganic nitrogen (DIN), and total phosphorus (TP) concentrations at continuous semi-monthly intervals for the three years between 1979-1983 and again at continuous 16-day intervals for 2018-2020. Between those two periods we observed the loss of a clear water phase that previously occurred in the months when the water column was fully mixed. Seasonal peaks in DIN coincident with mixing suggest that an enhanced accumulation of ammonium in the hypolimnion (the bottom layer of a stratified lake) during stratification, and release to the epilimnion (the top layer of a stratified lake) with mixing maintains high algal abundance and subsequently low secchi depth during what was previously the clear water phase. This interaction of nutrient loading and Lake Yojoa’s monomictic stratification regime illustrates a key phenomenon in how physical water column structure and nutrients interact in tropical monomictic lakes. This work highlights the need to consider nutrient dynamics of warm anoxic hypolimnions, not just surface water nutrient concentrations, to understand environmental change in these societally important but understudied ecosystems.
Preclinical study of DNA vaccines targeting SARS-CoV-2
Authors: Hayashi Hiroki , Sun Jiao , Yanagida Yuka , Otera Takako , Kubota-Kotetsu Ritsuko , Shioda Tatsuo , Ono Chikako , Matsuura Yoshiharu , Arase Hisashi , Yoshida Shota , Nakamaru Ryo , Ide Ryoko , Tenma Akiko , Kawabata Sotaro , Ehara Takako , Sakaguchi Makoto , Tomioka Hideki , Shimamura Munehisa , Okamoto Sachiko , Amaishi Yasunori , Chono Hideto , Mineno Junichi , Komatsuno Takano , Saito Yoshimi , Rakugi Hiromi , Morishita Ryuichi , Nakagami Hironori
Published: October 2020

To fight against the worldwide COVID-19 pandemic, the development of an effective and safe vaccine against SARS-CoV-2 is required. As potential pandemic vaccines, DNA/RNA vaccines, viral vector vaccines and protein-based vaccines have been rapidly developed to prevent pandemic spread worldwide. In this study, we designed plasmid DNA vaccine targeting the SARS-CoV-2 Spike glycoprotein (S protein) as pandemic vaccine, and the humoral, cellular, and functional immune responses were characterized to support proceeding to initial human clinical trials. After intramuscular injection of DNA vaccine encoding S protein with alum adjuvant (three times at 2-week intervals), the humoral immunoreaction, as assessed by anti-S protein or anti-receptor-binding domain (RBD) antibody titers, and the cellular immunoreaction, as assessed by antigen-induced IFNγ expression, were up-regulated. In IgG subclass analysis, IgG2b was induced as the main subclass. Based on these analyses, DNA vaccine with alum adjuvant preferentially induced Th1-type T cell polarization. We confirmed the neutralizing action of DNA vaccine-induced antibodies via two different methods, a binding assay of RBD recombinant protein with angiotensin-converting enzyme 2 (ACE2), a receptor of SARS-CoV-2, and pseudovirus assay. Further B cell epitope mapping analysis using a peptide array showed that most vaccine-induced antibodies recognized the S2 and RBD subunits, but not the S1 subunit. In conclusion, DNA vaccine targeting the spike glycoprotein of SARS-CoV-2 might be an effective and safe approach to combat the COVID-19 pandemic.
Dual RNA-Seq analysis ofin vitroinfection multiplicity inChlamydia-infected epithelial cells
Authors: Hayward Regan J. , Humphrys Michael S. , Huston Wilhelmina M. , Myers Garry S.A.
Published: October 2020

Dual RNA-seq experiments examining viral and bacterial pathogens are increasing, but vary considerably in their experimental designs, such as infection rates and RNA depletion methods. Here, we have applied dual RNA-seq toChlamydia trachomatisinfected epithelial cells to examine transcriptomic responses from both organisms. We compared two time points post infection (1 and 24 hours), three multiplicity of infection (MOI) ratios (0.1, 1 and 10) and two RNA depletion methods (rRNA and polyA). Capture of bacterial-specific RNA were greatest when combining rRNA and polyA depletion, and when using a higher MOI. However, under these conditions, host RNA capture was negatively impacted. Although it is tempting to use high infection rates, the implications on host cell survival, the potential reduced length of infection cycles and real world applicability should be considered. This data highlights the delicate nature of balancing host-pathogen RNA capture and will assist future transcriptomic-based studies to achieve more specific and relevant infection-related biological insights.
Lateral prefrontal cortex as a hub for music production with gradation from structural rules to movement sequences
Authors: Bianco R. , Novembre G. , Ringer H. , Kohler N. , Keller P.E. , Villringer A. , Sammler D.
Published: October 2020

Complex sequential behaviours, such as speaking or playing music, often entail the flexible, rule-based chaining of single acts. However, it remains unclear how the brain translates abstract structural rules into concrete series of movements. Here we demonstrate a multi-level contribution of anatomically distinct cognitive and motor networks to the execution of novel musical sequences. We combined functional and diffusion-weighted neuroimaging to dissociate high-level structural and low-level motor planning of musical chord sequences executed on a piano. Fronto-temporal and fronto-parietal neural networks were involved when sequences violated pianists’ structural or motor plans, respectively. Prefrontal cortex is identified as a hub where both networks converge within an anterior-to-posterior gradient of action control linking abstract structural rules to concrete movement sequences.
HPF1-dependent PARP activation promotes LIG3-XRCC1-mediated backup pathway of Okazaki fragment ligation
Authors: Kumamoto Soichiro , Nishiyama Atsuya , Chiba Yoshie , Miyashita Ryota , Konishi Chieko , Azuma Yoshiaki , Nakanishi Makoto
Published: October 2020

DNA Ligase 1 (LIG1) is known as the major DNA ligase responsible for Okazaki fragment joining. Recent studies have implicated LIG3 complexed with XRCC1 as an alternative player in Okazaki fragment joining in cases where LIG1 is not functional, although the underlying mechanisms are largely unknown. Here, using a cell-free system derived fromXenopusegg extracts, we demonstrated the essential role of PARP1-HPF1 in LIG3-dependent Okazaki fragment joining. We found that Okazaki fragments were eventually ligated even in the absence of LIG1, employing in its place LIG3-XRCC1 which was recruited onto chromatins. Concomitantly, LIG1 deficiency induces ADP-ribosylation of histone H3 in a PARP1-HPF1-dependent manner. The depletion of PARP1 or HPF1 resulted in a failure to recruit LIG3 onto chromatin and a subsequent failure in Okazaki fragment joining in LIG1-depleted extracts. Importantly, Okazaki fragments were not ligated at all when LIG1 and XRCC1 were co-depleted. Our results suggest that a unique form of ADP-ribosylation signalling promotes the recruitment of LIG3 on chromatins and its mediation of Okazaki fragment joining as a backup system for LIG1 perturbation.
Sediment-associated microbial community profiling: sample pre-processing through sequential membrane filtration for 16s rDNA amplicon sequencing
Authors: Serrana Joeselle M. , Watanabe Kozo
Published: October 2020

Sequential membrane filtration as a pre-processing step for the isolation of microorganisms could provide good quality and integrity DNA that can be preserved and kept at ambient temperatures before community profiling through culture-independent molecular techniques, e.g., 16s rDNA amplicon sequencing. Here, we assessed the impact of pre-processing sediment samples by sequential membrane filtration (from 10, 5 to 0.22 μm pore size membrane filters) for 16s rDNA-based community profiling of sediment-associated microorganisms. Specifically, we examined if there would be method-driven differences between non- and pre-processed sediment samples regarding the quality and quantity of extracted DNA, PCR amplicon, resulting high-throughput sequencing reads, microbial diversity, and community composition. We found no significant difference in the quality and quantity of extracted DNA and PCR amplicons between the two methods. Although we found a significant difference in raw and quality-filtered reads, read abundance after bioinformatics processing (i.e., denoising and the chimeric-read filtering steps) were not significantly different. These results suggest that read abundance after these read processing steps were not influenced by sediment processing or lack thereof. Although the non- and pre-processed sediment samples had more unique than shared amplicon sequence variants (ASVs), we report that their shared ASVs accounted for 74% of both methods’ absolute read abundance. More so at the genus level, the final collection filter identified most of the genera (95% of the reads) captured from the non-processed samples, with a total of 51 false-negative (2%) and 59 false-positive genera (3%). Accordingly, the diversity estimates and community composition were not significantly different between the non- and pre-processed samples. We demonstrate that while there were differences in shared and unique taxa, both methods revealed comparable microbial diversity and community composition. We also suggest the inclusion of sequential filters (i.e., pre- and mid-filters) in the community profiling, given the additional taxa not detected from the non-processed and the final collection filter. Our observations highlight the feasibility of pre-processing sediment samples for community analysis and the need to further assess sampling strategies to help conceptualize appropriate study designs for sediment-associated microbial community profiling.
Explainable Machine Learning Approach to Predict and Explain the Relationship between Task-based fMRI and Individual Differences in Cognition
Authors: Pat Narun , Wang Yue , Bartonicek Adam , Candia Julián , Stringaris Argyris
Published: October 2020

Despite decades of costly research, we still cannot accurately predict individual differences in cognition from task-based fMRI. Moreover, aiming for methods with higher prediction is not sufficient. To understand brain-cognition relationships, we need to explain how these methods draw brain information to make the prediction. Here we applied an explainable machine-learning (ML) framework to predict cognition from task-based fMRI during the n-back working-memory task, using data from the Adolescent Brain Cognitive Development (n=3,989). We compared nine predictive algorithms in their ability to predict 12 cognitive abilities. We found better out-of-sample prediction from ML algorithms over the mass-univariate and OLS multiple regression. Among ML algorithms, Elastic Net, a linear and additive algorithm, performed either similar to or better than non-linear and interactive algorithms. We explained how these algorithms drew information, using SHapley Additive explanation, eNetXplorer, Accumulated Local Effects and Friedman’s H-statistic. These explainers demonstrated benefits of ML over the OLS multiple regression. For example, ML provided some consistency in variable importance with a previous study (Sripada et al. 2020) and consistency with the mass-univariate approach in the directionality of brain-cognition relationships at different regions. Accordingly, our explainable-ML framework predicted cognition from task-based fMRI with boosted prediction and explainability over standard methodologies.
Gait variability is affected more by peripheral artery disease than by vascular occlusion
Authors: Rahman Hafizur , Pipinos Iraklis I. , Johanning Jason M. , Myers Sara A.
Published: October 2020

Background

Patients with peripheral artery disease (PAD) have altered gait variability from the first step they take, well before the onset of claudication pain. The mechanisms underlying these gait alterations are poorly understood.

Aims

This study sought to isolate the effect of reduced blood flow on gait variability by comparing healthy older controls and patients with PAD. We also determined the diagnostic value of gait variability parameters to identify the presence of PAD.

Methods

Thirty healthy older controls and thirty patients with PAD walked on a treadmill at their self-selected speed in rested (normal walking for controls; pain free for PAD) and reduced blood flow (post vascular occlusion with thigh tourniquet for controls; pain for PAD) conditions. Gait variability was assessed using the largest Lyapunov exponent, approximate entropy, standard deviation, and coefficient of variation of ankle, knee, and hip joints range of motion. Receiver operating characteristics curve analyses of the rested condition were performed to determine the optimal cut-off values for separating individuals with PAD from those without PAD.

Results and Discussion

Patients with PAD have increased amount of variability for knee and hip ranges of motion compared with healthy older group. Comparing for conditions, reduced blood flow demonstrated increased amount of variability compared with rested blood flow. Significant interactions between group and condition occurred at the ankle for Lyapunov exponent, approximate entropy, and coefficient of variation. A combination of gait variability parameters correctly identifies PAD disease 70% of the time or more.

Conclusions

Gait variability is affected both by PAD and by the mechanical induction of reduced blood flow.
Widespread occurrence of the droplet state of proteins in the human proteome
Authors: Hardenberg Maarten , Horvath Attila , Ambrus Viktor , Fuxreiter Monika , Vendruscolo Michele
Published: October 2020

A wide range of proteins have been reported to condensate into a dense liquid phase, forming a reversible droplet state. Failure in the control of the droplet state can lead to the formation of the more stable amyloid state, which is often disease-related. These observations prompt the question of how many proteins can undergo liquid-liquid phase separation. Here, in order to address this problem, we discuss the biophysical principles underlying the droplet state of proteins by analyzing current evidence for droplet-driver and droplet-client proteins. Based on the concept that the droplet state is stabilized by the large conformational entropy associated with non-specific side-chain interactions, we develop the FuzDrop method to predict droplet-promoting regions and proteins, which can spontaneously phase separate. We use this approach to carry out a proteome-level study to rank proteins according to their propensity to form the droplet state, spontaneously or via partner interactions. Our results lead to the conclusion that the droplet state could be, at least transiently, accessible to most proteins under conditions found in the cellular environment.

Significance

Liquid-liquid phase separation of proteins results in biomolecular condensates, which contribute to the organisation of cellular matter into membraneless organelles. It is still unclear, however, whether these condensates represent a common state of proteins. Here, based on biophysical principles driving phase separation, we report a proteome-wide ranking of proteins according to their propensity to condensate into a droplet state. We analyze two mechanisms for droplet formation - driver proteins can spontaneously phase separate, while client proteins require additional components. We conclude that the droplet state, as the native and amyloid states, is a fundamental state of proteins, with most proteins expected to be capable of undergoing liquid-liquid phase separation via either of these two mechanisms.
Context dependent activation and repression of enhancers by Hunchback binding sites inDrosophilaembryo
Authors: Ceolin Stefano , Hanf Monika , Schnepf Max , Unnerstall Ulrich , Jung Christophe , Gaul Ulrike
Published: October 2020

Hunchback (Hb) is considered a context-dependent transcription factor, able to activate or repress different enhancers duringDrosophilaembryo segmentation. The mechanism driving the contextdependent activity of Hb is however not well understood. Here we measure the activity of a large set of 20 synthetic enhancers that we design to elucidate the effect of Hb binding sites inDrosophilasegmentation. We obtain quantitative data on the spatiotemporal dynamics of activity of all synthetic enhancersin-vivo, by using a quantitative and sensitive reporter system we recently developed. Our data reveal the dual role of Hb binding sites in segmentation enhancers: on the one hand, Hb act as a typical short range repressor by binding to its cognate sequences; on the other hand, we report a novel effect of a sequence containing multiple Hb binding sites, which is able to increase enhancer activity independently from Hb binding. This sequence, which contains multiple Poly-dA stretches, increases the activity of enhancers driven by different activators, possibly by disfavoring nucleosome occupancy.

AUTHOR SUMMARY

The control of gene expression is a fundamental process that allows cells to respond to external stimuli and take on various identities in complex organisms. Enhancers are DNA sequences that play a key role in this process. In the simplest model of an enhancer, small parts of its sequence can be specifically bound by proteins called transcription factors and the occupancy pattern of these proteins on the enhancer determines the expression level of a specific gene. In this research work we have studied enhancers in the context of the development of a fruit fly embryo. We have built synthetic enhancer sequences containing binding sites for a few specific factors and measured their activity in living embryos using fluorescence microscopy. Our results revealed that binding sites for a particular protein, Hunchback, are able to influence the activity of the enhancer even independently from Hunchback binding to them. This discovery might help to explain the complex effects that have been observed when studying Hunchback binding sites in natural enhancers.
A deep learning algorithm for 3D cell detection in whole mouse brain image datasets
Authors: Tyson Adam L. , Rousseau Charly V. , Niedworok Christian J. , Keshavarzi Sepiedeh , Tsitoura Chryssanthi , Cossell Lee , Strom Molly , Margrie Troy W.
Published: October 2020

Understanding the function of the nervous system necessitates mapping the spatial distributions of its constituent cells defined by function, anatomy or gene expression. Recently, developments in tissue preparation and microscopy allow cellular populations to be imaged throughout the entire rodent brain. How-ever, mapping these neurons manually is prone to bias and is often impractically time consuming. Here we present an opensource algorithm for fully automated 3D detection of neuronal somata in mouse whole-brain microscopy images using standard desktop computer hardware. We demonstrate the applicability and power of our approach by mapping the brain-wide locations of large populations of cells labeled with cytoplasmic fluorescent proteins expressed via retrograde trans-synaptic viral infection.