bluuebunny/crossref_metadata_2025 huggingface dataset:
SGLT2 inhibition by intraperitoneal dapagliflozin mitigates peritoneal fibrosis and ultrafiltration failure in a mouse model of chronic peritoneal exposure to high-glucose dialysate
Authors: Balzer Michael S. , Rong Song , Nordlohne Johannes , Zemtsovski Jan D. , Schmidt Sonja , Stapel Britta , Bartosova Maria , von Vietinghoff Sibylle , Haller Hermann , Schmitt Claus P. , Shushakova Nelli
Published: November 2020

Peritoneal dialysis (PD) is limited by glucose-mediated peritoneal membrane (PM) fibrosis, angiogenesis and ultrafiltration failure. Influencing PM integrity by pharmacologically targeting sodium-dependent glucose transporter (SGLT)-mediated glucose uptake has not been studied. In this study wildtype C57Bl/6N mice were treated with high-glucose dialysate via an intraperitoneal catheter, with or without addition of selective SGLT2 inhibitor dapagliflozin. PM structural changes, ultrafiltration capacity and PET status for glucose, urea and creatinine were analyzed. Expression of SGLT and GLUT was analyzed by real-time PCR, immunofluorescence and immunohistochemistry. Peritoneal effluents were analyzed for cellular and cytokine composition. We found that peritoneal SGLT2 was expressed in mesothelial cells and in skeletal muscle. Dapagliflozin significantly reduced effluent TGF-β concentrations, peritoneal thickening and fibrosis as well as microvessel density, resulting in improved ultrafiltration, despite the fact that it did not affect development of high glucose transporter status.In vitro, dapagliflozin reduced monocyte chemoattractant protein-1 release under high glucose conditions in human and murine peritoneal mesothelial cells. Pro-inflammatory cytokine release in macrophages was reduced only when cultured in high glucose conditions with an additional inflammatory stimulus. In summary, dapagliflozin improved structural and functional peritoneal health in the context of high glucose PD.
The Establishment of Transgenerational Epigenetic Inheritance in theC. elegansGermline is Mediated by Lipid Metabolism
Authors: Peng Dan , Wang Chen , Li Kai-Le , Gan Zhi-Xue , Li Yong-Hao , Wang Hao-Wei , Li Qiu-Yu , Liu Xi-Wei , Sun He-Yuan , Jing Yuan-Ya , Fang Qiang , Zhao Qian , Zhang Lei , Chen Huan-Huan , Wei Hui-Min , Sun Jin , Tang Huan-Yin , Yang Xiao-Mei , Chang Jiang-Feng , Sun Feng , Jiang Ci-Zhong , Yuan Hong-Bin , Li Wei , Sun Fang-Lin
Published: November 2020

Environmental stress-induced epigenetic changes are inherited by germlines and profoundly affect the behavior and physiology of subsequent generations. However, the mechanisms by which acquired transgenerational epigenetic imprints are established in the parental germline remain poorly understood. In this study, we usedCaenorhabditis elegansas a model system and demonstrated that a key node of metabolism-Pod-2, an acetyl-CoA carboxylase, together with vitellogenins (Vits), cholesterol-binding/transport proteins, guide establishment of the acquired transgenerational epigenetic modifications H3K27me3 in the parental germline. The loss of function of a Vit; its transporter or receptor; or its binding partner, pod-2, resulted in the loss of acquired epigenetic memory in the germline. Our findings indicate that lipid metabolism is a critical mediator for establishing transgenerational epigenetic imprints in the germline.
A combined flow injection/reversed phase chromatography – high resolution mass spectrometry workflow for accurate absolute lipid quantification with13C- internal standards
Authors: Schoeny Harald , Rampler Evelyn , El Abiead Yasin , Hildebrand Felina , Zach Olivia , Hermann Gerrit , Koellensperger Gunda
Published: November 2020

We propose a fully automated novel workflow for lipidomics based on flow injection-followed by liquid chromatography high resolution mass spectrometry (FI/LC-HRMS). The workflow combined in-depth characterization of the lipidome achieved via reversed phase LC-HRMS with absolute quantification as obtained by a high number of lipid species-specific- and/or retention time (RT) matched/class-specific calibrants. The lipidome of13C labelled yeast (LILY) provided a cost efficient, large panel of internal standards covering triacylglycerols (TG), steryl esters (SE), free fatty acids (FA), diacylglycerols (DG), sterols (ST), ceramides (Cer), hexosyl ceramides (HexCer), phosphatidylglycerols (PG), phosphatidylethanolamines (PE), phosphatidic acids (PA), cardiolipins (CL), phosphatidylinositols (PI), phosphatidylserines (PS), phosphatidylcholines (PC), lysophosphatidylcholines (LPC) and lysophosphatidylethanolamines (LPE). In order to exploit the full potential of isotopically enriched biomass, LILY was absolutely quantified on demand via reversed isotope dilution analysis using FI-HRMS. Subsequent LC-HRMS analysis integrated different calibration strategies including lipid species-specific standards for >90 lipids. Extensive measures on quality control allowed to rank the calibration strategies and to automatically selected the calibration strategy of highest metrological order for the respective lipid species. Overall, the workflow enabled a streamlined analysis pipeline (identification and quantification in separate analytical runs) and provided validation tools together with absolute concentration values for >350 lipids in human plasma on a species level with an analytical run-time of less than 25 min per sample.

TOC
Computational identification of splicing phenotypes from single cell transcriptomic experiments
Authors: Huang Yuanhua , Sanguinetti Guido
Published: November 2020

RNA splicing is an important driver of heterogeneity in single cells, both through the expression of alternative transcripts and as a major determinant of transcriptional kinetics. However, the intrinsic coverage limitations of scRNA-seq technologies make it challenging to associate specific splicing events to cell-level phenotypes. Here, we present BRIE2, a scalable computational method that resolves these issues by regressing single-cell transcriptomic data against cell-level features. We show that BRIE2 effectively identifies differential alternative splicing events that are associated with a disease. Additionally, BRIE2 allows a principled selection of genes (differential momentum genes) that capture heterogeneity in transcriptional kinetics and improve quantitatively RNA velocity analyses. BRIE2, therefore, extends the scope of single-cell transcriptomic experiments towards the identification of splicing phenotypes associated with biological changes at the single-cell level.
Reproduction of a marine planktonic protist: Individual success versus population survival
Authors: Weinkauf Manuel F. G. , Siccha Michael , Weiner Agnes K. M.
Published: November 2020

Understanding the biology of reproduction is important for retracing key evolutionary processes in organisms, yet gaining detailed insights often poses major challenges. Planktonic Foraminifera are globally distributed marine microbial eukaryotes and important contributors to the global carbon cycle. Their extant biodiversity shows restricted distribution patterns of some species, whereas others are cosmopolitan in the world ocean. Planktonic Foraminifera cannot be bred under laboratory conditions, and thus details of their life cycle remain incomplete. Solely the production of flagellated gametes has been observed and taken as an indication for an exclusively sexual reproduction. Yet, sexual reproduction by spawning of gametes in the open ocean relies on sufficient gamete encounters to maintain viable populations, which represents a problem for organisms that lack the means of active propulsion and are marked by low population densities. To increase knowledge on the reproductive biology of planktonic Foraminifera, we applied a dynamic, individual-based modelling approach with parameters based on laboratory and field observations to test if random gamete encounters under commonly observed population densities are sufficient for maintaining viable populations. We show that temporal synchronization and potentially spatial concentration of gamete release seems inevitable for maintenance of the population. We argue that planktonic Foraminifera optimized their individual reproductive success at the expense of community-wide gene flow, which may explain their high degree of diversity. Our modelling approach helps to illuminate foraminiferal population dynamics and to predict the existence of necessary reproduction strategies, which may be detected in future field experiments. This study therefore contributes to our understanding of plankton ecology and evolution and their reproductive strategies in the open ocean.
Phosphonate production by marine microbes: exploring new sources and potential function
Authors: Acker Marianne , Hogle Shane L. , Berube Paul M. , Hackl Thomas , Stepanauskas Ramunas , Chisholm Sallie W. , Repeta Daniel J.
Published: November 2020

Phosphonates, organic compounds with a C-P bond, constitute 20-25% of phosphorus in high molecular weight dissolved organic matter and are a significant phosphorus source for marine microbes. However, little is known about phosphonate sources, biological function, or biogeochemical cycling. Here, we determine the biogeographic distribution and prevalence of phosphonate biosynthesis potential using thousands of genomes and metagenomes from the upper 250 meters of the global ocean. Potential phosphonate producers are taxonomically diverse, occur in widely distributed and abundant marine lineages (including SAR11 andProchlorococcus) and their abundance increases with depth. Within those lineages, phosphonate biosynthesis and catabolism pathways are mutually exclusive, indicating functional niche partitioning of organic phosphorus cycling in the marine microbiome. Surprisingly, one strain ofProchlorococcus(SB) can allocate more than 40% of its cellular P-quota towards phosphonate production. Chemical analyses and genomic evidence suggest that phosphonates in this strain are incorporated into surface layer glycoproteins that may act to reduce mortality from grazing or viral infection. Although phosphonate production is a low-frequency trait inProchlorococcuspopulations (~ 5% of genomes), experimentally derived production rates suggest thatProchlorococcuscould produce a significant fraction of the total phosphonate in the oligotrophic surface ocean. These results underscore the global biogeochemical impact of even relatively rare functional traits in abundant groups likeProchlorococcusand SAR11.
Lowering the Thermal Noise Barrier in Functional Brain Mapping with Magnetic Resonance Imaging
Authors: Vizioli L. , Moeller S. , Dowdle L. , Akçakaya M. , De Martino F. , Yacoub E. , Ugurbil K.
Published: November 2020

Functional magnetic resonance imaging (fMRI) has become one of the most powerful tools for investigating the human brain. However, virtually all fMRI studies have relatively poor signal-to-noise ratio (SNR). Here we introduce a novel fMRI denoising technique, which suppresses noise that is indistinguishable from zero-mean, Gaussian-distributed noise. Thermal noise, falling in this category, is a major source of noise in fMRI, particularly, but not exclusively, at high spatial and/or temporal resolutions. Using 7-Tesla high-resolution data, we demonstrate improvements in temporal-SNR, the detection of stimulus-induced signal changes, and functional maps, while leaving stimulus-induced signal change amplitudes, image spatial precision, and functional point-spread-function unaltered. We also show that the method is equally applicable when using supra-millimeter resolution 3- and 7-Tesla fMRI data, different cortical regions, stimulation/task paradigms, and acquisition strategies. This denoising approach improves key metrics of functional activation detection while preserving spatial precision.
Obligate cross-feeding expands the metabolic niche of bacteria
Authors: Oña Leonardo , Giri Samir , Avermann Neele , Kreienbaum Maximilian , Thormann Kai M. , Kost Christian
Published: November 2020

Bacteria frequently engage in obligate metabolic mutualisms with other microorganisms. However, it remains generally unclear how the resulting metabolic dependencies affect the ecological niche space accessible to the whole consortium relative to the niche space available to its constituent individuals. Here we address this issue by systematically cultivating metabolically dependent strains of different bacterial species either individually or as pairwise coculture in a wide range of carbon sources. Our results show that obligate cross-feeding is significantly more likely to expand the metabolic niche space of interacting bacterial populations than to contract it. Moreover, niche expansion occurred predominantly between two specialist taxa and correlated positively with the phylogenetic distance between interaction partners. Together, our results demonstrate that obligate cross-feeding can significantly expand the ecological niche space of interacting bacterial genotypes, thus explaining the widespread occurrence of this type of ecological interaction in natural microbiomes.
Bioarchaeological sex prediction from central Italy using generalized low rank imputation for cross-validated metric craniodental supervised ensemble machine learning with missing data
Authors: Muzzall Evan
Published: November 2020

I use a novel supervised ensemble machine learning approach to verify sex estimation of archaeological skeletons from central Italian bioarchaeological contexts with large amounts of missing data present. Eighteen cranial interlandmark distances and five maxillary metric distances were recorded fromn= 240 estimated males andn= 180 estimated females from four locations at Alfedena (600-400 BCE) and two locations at Campovalano (750-200 BCE and 9-11thCentury CE). A generalized low rank model (GLRM) was used to impute missing data and 20-fold external stratified cross-validation was used to fit an ensemble of eight machine learning algorithms to six different subsets of the data: 1) the face, 2) vault, 3) cranial base, 4) combined face/vault/base, 5) dentition, and 6) combined cranianiodental. Area under the receiver operator characteristic curve (AUC) was used to evaluate the predictive performance of six constituent algorithms, the discrete algorithmic winner(s), and the SuperLearner weighted ensemble’s classification of males and females from these six bony regions. This approach is useful for predicting male/female sex from central Italy. AUC for the combined craniodental data was the highest (0.9722), followed by the combined cranial data (0.9644), the face (0.9426), vault (0.9116), base (0.9060), and dentition (0.7421). Cross-validated ensemble machine learning of cranial and dental data shows strong potential for estimating sex in the bioarchaeological record and can contribute additional perspectives to help refine our understanding of human sex estimation. Additionally, GLRMs have the potential to handle missing data in ways previously unexplored in the discipline. The main limitation is that the biological sexes of the individuals estimated in this study are not certain, but were estimated macroscopically using common bioarchaeological methods. However, these methods show great promise for estimation of sex in bioarchaeological and forensic contexts and should be investigated on known-sex reference samples for confirmation.
Phylogenomic conflict coincides with rapid morphological innovation
Authors: Parins-Fukuchi Caroline , Stull Gregory W. , Smith Stephen A.
Published: November 2020

Evolutionary biologists have long been fascinated with the episodes of rapid phenotypic innovation that underlie the emergence of major lineages. Although our understanding of the environmental and ecological contexts of such episodes has steadily increased, it has remained unclear how population processes contribute to emergent macroevolutionary patterns. One insight gleaned from phylogenomics is that phylogenomic conflict, frequently caused by population-level processes, is often rampant during the origin of major lineages. With the understanding that phylogenomic conflict is often driven by complex population processes, we hypothesized that there may be a direct correspondence between areas of high conflict and elevated rates of phenotypic innovation if both patterns result from the same processes. We evaluated this hypothesis in six clades spanning vertebrates and plants. We found that the most conflict-rich regions of these six clades also tended to experience the highest rates of phenotypic innovation, suggesting that population processes shaping both phenotypic and genomic evolution may leave signatures at deep timescales. Closer examination of the biological significance of phylogenomic conflict may yield improved connections between micro- and macroevolution and increase our understanding of the processes that shape the origin of major lineages across the Tree of Life.
Performance of deep learning restoration methods for the extraction of particle dynamics in noisy microscopy image sequences
Authors: Kefer Paul , Iqbal Fadil , Locatelli Maelle , Lawrimore Josh , Zhang Mengdi , Bloom Kerry , Bonin Keith , Vidi Pierre-Alexandre , Liu Jing
Published: November 2020

Image-based particle tracking is an essential tool to answer research questions in cell biology and beyond. A major challenge of particle tracking in living systems is that low light exposure is required to avoid phototoxicity and photobleaching. In addition, high-speed imaging used to fully capture particle motion dictates fast image acquisition rates. Short exposure times come at the expense of tracking accuracy. This is generally true for quantitative microscopy approaches and particularly relevant to single molecule tracking where the number of photons emitted from a single chromophore is limited. Image restoration methods based on deep learning dramatically improve the signal-to-noise ratio in low-exposure datasets. However, it is not clear whether images generated by these methods yield accurate quantitative measurements such as diffusion parameters in (single) particle tracking experiments. Here, we evaluate the performance of two popular deep learning denoising software packages for particle tracking, using synthetic datasets and movies of diffusing chromatin as biological examples. With synthetic data, both supervised and unsupervised deep learning restored particle motions with high accuracy in two-dimensional datasets, whereas artifacts were introduced by the denoisers in 3D datasets. Experimentally, we found that, while both supervised and unsupervised approaches improved the number of trackable particles and tracking accuracy, supervised learning generally outperformed the unsupervised approach, as expected. We also highlight that with extremely noisy image sequences, deep learning algorithms produce deceiving artifacts, which underscores the need to carefully evaluate the results. Finally, we address the challenge of selecting hyper-parameters to train convolutional neural networks by implementing a frugal Bayesian optimizer that rapidly explores multidimensional parameter spaces, identifying networks yielding optional particle tracking accuracy. Our study provides quantitative outcome measures of image restoration using deep learning. We anticipate broad application of the approaches presented here to critically evaluate artificial intelligence solutions for quantitative microscopy.
Novel start codons introduce novel coding sequences in the human genomes
Authors: Zhang He , Xie Yang
Published: November 2020

Start-gain mutations can introduce novel start codons and generate novel coding sequences that may affect the function of genes. In this study, we systematically investigated the novel start codons that were either polymorphic or fixed in the human genomes. 829 polymorphic start-gain SNVs were identified in the human populations, and the novel start codons introduced by these SNVs have significantly higher activity in translation initiation. Some of these start-gain SNVs were reported to be associated with phenotypes and diseases in previous studies. By comparative genomic analysis, we found 26 human-specific start codons that were fixed after the divergence between the human and chimpanzee, and high-level translation initiation activity was observed on them. The negative selection signal was detected in the novel coding sequences introduced by these human-specific start codons, indicating the important function of these novel coding sequences. This study reveals start-gain mutations are keeping appearing in the human genomes during the evolution and may be important sources altering the function of genes which may further affect the phenotypes or cause diseases.
AMiGA: software for automated Analysis of Microbial Growth Assays
Authors: Midani Firas S. , Collins James , Britton Robert A.
Published: November 2020

The analysis of microbial growth is one of the central methods in the field of microbiology. Microbial growth dynamics can be characterized by growth parameters including carrying capacity, exponential growth rate, and growth lag. However, growth assays with clinical isolates, fastidious organisms, or microbes under stress often produce atypical growth shapes that do not follow the classical microbial growth pattern. Here, we introduce the Analysis of Microbial Growth Assays (AMiGA) software which streamlines the analysis of growth curves without any assumptions about their shapes. AMiGA can pool replicates of growth curves and infer summary statistics for biologically meaningful growth parameters. In addition, AMiGA can quantify death phases and characterize diauxic shifts. It can also statistically test for differential growth under distinct experimental conditions. Altogether, AMiGA streamlines the organization, analysis, and visualization of microbial growth assays.

IMPORTANCE

Our current understanding of microbial physiology relies on the simple method of measuring microbial populations’ size over time and under different conditions. Many advances have increased the throughput of those assays and enabled the study of non-lab adapted microbes under diverse conditions that widely affect their growth dynamics. Our software provides an all-in-one tool for estimating the growth parameters of microbial cultures and testing for differential growth in a high-throughput and user-friendly fashion without any underlying assumptions about how microbes respond to their growth conditions.
Cytokinin inhibits fungal development and virulence by targeting the cytoskeleton and cellular trafficking
Authors: Gupta Rupali , Anand Gautam , Pizarro Lorena , Laor Dana , Kovetz Neta , Sela Noa , Yehuda Tal , Gazit Ehud , Bar Maya
Published: November 2020

Cytokinin (CK) is an important plant developmental regulator, having activities in many aspects of plant life and its response to the environment. CKs are involved in diverse processes in the plant, including stem-cell maintenance, vascular differentiation, growth and branching of roots and shoots, leaf senescence, nutrient balance and stress tolerance. In some cases, phytopathogens secrete CKs. It has been suggested that to achieve pathogenesis in the host, CK-secreting biotrophs manipulate CK signaling to regulate the host cell cycle and nutrient allocation. CK is known to induce host plant resistance to several classes of phytopathogens from a handful of works, with induced host immunityviasalicylic acid signaling suggested to be the prevalent mechanism for this host resistance.

Here, we show that CK directly inhibits the growth, development, and virulence of fungal phytopathogens. Focusing onBotrytis cinerea (Bc), we demonstrate that various aspects of fungal development can be reversibly inhibited by CK. We also found that CK affects both budding and fission yeast in a similar manner. Investigating the mechanism by which CK influences fungal development, we conducted RNA-NGS on mock and CK treatedB. cinereasamples, finding that CK inhibits the cell cycle, cytoskeleton, and endocytosis. Cell biology experiments demonstrated that CK affects cytoskeleton structure and cellular trafficking inBc, lowering endocytic rates and endomembrane compartment sizes, likely leading to reduced growth rates and arrested developmental programs. Mutant analyses in yeast confirmed that the endocytic pathway is altered by CK.

Our work uncovers a remarkably conserved role for a plant growth hormone in fungal biology, suggesting that pathogen-host interactions resulted in fascinating molecular adaptations on fundamental processes in eukaryotic biology.

Importance

Cytokinins (CKs), important plant growth/ developmental hormones, have previously been associated with host disease resistance. Here, we demonstrate that CK directly inhibits the growth, development, and virulence ofB. cinerea(Bc) and many additional phytopathogenic fungi. Molecular and cellular analyses revealed that CK is not toxic toBc, but rather,Bclikely recognizes CK and responds to it, resulting in cell cycle and individual cell growth retardation, via downregulation of cytoskeletal components and endocytic trafficking. Mutant analyses in yeast confirmed that the endocytic pathway is a CK target. Our work demonstrates a conserved role for CK in yeast and fungal biology, suggesting that suggesting that pathogen-host interactions may cause molecular adaptations on fundamental processes in eukaryotic biology.
Remote effects of temporal lobe epilepsy surgery: long-term morphological changes after surgical resection
Authors: Arnold T. Campbell , Kini Lohith G. , Bernabei John M. , Revell Andrew Y. , Das Sandhitsu R. , Stein Joel M. , Lucas Tim H. , Englot Dario J. , Morgan Victoria L. , Litt Brian , Davis Kathryn A.
Published: November 2020

Objective

We present a semi-automated method for quantifying structural changes after epilepsy surgery that accounts for tissue deformation caused by resection. We demonstrate its utility by comparing the remote structural effects of two surgical approaches, the anterior temporal lobectomy (ATL) and the selective amygdalohippocampectomy (SAH).

Methods

We studied 37 temporal lobe epilepsy (TLE) patients who underwent resective surgery. Patients were treated with either an anterior temporal lobectomy (ATL, N=21) or a selective amygdalohippocampectomy (SAH, N=16). All patients received same-scanner MR imaging preoperatively and postoperatively (5+ months after surgery). To analyze structural changes in remote brain regions, we (1) implemented an automated method for segmenting resections with manual review, (2) applied cost function masking to the resection zone, and (3) estimated longitudinal cortical thickness changes using Advanced Normalization Tools (ANTs). We then compared post-operative changes in cortical thickness between the two surgical groups in brain regions outside the resected area.

Results

Patients treated with ATL exhibited significantly greater cortical thinning globally when compared to patients treated with SAH (p = 0.049). There were significant focal differences between the two treatment groups in the ipsilateral frontal lobe (superior medial and medial orbital regions) and insula (p > 0.001, α = 0.05 Bonferroni corrected). No significant effects were seen in the contralateral hemisphere.

Significance

We present and share a semi-automated pipeline for quantifying remote longitudinal changes in cortical thickness after neurosurgery. The technique is applicable to a broad array of applications, including surgical planning and mapping neuropsychological function to brain structure. Using this tool, we demonstrate that patients treated with SAH for refractory temporal lobe epilepsy have less postoperative cortical thinning in remote brain regions than those treated with ATL. We share all algorithm code and results to accelerate collaboration and clinical translation of our work.

KEY POINTS BOX

Different epilepsy surgical approaches lead to distinct patterns of postoperative cortical atrophy in remote brain regions

Patients treated with SAH have less postoperative cortical thinning than patients treated with ATL

The insula and frontal lobe demonstrated the greatest focal differences in postoperative cortical thinning when comparing SAH and ATL

Postoperative cortical thinning analyses may inform surgical planning and our understanding of cognitive sequelae
Changes in physical activity, sitting and sleep across the COVID-19 national lockdown period in Scotland
Authors: Janssen Xanne , Fleming Leanne , Kirk Alison , Rollins Lesley , Young David , Grealy Madeleine , MacDonald Bradley , Flowers Paul , Williams Lynn
Published: November 2020

We examine the impact of the COVID-19 outbreak and concomitant restrictions (i.e. lockdown) on 24-hour movement behaviors (i.e. physical activity, sitting, sleep) in a purposive sample of people (n=3230) reporting change recruited on-line. Participants’ self-reported time spent in moderate-to-vigorous physical activity (MVPA), walking, sitting and sleep prior to lockdown (T1), during the first national lockdown (T2) and as restrictions initially started to ease (T3). For each 24-hour movement behavior, category-shifts are reported (positive, negative or did not change), as well as the percentage of participants recording positive/negative changes across clusters of behaviors and the percentage of participants recording improvement or maintenance of change across time. From T1 to T2 walking decreased, whereas MVPA, sitting and sleep increased, from T2 to T3 levels returned to pre-lockdown for all but MVPA. Participants who changed one behavior positively were more likely to report a positive change in another and 50% of those who reported positive changes from T1 to T2 maintained or improved further when restrictions started to ease. The current study showed that a large proportion of the sample reported positive changes, most notably those displaying initially poor levels of each behavior. These findings will inform salutogenic intervention development.
Single-cell RNA-seq uncovers shared and distinct axes of variation in dorsal LGN neurons in mice, non-human primates and humans
Authors: Bakken Trygve E. , van Velthoven Cindy T.J. , Menon Vilas , Hodge Rebecca D. , Yao Zizhen , Nguyen Thuc Nghi , Graybuck Lucas T. , Horwitz Gregory D. , Bertagnolli Darren , Goldy Jeff , Garren Emma , Parry Sheana , Casper Tamara , Shehata Soraya I. , Barkan Eliza R. , Szafer Aaron , Levi Boaz P. , Dee Nick , Smith Kimberly A. , Sunkin Susan M. , Bernard Amy , Phillips John W. , Hawrylycz Michael , Koch Christof , Murphy Gabe , Lein Ed , Zeng Hongkui , Tasic Bosiljka
Published: November 2020

Abundant anatomical and physiological evidence supports the presence of at least three distinct types of relay glutamatergic neurons in the primate dorsal lateral geniculate nucleus (dLGN) of the thalamus, the brain region that conveys visual information from the retina to the primary visual cortex. Relay neuron diversity has also been described in the mouse dLGN (also known as LGd). Different types of relay neurons in mice, humans and macaques have distinct morphologies, distinct connectivity patterns, and convey different aspects of visual information to the cortex. To investigate the molecular underpinnings of these cell types, and how these relate to other cellular properties and differences in dLGN between human, macaque, and mice, we profiled gene expression in single nuclei and cells using RNA-sequencing. These efforts identified four distinct types of relay neurons in the primate dLGN, magnocellular neurons, parvocellular neurons, and two cell types expressing canonical marker genes for koniocellular neurons. Surprisingly, despite extensive documented morphological and physiological differences between magno- and parvocellular neurons, we identified few genes with significant differential expression between transcriptomic cell types corresponding to these two neuronal populations. We also detected strong donor-specific gene expression signatures in both macaque and human relay neurons. Likewise, the dominant feature of relay neurons of the adult mouse dLGN is high transcriptomic similarity, with an axis of heterogeneity that aligns with core vs. shell portions of mouse dLGN. Together, these data show that transcriptomic differences between principal cell types in the mature mammalian dLGN are subtle relative to striking differences in morphology and cortical projection targets. Finally, we align cellular expression profiles across species and find homologous types of relay neurons in macaque and human, and distinct relay neurons in mouse.
PDE1 inhibition modulates Cav1.2 channel to stimulate cardiomyocyte contraction
Authors: Muller Grace K , Song Joy , Jani Vivek , Wu Yuejin , Anderson Mark E , Kass David A
Published: November 2020

Rationale

Cyclic adenosine monophosphate (cAMP) activation of protein kinase A (PKA) stimulates excitation-contraction coupling, increasing cardiac contractility. This is clinically leveraged by beta-adrenergic stimulation (β-ARs) or phosphodiesterase-3 inhibition (PDE3i), though both approaches are limited by arrhythmia and chronic myocardial toxicity. Phosphodiesterase-1 inhibition (PDE1i) also augments cAMP and was recently shown in rabbit cardiomyocytes to augment contraction independent of β-AR stimulation or blockade, and with less intracellular calcium rise than β-ARs or PDE3i. Early testing of PDE1 inhibition in humans with neuro-degenerative disease and dilated heart failure has commenced. Yet, the molecular mechanisms for PDE1i inotropic effects remain largely unknown.

Objective

Define the mechanism(s) whereby PDE1i increases contractility.

Methods and Results

Primary guinea pig myocytes which express the cAMP-hydrolyzing PDE1C isoform found in larger mammals and humans were studied. The potent, selective PDE1i (ITI-214) did not alter cell shortening or Ca2+transients under resting conditions whereas both increased with β-ARs or PDE3i. However, PDE1i enhanced shortening with less Ca2+rise in a PKA-dependent manner when combined with low-dose adenylate cyclase stimulation (Forskolin). Unlike PDE3i, PDE1i did not augment β-AR responses. Whereas β-ARs reduced myofilament Ca2+sensitivity and increased sarcoplasmic reticular Ca2+content in conjunction with greater phosphorylation of troponin I, myosin binding protein C, and phospholamban, PDE1i did none of this. However, PDE1i increased Cav1.2 channel conductance similar to PDE3i in a PKA-dependent manner. Myocyte shortening and peak Ca2+transients were more sensitive to Cav1.2 blockade with nitrendipine combined with PDE1i versus PDE3i. Lastly, PDE1i was found to be far less arrythmogenic than PDE3i.

Conclusions

PDE1i enhances contractility by a PKA-dependent increase in Cav1.2 conductance without concomitant myofilament desensitization. The result is less rise in intracellular Ca2+and arrhythmia compared to β-ARs and/or PDE3i. PDE1i could be a novel positive inotrope for failing hearts without the toxicities of β-ARs and PDE3i.
Aryl hydrocarbon receptor and TGF-β inducible early gene mediate a transcriptional axis modulating immune homeostasis in mosquitoes
Authors: Kulkarni Aditi , Pandey Ashmita , Trainor Patrick , Carlisle Samantha , Yu Wanqin , Kukutla Phanidhar , Xu Jiannong
Published: November 2020

Immune homeostasis ensures effective pathogen defense and avoids overactivity, which is achieved through an orchestrated transcriptional network. Here we demonstrate that mosquito AhR and TIEG mediate a transcriptional axis to modulate the immune response. The AhR agonist compromised the immunity with reduced survival upon the challenge with bacteriumSerratia fonticola, while the AhR antagonists enhanced the immunity with increased survival. The phenotype of pharmacological immune enhancement was corroborated genetically by theAhRgene silencing. The transcriptome comparison following AhR manipulations highlighted a set of AhR regulated genes, from which transcription factor TIEG, the ortholog of Krüppel-like factor 10, was chosen for further study. TIEG was required for the AhR mediated immune modulation. SilencingTIEGincreased survival and reversed the immune suppression mediated by agonist-activated AhR. Among the transcriptomes, there were genes sharing co-expression patterns in the cohorts with AhR manipulation pharmacologically or genetically. Moreover, the mosquitoes with silencedTIEGandAhRshared ~68% altered genes upon infection. Together, the data suggest TIEG is downstream of AhR, acting as a major transcription factor mediating the immune modulation. The TIEG targets include genes involved in sugar metabolism and circadian rhythms, both processes are critical for immune homeostasis. In the naïve mosquitoes, the AhR-TIEG axis prevents the adverse effect of the overactivated IMD pathway created by silencing the inhibitorCaspar. In summary, AhR and TIEG constitute a transcriptional axis that mediates a gene network critical for maintaining immune homeostasis.

Significance

Immune homeostasis is sustained by various parameters involving different transcriptional regulatory networks. Such knowledge in mosquitoes remains scarce. Here, using AhR manipulation and transcriptome interrogation, we demonstrate that AhR and TIEG (a KLF10 ortholog) constitute a transcriptional axis to mediate immune modulation using an antibacterial immune model in the malaria vectorAnopheles gambiae. AhR is a ligand-activated transcription factor that senses environmental signals and transcribes relevant genes to modulate immune responses. TIEG/KLF10, conserved from invertebrates to mammals, mediates various transcriptional networks. Our data show that the AhR-TIEG axis controls the genes involving in sugar sensing and circadian rhythms in the infection context. This finding warrants further study to elucidate the transcriptional control of metabolic and circadian behind immune homeostasis.
Metabolomic investigation of the pseudouridimycin producer, a prolific streptomycete
Authors: Iorio Marianna , Davatgarbenam Sahar , Serina Stefania , Criscenzo Paolo , Zdouc Mitja M. , Simone Matteo , Maffioli Sonia I. , Ebright Richard H. , Donadio Stefano , Sosio Margherita
Published: November 2020

We report a metabolomic analysis of Streptomyces sp. ID38640, a soil isolate that produces the bacterial RNA polymerase inhibitor pseudouridimycin. The analysis was performed on the wild type and on ten different pum mutants blocked at different steps in pseudouridimycin biosynthesis. The results indicate that Streptomyces sp. ID38640 is able to produce, in addition to pseudouridimcyin, lydicamycins and deferroxiamines, as previously reported, also the lassopeptide ulleungdin, the non-ribosomal peptide antipain and the osmoprotectant ectoine. The corresponding biosynthetic gene clusters were readily identified in the strain genome. We also detected the known compound pyridindolol, for which we propose a previously unreported biosynthetic gene cluster, as well as three families of unknown metabolites. Remarkably, the levels of the different metabolites varied strongly in the different mutant strains, allowing detection of metabolites not normally seen in the wild type. Three newly constructed pum mutants, along with systematic investigation of the accumulated metabolites, shed further lights on pseudouridimycin biosynthesis. We also show that several Streptomyces strains, harboring the pum biosynthetic gene cluster and unrelated to ID38640, readily produce pseudouridimycin.
A Fast Lysine Cross-linker DOPA Enables Mass Spectrometry Analyses of Protein Unfolding and Weak Protein-protein Interactions
Authors: Wang Jian-Hua , Tang Yu-Liang , Jain Rohit , Xiao Fan , Gong Zhou , Zhou Yu , Tan Dan , Li Qiang , Dong Xu , Liu Shu-Qun , Tang Chun , Huang Niu , Ye Keqiong , Dong Meng-Qiu , Lei Xiaoguang
Published: November 2020

Chemical cross-linking of proteins coupled with mass spectrometry analysis (CXMS) has become a widely used method for protein structure analysis. Central to this technology are chemical cross-linkers. The most popular cross-linkers are N-hydroxysuccinimide (NHS) esters, which react with protein amino groups relatively slowly over 10 minutes or more while in competition with the hydrolysis reaction of NHS esters. To improve the speed of cross-linking, we developed a new class of amine-selective and non-hydrolyzabledi-ortho-phthalaldehyde (DOPA) cross-linkers. DOPA can cross-link proteins in 10 seconds under near physiological conditions, which is 60 times faster than the NHS ester cross-linker DSS. DOPA also works at low pH, low temperature, or in the presence of high concentrations of denaturants such as 8 M urea or 6 M guanidine hydrochloride. Further, DOPA-mediated pulse cross-linking captured the dynamic conformational changes associated with RNase A unfolding. Lastly, DOPA outperformed DSS at capturing weak but specific protein-protein interactions.
Liver FoxO1 overexpression is positively associated with the degree of liver injury in cirrhotic patients
Authors: Fernandez-Galán Esther , Sandalinas Silvia , Morales-Romero Blai , Macias Laura , Pauta Montse , Ribera Jordi , Casals Gregori , Boix Loreto , Bruix Jordi , Jimenez Wladimiro , Morales-Ruiz Manuel
Published: November 2020

Introduction

Chronic liver disease is associated with high mortality. Liver transplantation is the definitive treatment for patients with end-stage liver disease, improving their survival and quality of life. However, chronic rejection of the graft and the imbalance between the demand and the availability of organs limit its applicability. Therefore, finding therapeutic and/or diagnostic alternatives for these patients is a priority. In this context, preclinical studies in rodents have demonstrated that Akt plays a key role in liver dysfunction. Even with all this evidence, the activation status of Akt and its downstream targets in the liver of patients with chronic hepatopathy is still unknown. Hence, the present study aims to determine the activation status of the molecules involved in the Akt signaling pathway in livers of cirrhotic patients.

Materials and Methods

In this study, 36 liver tissue samples from a cohort of 27 cirrhotic patients and 9 patients without cirrhosis were included. A total of 10 proteins involved in Akt/mTOR pathway (GSK3β, IGF1R, IRS1, mTOR, p70S6K, IR, PTEN, GSK3α, TSC2, and RPS6) were analyzed using a multiplex immunoassay based on Luminex® technology.

Results

Significant differences were found in several Akt/mTOR target proteins between the groups of cirrhotic patients vs. non-cirrhotic: FoxO1 (9.5 vs. 4.4;p<0.01), p-Akt (2.1 vs. 1.0;p<0.01), PTEN (3.061 vs. 1.877;p<0.05) and p70S6K (196.3 vs. 270.5;p<0.001). FoxO1 showed the best correlation with biochemical markers of liver injury aspartate aminotransferase and serum alanine aminotransferase (ASAT: r=0.51,p<0.05; ALAT: r=0.49,p<0.05). Moreover, the individual influence of FoxO1 on these parameters was confirmed by multiple regression analysis. It was the only enzyme in the Akt signaling pathway identified as a positive independent predictor of increased ASAT and ALAT levels.

Conclusion

FoxO1 is overexpressed in the liver of cirrhotic patients after partial hepatectomy. FoxO1 levels are also associated with the degree of liver injury, showing a positive correlation with current biomarkers used in clinical practice to detect liver injury.
Single-molecule analysis reveals cooperative stimulation of Rad51 filament nucleation and growth by mediator proteins
Authors: Belan Ondrej , Barroso Consuelo , Kaczmarczyk Artur , Anand Roopesh , Federico Stefania , O’Reilly Nicola , Newton Matthew D. , Maeots Erik , Enchev Radoslav I. , Martinez-Perez Enrique , Rueda David S. , Boulton Simon J.
Published: November 2020

Homologous recombination (HR) is an essential DNA double-strand break (DSBs) repair mechanism frequently inactivated in cancer. During HR, RAD51 forms nucleoprotein filaments on RPA-coated resected DNA and catalyses strand invasion into homologous duplex DNA. How RAD51 displaces RPA and assembles into long HR-proficient filaments remains uncertain. Here, we employ single-molecule imaging to investigate the mechanism of nematode RAD-51 filament growth in the presence of BRC-2 (BRCA2) and RAD-51 paralogs, RFS-1/RIP-1. BRC-2 nucleates RAD-51 on RPA-coated DNA, while RFS-1/RIP-1 acts as a ‘chaperone’ to promote 3’ to 5’ filament growth via highly dynamic engagement with 5’ filament ends. Inhibiting ATPase or mutation in RFS-1 Walker box leads to RFS-1/RIP-1 retention on RAD-51 filaments and hinders growth.rfs-1Walker box mutants display sensitivity to DNA damage and accumulate RAD-51 complexes non-functional for HRin vivo. Our work reveals the mechanism of RAD-51 nucleation and filament growth in the presence of recombination mediators.
A Minimal, Adaptive Binning Scheme for Weighted Ensemble Simulations
Authors: Torrillo Paul A. , Bogetti Anthony T. , Chong Lillian T.
Published: November 2020

A promising approach for simulating rare events with rigorous kinetics is the weighted ensemble path sampling strategy. One challenge of this strategy is the division of configurational space into bins for sampling. Here we present a minimal adaptive binning (MAB) scheme for the automated, adaptive placement of bins along a progress coordinate within the framework of the weighted ensemble strategy. Results reveal that the MAB binning scheme, despite its simplicity, is more efficient than a manual, fixed binning scheme in generating transitions over large free energy barriers, generating a diversity of pathways, estimating rate constants, and sampling conformations. The scheme is general and extensible to any rare-events sampling strategy that employs progress coordinates.
GR chaperone cycle mechanism revealed by cryo-EM: inactivation of GR by GR:Hsp90:Hsp70:Hop client-loading complex
Authors: Wang Ray Yu-Ruei , Noddings Chari M. , Kirschke Elaine , Myasnikov Alexander G. , Johnson Jill L. , Agard David A.
Published: November 2020

Maintaining a healthy proteome is fundamental for organism survival1,2. Integral to this are Hsp90 and Hsp70 molecular chaperones that together facilitate the folding, remodeling and maturation of Hsp90’s many “client” proteins3–7. The glucocorticoid receptor (GR) is a model client strictly dependent upon Hsp90/Hsp70 for activity8–13. Chaperoning GR involves a cycle of inactivation by Hsp70, formation of an inactive GR:Hsp90:Hsp70:Hop “loading” complex, conversion to an active GR:Hsp90:p23 “maturation” complex, and subsequent GR release14. Unfortunately, a molecular understanding of this intricate chaperone cycle is lacking for any client. Here, we report the cryo-EM structure of the GR loading complex, in which Hsp70 loads GR onto Hsp90, revealing the molecular basis of direct Hsp90/Hsp70 coordination. The structure reveals two Hsp70s—one delivering GR and the other scaffolding Hop. Unexpectedly, the Hop cochaperone interacts with all components of the complex including GR, poising Hsp90 for subsequent ATP hydrolysis. GR is partially unfolded and recognized via an extended binding pocket composed of Hsp90, Hsp70 and Hop, revealing the mechanism of GR loading and inactivation. Together with the GR maturation complex (Noddings et al., 2020), we present the first complete molecular mechanism of chaperone-dependent client remodeling, establishing general principles of client recognition, inhibition, transfer and activation.