bluuebunny/crossref_metadata_2025 huggingface dataset:
Nucleosome conformational variability in solution and in interphase nuclei evidenced by cryo-electron miocroscopy of vitreous sections
Authors: Eltsov Mikhail , Grewe Diana , Lemercier Nicolas , Frangakis Achilleas , Livolant Françoise , Leforestier Amélie
Published: April 2018

In Eukaryotes, DNA is wound around the histone core octamer to form the basic chromatin unit, the nucleosome. Atomic resolution structures have been obtained from crystallography and single particle cryo-electron microscopy of identical engineered particles. But native nucleosomes are dynamical entities with diverse DNA sequence and histone content, and little is known about their conformational variability, especially in the cellular context. Using cryo-electron microscopy and tomography of vitreous sections we analyse the conformation of native nucleosomes, bothin vitro, using purified particles solubilised at physiologically relevant concentrations (25-50 %), andin situ, within interphase nuclei. We visualise individual nucleosomes at a level of detail that allows us to analyse the conformation of the DNA wrapped around, and measure the distance between the DNA gyres. We evidence a variety of conformations. In interphase nuclei open nucleosomes predominate, with an average inter-gyre distance larger than that of the canonical particle. In concentrated solutions, we evidence a salt–dependant transition, with high salt compact conformations resembling the canonical nucleosome, and open low salt ones, closer to nuclear nucleosomes. Although further particle characterisation and cartography are needed to understand the relationship between this conformational variability and chromatin functional states, this work opens a route to chromatin explorationin situ.
Accurate informatic modeling of tooth enamel pellicle interactions by training substitution matrices with Mat4Pep
Authors: Horst Jeremy A. , Seto Jong , Oren Ersin Emre , Horst Orapin V. , Hung Ling-Hong , Samudrala Ram
Published: April 2018

Motivation

Protein-hydroxyapatite interactions govern the development and homeostasis of teeth and bone. Characterization would enable design of peptides to regenerate mineralized tissues and control attachments such as ligaments and dental plaque. Progress has been limited because no available methods produce robust data for assessing phase interfaces.

Results

We show that tooth enamel pellicle peptides contain subtle sequence similarities that encode hydroxyapatite binding mechanisms, by segregating pellicle peptides from control sequences using our previously developed substitution matrix-based peptide comparison protocol (Oren et al., 2007), with improvements. Sampling diverse matrices, adding biological control sequences, and optimizing matrix refinement algorithms improves discrimination from 0.81 to 0.99 AUC in leave-one-out experiments. Other contemporary methods fail on this problem. We find hydroxyapatite interaction sequence patterns by applying the resulting selected refined matrix (“pellitrix”) to cluster the peptides and build subgroup alignments. We identify putative hydroxyapatite maturation domains by application to enamel biomineralization proteins and prioritize putative novel pellicle peptides identified by In stageTip (iST) mass spectrometry. The sequence comparison protocol outperforms other contemporary options for this small and heterogeneous group, and is generalized for application to any group of peptides.

Availability

Software to apply this protocol is freely available at github.com/JeremyHorst/Mat4Pep and compbio.org/protinfo/ Mat4Pep.

Contact

jahorst@gmail.com, ram@compbio.org.

Supplementary information

Available at Bioinformatics online.
Prefrontal Cortex as a Meta-Reinforcement Learning System
Authors: Wang Jane X. , Kurth-Nelson Zeb , Kumaran Dharshan , Tirumala Dhruva , Soyer Hubert , Leibo Joel Z. , Hassabis Demis , Botvinick Matthew
Published: April 2018

Over the past twenty years, neuroscience research on reward-based learning has converged on a canonical model, under which the neurotransmitter dopamine ‘stamps in’ associations between situations, actions and rewards by modulating the strength of synaptic connections between neurons. However, a growing number of recent findings have placed this standard model under strain. In the present work, we draw on recent advances in artificial intelligence to introduce a new theory of reward-based learning. Here, the dopamine system trains another part of the brain, the prefrontal cortex, to operate as its own free-standing learning system. This new perspective accommodates the findings that motivated the standard model, but also deals gracefully with a wider range of observations, providing a fresh foundation for future research.
Rearing temperature and fatty acid supplementation jointly affect membrane fluidity and heat tolerance inDaphnia
Authors: Martin-Creuzburg D. , Coggins B.L. , Ebert D. , Yampolsky L.Y.
Published: April 2018

The homeoviscous adaptation hypothesis states that the relative abundance of polyunsaturated fatty acids (PUFA) decreases in the membrane phospholipids of ectothermic organisms at higher temperatures to maintain vital membrane properties. We hypothesized that the well-documented reduced heat tolerance of cold-rearedDaphniais due to the accumulation of PUFA in their body tissues and that heat-rearedDaphniacontain reduced amounts of PUFA even when receiving a high dietary supply of PUFA. InDaphniareared at 15°C, supplementation of a PUFA-deficient food with the long-chain PUFA eicosapentaenoic acid (EPA) resulted in an increase in the relative abundance of EPA in body tissues and a decrease in heat tolerance. However, the same was observed inDaphniareared at 25°C, indicating that the ability of heat-acclimatedDaphniato adjust EPA body concentrations is limited when exposed to high dietary EPA concentrations.Daphniareared at 25°C showed the lowest change in membrane fluidity, measured as fluorescence polarization. ForDaphniareared at three different temperatures, thermal tolerance (time to immobility at a lethally high temperature) and increasing dietary EPA concentrations correlated with fluorescence polarization and the degree of fatty acid unsaturation. Overall, our results support the homeoviscous adaptation hypothesis by showing that cold-rearedDaphnia,which accumulate PUFA within their tissues, are more susceptible to heat than hot-rearedDaphnia,which contain less PUFA.
Development of a GFP Fluorescent Bacterial Biosensor for the Detection and Quantification of Silver and Copper Ions
Authors: Martinez Adam R. , Heil John R. , Charles Trevor C.
Published: April 2018

Ionic silver is known to be an effective antimicrobial agent widely used in the cleaning and medical industries, however, there are several concerns regarding the release of silver pollutants into the environment. Presented here are two engineered bacterial biosensors for the detection and quantification of silver. The biosensors contain a silver resistance operon and a GFP gene that is strictly regulated through silver activated regulatory regions that control expression of thesiloperons. The two biosensors are responsive to a wide range of silver ion concentrations, and a correlation between silver and GFP signal is seen at select concentration ranges. The biosensors were shown to detect silver ions released from silver nanoparticles, and have the potential to become a method for monitoring ion release rates of different nanoparticles. Interestingly, the close homology of the silver resistance and copper resistance genes allowed for the biosensor to also be responsive to copper ions, implying that copper ions activate silver resistance. Further development of this biosensor could lead to commercial applications for environmental monitoring.

Importance

Ionic silver is known to have many harmful environmental effects. Silver pollutants have been found in various environmental settings such as natural waterways and tailings from mining operations, raising concern. In addition, persistent exposure to silver in medical and environmental settings has led to the development of silver resistant bacteria, many of which are also resistant to a wide range of antibiotics. Some of these have the potential to develop into human pathogens. It then becomes important to have standardized methods for detecting and monitoring silver concentrations in various environments so that appropriate measures can be taken to prevent further silver ion release. This research shows that bacterial biosensors engineered to detect and quantify silver ions can be developed as effective alternatives to traditional analytical techniques. Further development of such biosensors could result in a commercial system for short and long term environmental monitoring, which is important as products containing silver and other heavy metals become increasingly popular.
Integrative visual omics of the white-rot fungus Polyporus brumalis exposes the biotechnological potential of its oxidative enzymes for delignifying raw plant biomass
Authors: Miyauchi Shingo , Rancon Anaïs , Drula Elodie , Chaduli Delphine , Favel Anne , Grisel Sacha , Henrissat Bernard , Herpoël-Gimbert Isabelle , Ruiz-Dueñas Francisco J. , Chevret Didier , Heinaut Matthieu , Lin Junyan , Wang Mei , Pangilinan Jasmyn , Lipzen Anna , Lesage-Meessen Laurence , Navarro David , Riley Robert , Grigoriev Igor V. , Zhou Simeng , Raouche Sana , Rosso Marie-Noëlle
Published: April 2018

White-rot fungi are wood decayers able to degrade all polymers from lignocellulosic biomass including cellulose, hemicelluloses, and lignin. The white-rot fungus Polyporus brumalis efficiently breaks down lignin and is regarded as having a high potential for the initial treatment of plant biomass in its conversion to bio-energy. We performed integrative multi-omics analyses by combining data from the fungal genome, transcriptomes, and secretomes. We found the fungus possessed an unexpectedly large set of genes coding for enzymes related to lignin degradation, and that these were highly expressed and massively secreted under solid-state fermentation conditions. The examination of interrelated multi-omics patterns revealed the coordinated regulation of lignin-active peroxidases and H2O2-generating enzymes along with the activation of cellular mechanisms for detoxification, which combined to result in the efficient lignin breakdown by the fungus.

Importance

Plant biomass conversion for green chemistry and bio-energy is a current challenge for a modern sustainable bioeconomy. The complex polyaromatic lignin polymers in raw biomass feedstocks (i.e. agriculture and forestry by-products) are major obstacles for biomass conversions. From a biotechnological aspect, these compounds could be a potential source of aromatic platform molecules for bio-based polymers. Here we describe the extraordinary ability of Polyporus brumalis for lignin degradation using its enzymatic arsenal to break down wheat straw, a lignocellulosic substrate that is considered as a biomass feedstock worldwide. We observed unusual expansions of gene families coding for; 1) Class II peroxidases involved in lignin degradation; and 2) GMC oxidoreductases/dehydrogenases involved in generating the hydrogen peroxide required for lignin peroxidase activity. Our findings suggested the fungus massively mobilizes this oxidative machinery during growth on wheat straw. Overall, we identified sets of co-regulated enzymes, which could potentially augment the efficiency of biotechnological plant biomass conversions.
Pathological Oxidation of PTPN12 Underlies ABL1 Phosphorylation in HLRCC
Authors: Xu Yang , Taylor Paul , Andrade Joshua , Ueberheide Beatrix , Shuch Brian , Glazer Peter M. , Bindra Ranjit S. , Moran Michael F. , Linehan Marston W. , Neel Benjamin G.
Published: April 2018

Hereditary Leiomyomatosis and Renal Cell Cancer (HLRCC) is an inherited cancer syndrome associated with a highly aggressive form of type 2 papillary renal cell carcinoma (PRCC). Germ line inactivating alterations in Fumarate Hydratase (FH) cause HLRCC, and result in elevated levels of reactive oxygen species (ROS). Recent work indicates that FH -/-PRCC cells have increased ABL1 activation, which promotes tumor growth, but how ABL1 is activated remained unclear. Oxidation can regulate protein-tyrosine phosphatase (PTP) catalytic activity; conceivably, ROS-catalyzed inactivation of an ABL-directed PTP might account for ABL1 activation in this malignancy. Previously, our group developed “q-oxPTPome,” a method that can globally monitor the oxidation of classical PTPs. We have now refined the q-oxPTPome approach, increasing its sensitivity by >10X. Applying q-oxPTPome to FH-deficient cell models shows that multiple PTPs are either highly oxidized (including PTPN12) or overexpressed. In general, highly oxidized PTPs were those that have relatively high sensitivity to exogenous H2O2. Most PTP oxidation in FH-deficient cells is reversible, although nearly 40% of PTPN13 is oxidized irreversibly to the sulfonic acid state. Using “substrate-trapping mutants”, we mapped PTPs to their putative substrates, and found that only PTPN12 could target ABL1. Furthermore, knockdown experiments identify PTPN12 as the major ABL1 phosphatase in HLRCC. Overall, our results show that ROS-induced PTPN12 oxidation accounts for ABL1 phosphorylation in HLRCC-associated PRCC, reveal a novel mechanism for inactivating a tumor suppressor gene product, and establish a direct link between pathological PTP oxidation and neoplastic disease.
Convergence of socio-ecological dynamics in disparate ecological systems under strong coupling to human social systems
Authors: Sigdel Ram , Anand Madhur , Bauch Chris T.
Published: April 2018

It is widely recognized that coupled socio-ecological dynamics can be qualitatively different from the dynamics of social or ecological systems in isolation from one another. The influence of the type of ecological dynamics on the dynamics of the larger socio-ecological system is less well studied, however. Here, we carry out such a comparison using a mathematical model of a common pool resource problem. A population must make decisions about harvesting a renewable resource. Individuals may either be cooperators, who harvest at a sustainable level, or defectors, who over-harvest. Cooperators punish defectors through social ostracism. Individuals can switch strategies according the costs and benefits of harvesting and the strength of social ostracism. These mechanisms are represented by a differential equation for social dynamics which is coupled to three different types of resource dynamics: logistic growth, constant inflow, and threshold growth. We find that when human influence is sufficiently weak, the form of natural dynamics leaves a strong imprint on the socio-ecological dynamics, and human social dynamics are qualitatively very different from natural dynamics. However, stronger human influence introduces a broad intermediate parameter regime where dynamical patterns converge to a common type: the three types of ecological systems exhibit similar dynamics, but also, social and ecological dynamics strongly mirror one another. This is a consequence of stronger coupling and is reminiscent of synchrony from other fields, such as the classic problem of coupled oscillators in physics. Socio-ecological convergence has implications for how we understand and manage complex socio-ecological systems. In an era of growing human influence on ecological systems, further empirical and theoretical work is required to determine whether socio-ecological convergence is present in real systems.
Better than maximum likelihood estimation of model-based and model-free learning style
Authors: Yazdani Sadjad , Vahabie Abdol-Hossein , Araabi Babak Nadjar , Ahmadabadi Majid Nili
Published: April 2018

Multiple decision making systems work together to shape the final choices in human behavior. Habitual and goal-directed systems are the two most important systems that are studied in the reinforcement learning (RL) literature by model-free and model-based learning methods. Human behavior resembles the weighted combination of these systems and such a combination is modeled by weighted summation of action’s value from the model based and model free systems. Extraction of this weighted parameter, which is important for many applications and computational modeling, has been mostly based on the maximum likelihood or maximum a posteriori methods. We show these methods bring many challenges and their respective extracted values are less reliable especially in the proximity of extremes values. We propose that using a free format learning method (k-nearest neighbor) which uses more information besides the fitted values e.g. global information like stay probability instead of trial by trial information can ameliorate the estimation error. The proposed method is examined by simulation and results show the advantage of the proposed method. In addition, investigation of the human behavior data from previous researchers proved the proposed method to result in more statistically robust results in predicting other behavioral indices such as the number of gaze directions toward each target. In brief, the proposed method increases the reliability of the estimated parameters and enhances the applicability of reinforcement learning paradigms in clinical trials.
Large and fast human pyramidal neurons associate with intelligence
Authors: Goriounova Natalia A. , Heyer Djai B. , Wilbers René , Verhoog Matthijs B. , Giugliano Michele , Verbist Christophe , Obermayer Joshua , Kerkhofs Amber , Smeding Harriët , Verberne Maaike , Idema Sander , Baayen Johannes C. , Pieneman Anton W. , de Kock Christiaan P.J. , Klein Martin , Mansvelder Huibert D.
Published: April 2018

It is generally assumed that human intelligence relies on efficient processing by neurons in our brain. Behavioral and brain-imaging studies robustly show that higher intelligence associates with faster reaction times and thicker gray matter in temporal and frontal cortical areas. However, no direct evidence exists that links individual neuron activity and structure to human intelligence. Since a large part of cortical grey matter consists of dendrites, these structures likely determine cortical architecture. In addition, dendrites strongly affect functional properties of neurons, including action potential speed. Thereby, dendritic size and action potential firing may constitute variation in cortical thickness, processing speed, and ultimately IQ.

To investigate this, we took advantage of brain tissue available from neurosurgery and recorded from pyramidal neurons in the medial temporal cortex, an area showing high association between cortical thickness, cortical activity and intelligence. Next, we reconstructed full dendritic structures of recorded neurons and combined these with brain-imaging data and IQ scores from the same subjects. We find that high IQ scores and large temporal cortical thickness associate with larger, more complex dendrites of human pyramidal neurons. We show in silico that larger dendrites enable pyramidal neurons to track activity of synaptic inputs with higher temporal precision, due to fast action potential initiation. Finally, we find that human pyramidal neurons of individuals with higher IQ scores sustain faster action potentials during repeated firing. These findings provide first evidence that human intelligence is associated with neuronal complexity, action potential speed and efficient information transfer in cortical neurons.
Quantitative proteomics identification of seminal fluid proteins in male Drosophila melanogaster
Authors: Sepil Irem , Hopkins Ben R , Dean Rebecca , ThÃ©zÃ©nas Marie-LaÃ«titia , Charles Philip D , Konietzny Rebecca , Fischer Roman , Kessler Benedikt M , Wigby Stuart
Published: April 2018

Seminal fluid contains some of the fastest evolving proteins currently known. These seminal fluid proteins (Sfps) play crucial roles in reproduction, such as supporting sperm function, and – particularly in insects – modifying female physiology and behaviour. Identification of Sfps in small animals is challenging, and often relies on samples taken from the female reproductive tract after mating. A key pitfall of this method is that it might miss Sfps that are of low abundance due to dilution in the female-derived sample or rapid processing in females. Here we present a new and complimentary method, which provides added sensitivity to Sfp identification. We applied label-free quantitative proteomics to Drosophila melanogaster male reproductive tissue – where Sfps are unprocessed, and highly abundant – and quantified Sfps before and immediately after mating, to infer those transferred during copulation. We also analysed female reproductive tracts immediately before and after copulation to confirm the presence and abundance of known and candidate Sfps, where possible. Results were cross-referenced with transcriptomic and sequence databases to improve confidence in Sfp detection. Our data was consistent with 124 previously reported Sfps. We found 8 high-confidence novel candidate Sfps, which were both depleted in mated versus unmated males and identified within the reproductive tract of mated but not virgin females. We also identified 31 more candidates that are likely Sfps based on their abundance, known expression and predicted characteristics, and revealed that four proteins previously identified as Sfps are at best minor contributors to the ejaculate. The estimated copy numbers for our candidate Sfps were lower than for previously identified Sfps, supporting the idea that our technique provides a deeper analysis of the Sfp proteome than previous studies. Our results demonstrate a novel, high-sensitivity approach to the analysis of seminal fluid proteomes, whose application will further our understanding of reproductive biology.
Response of the multiple-demand network during simple stimulus discriminations
Authors: Wen Tanya , Mitchell Daniel J , Duncan John
Published: April 2018

The multiple-demand (MD) network is sensitive to many aspects of task difficulty, including such factors as rule complexity, memory load, attentional switching and inhibition. Many accounts link MD activity to top-down task control, raising the question of response when performance is limited by the quality of sensory input, and indeed, some prior results suggest little effect of sensory manipulations. Here we examined judgments of motion direction, manipulating difficulty by either motion coherence or salience of irrelevant dots. We manipulated each difficulty type across six levels, from very easy to very hard, and additionally manipulated whether difficulty level was blocked, and thus known in advance, or randomized. Despite the very large manipulations employed, difficulty had little effect on MD activity, especially for the coherence manipulation. Contrasting with these small or absent effects, we observed the usual increase of MD activity with increased rule complexity. We suggest that, for simple sensory discriminations, it may be impossible to compensate for reduced stimulus information by increased top-down control.
Golgi Renaissance: the pivotal role of the largest Golgi protein giantin
Authors: Casey Carol A. , Thomes Paul , Manca Sonia , Riethoven Jean-Jack M. , Clarke Jennifer , Petrosyan Armen
Published: April 2018

Golgi undergoes disorganization in response to the drugs or alcohol, but it is able to restore compact structure under recovery. This self-organization mechanism remains mostly elusive, as does the role of giantin, the largest Golgi matrix dimeric protein. Here, we found that in cells treated with Brefeldin A (BFA) or ethanol (EtOH), Golgi disassembly is associated with giantin de-dimerization, which was restored to the dimer form after BFA or EtOH washout. Cells lacking giantin are disabled for the restoration of the classical ribbon Golgi, and they demonstrate altered trafficking of proteins to the cell surface. The fusion of the nascent Golgi membranes is mediated by the cross-membrane interaction of Rab6a GTPase and giantin. Giantin is involved in the formation of long intercisternal connections, which in giantin-depleted cells was replaced by the short bridges that formed via oligomerization of GRASP65. This phenomenon occurs in advanced prostate cancer cells, in which a fragmented Golgi phenotype is maintained by the dimerization of GRASP65. Thus, we provide a model of Golgi Renaissance, which is impaired in aggressive prostate cancer.
Epigenetic Age-Predictor for Mice based on Three CpG Sites
Authors: Han Yang , Eipel Monika , Sakk Vadim , Dethmers-Ausema Bertien , de Haan Gerald , Geiger Hartmut , Wagner Wolfgang
Published: April 2018

Epigenetic clocks for mice were generated based on deep-sequencing analysis of the methylome. In this study we demonstrate that site-specific analysis of DNA methylation levels by pyrosequencing at only three CG dinucleotides (CpGs) in the genes Prima1, Hsf4, and Kcns1 facilitates precise estimation of chronological age in murine blood samples, too. DBA/2J mice revealed accelerated epigenetic aging as compared to C57BL6 mice, which is in line with their shorter life-expectancy. The three-CpG-predictor provides a simple and cost-effective biomarker to determine biological age in large intervention studies with mice.
Synaptobrevin-2 C-terminal Flexible Region Regulates the Discharge of Catecholamine through the Fusion Pore
Authors: Weiss Annita N.
Published: April 2018

The discharge of neurotransmitters from vesicles is a regulated process. Synaptobrevin-2 a SNARE protein, participates in this process through its interaction with other SNARE and associate proteins. Synaptobrevin-2 transmembrane domain is embedded into the vesicle lipid bilayer except for its last three residues. These residues are hydrophilic and constitute synaptobrevin-2 C-terminal flexible region. This region interacts with the intravesicular lipid bilayer phosphate head groups to initiate the fusion pore formation. Here it is shown that, this region also modulates the intravesicular membrane potential thereby the discharged of catecholamine. Synapotobrevin-2 Y113 residue was mutated to lysine or glutamate. The effects of these mutations on the exocytotic process in chromaffin cells were assessed using capacitance measurements, combined with amperometry and stimulation by flash photolysis of caged Ca2+. Both Y113E and Y113K mutations reduced the amplitudes of vesicle fusions and reduced the rates of release of catecholamine molecules in quanta release events. Further investigation revealed that the proximity of these charged residues near the vesicle lipid bilayer most likely changed the intravesicular potential, thereby slowing the flux of ions through the fusion pore, hence reducing the rate of catecholamine secretion. These results suggest that catecholamine efflux is couple with the intravesicular membrane potential.
Ref-1/APE1 inhibition with novel small molecules blocks ocular neovascularization
Authors: Pran Babu Sardar Pasha Sheik , Sishtla Kamakshi , Sulaiman Rania S. , Park Bomina , Shetty Trupti , Shah Fenil , Fishel Melissa L. , Wikel James H. , Kelley Mark R. , Corson Timothy W.
Published: April 2018

Ocular neovascular diseases like wet age-related macular degeneration are a major cause of blindness. Novel therapies are greatly needed for these diseases. One appealing antiangiogenic target is reduction-oxidation factor 1-apurinic/apyrimidinic endonuclease 1 (Ref-1/APE1). This protein can act as a redox-sensitive transcriptional activator for NF-κB and other pro-angiogenic transcription factors. An existing inhibitor of Ref-1’s function, APX3330, previously showed antiangiogenic effects. Here, we developed improved APX3330 derivatives and assessed their antiangiogenic activity. We synthesized APX2009 and APX2014 and demonstrated enhanced inhibition of Ref-1 function in a DNA-binding assay compared to APX3330. Both compounds were antiproliferative against human retinal microvascular endothelial cells (HRECs; GI50 APX2009: 1.1 μM, APX2014: 110 nM) and macaque choroidal endothelial cells (Rf/6a GI50APX2009: 26 μM, APX2014: 5.0 μM). Both compounds significantly reduced the ability of HRECs and Rf/6a cells to form tubes at mid nanomolar concentrations compared to control, and both significantly inhibited HREC and Rf/6a cell migration in a scratch wound assay, reducing NF-κB activation and downstream targets.Ex vivo, both APX2009 and APX2014 inhibited choroidal sprouting at low micromolar and high nanomolar concentrations respectively. In the laser-induced choroidal neovascularization mouse model, intraperitoneal APX2009 treatment significantly decreased lesion volume by 4-fold compared to vehicle (p< 0.0001, ANOVA with Dunnett’s post hoc tests), without obvious intraocular or systemic toxicity. Thus, Ref-1 inhibition with APX2009 and APX2014 blocks ocular angiogenesisin vitroandex vivo, and APX2009 is an effective systemic therapy for CNVin vivo, establishing Ref-1 inhibition as a promising therapeutic approach for ocular neovascularization.
Single-Cell Transcriptomic Analysis of Human Lung Reveals Complex Multicellular Changes During Pulmonary Fibrosis
Authors: Reyfman Paul A. , Walter James M. , Joshi Nikita , Anekalla Kishore R. , McQuattie-Pimentel Alexandra C. , Chiu Stephen , Fernandez Ramiro , Akbarpour Mahzad , Chen Ching-I , Ren Ziyou , Verma Rohan , Abdala-Valencia Hiam , Nam Kiwon , Chi Monica , Han SeungHye , Gonzalez-Gonzalez Francisco J. , Soberanes Saul , Watanabe Satoshi , Williams Kinola J.N. , Flozak Annette S , Nicholson Trevor T. , Morgan Vince K. , Hrusch Cara L. , Guzy Robert D. , Bonham Catherine A. , Sperling Anne I. , Bag Remzi , Hamanaka Robert B. , Mutlu Gökhan M. , Yeldandi Anjana V. , Marshall Stacy A. , Shilatifard Ali , Amaral Luis A.N. , Perlman Harris , Sznajder Jacob I. , Winter Deborah R. , Hinchcliff Monique , Argento A. Christine , Gillespie Colin T. , D’Amico Dematte Jane , Jain Manu , Singer Benjamin D. , Ridge Karen M. , Gottardi Cara J. , Lam Anna P. , Bharat Ankit , Bhorade Sangeeta M. , Budinger G.R. Scott , Misharin Alexander V.
Published: April 2018

Pulmonary fibrosis is a devastating disorder that results in the progressive replacement of normal lung tissue with fibrotic scar. Available therapies slow disease progression, but most patients go on to die or require lung transplantation. Single-cell RNA-seq is a powerful tool that can reveal cellular identity via analysis of the transcriptome, but its ability to provide biologically or clinically meaningful insights in a disease context is largely unexplored. Accordingly, we performed single-cell RNA-seq on lung tissue obtained from eight transplant donors and eight recipients with pulmonary fibrosis and one bronchoscopic cryobiospy sample. Integrated single-cell transcriptomic analysis of donors and patients with pulmonary fibrosis identified the emergence of distinct populations of epithelial cells and macrophages that were common to all patients with lung fibrosis. Analysis of transcripts in the Wnt pathway suggested that within the same cell type, Wnt secretion and response are restricted to distinct non-overlapping cells, which was confirmed using in situ RNA hybridization. Single-cell RNA-seq revealed heterogeneity within alveolar macrophages from individual patients, which was confirmed by immunohistochemistry. These results support the feasibility of discovery-based approaches applying next generation sequencing technologies to clinically obtained samples with a goal of developing personalized therapies.

One Sentence Summary

Single-cell RNA-seq applied to tissue from diseased and donor lungs and a living patient with pulmonary fibrosis identifies cell type-specific disease-associated molecular pathways.
Transient protein accumulation at the center of the T cell antigen presenting cell interface drives efficient IL-2 secretion
Authors: Clark Danielle J. , McMillan Laura E. , Tan Sin Lih , Bellomo Gaia , Massoué Clémentine , Thompson Harry , Mykhaylechko Lidiya , Alibhai Dominic , Ruan Xiongtao , Singleton Kentner L. , Du Minna , Hedges Alan J. , Schwartzberg Pamela L. , Verkade Paul , Murphy Robert F. , Wülfing Christoph
Published: April 2018

Supramolecular signaling assemblies are of interest for their unique signaling properties. A µm scale signaling assembly, the central supramolecular signaling cluster (cSMAC), forms at the center of the interface of T cells activated by antigen presenting cells. We have determined that it is composed of multiple complexes of a supramolecular volume of up to 0.5µm3 and associated with extensive membrane undulations. To determine cSMAC function, we have systematically manipulated the localization of three adaptor proteins, LAT, SLP-76, and Grb2. cSMAC localization varied between the adaptors and was diminished upon blockade of the costimulatory receptor CD28 and deficiency of the signal amplifying kinase Itk. Reconstitution of cSMAC localization restored IL-2 secretion which is a key T cell effector function as dependent on reconstitution dynamics. Our data suggest that the cSMAC enhances early signaling by facilitating signaling interactions and attenuates signaling thereafter through sequestration of a more limited set of signaling intermediates.
Hybridization, sex specific genomic architecture and local adaptation
Authors: Runemark Anna , Eroukhmanoff Fabrice , Nava-Bolaños Angela , Hermansen Jo S , Meier Joana I
Published: April 2018

While gene flow can reduce the potential for local adaptation, hybridization may conversely provide genetic variation that increases the potential for local adaptation. Hybridization may also affect adaptation through altering sexual dimorphism and sexual conflict, but this remains largely unstudied. Here, we discuss how hybridization may affect sexual dimorphism and conflict due to differential effects of hybridization on males and females, and then how this in turn may affect local adaptation. First, the lower viability of the heterogametic sex in hybrids could shift the balance in sexual conflict. Second, sex-specific inheritance of the mitochondrial genome in hybrids may lead to cyto-nuclear mismatches, for example in the form of “mother’s curse”, with potential consequences for sex-ratio and sex specific expression. Third, transgressive segregation of sexually antagonistic alleles could lead to greater sexual dimorphism in hybrid populations. These mechanisms can reduce sexual conflict and enhance intersexual niche partitioning, increasing the fitness of hybrids. Adaptive introgression of alleles reducing sexual conflict or enhancing intersexual niche partitioning may facilitate local adaptation, and could favour the colonization of novel habitats. We review these consequences of hybridization on sex differences and local adaptation, and discuss how their prevalence and importance could be tested empirically.
Organizing neuronal ER-PM junctions is a conserved nonconducting function of Kv2 plasma membrane ion channels
Authors: Kirmiz Michael , Palacio Stephanie , Thapa Parashar , King Anna N. , Sack Jon T. , Trimmer James S.
Published: April 2018

Endoplasmic reticulum (ER) and plasma membrane (PM) form junctions crucial to ion and lipid signaling and homeostasis. The Kv2.1 ion channel is unique among PM proteins in organizing ER-PM junctions. Here, we show that this organizing function is conserved between Kv2 family members that differ in their biophysical properties, modulation and cellular expression. Manipulation of actin cytoskeleton surrounding Kv2 ER-PM junctions affects their spatial organization. Kv2-containing ER-PM junctions overlap with those formed by canonical ER-PM tethers. ER-PM junction organization by Kv2 channels is unchanged by point mutations that eliminate ion conduction, but abolished by those that eliminate PM clustering without impacting ion channel function. Kv2.2 is distinct in lacking the reversible modulation of junction organization present in Kv2.1. Brain neurons in Kv2 double knockout mice have altered ER-PM junctions, demonstrating a conserved in vivo function for Kv2 family members distinct from their canonical role as ion-conducting channels shaping neuronal excitability.
Maternal tamoxifen treatment expands the macrophage population of early mouse embryos
Authors: Rojo Rocío , Sauter Kristin A. , Lefevre Lucas , Hume David A. , Pridans Clare
Published: April 2018

Several different transgenic tamoxifen-inducible cre reporter lines have been used to analyse the contribution of embryonic precursors to the development of the mononuclear phagocyte system in mice. Here we show that tamoxifen treatment of the mother at 8.5dpc with doses commonly-used in lineage trace studies produces a 4-5-fold expansion of the embryonic leukocyte populations by 10.5dpc, detected in whole mounts of embryos using aCsf1rreporter gene or separately by expression ofCsf1r, Itgam(CD11b),Adgre1(F4/80) orPtprc(CD45) mRNA. These findings indicate that tamoxifen cannot be considered a neutral agonist in macrophage lineage trace studies.

Summary sentence

Treatment of pregnant mice with tamoxifen in early gestation produces a large expansion of the embryonic macrophage population.
Interspecies Social Spreading: Interaction between two sessile soil bacteria leads to emergence of surface motility
Authors: McCully Lucy M. , Bitzer Adam S. , Seaton Sarah C. , Smith Leah M. , Silby Mark W.
Published: April 2018

Bacteria often live in complex communities in which they interact with other organisms. Consideration of the social environment of bacteria can reveal emergent traits and behaviors that would be overlooked by studying bacteria in isolation. Here we characterize a social trait which emerges upon interaction between the distantly-related soil bacteriaPseudomonas fluorescensPf0-1 andPedobactersp. V48. On hard agar, which is not permissive for motility of the mono-culture of either species, co-culture reveals an emergent phenotype we term ‘interspecies social spreading,’ where the mixed colony spreads across the hard surface. We show that initiation of social spreading requires close association between the two species of bacteria. Both species remain associated throughout the spreading colony, with reproducible and non-homogenous patterns of distribution. The nutritional environment influences social spreading; no social behavior is observed under high nutrient conditions, but low nutrient conditions are insufficient to promote social spreading without high salt concentrations. This simple two-species consortium is a tractable model system that will facilitate mechanistic investigations of interspecies interactions and provide insight into emergent properties of interacting species. These studies will contribute to the broader knowledge of how bacterial interactions influence the functions of communities they inhabit.

Importance

The wealth of studies on microbial communities has revealed the complexity and dynamics of the composition of communities in many ecological settings. Fewer studies probe the functional interactions of the community members. Function of the community as a whole may not be fully revealed by characterizing the individuals. In our two-species model community, we find an emergent trait resulting from the interaction of the soil bacteriaPseudomonas fluorescensPf0-1 andPedobactersp. V48. Observation of emergent traits suggests there may be many functions of a community that are not predicted based ona prioriknowledge of the community members. These types of studies will provide a more holistic understanding of microbial communities, allowing us to connect information about community composition with behaviors determined by interspecific interactions. These studies increase our ability to understand communities, such as the soil microbiome, plant-root microbiome, and human gut microbiome, with the final goal of being able to manipulate and rationally improve these communities.
Viral Invasion Fitness Across a Continuum from Lysis to Latency
Authors: Weitz Joshua S. , Li Guanlin , Gulbudak Hayriye , Cortez Michael H. , Whitaker Rachel J.
Published: April 2018

The prevailing paradigm in ecological studies of viruses and their microbial hosts is that the reproductive success of viruses depends on the proliferation of the “predator”, i.e., the virus particle. Yet, viruses are obligate intracellular parasites, and the virus genome – the actual unit of selection – can persist and proliferate from one cell generation to the next without lysis or the production of new virus particles. Here, we propose a theoretical framework to quantify the invasion fitness of viruses using an epidemiological cell-centric metric that focuses on the proliferation of viral genomes inside cells instead of virus particles outside cells. This cell-centric metric enables direct comparison of viral strategies characterized by obligate killing of hosts (e.g., via lysis), persistence of viral genomes inside hosts (e.g., via lysogeny), and strategies along a continuum between these extremes (e.g., via chronic infections). As a result, we can identify environmental drivers, life history traits, and key feedbacks that govern variation in viral propagation in nonlinear population models. For example, we identify threshold conditions given relatively low densities of susceptible cells and relatively high growth rates of infected cells in which lysogenic and other chronic strategies have higher potential viral reproduction than lytic strategies. Altogether, the theoretical framework helps unify the ongoing study of eco-evolutionary drivers of viral strategies in natural environments.
Syntheses, Raman spectroscopy and crystal structures of alkali hexafluoridorhenates(IV) revisited
Authors: Louis-Jean James , Mariappan Balasekaran Samundeeswari , Smith Dean , Salamat Ashkan , Pham Chien Thang , Poineau Frederic
Published: April 2018

The A
2[ReF6] (A = K, Rb and Cs) salts are isotypic and crystallize in the trigonal space group type P\overline{3}m1, adopting the K2[GeF6] structure type. Common to all A
2[ReF6] structures are slightly distorted octahedral [ReF6]2− anions with an average Re—F bond length of 1.951 (8) Å. In those salts, symmetry lowering on the local [ReF6]2− anions from Oh
(free anion) to D
3d
(solid-state structure) occur. The distortions of the [ReF6]2− anions, as observed in their Raman spectra, are correlated to the size of the counter-cations.
The oxygenating constituent of 3,6-diketocamphane monooxygenase from the CAM plasmid ofPseudomonas putida: the first crystal structure of a type II Baeyer–Villiger monooxygenase. Corrigendum
Authors: Isupov Michail N. , Schröder Ewald , Gibson Robert P. , Beecher Jean , Donadio Giuliana , Saneei Vahid , Dcunha Stephlina A. , McGhie Emma J. , Sayer Christopher , Davenport Colin F. , Lau Peter C. K. , Hasegawa Yoshie , Iwaki Hiroaki , Kadow Maria , Balke Kathleen , Bornscheuer Uwe T. , Bourenkov Gleb , Littlechild Jennifer A.
Published: April 2018

A statement is amended in the article by Isupovet al.[(2015).Acta Cryst.D71, 2344–2353].
Structural and functional roles of dynamically correlated residues in thymidylate kinase
Authors: Chaudhary Santosh Kumar , Jeyakanthan Jeyaraman , Sekar Kanagaraj
Published: April 2018

Thymidylate kinase is an important enzyme in DNA synthesis. It catalyzes the conversion of thymidine monophosphate to thymidine diphosphate, with ATP as the preferred phosphoryl donor, in the presence of Mg2+. In this study, the dynamics of the active site and the communication paths between the substrates, ATP and TMP, are reported for thymidylate kinase fromThermus thermophilus. Conformational changes upon ligand binding and the path for communication between the substrates and the protein are important in understanding the catalytic mechanism of the enzyme. High-resolution X-ray crystal structures of thymidylate kinase in apo and ligand-bound states were solved. This is the first report of structures of binary and ternary complexes of thymidylate kinase with its natural substrates ATP and ATP–TMP, respectively. Distinct conformations of the active-site residues, the P-loop and the LID region observed in the apo and ligand-bound structures revealed that their concerted motion is required for the binding and proper positioning of the substrate TMP. Structural analyses provide an insight into the mode of substrate binding at the active site. The residues involved in communication between the substrates were identified through network analysis using molecular-dynamics simulations. The residues identified showed high sequence conservation across species. Biochemical analyses show that mutations of these residues either resulted in a loss of activity or affected the thermal stability of the protein. Further, molecular-dynamics analyses of mutants suggest that the proper positioning of TMP is important for catalysis. These data also provide an insight into the phosphoryl-transfer mechanism.
The complex analysis of X-ray mesh scans for macromolecular crystallography
Authors: Melnikov Igor , Svensson Olof , Bourenkov Gleb , Leonard Gordon , Popov Alexander
Published: April 2018

In macromolecular crystallography, mesh (raster) scans are carried out either as part of X-ray-based crystal-centring routines or to identify positions on the sample holder from which diffraction images can be collected. Here, the methods used inMeshBest, software which automatically analyses diffraction images collected during a mesh scan and produces a two-dimensional crystal map showing estimates of the dimensions, centre positions and diffraction qualities of each crystal contained in the mesh area, are presented. Sample regions producing diffraction images resulting from the superposition of more than one crystal are also distinguished from regions with single-crystal diffraction. The applicability of the method is demonstrated using several cases.
Hydrogen bonds are a primary driving force forde novoprotein folding. Corrigendum
Authors: Lee Schuyler , Wang Chao , Liu Haolin , Xiong Jian , Jiji Renee , Hong Xia , Yan Xiaoxue , Chen Zhangguo , Hammel Michal , Wang Yang , Dai Shaodong , Wang Jing , Jiang Chengyu , Zhang Gongyi
Published: April 2018

The paper by Leeet al.[(2017).Acta Cryst.D73, 955–969] is withdrawn.
On the application of the expected log-likelihood gain to decision making in molecular replacement
Authors: Oeffner Robert D. , Afonine Pavel V. , Millán Claudia , Sammito Massimo , Usón Isabel , Read Randy J. , McCoy Airlie J.
Published: April 2018

Molecular-replacement phasing of macromolecular crystal structures is often fast, but if a molecular-replacement solution is not immediately obtained the crystallographer must judge whether to pursue molecular replacement or to attempt experimental phasing as the quickest path to structure solution. The introduction of the expected log-likelihood gain [eLLG; McCoyet al.(2017),Proc. Natl Acad. Sci. USA,114, 3637–3641] has given the crystallographer a powerful new tool to aid in making this decision. The eLLG is the log-likelihood gain on intensity [LLGI; Read & McCoy (2016),Acta Cryst.D72, 375–387] expected from a correctly placed model. It is calculated as a sum over the reflections of a function dependent on the fraction of the scattering for which the model accounts, the estimated model coordinate error and the measurement errors in the data. It is shown how the eLLG may be used to answer the question `can I solve my structure by molecular replacement?'. However, this is only the most obvious of the applications of the eLLG. It is also discussed how the eLLG may be used to determine the search order and minimal data requirements for obtaining a molecular-replacement solution using a given model, and for decision making in fragment-based molecular replacement, single-atom molecular replacement and likelihood-guided model pruning.