bluuebunny/crossref_metadata_2025_split huggingface dataset:
Applications for deep learning in ecology
Authors: Christin Sylvain , Hervet Éric , Lecomte Nicolas 
Published: May 2018

AbstractA lot of hype has recently been generated around deep learning, a group of artificial intelligence approaches able to break accuracy records in pattern recognition. Over the course of just a few years, deep learning revolutionized several research fields such as bioinformatics or medicine. Yet such a surge of tools and knowledge is still in its infancy in ecology despite the ever-growing size and the complexity of ecological datasets. Here we performed a literature review of deep learning implementations in ecology to identify its benefits in most ecological disciplines, even in applied ecology, up to decision makers and conservationists alike. We also provide guidelines on useful resources and recommendations for ecologists to start adding deep learning to their toolkit. At a time when automatic monitoring of populations and ecosystems generates a vast amount of data that cannot be processed by humans anymore, deep learning could become a necessity in ecology.
Overcoming bottlenecks for in vitro synthesis and initial structural insight of ice nucleating protein InaZ
Authors: Novikova Irina V. , China Swarup , Evans James E. 
Published: May 2018

AbstractUnlike inorganic or other synthetic alternatives, ice nucleating proteins (INPs) remain the most efficient ice nuclei today. Their potential applications in cryo-preservation, biomedicine, food industry and in the modulation of climate are widespread. Nevertheless, over several decades, cell-based recombinant methods have experienced multiple difficulties expressing these large proteins in full-length and in necessary yields while retaining functionality. As a result, our understanding of the structure and ice nucleation mechanism for this class of proteins is incomplete, and, most importantly, the full extent of possible applications unrealized. Using a wheat-germ cell-free expression pipeline, we successfully expressed and purified full-length ice nucleating protein InaZ fromPseudomonas syringae, known as a model INP. High protein yield and solubility has been achieved using this system. Ice nucleation experiments inside a dynamic environmental scanning electron microscope (ESEM) confirmed that the produced InaZ products remain functional. Preliminary structural assessments of these proteins using Transmission Electron Microscopy (TEM) showed experimental evidence for their structural organization as fibrils. We believe that the current platform will be suitable for expressing other INPs of interest and can be further employed as new engineering system either for industrial or scientific needs.
Genome sequence ofJaltomataaddresses rapid reproductive trait evolution and enhances comparative genomics in the hyper-diverse Solanaceae
Authors: Wu Meng , Kostyun Jamie L. , Moyle Leonie C. 
Published: May 2018

ABSTRACTWithin the economically important plant family Solanaceae,Jaltomatais a rapidly evolving genus that has extensive diversity in flower size and shape, as well as fruit and nectar color, among its ∼80 species. Here we report the whole-genome sequencing, assembly, and annotation, of one representative species (Jaltomata sinuosa) from this genus. Combining PacBio long-reads (25X) and Illumina short-reads (148X) achieved an assembly of approximately 1.45 Gb, spanning ∼96% of the estimated genome. 96% of curated single-copy orthologs in plants were detected in the assembly, supporting a high level of completeness of the genome. Similar to other Solanaceous species, repetitive elements made up a large fraction (∼80%) of the genome, with the most recently active element,Gypsy, expanding across the genome in the last 1-2 million years.Computational gene prediction, in conjunction with a merged transcriptome dataset from 11 tissues, identified 34725 protein-coding genes. Comparative phylogenetic analyses with six other sequenced Solanaceae species determined thatJaltomatais most likely sister toSolanum, although a large fraction of gene trees supported a conflicting bipartition consistent with substantial introgression betweenJaltomataandCapsicumafter these species split. We also identified gene family dynamics specific toJaltomata, including expansion of gene families potentially involved in novel reproductive trait development, and loss of gene families that accompanied the loss of self-incompatibility. This high-quality genome will facilitate studies of phenotypic diversification in this rapidly radiating group, and provide a new point of comparison for broader analyses of genomic evolution across the Solanaceae.
The evolutionary game of interspecific mutualism in the multi-species model
Authors: Shibasaki Shota 
Published: May 2018

AbstractMutualistic interspecific interactions, including Müllerian mimicry and division of labor, are common in nature. In contrast to antagonistic interactions, where faster evolution is favored, mutualism can favor slower evolution under some conditions. This is called the Red King effect. After Bergstrom and Lachmann (2003) proposed Red King effect, it has been investigated in two species models. However, biological examples suggest that the mutualisms can include three or more species. Here, I modeled the evolutionary dynamics of mutualism in communities where there exist two or more species, and all species mutually interact with one another. Regardless of the number of species in the community, it is possible to derive conditions for the stable equilibria. Although there exist nonlinear relationship between the evolutionary rates and the evolutionary fate of each species in the multi-species communities, the model suggests that it is possible to predict whether the faster evolution is favored or disfavored for the relatively fast species; on the other hand, it is difficult to predict the evolutionary fate of relatively slow species because the evolutionary dynamics of the slow species is affected by the evolutionary fate of the fast species.
Multiple Flagellin Proteins Have Distinct and Synergistic Roles inAgrobacterium tumefaciensMotility
Authors: Mohari Bitan , Thompson Melene A. , Trinidad Jonathan C , Fuqua Clay 
Published: May 2018

AbstractRotary flagella propel bacteria through liquid and across semi-solid environments. Flagella are composed of the basal body that constitutes the motor for rotation, the curved hook that connects to the basal body, and the flagellar filament that propels the cell. Flagellar filaments can be comprised of a single flagellin protein such as inEscherichia colior with multiple flagellins such is inAgrobacterium tumefaciens. The four distinct flagellins FlaA, FlaB, FlaC and FlaD produced by wild typeA. tumefaciens, are not redundant in function, but have specific properties. FlaA and FlaB are much more abundant than FlaC and FlaD and are readily observable in mature flagellar filaments, when either FlaA or FlaB is fluorescently labeled. Cells having FlaA with any one of the other three flagellins can generate functional filaments and thus are motile, but FlaA alone cannot constitute a functional filament. InflaAmutants that manifest swimming deficiencies, there are multiple ways by which these mutations can be phenotypically suppressed. These suppressor mutations primarily occur within or upstream of theflaBflagellin gene or in the transcriptional factorsciPregulating flagellar expression. The helical conformation of the flagellar filament appears to require a key asparagine residue present in FlaA and absent in other flagellins. However, FlaB can be spontaneously mutated to render helical flagella in absence of FlaA, reflecting their overall similarity and perhaps the subtle differences in the specific functions they have evolved to fulfill.ImportanceFlagellins are abundant bacterial proteins comprising the flagellar filaments that propel bacterial movement. Several members of the Alphaproteobacterial group express multiple flagellins, in contrast to model systems such asEscherichia colithat has only one flagellin protein. The plant pathogenAgrobacterium tumefacienshas four flagellins, the abundant and readily detected FlaA and FlaB, and lower levels of FlaC and FlaD. Mutational analysis reveals that FlaA requires at least one of the other flagellins to function -flaAmutants produce non-helical flagella and cannot swim efficiently. Suppressor mutations can rescue this swimming defect through mutations in the remaining flagellins, including structural changes imparting flagellar helical shape, and putative regulators. Our findings shed light on how multiple flagellins contribute to motility.
Virus-Like Particles and Magnetic Microspheres Provide a Flexible and Sustainable Multiplexed Alphavirus Immunodiagnostic Platform
Authors: Ricks Keersten M. , Shoemaker Charles J. , Dupuy Lesley C. , Flusin Olivier , Voorhees Matthew A. , Fulmer Ashley N. , Six Carolyn M. , Badger Catherine V. , Schmaljohn Connie S. , Schoepp Randal J. 
Published: May 2018

AbstractThere is a pressing need for sustainable and sensitive immunodiagnostics for use in public health efforts to understand and combat the threat of endemic and emerging infectious diseases. We describe a novel approach to immunodiagnostics based on virus-like particles (VLPs) attached to magnetic beads. This flexible, innovative immunoassay system, based on the MAGPIX® platform, improves sensitivity by up to 2-logs and has faster sample-to-answer time over traditional methods. As a proof of concept, a retroviral-based VLP, that presents the Venezuelan equine encephalitis virus E1/E2 glycoprotein antigen on its surface, was generated and coupled to magnetic beads to create VLP-conjugated microspheres (VCMs). Using these VCMs, IgG and IgM antibodies were detectable in nonhuman primate (NHP) and human clinical serum samples at dilutions of 1 × 104 and greater. We extended the VCM methodology to two other New-World alphaviruses, eastern and western equine encephalitis viruses, as well as an Old-World alphavirus, Chikungunya virus, demonstrating the flexibility of this approach toward different VLP architectures. When multiplexed on the MAGPIX® platform, the VCMs provided differential diagnosis between Old-World and New-World alphaviruses and well as a route toward assessing the humoral response to both natural infection and vaccination. This VCM system will allow more rapid and efficient detection of endemic and emerging viral pathogens in human populations.
Cell shape independent FtsZ dynamics in synthetically remodeled cells
Authors: Söderström Bill , Badrutdinov Alexander , Chan Helena , Skoglund Ulf 
Published: May 2018

AbstractThe FtsZ protein is a key regulator of bacterial cell division. It has been implicated in acting as a scaffolding protein for other division proteins, being a force generator during constriction, and more recently, as an active regulator of septal cell wall production. During an early stage of the division cycle, FtsZ assembles into a heterogeneous structure coined the “Z-ring” due to its resemblance to a ring confined by the midcell geometry. Whilein vitroexperiments on supported lipid bilayers have shown that purified FtsZ can self-organize into a swirling ring roughly the diameter of a bacterial cell, it is not known how, and if, membrane curvature affects FtsZ assembly and dynamicsin vivo.To establish a framework for examining geometrical influences on proper Z-ring assembly and dynamics, we sculpturedEscherichia colicells into unnatural shapes, such as squares and hearts, using division- and cell wall-specific inhibitors in a micro fabrication scheme. This approach allowed us to examine FtsZ behavior in engineered “Z-squares” and “Z-hearts”, and in giant cells up to 50 times their normal volume. Quantification of super-resolution STimulated Emission Depletion (STED) nanoscopy data showed that FtsZ densities in sculptured cells maintained the same dimensions as their wild-type counterparts. Additionally, time-resolved fluorescence measurements revealed that FtsZ dynamics were generally conserved in a wide range of cell shapes. Based on our results, we conclude that the underlying membrane environment is not a deciding factor for FtsZ filament maintenance and treadmillingin vivo.
Widespread inter-individual gene expression variability inArabidopsis thaliana
Authors: Cortijo Sandra , Aydin Zeynep , Ahnert Sebastian , Locke James 
Published: May 2018

AbstractA fundamental question in biology is how gene expression is regulated to give rise to a phenotype. However, transcriptional variability is rarely considered and could influence the relationship between genotype and phenotype. It is known in unicellular organisms that gene expression is often noisy rather than uniform and this has been proposed to be beneficial when environmental conditions are unpredictable. However, little is known about transcriptional variability in plants. Using transcriptomic approaches, we analysed gene expression variability between individualArabidopsis thalianaplants growing in identical conditions over a 24 hour time-course. We identified hundreds of genes that exhibit high inter-individual variability and found that many are involved in environmental responses. We also identified factors that might facilitate gene expression variability, such as gene length, the number of transcription factors regulating the genes and the chromatin environment. These results shed new light on the impact of transcriptional variability in gene expression regulation in plants.
Biophysical basis of alpha rhythm disruption in Alzheimer’s disease
Authors: Sharma Rohan , Nadkarni Suhita 
Published: May 2018

AbstractAlpha is one of the most prominent rhythms (7.5–12.5 Hz) detected in electroencephalography (EEG) during wakeful relaxation with closed eyes. In response to elevated ambient acetylcholine levels, a subclass of thalamic pacemaker cells generate alpha. This rhythm is intrinsic to the cell and is robustly orchestrated by an interplay of hyperpolarization activated cyclic nucleotide gated channels(HCN) and calcium-ion channels. It has been shown that decreased expression of HCN channels is correlated to Alzheimer's Diseased (AD). In early stages of AD, alpha is known to be down-regulated and lowered in coherence. We use this well characterized and quantified rhythm to understand the changes in ion channel properties that lead to disruption of alpha as seen in AD in a biophysically detailed network model of the thalamo-cortical circuit that generates the alpha-rhythm. Our computational model allows us to explore the causal links between alpha rhythms, HCN channels and amyloid-beta aggregation. The most commonly used drugs(acetylcholinesterase inhibitors) in AD increase the duration and level of acetylcholine and provide temporary symptomatic relief in some cases. Our simulations show how increasing acetylcholine can provide rescue for a small range of aberrant HCN expression. We hypothesize that reduced alpha rhythm frequency and coherence is a result of down-regulated HCN expression, rather then compromised cholinergic modulation(as is currently thought). The model predicts that lowering of the alpha-rhythm can modify the network activity in the thalamo-cortical circuit and lead to an increase in the inhibitory drive to the thalamus.
The scent of symbiosis: gut bacteria affect social interactions in leafcutting ants
Authors: Teseo Serafino , van Zweden Jelle S. , Pontieri Luigi , Kooij Pepijn W. , Sørensen Søren J. , Wenseleers Tom , Poulsen Michael , Boomsma Jacobus J. , Sapountzis Panagiotis 
Published: May 2018

AbstractAnimal gut microbiota affect host physiology and behaviour. In eusocial Hymenoptera, where colony-level integrity is preserved via a nestmate discrimination system based on cuticular hydrocarbon mixtures, microorganismal effects may influence social dynamics. Although nestmate recognition has undergone a thorough exploration during the last four decades, few studies have investigated the putative role of gut microbes. Here we integrate metagenomic, chemical and behavioural approaches to test whether gut microbes affect nestmate recognition inAcromyrmex echinatiorleaf-cutting ants. Treating workers with a sterile diet or with antibiotics resulted in a substantial alteration of their gut microbial communities. In pairwise social interactions, untreated vs. antibiotic-treated nestmates behaved more aggressively than other nestmate and non-nestmate pairs, suggesting that the suppression of microbes indirectly alters chemical social cues and triggers aggressive behaviour. Chemical analyses on treated individuals revealed a decrease in the abundance of two metapleural gland antifungal compounds, and we confirmed the correspondence between aggression levels and chemical profile differences. Feeding microbiota-remodelled ants with conspecific faecal droplets partially restored the original bacterial communities. Furthermore, non-nestmates fed with faecal droplets from different colonies were unusually aggressive compared to pairs fed with faecal droplets from the same colony. This suggests that chemicals derived from microbial strains may shape nestmate recognition, opening novel questions about the role of microorganisms in the evolution of social behaviour.
CellTag Indexing: genetic barcode-based sample multiplexing for single-cell genomics
Authors: Guo Chuner , Kong Wenjun , Kamimoto Kenji , Rivera-Gonzalez Guillermo C. , Yang Xue , Kirita Yuhei , Morris Samantha A 
Published: May 2018

ABSTRACTSingle-cell technologies have seen rapid advancements in recent years, presenting new analytical challenges and opportunities. These high-throughput assays increasingly require special consideration in experimental design, sample multiplexing, batch effect removal, and data interpretation. Here, we describe a lentiviral barcode-based multiplexing approach, ‘CellTag Indexing’, where we transduce and label samples that can then be pooled together for downstream experimentation and analysis. By introducing predefined genetic barcodes that are transcribed and readily detected, we can reliably read out sample identity and transcriptional state via single-cell profiling. We validate and demonstrate the utility of CellTag Indexing by sequencing transcriptomes at single-cell resolution using a variety of cell types including mouse pre-B cells, primary mouse embryonic fibroblasts, and human HEK293T cells. A unique feature of CellTag Indexing is that the barcodes are heritable. This enables cell populations to be tagged, pooled and tracked over time within the same experimental replicate, then processed together to minimize unwanted biological and technical variation. We demonstrate this feature of CellTagging in long-term tracking of cell engraftment and differentiation, in vivo, in a mouse model of competitive transplant into the large intestine. Together, this presents CellTag Indexing as a broadly applicable genetic multiplexing tool that is complementary with existing single-cell technologies.
Bile acids target proteolipid nano-assemblies of EGFR and phosphatidic acid in the plasma membrane for stimulation of MAPK signaling
Authors: Liang Hong , Estes Mary K. , Zhang Huiling , Du Guangwei , Zhou Yong 
Published: May 2018

AbstractBile acids are critical biological detergents in the gastrointestinal tract and also act as messengers to regulate a multitude of intracellular signaling events, including mitogenic signaling, lipid metabolism and endo/exocytosis. In particular, bile acids stimulate many receptors and ion channels on the cell surface, the mechanisms of which are still poorly understood. Membrane-associating proteins depend on the local spatial distribution of lipids in the plasma membrane (PM) for their function. Here, we report that the highly amphipathic secondary bile acid deoxycholic acid (DCA), a major constituent in the human bile, at doses <1μM enhances the nanoclustering of phosphatidic acid (PA) but disrupts the local segregation of phosphoinositol 4,5-bisphosphate (PIP2) in the basolateral PM of the human colorectal adenocarcinoma Caco-2 cells. PA has been shown to be a key structural component of the signaling nano-domains of epidermal growth factor receptor (EGFR) on the cell surface. We show that DCA promotes the co-localization between PA and EGFR, the PA-driven EGFR dimerization/oligomerization and EGFR signaling. Depletion of PA abolishes the stimulatory effects of DCA on the EGFR oligomerization and signaling. This effect occurs in the cultured Caco-2 cells and the ex vivo human intestinal enteroids. We propose a novel mechanism, where the amphiphilic DCA monomers alter the nano-assemblies of anionic phospholipids and in turn change the dynamic structural integrity of the lipid-driven oligomerization of cell surface receptors and their signal transduction.
CRISPR-Cas9 interrogation of a putative fetal globin repressor in human erythroid cells
Authors: Chung Jennifer , Magis Wendy , Vu Jonathan , Heo Seok-Jin , Wartiovaara Kirmo , Walters Mark C. , Kurita Ryo , Nakamura Yukio , Boffelli Dario , Martin David I. K. , Corn Jacob E. , Dewitt Mark A. 
Published: May 2018

AbstractSickle Cell Disease and ß-thalassemia, which are caused by defective or deficient adult ß-globin (HBB) respectively, are the most common serious genetic blood diseases in the world. Expression of the fetal ß-like globin, also known as γ-globin, can ameliorate both disorders by serving in place of the adult ß-globin. Here we use CRISPR-Cas9 gene editing to explore a putative γ-globin silencer region identified by comparison of naturally-occurring deletion mutations associated with up-regulated γ-globin. We find that deletion of a 1.7 kb consensus element or select 350 bp sub-regions from bulk populations of cells increases levels of fetal hemoglobin (HbF) or γ-globin. Screening of individual sgRNAs in one sub-region revealed three single guides that caused mild increases in γ-globin expression. However, clonal cell lines with the 1.7 kb region deleted did not up-regulate γ-globin and neither did lines with either of two of sub-regions identified in the screen deleted. These data suggest that the region is not an autonomous γ-globin silencer, and thus by itself is not a suitable therapeutic target in the ß-hemoglobinopathies.