Elife , IF:7.08 , 2020 Mar , V9 doi: 10.7554/eLife.53432
Theoretical relation between axon initial segment geometry and excitability.
Sorbonne Universite, INSERM, CNRS, Institut de la Vision, Paris, France.
In most vertebrate neurons, action potentials are triggered at the distal end of the axon initial segment (AIS). Both position and length of the AIS vary across and within neuron types, with activity, development and pathology. What is the impact of AIS geometry on excitability? Direct empirical assessment has proven difficult because of the many potential confounding factors. Here, we carried a principled theoretical analysis to answer this question. We provide a simple formula relating AIS geometry and sodium conductance density to the somatic voltage threshold. A distal shift of the AIS normally produces a (modest) increase in excitability, but we explain how this pattern can reverse if a hyperpolarizing current is present at the AIS, due to resistive coupling with the soma. This work provides a theoretical tool to assess the significance of structural AIS plasticity for electrical function.
PMID: 32223890
Elife , IF:7.08 , 2020 Mar , V9 doi: 10.7554/eLife.52614
Wikidata as a knowledge graph for the life sciences.
Micelio, Antwerpen, Belgium.; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States.; Center for Integrative Bioinformatics Vienna, Max Perutz Laboratories, University of Vienna and Medical University of Vienna, Vienna, Austria.; McDonnell Genome Institute, Washington University School of Medicine, St. Louis, United States.; Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, United States.; European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom.; School of Chemistry, The University of Sydney, Sydney, Australia.; Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, United States.; Wellcome Trust Sanger Institute, Cambridge, United Kingdom.; School of Data Science, University of Virginia, Charlottesville, United States.; University of Maryland School of Medicine, Baltimore, United States.; Department of Animal Plant and Soil Sciences, La Trobe University, Melbourne, Australia.; Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands.; Retired researcher, Berlin, Germany.; Yale University Library, Yale University, New Haven, United States.
Wikidata is a community-maintained knowledge base that has been assembled from repositories in the fields of genomics, proteomics, genetic variants, pathways, chemical compounds, and diseases, and that adheres to the FAIR principles of findability, accessibility, interoperability and reusability. Here we describe the breadth and depth of the biomedical knowledge contained within Wikidata, and discuss the open-source tools we have built to add information to Wikidata and to synchronize it with source databases. We also demonstrate several use cases for Wikidata, including the crowdsourced curation of biomedical ontologies, phenotype-based diagnosis of disease, and drug repurposing.
PMID: 32180547
Genomics , IF:6.205 , 2020 Mar , V112 (2) : P1233-1244 doi: 10.1016/j.ygeno.2019.07.009
Genome-wide identification, expression profiling, and network analysis of AT-hook gene family in maize.
Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA.; School of Computing, Clemson University, 210 McAdams Hall, Clemson, SC 29634, USA.; Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA.; Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA. Electronic address: sekhon@clemson.edu.
AT-hook motif nuclear localized (AHL) genes have diverse but poorly understood biological functions. We identified and analyzed 37 AHL genes in maize. We also discovered four and one additional AHLs in rice and sorghum, respectively, besides those reported earlier. The maize AHLs were classified into two clades (A and B) and three distinct types (I, II, and III) as also reported in Arabidopsis. Phylogenetic and ortholog analyses showed that, while the evolutionary classification was conserved in plants, expansion of the AHL gene family in maize was accompanied with new biological functions. Gene structure analysis showed that, while all but one Type-I AHLs lacked an intron, origin of Type-II and Type-III AHLs was associated with the gain of introns suggesting evolutionarily distinct temporal and spatial expression patterns and, likely, neofunctionalization. Gene duplication analysis revealed that AHLs in maize expanded via dispersive duplication further supporting their functional diversity. To discern these functions, we analyzed 71 transcriptomes from diverse tissues and developmental stages of maize and classified AHLs into eight groups with distinct temporal/spatial expression profiles. Coexpression analysis implicated 5 AHLs and 33 novel genes in networks specific to endosperm, seed, root, leaf, and reproductive tissues indicating their role in the development of these organs. Major processes coregulated by AHLs include pollen development, drought response, senescence, and wound response. We also identified interactions of AHL proteins in coregulating important processes including stress response. These novel insights into the role of AHLs in plant development provide a platform for functional analyses in maize and related grasses.
PMID: 31323298
J Exp Bot , IF:5.908 , 2020 Mar , V71 (6) : P2198-2209 doi: 10.1093/jxb/erz572
Unique bacterial assembly, composition, and interactions in a parasitic plant and its host.
Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada.; Department of Integrative Biology, University of California, Berkeley, CA, USA.
How plant-associated microbiota are shaped by, and potentially contribute to, the unique ecology and heterotrophic life history of parasitic plants is relatively unknown. Here, we investigate the leaf and root bacterial communities of the root holoparasite Orobanche hederae and its host Hedera spp. from natural populations. Root bacteria inhabiting Orobanche were less diverse, had fewer co-associations, and displayed increased compositional similarity to leaf bacteria relative to Hedera. Overall, Orobanche bacteria exhibited significant congruency with Hedera root bacteria across sites, but not the surrounding soil. Infection had localized and systemic effects on Hedera bacteria, which included effects on the abundance of individual taxa and root network properties. Collectively, our results indicate that the parasitic plant microbiome is derived but distinct from the host plant microbiota, exhibits increased homogenization between shoot and root tissues, and displays far fewer co-associations among individual bacterial members. Host plant infection is accompanied by modest changes of associated microbiota at both local and systemic scales compared with uninfected individuals. Our results are a first step towards extending the growing insight into the assembly and function of the plant microbiome to include the ecologically unique but often overlooked guild of heterotrophic plants.
PMID: 31912143
J Anim Ecol , IF:4.554 , 2020 Mar doi: 10.1111/1365-2656.13198
Ant colony nest networks adapt to resource disruption.
Department of Biology, University of York, York, UK.; York Cross-disciplinary Centre for Systems Analysis, University of York, York, UK.; Department of Computer Science, University of York, York, UK.; Department of Earth, Ocean and Ecological Sciences, University of Liverpool, Liverpool, UK.; Centre for African Ecology, School of Animal, Plant and Environmental Sciences, University of Witwatersrand, Johannesburg, South Africa.; Department of Zoology & Entomology, University of Pretoria, Pretoria, South Africa.
Animal social structure is shaped by environmental conditions, such as food availability. This is important as conditions are likely to change in the future and changes to social structure can have cascading ecological effects. Wood ants are a useful taxon for the study of the relationship between social structure and environmental conditions, as some populations form large nest networks and they are ecologically dominant in many northern hemisphere woodlands. Nest networks are formed when a colony inhabits more than one nest, known as polydomy. Polydomous colonies are composed of distinct sub-colonies that inhabit spatially distinct nests and that share resources with each other. In this study, we performed a controlled experiment on 10 polydomous wood ant (Formica lugubris) colonies to test how changing the resource environment affects the social structure of a polydomous colony. We took network maps of all colonies for 5 years before the experiment to assess how the networks changes under natural conditions. After this period, we prevented ants from accessing an important food source for a year in five colonies and left the other five colonies undisturbed. We found that preventing access to an important food source causes polydomous wood ant colony networks to fragment into smaller components and begin foraging on previously unused food sources. These changes were not associated with a reduction in the growth of populations inhabiting individual nests (sub-colonies), foundation of new nests or survival, when compared with control colonies. Colony splitting likely occurred as the availability of food in each nest changed causing sub-colonies to change their inter-nest connections. Consequently, our results demonstrate that polydomous colonies can adjust to environmental changes by altering their social network.
PMID: 32141609
Hum Brain Mapp , IF:4.421 , 2020 Mar , V41 (4) : P917-927 doi: 10.1002/hbm.24849
Gray matter integrity predicts white matter network reorganization in multiple sclerosis.
Department of Neurology and Neuroimaging Center (NIC) of the Focus Program Translational Neuroscience (FTN), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.; Department of Neurology, University of Munster, Munster, Germany.
Multiple sclerosis (MS) is a chronic inflammatory and neurodegenerative disease leading to gray matter atrophy and brain network reconfiguration as a response to increasing tissue damage. We evaluated whether white matter network reconfiguration appears subsequently to gray matter damage, or whether the gray matter degenerates following alterations in white matter networks. MRI data from 83 patients with clinically isolated syndrome and early relapsing-remitting MS were acquired at two time points with a follow-up after 1 year. White matter network integrity was assessed based on probabilistic tractography performed on diffusion-weighted data using graph theoretical analyses. We evaluated gray matter integrity by computing cortical thickness and deep gray matter volume in 94 regions at both time points. The thickness of middle temporal cortex and the volume of deep gray matter regions including thalamus, caudate, putamen, and brain stem showed significant atrophy between baseline and follow-up. White matter network dynamics, as defined by modularity and distance measure changes over time, were predicted by deep gray matter volume of the atrophying anatomical structures. Initial white matter network properties, on the other hand, did not predict atrophy. Furthermore, gray matter integrity at baseline significantly predicted physical disability at 1-year follow-up. In a sub-analysis, deep gray matter volume was significantly related to cognitive performance at baseline. Hence, we postulate that atrophy of deep gray matter structures drives the adaptation of white matter networks. Moreover, deep gray matter volumes are highly predictive for disability progression and cognitive performance.
PMID: 32026599
Microorganisms , IF:4.152 , 2020 Mar , V8 (3) doi: 10.3390/microorganisms8030385
Insights into Thermophilic Plant Biomass Hydrolysis from Caldicellulosiruptor Systems Biology.
Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA.
Plant polysaccharides continue to serve as a promising feedstock for bioproduct fermentation. However, the recalcitrant nature of plant biomass requires certain key enzymes, including cellobiohydrolases, for efficient solubilization of polysaccharides. Thermostable carbohydrate-active enzymes are sought for their stability and tolerance to other process parameters. Plant biomass degrading microbes found in biotopes like geothermally heated water sources, compost piles, and thermophilic digesters are a common source of thermostable enzymes. While traditional thermophilic enzyme discovery first focused on microbe isolation followed by functional characterization, metagenomic sequences are negating the initial need for species isolation. Here, we summarize the current state of knowledge about the extremely thermophilic genus Caldicellulosiruptor, including genomic and metagenomic analyses in addition to recent breakthroughs in enzymology and genetic manipulation of the genus. Ten years after completing the first Caldicellulosiruptor genome sequence, the tools required for systems biology of this non-model environmental microorganism are in place.
PMID: 32164310
Brain Behav , IF:2.091 , 2020 Mar , V10 (3) : Pe01524 doi: 10.1002/brb3.1524
Exploring the social cognition network in young adults with autism spectrum disorder using graph analysis.
Department of Applied Clinical Sciences and Biotechnology, University of L'Aquila, L'Aquila, Italy.; Regional Centre for Autism, Abruzzo Region Health System, L'Aquila, Italy.; Department of Mental Health of Modena, AUSL Modena, Modena, Italy.
BACKGROUND: Autism spectrum disorder (ASD) is characterized by an impairment in social cognition (SC). SC is a cognitive construct that refers to the capacity to process information about social situations. It is a complex network that includes distinct components. Exploring how SC components work together leads to a better understanding of how their interactions promote adequate social functioning. Our main goal was to use a novel statistical method, graph theory, to analyze SC relationships in ASD and Typically Developing (TD) individuals. METHODS: We applied graph theory to SC measures to verify how the SC components interact and to establish which of them are important within the interacting SC network for TD and ASD groups. RESULTS: The results showed that, in the TD group, the SC nodes are connected; their network showed increased betweenness among nodes, especially for the Theory of Mind. By contrast, in the SC network in the ASD group the nodes are highly disconnected, and the efficient connection among the components is absent. CONCLUSION: ASD adults do not show SC competencies and functional communication among these skills. Under this regard, specific components are crucial, suggesting they could represent critical domains for ASD SC.
PMID: 31971664
Heliyon , 2020 Mar , V6 (3) : Pe03489 doi: 10.1016/j.heliyon.2020.e03489
Response of grass interplanting on bacterial and fungal communities in a jujube orchard in Ningxia, northwest China.
School of Agricultural, Ningxia University, Yinchuan, Ningxia 750021, PR China.
Orchard grass is an important soil management method that improves pest resistance in fruit trees and it reduces the usage of chemical fertilizer to protect the environment. In this study, we investigated the bacterial and fungi communities in the rhizosphere of Ziziphus jujuba Mill cv. 'lingwuchangzao' by high-throughput sequencing to test the effects of different sward types. The soil organic matter, available phosphorus, available potassium, and total nitrogen contents were higher with cleared tillage compared with the other planting grass treatments. Ascomycota, Basidiomycota, and Mortierellomycota were the dominant fungal groups. Most of the soil nutrient levels were lower in the treatments with grass (except for planting with ryegrass and pea grass) than cleared tillage, but there were no significant differences in the bacterial and fungi diversity. pH and total phosphorus were the main contributors to variations in the bacterial communities. The variations in the fungal communities were mainly attributed to the soil nutrient levels. The changes in the titratable acids and vitamin C contents were clearly correlated with the dynamics of the bacterial and fungi communities. Network analysis showed that 60% of the bacteria had close connections with fungi, including the dominant bacteria comprising Proteobacteria, Actinobacteria, and Bacteroidetes. Our findings demonstrated that different types of grass treatments affected the abundances of microbes rather than their composition.
PMID: 32154422