Abstract：
:Previous studies of protein fold space suggest that fold coverage is plateauing. However, sequence sampling has been -and remains to a large extent- heavily biased, focusing on culturable phyla. Sustained technological developments have fuelled the advent of metagenomics and single-cell sequencing, which might correct the current sequencing bias. The extent to which these efforts affect structural diversity remains unclear, although preliminary results suggest that uncultured organisms could constitute a source of new folds. We investigate to what extent genomes from uncultured and under-sampled phyla accessed through single cell sequencing, metagenomics and high-throughput culturing efforts have the potential to increase protein fold space, and conclude that i) genomes from under-sampled phyla appear enriched in sequences not covered by current protein family and fold profile libraries, ii) this enrichment is linked to an excess of short (and possibly partly spurious) sequences in some of the datasets, iii) the discovery rate of novel folds among sequences uncovered by current fold and family profile libraries may be as high as 36%, but would ultimately translate into a marginal increase in global discovery of novel folds. Thus, genomes from under-sampled phyla should have a rather limited impact on increasing coarse grained tertiary structure level novelty.
journal_name
Sci Repjournal_title
Scientific reportsauthors
Barry Roche D,Brüls Tdoi
10.1038/srep14717subject
Has Abstractpub_date
2015-10-05 00:00:00pages
14717issn
2045-2322pii
srep14717journal_volume
5pub_type
杂志文章abstract：:An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...
journal_title：Scientific reports
pub_type： 已发布勘误
doi：10.1038/s41598-020-58753-6
更新日期：2020-01-29 00:00:00
abstract：:Unlike individual, free-floating planktonic bacteria, biofilms are surface-attached communities of slow- or non-replicating bacteria encased within a protective extracellular polymeric matrix enabling persistent bacterial populations to tolerate high concentrations of antimicrobials. Our current antibacterial arsenal ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-017-01045-3
更新日期：2017-05-17 00:00:00
abstract：:A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper. ...
journal_title：Scientific reports
pub_type： 已发布勘误
doi：10.1038/s41598-018-23445-9
更新日期：2018-03-22 00:00:00
abstract：:Obesity is associated with dysregulated lipid metabolism and adipokine secretion. Our group has previously reported obesity and adipokines are associated with % total fatty acid (FA) differences in plasma phospholipids. The objective of our current study was to identify in which complex lipid species (i.e., phosphatid...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-017-05785-0
更新日期：2017-07-24 00:00:00
abstract：:People with normal hearing thresholds can nonetheless have difficulty with understanding speech in noisy backgrounds. The origins of such supra-threshold hearing deficits remain largely unclear. Previously we showed that the auditory brainstem response to running speech is modulated by selective attention, evidencing ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-50773-1
更新日期：2019-10-01 00:00:00
abstract：:Cerebellar involvement in cognition, as well as in sensorimotor control, is increasingly recognized and is thought to depend on connections with the cerebral cortex. Anatomical investigations in animals and post-mortem humans have established that cerebro-cerebellar connections are contralateral to each other and incl...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-017-13079-8
更新日期：2017-10-09 00:00:00
abstract：:The atomic-scale response of dielectrics/ferroelectrics to electric fields is central to their functionality. Here we introduce an in situ characterization method that reveals changes in the local atomic structure in polycrystalline materials under fields. The method employs atomic pair distribution functions (PDFs), ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep14678
更新日期：2015-10-01 00:00:00
abstract：:The opening of connexin (Cx) hemichannels in the membrane is tightly regulated by calcium (Ca2+) and membrane voltage. Electrophysiological and atomic force microscopy experiments indicate that Ca2+ stabilizes the hemichannel closed state. However, structural data show that Ca2+ binding induces an electrostatic seal p...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-017-15975-5
更新日期：2017-11-20 00:00:00
abstract：:The effect of free mate choice on the relative magnitude of fitness benefits has been examined among various species. The majority of the data show significant fitness benefits of mating with partners of an individual's own choice, highlighting elevated behavioral compatibility between partners with free mate choice. ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-017-10484-x
更新日期：2017-08-31 00:00:00
abstract：:Generally, the length of the oxide nanowires grown by vapor phase transport is limited by the degradation of the source materials. Furthermore, the source material is used once for the nanowires growth. By exploiting the Si-Zn phase diagram, we have developed a simple methodology for the non-catalytic growth of ultral...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep01172
更新日期：2013-01-01 00:00:00
abstract：:The numerous species that make up the oral microbiome are now understood to play a key role in establishment and maintenance of oral health. The ability to taxonomically identify community members at the species level is important to elucidating its diversity and association to health and disease. We report the overal...
journal_title：Scientific reports
pub_type： 杂志文章,随机对照试验
doi：10.1038/srep43344
更新日期：2017-02-27 00:00:00
abstract：:Countries in the Asia Pacific region aim to eliminate malaria by 2030. A cornerstone of malaria elimination is the effective management of Anopheles mosquito vectors. Current control tools such as insecticide treated nets or indoor residual sprays target mosquitoes in human dwellings. We find in a high transmission re...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep40551
更新日期：2017-01-16 00:00:00
abstract：:Barley (Hordeum vulgare L.) produces five leucine-derived hydroxynitrile glucosides, potentially involved in alleviating pathogen and environmental stresses. These compounds include the cyanogenic glucoside epiheterodendrin. The biosynthetic genes are clustered. Total hydroxynitrile glucoside contents were previously ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-41884-w
更新日期：2019-04-05 00:00:00
abstract：:Tuberculosis (TB) is the leading cause of death due to an infectious agent, but only a small fraction of those infected develop the disease. Cytokines are involved in the mediation and regulation of immunity, and their secretion patterns may reflect the infection status. To increase our understanding of immune respons...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-44294-0
更新日期：2019-06-03 00:00:00
abstract：:Transcriptomic analysis showed that the central circadian pathway genes had significantly altered expression in fracture calluses from mice fed a low phosphate diet. This led us to hypothesize that phosphate deficiency altered the circadian cycle in peripheral tissues. Analysis of the expression of the central clock g...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-018-31830-7
更新日期：2018-09-13 00:00:00
abstract：:Increasing the thermostability of proteins is often crucial for their successful use as analytic, synthetic or therapeutic tools. Most rational thermostabilization strategies were developed on small two-state proteins and, unsurprisingly, they tend to fail when applied to the much more abundant, larger, non-fully coop...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep09129
更新日期：2015-03-16 00:00:00
abstract：:Electronic textiles have garnered significant attention as smart technology for next-generation wearable electronic devices. The existing power sources lack compatibility with wearable devices due to their limited flexibility, high cost, and environment unfriendliness. In this work, we demonstrate bamboo fabric as a s...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-70182-z
更新日期：2020-08-06 00:00:00
abstract：:Inherited the advantages of inorganic salts and organic solvents, ionic liquids (ILs) exhibit many superior properties allowing them promising green solvents for the future. Although it has been widely acknowledged that the unique features of ILs originate from their dual ionic and organic nature, its microscopic phys...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep19644
更新日期：2016-01-19 00:00:00
abstract：:Sex-based variations in the immune response to the influenza vaccines was reported, however, the genetic basis responsible for the sex variations in the immune response toward the influenza vaccines remains unclear. Here, the genes responsible for sex-specific responses after vaccination with trivalent inactivated inf...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-018-31999-x
更新日期：2018-09-10 00:00:00
abstract：:The myxozoan parasite, Tetracapsuloides bryosalmonae has a two-host life cycle alternating between freshwater bryozoans and salmonid fish. Infected fish can develop Proliferative Kidney Disease, characterised by a gross lymphoid-driven kidney pathology in wild and farmed salmonids. To facilitate an in-depth understand...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-77881-7
更新日期：2021-01-25 00:00:00
abstract：:Here we report exquisitely distinct material properties of primary vascular smooth muscle (VSM) cells isolated from the thoracic aorta of adult (8 months) vs. aged (30 months) F344XBN rats. Individual VSM cells derived from the aged animals showed a tense internal network of the actin cytoskeleton (CSK), exhibiting in...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-018-20763-w
更新日期：2018-02-08 00:00:00
abstract：:The ongoing global intensification of wheat production will likely be accompanied by a rising pressure of Fusarium diseases. While utmost attention was given to Fusarium head blight (FHB) belowground plant infections of the pathogen have largely been ignored. The current knowledge about the impact of soil borne Fusari...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-018-31544-w
更新日期：2018-09-03 00:00:00
abstract：:A wide network of interconnected areas was previously found in neuroimaging studies involving normal as well as pathological subjects; however literature seems to suffer from a lack of investigation in glucose metabolism behaviour under olfactory condition. Thus, the present work describe for the first time a pure olf...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep05146
更新日期：2014-06-03 00:00:00
abstract：:This corrects the article DOI: 10.1038/srep46290. ...
journal_title：Scientific reports
pub_type： 杂志文章,已发布勘误
doi：10.1038/srep46823
更新日期：2017-05-22 00:00:00
abstract：:Long interspersed nuclear elements-1 (L1s) are a large family of retrotransposons. Retrotransposons are repetitive sequences that are capable of autonomous mobility via a copy-and-paste mechanism. In most copy events, only the L1 sequence is inserted, however, they can also mobilize the flanking non-repetitive region ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-017-15076-3
更新日期：2017-11-06 00:00:00
abstract：:The ability to harvest thermal energy and manipulate heat fluxes has recently attracted a great deal of research interest because this is critical to achieve efficient solar-to-thermal energy conversion in the technology of concentrated solar thermal collectors. Thermal metamaterials with engineered thermal conduction...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep11552
更新日期：2015-06-25 00:00:00
abstract：:Light-sheet microscopy enables considerable speed and phototoxicity gains, while quantitative-phase imaging confers label-free recognition of cells and organelles, and quantifies their number-density that, thermodynamically, is more representative of metabolism than size. Here, we report the fusion of these two imagin...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-76730-x
更新日期：2020-11-19 00:00:00
abstract：:Plant cell cultures are an attractive platform for the production of recombinant proteins. A major drawback, hindering the establishment of plant cell suspensions as an industrial platform, is the low product yield obtained thus far. Histone acetylation is associated with increased transcription levels, therefore it i...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-017-17006-9
更新日期：2017-12-01 00:00:00
abstract：:Several proteins and peptides in saliva were shown to stimulate gingival wound repair, but the role of salivary metabolites in this process remains unexplored. In vitro gingival re-epithelialization kinetics were determined using unstimulated saliva samples from healthy individuals collected during an experimental gin...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-59988-z
更新日期：2020-02-20 00:00:00
abstract：:Pseudomonas aeruginosa is a major threat for immune-compromised patients. Bacterial pneumonia can induce uncontrolled and massive neutrophil recruitment ultimately leading to acute respiratory distress syndrome and epithelium damage. Interleukin-22 plays a central role in the protection of the epithelium. In this stud...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-017-11518-0
更新日期：2017-09-08 00:00:00
