Overcoming challenges in human saliva gene expression measurements.

Abstract:

:Saliva, as a non-invasive and easily accessible biofluid, has been shown to contain RNA biomarkers for prediction and diagnosis of several diseases. However, systematic analysis done by our group identified two problematic issues not coherently described before: (1) most of the isolated RNA originates from the oral microbiome and (2) the amount of isolated human RNA is comparatively low. The degree of bacterial contamination showed ratios up to 1:900,000, so that only about one out of 900,000 RNA copies was of human origin, but the RNA quality (average RIN 6.7 + /- 0.8) allowed for qRT-PCR. Using 12 saliva samples from healthy donors, we modified the methodology to (1) select only human RNA during cDNA synthesis by aiming at the poly(A)+-tail and (2) introduced a pre-amplification of human RNA before qRT-PCR. Further, the manufacturer's criteria for successful pre-amplification (Ct values ≤ 35 for unamplified cDNA) had to be replaced by (3) proofing linear pre-amplification for each gene, thus, increasing the number of evaluable samples up to 70.6%. When considering theses three modifications unbiased gene expression analysis on human salivary RNA can be performed.

journal_name

Sci Rep

journal_title

Scientific reports

authors

Ostheim P,Tichý A,Sirak I,Davidkova M,Stastna MM,Kultova G,Paunesku T,Woloschak G,Majewski M,Port M,Abend M

doi

10.1038/s41598-020-67825-6

subject

Has Abstract

pub_date

2020-07-07 00:00:00

pages

11147

issue

1

issn

2045-2322

pii

10.1038/s41598-020-67825-6

journal_volume

10

pub_type

杂志文章
  • Inducible EphA4 knockout causes motor deficits in young mice and is not protective in the SOD1G93A mouse model of ALS.

    abstract::Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by motor neuron loss that ultimately leads to fatal paralysis. Reducing levels or function of the tyrosine kinase, ephrin type-A receptor 4 (EphA4), has been suggested as a potential approach for slowing disease progression in ALS. Becaus...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-72723-y

    authors: Dominguez SL,Earr T,Dourado M,Ngu H,Meilandt WJ,Hanson JE

    更新日期:2020-09-24 00:00:00

  • Relationship between lumbar lordosis and the ratio of the spinous process height to the anterior spinal column height.

    abstract::Purpose Global sagittal imbalance with lumbar hypo-lordosis leads to various problems in elderly populations and is often treated with long-segment fusion and osteotomy. These highly invasive procedures result in a wide range of rigid spines with a high rate of complications. Although some reports have mentioned the p...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-63648-7

    authors: Inanami H,Iwai H,Kaneko T,Oshina M,Manabe N,Takano Y,Yuzawa Y,Segawa T,Yanagisawa K,Hirai S,Saiki F,Fukushima M,Oka H,Matsudaira K,Oshima Y,Koga H

    更新日期:2020-04-21 00:00:00

  • Deletion of CD38 and supplementation of NAD+ attenuate axon degeneration in a mouse facial nerve axotomy model.

    abstract::Following facial nerve axotomy, nerve function is not fully restored even after reconstruction. This may be attributed to axon degeneration/neuronal death and sustained neuroinflammation. CD38 is an enzyme that catalyses the hydrolysis of nicotinamide adenine dinucleotide (NAD+) and is a candidate molecule for regulat...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-73984-3

    authors: Takaso Y,Noda M,Hattori T,Roboon J,Hatano M,Sugimoto H,Brenner C,Yamamoto Y,Okamoto H,Higashida H,Ito M,Yoshizaki T,Hori O

    更新日期:2020-10-20 00:00:00

  • Brazilian Maternal and Child Nutrition Consortium: establishment, data harmonization and basic characteristics.

    abstract::Pooled data analysis in the field of maternal and child nutrition rarely incorporates data from low- and middle-income countries and existing studies lack a description of the methods used to harmonize the data and to assess heterogeneity. We describe the creation of the Brazilian Maternal and Child Nutrition Consorti...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-71612-8

    authors: Carrilho TRB,Farias DR,Batalha MA,Costa NCF,Rasmussen KM,Reichenheim ME,Ohuma EO,Hutcheon JA,Kac G,Brazilian Maternal and Child Nutrition Consortium.

    更新日期:2020-09-10 00:00:00

  • On the first evidence of exchange-bias feature in magnetically contrasted consolidates made from CoFe2O4-CoO core-shell nanoparticles.

    abstract::Hetero-nanostructures based on magnetic contrast oxides have been prepared as highly dense nanoconsolidates. Cobalt ferrite-cobalt oxide core-shell type nanoparticles (NPs) were synthesized by seed mediated growth in polyol and subsequently consolidated by Spark Plasma Sintering (SPS) at 500 °C for a few minutes while...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-55649-y

    authors: Flores-Martinez N,Franceschin G,Gaudisson T,Haj-Khlifa S,Derouich SG,Yaacoub N,Grenèche JM,Menguy N,Valenzuela R,Ammar S

    更新日期:2019-12-19 00:00:00

  • Homogeneity of lithium distribution in cylinder-type Li-ion batteries.

    abstract::Spatially-resolved neutron powder diffraction with a gauge volume of 2 × 2 × 20 mm(3) has been applied as an in situ method to probe the lithium concentration in the graphite anode of different Li-ion cells of 18650-type in charged state. Structural studies performed in combination with electrochemical measurements an...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep18380

    authors: Senyshyn A,Mühlbauer MJ,Dolotko O,Hofmann M,Ehrenberg H

    更新日期:2015-12-18 00:00:00

  • Frontal cortex function as derived from hierarchical predictive coding.

    abstract::The frontal lobes are essential for human volition and goal-directed behavior, yet their function remains unclear. While various models have highlighted working memory, reinforcement learning, and cognitive control as key functions, a single framework for interpreting the range of effects observed in prefrontal cortex...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-21407-9

    authors: Alexander WH,Brown JW

    更新日期:2018-03-01 00:00:00

  • A negative covariation between toxoplasmosis and CoVID-19 with alternative interpretations.

    abstract::Coronaviruses may exert severely negative effects on the mortality and morbidity of birds and mammals including humans and domestic animals. Most recently CoVID-19 has killed about half million people (27th of June, 2020). Susceptibility to this disease appears to differ markedly across different societies but the fac...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-69351-x

    authors: Jankowiak Ł,Rozsa L,Tryjanowski P,Møller AP

    更新日期:2020-07-27 00:00:00

  • A Canonical Biophysical Model of the CsrA Global Regulator Suggests Flexible Regulator-Target Interactions.

    abstract::Bacterial global post-transcriptional regulators execute hundreds of interactions with targets that display varying molecular features while retaining specificity. Herein, we develop, validate, and apply a biophysical, statistical thermodynamic model of canonical target mRNA interactions with the CsrA global post-tran...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-27474-2

    authors: Leistra AN,Gelderman G,Sowa SW,Moon-Walker A,Salis HM,Contreras LM

    更新日期:2018-07-02 00:00:00

  • Cellular reprogramming for successful CNS axon regeneration is driven by a temporally changing cast of transcription factors.

    abstract::In contrast to mammals, adult fish display a remarkable ability to fully regenerate central nervous system (CNS) axons, enabling functional recovery from CNS injury. Both fish and mammals normally undergo a developmental downregulation of axon growth activity as neurons mature. Fish are able to undergo damage-induced ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-50485-6

    authors: Dhara SP,Rau A,Flister MJ,Recka NM,Laiosa MD,Auer PL,Udvadia AJ

    更新日期:2019-10-02 00:00:00

  • Low Complexity Compression and Speed Enhancement for Optical Scanning Holography.

    abstract::In this paper we report a low complexity compression method that is suitable for compact optical scanning holography (OSH) systems with different optical settings. Our proposed method can be divided into 2 major parts. First, an automatic decision maker is applied to select the rows of holographic pixels to be scanned...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep34724

    authors: Tsang PW,Poon TC,Liu JP,Kim T,Kim YS

    更新日期:2016-10-06 00:00:00

  • Abundance and sinking of particulate black carbon in the western Arctic and Subarctic Oceans.

    abstract::The abundance and sinking of particulate black carbon (PBC) were examined for the first time in the western Arctic and Subarctic Oceans. In the central Arctic Ocean, high PBC concentrations with a mean of 0.021 ± 0.016 μmol L(-1) were observed in the marginal ice zone (MIZ). A number of parameters, including temperatu...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep29959

    authors: Fang Z,Yang W,Chen M,Zheng M,Hu W

    更新日期:2016-07-15 00:00:00

  • Author Correction: Activation of endothelial β-catenin signaling induces heart failure.

    abstract::A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper. ...

    journal_title:Scientific reports

    pub_type: 已发布勘误

    doi:10.1038/s41598-018-34062-x

    authors: Nakagawa A,Naito AT,Sumida T,Nomura S,Shibamoto M,Higo T,Okada K,Sakai T,Hashimoto A,Kuramoto Y,Oka T,Lee JK,Harada M,Ueda K,Shiojima I,Limbourg FP,Adams RH,Noda T,Sakata Y,Akazawa H,Komuro I

    更新日期:2018-10-29 00:00:00

  • Genetic and scRNA-seq Analysis Reveals Distinct Cell Populations that Contribute to Salivary Gland Development and Maintenance.

    abstract::Stem and progenitor cells of the submandibular salivary gland (SMG) give rise to, maintain, and regenerate the multiple lineages of mature epithelial cells including those belonging to the ductal, acinar, basal and myoepithelial subtypes. Here we have exploited single cell RNA-sequencing and in vivo genetic lineage tr...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-32343-z

    authors: Song EC,Min S,Oyelakin A,Smalley K,Bard JE,Liao L,Xu J,Romano RA

    更新日期:2018-09-19 00:00:00

  • Effects of pirfenidone targeting the tumor microenvironment and tumor-stroma interaction as a novel treatment for non-small cell lung cancer.

    abstract::Targeting cancer-associated fibroblasts (CAFs), as well as the crosstalk between stroma and cancer cells, could be of value in managing cancers. Pirfenidone (PFD) is an anti-fibrotic agent for idiopathic pulmonary fibrosis. This study aimed to investigate the possibility that PFD might exert an anti-tumor effect throu...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-67904-8

    authors: Fujiwara A,Funaki S,Fukui E,Kimura K,Kanou T,Ose N,Minami M,Shintani Y

    更新日期:2020-07-02 00:00:00

  • Juvenile hormone regulation of female reproduction in the common bed bug, Cimex lectularius.

    abstract::To begin studies on reproduction in common bed bug, Cimex lectularius, we identified three genes coding for vitellogenin (Vg, a protein required for the reproductive success of insects) and studied their hormonal regulation. RNA interference studied showed that expression of Vg3 gene in the adult females is a prerequi...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep35546

    authors: Gujar H,Palli SR

    更新日期:2016-10-20 00:00:00

  • Non-classical MHC I-E negatively regulates macrophage activation and Th17 cell development in NOD mice.

    abstract::Transgenic expression of I-E molecules prevents diabetes in NOD mice. So far, the precise role of these non-classical MHC II molecules remains elusive. Here, we showed that transgenic expression of I-E(k) alpha 16 molecule in NOD mice selectively reduced Th17 cells in the thymus and pancreatic draining lymph nodes. Th...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep12941

    authors: Yang C,Guo N,Liu J,Yang J,Zhu K,Xiao H,Leng Q

    更新日期:2015-08-07 00:00:00

  • The impact of climate change and glacier mass loss on the hydrology in the Mont-Blanc massif.

    abstract::The Mont-Blanc massif, being iconic with its large glaciers and peaks of over 4,000 m, will experience a sharp increase in summer temperatures during the twenty-first century. By 2100, the impact of climate change on the cryosphere and hydrosphere in the Alps is expected to lead to a decrease in annual river discharge...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-67379-7

    authors: Laurent L,Buoncristiani JF,Pohl B,Zekollari H,Farinotti D,Huss M,Mugnier JL,Pergaud J

    更新日期:2020-06-26 00:00:00

  • Adalimumab Reduces Photoreceptor Cell Death in A Mouse Model of Retinal Degeneration.

    abstract::Growing evidence suggests that inflammation is involved in the progression of retinitis pigmentosa (RP) both in patients and in animal models. The aim of this study was to investigate the effect of Adalimumab, a monoclonal anti-TNFα antibody, on retinal degeneration in a murine model of human autosomal recessive RP, t...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep11764

    authors: Martínez-Fernández de la Cámara C,Hernández-Pinto AM,Olivares-González L,Cuevas-Martín C,Sánchez-Aragó M,Hervás D,Salom D,Cuezva JM,de la Rosa EJ,Millán JM,Rodrigo R

    更新日期:2015-07-14 00:00:00

  • Enhancing nanoparticle-based visible detection by controlling the extent of aggregation.

    abstract::Visible indication based on the aggregation of colloidal nanoparticles (NPs) is highly advantageous for rapid on-site detection of biological entities, which even untrained persons can perform without specialized instrumentation. However, since the extent of aggregation should exceed a certain minimum threshold to pro...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep00456

    authors: Lim S,Koo OK,You YS,Lee YE,Kim MS,Chang PS,Kang DH,Yu JH,Choi YJ,Gunasekaran S

    更新日期:2012-01-01 00:00:00

  • Changes in the adhesive properties of spider aggregate glue during the evolution of cobwebs.

    abstract::We compare the prey capture glues produced by orb-weaving spiders (viscid glue) and their evolutionary descendents, the cobweb-weaving spiders (gumfoot glue). These glues are produced in homologous glands but exhibit contrasting structure, properties and response to changing humidity. Individual glue droplet stretchin...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep00041

    authors: Sahni V,Blackledge TA,Dhinojwala A

    更新日期:2011-01-01 00:00:00

  • A national assessment of the epidemiology of severe fever with thrombocytopenia syndrome, China.

    abstract::First discovered in rural areas of middle-eastern China in 2009, severe fever with thrombocytopenia syndrome (SFTS) is an emerging tick-borne zoonosis affecting hundreds of cases reported in China each year. Using the national surveillance data from 2010 to 2013, we conducted this retrospective epidemiological study a...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep09679

    authors: Liu K,Zhou H,Sun RX,Yao HW,Li Y,Wang LP,Di Mu,Li XL,Yang Y,Gray GC,Cui N,Yin WW,Fang LQ,Yu HJ,Cao WC

    更新日期:2015-04-23 00:00:00

  • Ion-ion interactions in the denatured state contribute to the stabilization of CutA1 proteins.

    abstract::In order to elucidate features of the denatured state ensembles that exist in equilibrium with the native state under physiological conditions, we performed 1.4-μs molecular dynamics (MD) simulations at 400 K and 450 K using the monomer subunits of three CutA1 mutants from Escherichia coli: an SH-free mutant (Ec0SH) w...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-25825-7

    authors: Yutani K,Matsuura Y,Naitow H,Joti Y

    更新日期:2018-05-16 00:00:00

  • Laundry wastewater treatment using a combination of sand filter, bio-char and teff straw media.

    abstract::Numerous researchers have expressed concern over the emerging water scarcity issues around the globe. Economic water scarcity is severe in the developing countries; thus, the use of inexpensive wastewater treatment strategies can help minimize this issue. An abundant amount of laundry wastewater (LWW) is generated dai...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-54888-3

    authors: Yaseen ZM,Zigale TT,Tiyasha,D RK,Salih SQ,Awasthi S,Tung TM,Al-Ansari N,Bhagat SK

    更新日期:2019-12-10 00:00:00

  • Phylogenetic analysis of small ruminant lentiviruses in Germany and Iran suggests their expansion with domestic sheep.

    abstract::Small ruminant lentiviruses (SRLVs) are found in sheep in Germany and Iran. SRLVs have been classified into four genotypes: A-C and E. Genotype A has been subdivided into 20 subtypes. Previous studies suggested that, first, the ancestors of genotype A are those SRLVs found in Turkey, second, the evolution of SRLVs is ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-58990-9

    authors: Molaee V,Bazzucchi M,De Mia GM,Otarod V,Abdollahi D,Rosati S,Lühken G

    更新日期:2020-02-10 00:00:00

  • Emergence of life in an inflationary universe.

    abstract::Abiotic emergence of ordered information stored in the form of RNA is an important unresolved problem concerning the origin of life. A polymer longer than 40-100 nucleotides is necessary to expect a self-replicating activity, but the formation of such a long polymer having a correct nucleotide sequence by random react...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-58060-0

    authors: Totani T

    更新日期:2020-02-03 00:00:00

  • Friedelin Synthase from Maytenus ilicifolia: Leucine 482 Plays an Essential Role in the Production of the Most Rearranged Pentacyclic Triterpene.

    abstract::Among the biologically active triterpenes, friedelin has the most-rearranged structure produced by the oxidosqualene cyclases and is the only one containing a cetonic group. In this study, we cloned and functionally characterized friedelin synthase and one cycloartenol synthase from Maytenus ilicifolia (Celastraceae)....

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep36858

    authors: Souza-Moreira TM,Alves TB,Pinheiro KA,Felippe LG,De Lima GM,Watanabe TF,Barbosa CC,Santos VA,Lopes NP,Valentini SR,Guido RV,Furlan M,Zanelli CF

    更新日期:2016-11-22 00:00:00

  • Development of miniaturized walking biological machines.

    abstract::The quest to 'forward-engineer' and fabricate biological machines remains a grand challenge. Towards this end, we have fabricated locomotive "bio-bots" from hydrogels and cardiomyocytes using a 3D printer. The multi-material bio-bot consisted of a 'biological bimorph' cantilever structure as the actuator to power the ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep00857

    authors: Chan V,Park K,Collens MB,Kong H,Saif TA,Bashir R

    更新日期:2012-01-01 00:00:00

  • Cost-Effective and Highly Photoresponsive Nanophosphor-P3HT Photoconductive Nanocomposite for Near-Infrared Detection.

    abstract::The advent of flexible optoelectronic devices has accelerated the development of semiconducting polymeric materials. We seek to replace conventional expensive semiconducting photodetector materials with our cost-effective composite system. We demonstrate in this work the successful fabrication of a photoconductive com...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep16761

    authors: Tong Y,Zhao X,Tan MC,Zhao R

    更新日期:2015-11-16 00:00:00

  • Revelation of early detection of co-seismic ionospheric perturbations in GPS-TEC from realistic modelling approach: Case study.

    abstract::GPS-derived Total Electron Content (TEC) is an integrated quantity; hence it is difficult to relate the detection of ionospheric perturbations in TEC to a precise altitude. As TEC is weighted by the maximum ionospheric density, the corresponding altitude (hmF2) is, generally, assumed as the perturbation detection alti...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-30476-9

    authors: Thomas D,Bagiya MS,Sunil PS,Rolland L,Sunil AS,Mikesell TD,Nayak S,Mangalampalli S,Ramesh DS

    更新日期:2018-08-14 00:00:00