Direct Saliva Transcriptome Analysis

BACKGROUND Current standard operating procedures for salivary transcriptomic analysis require low temperatures and lengthy mRNA isolation, which substantially hamper its use in the clinic. We developed a streamlined, ambient-temperature processing, stabilization, and storage protocol for clinical analysis of salivary RNA. METHODS The direct saliva transcriptome analysis (DSTA) used cell-free saliva supernatant instead of isolated mRNA for saliva transcriptomic detection, and all procedures, including processing, stabilization, and storage of saliva samples, were performed at ambient temperature without a stabilizing reagent. We evaluated this streamlined protocol by comparing the mRNA expression levels of 3 saliva internal reference genes [glyceraldehyde-3-phosphate dehydrogenase (GAPDH); actin, beta (ACTB); and ribosomal protein S9 (RPS9)] to levels measured with standard procedures, and detecting the variation of their expression levels under long-term ambient temperature storage. The clinical utility of DSTA was assessed by use of 7 oral cancer salivary mRNA biomarkers in a clinical study. RESULTS Each saliva internal reference gene mRNA showed similar expression levels when assayed by the DSTA or standard procedures, and remained stable under ambient temperature storage for at least 10 weeks without significant degradation (P = 0.918, 0.288, and 0.242 for GAPDH, ACTB, and RPS9, respectively). Compared with standard procedures, the performance characteristics of oral cancer salivary transcriptomic markers were retained as assayed by DSTA after 10 weeks of storage at ambient temperature. These results indicate that the DSTA is a suitable alternative method for saliva transcriptomic analysis and is feasible for use in clinical cancer research applications. CONCLUSIONS The streamlined DSTA protocol can impact the saliva-handling method and improve the standard operating procedures for clinical saliva transcriptomic diagnostics.

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Virtual Global Transplant Laboratory Standard Operating Procedures for Blood Collection, PBMC Isolation, and Storage

Transplantation Direct ◽

10.1097/txd.0000000000000613 ◽

2016 ◽

Vol 2 (9) ◽

pp. e101 ◽

Cited By ~ 23

Author(s):

Lauren E. Higdon ◽

Karim Lee ◽

Qizhi Tang ◽

Jonathan S. Maltzman

Keyword(s):

Standard Operating Procedures ◽

Blood Collection ◽

Standard Operating ◽

And Storage

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Standard Operating Procedures for Biospecimen Collection, Processing, and Storage

Pancreas ◽

10.1097/mpa.0000000000001171 ◽

2018 ◽

Vol 47 (10) ◽

pp. 1213-1221 ◽

Cited By ~ 6

Author(s):

William E. Fisher ◽

Zobeida Cruz-Monserrate ◽

Amy L. McElhany ◽

Gregory B. Lesinski ◽

Phil A. Hart ◽

...

Keyword(s):

Standard Operating Procedures ◽

Biospecimen Collection ◽

Standard Operating ◽

Processing And Storage ◽

And Storage

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Stability of black grass jelly (Mesona chinensis) probioticated by encapsulation of Lactobacillus plantarum Mar8 with agar and gum Arabic

Nusantara Bioscience ◽

10.13057/nusbiosci/n110114 ◽

2019 ◽

Vol 11 (1) ◽

pp. 84-88 ◽

Cited By ~ 1

Author(s):

NILAM FADMAULIDHA WULANDARI ◽

TITIN YULINERY ◽

NANDANG SUHARNA ◽

NOVIK NURHIDAYAT

Keyword(s):

Ambient Temperature ◽

Lactobacillus Plantarum ◽

Storage Temperature ◽

Gum Arabic ◽

Gelling Agent ◽

Traditional Food ◽

Food Ingredients ◽

Agar Concentration ◽

And Storage ◽

Temperature Storage

Abstract. Wulandari NF, Yulinery T, Suharna N, Nurhidayat N. 2019. Stability of black grass jelly (Mesona chinensis) probioticated by encapsulation of Lactobacillus plantarum Mar8 with agar and gum Arabic. Nusantara Bioscience 11: 84-88. Black grass jelly [Mesona chinensis (Benth)] is one of the traditional food ingredients that can be used as the encapsulation material. However, syneresis easily occurs so that becomes a problem during storage. This study was conducted to evaluate the effect of type of stabilizers (agar and gum Arabic) and storage temperature (cold/4oC and ambient temperature/37oC) on black grass jelly stability and the viability of encapsulated Lactobacillus plantarum Mar8 in probiotication. The concentrations of stabilizers were 0.5%; 1.0%; 1.5% and 2.0% (w/v). The result showed that the syneresis rate was stable up to 2% of agar concentration at low storage temperature, while gum Arabic in the concentration of >1% resulted in increasing syneresis rate. Ambient temperature storage increased the syneresis rate. This study showed that agar or gum Arabic was supporting the probiotication as good encapsulant. Moreover, it was suitable for stabilizing or gelling agent at 0.5%-1% concentration to produce black grass jelly as RTD.

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Transcriptome Analysis Provides Insights into the Mechanism of Astaxanthin Enrichment in a Mutant of the Ridgetail White Prawn Exopalaemon carinicauda

Genes ◽

10.3390/genes12050618 ◽

2021 ◽

Vol 12 (5) ◽

pp. 618

Author(s):

Yue Jin ◽

Shihao Li ◽

Yang Yu ◽

Chengsong Zhang ◽

Xiaojun Zhang ◽

...

Keyword(s):

Transcriptome Analysis ◽

Underlying Mechanism ◽

Biological Processes ◽

Wild Type ◽

Expression Levels ◽

In The Wild ◽

Cuticle Proteins ◽

Apolipoprotein D ◽

High Level ◽

Lower Expression

A mutant of the ridgetail white prawn, which exhibited rare orange-red body color with a higher level of free astaxanthin (ASTX) concentration than that in the wild-type prawn, was obtained in our lab. In order to understand the underlying mechanism for the existence of a high level of free astaxanthin, transcriptome analysis was performed to identify the differentially expressed genes (DEGs) between the mutant and wild-type prawns. A total of 78,224 unigenes were obtained, and 1863 were identified as DEGs, in which 902 unigenes showed higher expression levels, while 961 unigenes presented lower expression levels in the mutant in comparison with the wild-type prawns. Based on Gene Ontology analysis and Kyoto Encyclopedia of Genes and Genomes analysis, as well as further investigation of annotated DEGs, we found that the biological processes related to astaxanthin binding, transport, and metabolism presented significant differences between the mutant and the wild-type prawns. Some genes related to these processes, including crustacyanin, apolipoprotein D (ApoD), cathepsin, and cuticle proteins, were identified as DEGs between the two types of prawns. These data may provide important information for us to understand the molecular mechanism of the existence of a high level of free astaxanthin in the prawn.

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Management of oxygen saturation monitoring in preterm newborns in the NICU: the Italian picture

Italian Journal of Pediatrics ◽

10.1186/s13052-021-01050-3 ◽

2021 ◽

Vol 47 (1) ◽

Author(s):

Serafina Perrone ◽

◽

Maurizio Giordano ◽

Giuseppe De Bernardo ◽

Paola Lugani ◽

...

Keyword(s):

Oxygen Saturation ◽

Healthcare Professionals ◽

Cross Sectional Study ◽

Standard Operating Procedures ◽

Specific Training ◽

Related Factors ◽

Cross Sectional ◽

Survey Form ◽

Standard Operating ◽

Oxygen Monitoring

Abstract Background Although many studies emphasize the importance of using oxygen saturation (SpO2) targets in the NICUs, there is a wide variability in used saturation ranges among centers. Primary aim was to draw a representative picture on how the management of oxygen monitoring is performed in the Italian NICUs. Second aim was to identify healthcare-professionals related factors associated with oxygen targeting in the preterm population. Methods Cross-sectional study with data collection via an electronic survey form. A questionnaire containing pre-piloted and open questions on monitoring and management of the SpO2 was administered to neonatologists across the network of the Italian Society of Neonatology. The questions focused on: the infrastructure, specific training, healthcare professionals and patients-related factors. The results of the survey were anonymously collected, summarized and analyzed. Results Out of 378 questionnaires, 93 were correctly filled. Thirty-six different SpO2 ranges were observed. Centers using written standard operating procedures on oxygen management and SpO2 monitoring maintained a correct average range of SpO2 90–95%, avoided hyperoxia and reconsidered saturation targets in relation to comorbidities. 39.8% of responders disabled alarms during neonatal care. One center used biomarkers for complete monitoring of neonatal oxygenation status. Conclusions There is considerable variation in SpO2 targets for preterm infants in the Italian NICUs. Standard operating procedures and specific training for health care personnel are the main factors playing a role for the correct maintenance of the recommended oxygen targets in preterms.

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O19 SBE, SOPs and COVID-19: Using simulation-based education (SBE) to facilitate the development of paediatric COVID-19 standard operating procedures (SOP)

10.1136/bmjstel-2020-aspihconf.19 ◽

2020 ◽

Author(s):

Frances Louise Hanlon ◽

Rosie Fish ◽

Emily Suckling ◽

Kirsty Brown

Keyword(s):

Standard Operating Procedures ◽

Simulation Based ◽

Standard Operating

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Improving Water Quality Can Reduce Pyrogenic Reactions Associated With Reuse of Cardiac Catheters

Infection Control and Hospital Epidemiology ◽

10.1086/502166 ◽

2003 ◽

Vol 24 (12) ◽

pp. 955-960 ◽

Cited By ~ 2

Author(s):

Rosemary E. Duffy ◽

Braulio Couto ◽

Jussara M. Pessoa ◽

Carlos Starling ◽

Silma Pinheiro ◽

...

Keyword(s):

Water Quality ◽

Cardiac Catheterization ◽

Linear Trend ◽

Phase 1 ◽

Standard Operating Procedures ◽

Chi Square ◽

Cardiac Catheters ◽

Standard Operating ◽

Chi Square Test ◽

Belo Horizonte

AbstractObjective:To report the results of our preintervention investigation and subsequent 19-month three-phase intervention study designed to reduce pyrogenic reactions among patients undergoing cardiac catheterization using reprocessed catheters.Design:A case-control study for the preintervention period and a prospective cohort study for the intervention period.Setting:A 400-bed hospital in Belo Horizonte, Brazil.Participants:Any patient undergoing cardiac catheterization in the hospital.Interventions:Three intervention phases were implemented to improve the quality of the water supplied to the cardiac catheter reprocessing laboratory. Standard operating procedures for reprocessing cardiac catheters were established and reprocessing staff were trained and educated.Results:The rate of pyrogenic reactions decreased significantly during the intervention phases, from 12.8% (159 of 1,239) in phase 1 to 5.3% (38 of 712) in phase 2 to 0.5% (4 of 769) in phase 3 (chi-square test for linear trend, 97.5;P< .001).Conclusion:Improving water quality and using standard operating procedures for reprocessing catheters can prevent pyrogenic reactions in hospitalized patients.

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