RESUMEN

Using histological cross-sections, the chondrocranium anatomy was reconstructed for two developmental stages of Hermann's tortoise (Testudo hermanni). The morphology differs from the chondrocrania of most other turtles by a process above the ectochoanal cartilage with Pelodiscus sinensis being the only other known species with such a structure. The anterior and posterior processes of the tectum synoticum are better developed than in most other turtles and an ascending process of the palatoquadrate is missing, which is otherwise only the case in pleurodiran turtles. The nasal region gets proportionally larger during development. We interpret the enlargement of the nasal capsules as an adaption to increase the surface area of the olfactory epithelium for better perception of volant odors. Elongation of the nasal capsules in trionychids, in contrast, is unlikely to be related to olfaction, while it is ambiguous in the case of Sternotherus odoratus. However, we have to conclude that research on chondrocranium anatomy is still at its beginning and more comprehensive detailed descriptions in relation to other parts of the anatomy are needed before providing broad-scale ecological and phylogenetic interpretations.

Asunto(s)

RESUMEN

Background: Ensuring the rapidity and accuracy of emergency laboratory test results is especially important to save the lives of patients with acute and critical conditions. To better meet the needs of clinicians and patients, detection efficiency can be improved by reducing extra-laboratory sample turnaround times (TATs) through the use of innovative pneumatic tube system (PTS) transport for sample transport. However, concerns remain regarding the potential compromise of sample quality during PTS transit relative to that occurring with manual transportation. This study was performed to evaluate the efficacy of an innovative PTS (Tempus600 PTS) relative to a traditional PTS in terms of sample transit time, sample quality, and the concordance of analytical results with those obtained from manually transported samples. Methods: In total, 30 healthy volunteers aged >18 years were recruited for this study, conducted for five consecutive days. Venous blood samples were collected from six volunteers per day at fixed timepoints. From each volunteer, nine blood samples were collected into tubes with tripotassium ethylene diamine tetraacetic acid anticoagulant, tubes with 3.2 % sodium citrate, and serum tubes with separation gel (n = 3 each) and subjected to all tests conducted in the emergency laboratory in our hospital. 270 blood samples from 30 healthy volunteers were transported and analyzed, yielding 6300 test results. The blood samples were divided randomly into three groups (each containing one tube of each type) and transported to the emergency laboratory manually and with Tempus600 PTS and conventional Swisslog PTS, respectively. The extra-laboratory TATs, sample quality, and test results of the transported blood samples were compared. Results: The sample quality and test results did not differ according to the delivery method. The TAT was much shorter with the Tempus600 than with the other two transport modes (58.40 ± 1.52 s vs. 1711.20 ± 77.56 s for manual delivery and 146.60 ± 1.82 s for the Swisslog PTS; P = 0.002). Conclusion: Blood sample transport with the Tempus600 PTS significantly reduced the extra-laboratory TAT without compromising sample quality or test result accuracy, thereby improving the efficiency of sample analysis and the services provided to clinicians and patients.

RESUMEN

OBJECTIVES: Efficient and timely transportation of clinical samples is pivotal to ensure accurate diagnoses and effective patient care. During the transportation process, preservation of sample integrity is crucial to avoid pre-analytical aberrations on laboratory results. Here, we present a comparative analysis between a two-step Tempus600 hub solution single-tube and a one-step, container-based pneumatic transport system (PTS) from Airco, for the in-house transportation of blood samples. METHODS: Ten blood samples from healthy volunteers were split in 10 mL collection tubes filled at full or half capacity for transportation with the two PTS (about 250 m). To compare the impact of transportation, markers of hemolysis such as lactate dehydrogenase (LDH), potassium (K+), and the hemolysis index (HI), were determined. Additionally, differences in HI in routine samples and repeated transportation was investigated. To assess and compare the mechanistic impact profiles, we recorded the acceleration profiles of the two PTS using a shock data logger. RESULTS: Transportation using the Tempus600 hub solution resulted in 49 and 46 % higher HI with samples filled to total or half capacity, respectively. Routine samples transported with the Tempus600 hub solution showed a higher median HI by 23 and 33 %. Additionally, shock logger analysis showed an elevated amount of shocks (6.5 fold) and shock intensities (1.8 fold). CONCLUSIONS: The Tempus600 hub solution caused an increased number of unreportable LDH or K+ results based on the hemolysis index. However, it was only statistically significant for LDH (p<0.01 and p<0.08) - while the comparisons for K+ were not statistically significant (p<0.28 and p<0.56).

RESUMEN

In this case report, we describe a patient who developed metastatic liver cancer of unknown primary origin one year following the surgical removal of a retroperitoneal adenocarcinoma. The retroperitoneal adenocarcinoma is considered a malignant transformation of teratoma (MTT), given the patient's distant history of testicular tumor excised 25 years prior and treated with chemotherapy. Despite no primary tumor being identified, the leading primary hypothesis is that the liver metastasis stemmed from the resected retroperitoneal adenocarcinoma from one year prior. We theorize that the patient's cisplatin-based chemotherapy 25 years ago may have triggered the MTT, as documented in the existing literature. Using TEMPUS gene testing on both the retroperitoneal adenocarcinoma and the recently discovered liver metastasis, we identified several genes with variants of unknown significance (VUS) that could potentially be linked to cisplatin chemotherapy resistance. While we cannot conclude that this patient definitively underwent MTT, it remains the most plausible explanation. Future research should investigate both the validity of the genes we have uncovered with respect to cisplatin resistance, as well as other genes associated with cisplatin resistance to further understand the pathogenesis of cisplatin resistance for better prediction of treatment response. As the world of medicine shifts towards individualized therapies and precision medicine, reporting and analyzing genetic mutations derived from tumors remains imperative. Our case report aims to contribute to the growing database of defined mutations and underscores the immense potential of genetic analysis in directing personalized treatment options.

RESUMEN

Based on histological cross-sections, the chondrocranium of the common musk turtle (Sternotherus odoratus) was reconstructed, described, and compared with other turtles. It differs from that of other turtle chondrocrania by possessing elongated, slightly dorsally orientated nasal capsules with three dorsolateral foramina, which might be homologous to the foramen epiphaniale, and by having an enlarged crista parotica. Additionally, the posterior part of the palatoquadrate is more elongated and more slender than in other turtles, while its ascending process is connected to the otic capsule by appositional bone. The proportions of the chondrocranium were also compared with those of "mature" chondrocrania of other turtle species in a Principal Component Analysis (PCA). Other than expected, the S. odoratus chondrocranium is not similar in proportions to those of chelydrids, the closest related species in the sample. The results indicate to differences in the proportions among larger turtle clades (e.g., Durocryptodira, Pleurodira, and Trionychia). S. odoratus is an exception to this pattern since it shows elongated nasal capsules similar to the trionychid Pelodiscus sinensis. A second PCA comparing the chondrocranial proportions of multiple developmental "stages" mostly shows differences between trionychids and all other turtles. S. odoratus is again similar to trionychids along PC1, but its proportions are the most similar along PC2 and PC3 to older "stages" of americhelydians, including the chelydrid Chelydra serpentina, which is related to chondrocranium height and quadrate width. We discuss potential ecological correlations of our findings mirrored in late embryonic stages.

RESUMEN

Whole-blood-derived transcriptional profiling is widely used in biomarker discovery, immunological research, and therapeutic development. Traditional molecular and high-throughput transcriptomic platforms, including molecular assays with quantitative PCR (qPCR) and RNA-sequencing (RNA-seq), are dependent upon high-quality and intact RNA. However, collecting high-quality RNA from field studies in remote tropical locations can be challenging due to resource restrictions and logistics of post-collection processing. The current study tested the relative performance of the two most widely used whole-blood RNA collection systems, PAXgene® and Tempus™, in optimal laboratory conditions as well as suboptimal conditions in tropical field sites, including the effects of extended storage times and high storage temperatures. We found that Tempus™ tubes maintained a slightly higher RNA quantity and integrity relative to PAXgene® tubes at suboptimal tropical conditions. Both PAXgene® and Tempus™ tubes gave similar RNA purity (A260/A280). Additionally, Tempus™ tubes preferentially maintained the stability of mRNA transcripts for two reference genes tested, Succinate dehydrogenase complex, subunit A (SDHA) and TATA-box-binding protein (TBP), even when RNA quality decreased with storage length and temperature. Both tube types preserved the rRNA transcript 18S ribosomal RNA (18S) equally. Our results suggest that Tempus™ blood RNA collection tubes are preferable to PAXgene® for whole-blood collection in suboptimal tropical conditions for RNA-based studies in resource-limited settings.

Asunto(s)

RESUMEN

OBJECTIVES: Pneumatic tube transportation of samples is an effective way of reducing turn-around-time, but evidence of the effect of pneumatic tube transportation on urine samples is lacking. We thus wished to investigate the effect of pneumatic tube transportation on various components in urine, in order to determine if pneumatic tube transportation of these samples is feasible. METHODS: One-hundred fresh urine samples were collected in outpatient clinics and partitioned with one partition being carried by courier to the laboratory, while the other was sent by pneumatic tube system (Tempus600). Both partitions were then analysed for soluble components and particles, and the resulting mean difference and limits of agreement were calculated. RESULTS: Albumin, urea nitrogen, creatinine, protein and squamous epithelial cells were unaffected by transportation in the Tempus600 system, while bacteria, renal tubular epithelial cells, white blood cells and red blood cells were affected and potassium and sodium may have been affected. CONCLUSIONS: Though pneumatic tube transportation did affect some of the investigated components, in most cases the changes induced were clinically acceptable, and hence samples could be safely transported by the Tempus600 pneumatic tube system. For bacteria, white blood cells and red blood cells local quality demands will determine if pneumatic tube transportation is appropriate.

Asunto(s)

RESUMEN

OBJECTIVE: Transcriptome analysis of human whole blood is used to discover biomarkers of diseases and to assess phenotypic traits. Here we have collected small volumes of blood in Tempus solution and tested whether different storage conditions have an impact on transcriptomic profiling. Fifty µl of blood were collected in 100µl of Tempus solutions, freezed at - 20 °C for 1 day and eventually thawed, stored and processed under five different conditions: (i) - 20 °C for 1 week; (ii) +4 °C for 1 week; (iii) room temperature for 1 week; (iv) room temperature for 1 day, - 20 °C for 1 day, room temperature until testing at day 7, (v) - 20 °C for 1 week, RNA was isolated and stored in GenTegra solution. We used 272 immune transcript specific assays to test the expression profiling using qPCR based Fluidigm BioMark HD dynamic array. RESULTS: RNA yield ranged between 0.17 and 1.39µg. Except for one sample, RIN values were > 7. Using Principal Component Analysis, we saw that the storage conditions did not drive sample distribution. The condition that showed larger variability was the RT-FR-RT (room temperature-freezing-room temperature), suggesting that freezing-thawing cycles may have a worse effect on data reproducibility than keeping the samples at room temperature.

Asunto(s)

RESUMEN

OBJECTIVE: Type I interferons (IFN) have important roles in many immune-mediated inflammatory diseases (IMIDs) and are a relatively new therapeutic target. Direct detection of type I IFNs has proved challenging, thus their presence is often inferred from the expression of interferon-stimulated genes (ISGs) and calculation of an interferon score (IS). The objective of this research was to determine if the expression of six common ISGs and subsequent IS were comparable when RNA was derived from the Tempus and PAXgene whole blood RNA collection systems. RESULTS: Whole blood was obtained from ten healthy adults, incubated ex vivo in the absence and presence of recombinant human IFNα then divided into PAXgene and Tempus tubes. Despite reports of tube-specific patterns of gene expression, quantitative PCR (qPCR) analysis revealed no significant differences between PAXgene and Tempus tubes in either the homeostatic or IFNα-induced expression of six ISGs (IFI27, IFI44L, IFIT1, ISG15, RSAD2, SIGLEC1). Overall there was a strong correlation in the IS between unstimulated (r = 0.92, p = 0.0005) and IFNα-stimulated (r = 0.71, p = 0.0268) samples derived from the PAXgene and Tempus tubes.

Asunto(s)

RESUMEN

Background Efficient blood stabilization is essential to obtaining reliable and comparable RNA analysis data in preclinical operations. PAXgene (Qiagen, Becton Dickinson) and Tempus (Applied Biosystems, Life Technologies) blood collection tubes with RNA stabilizers both avoid preanalytical degradation of mRNA by endogenous nucleases and modifications in specific mRNA concentrations by unintentional up- or down-regulation of gene expression. Methods Sixteen different preanalytical conditions were tested in PAXgene and Tempus blood samples from seven donors: different mixing after collection, different fill volumes and different 24-h transport temperature conditions after collection. RNA was extracted by column-based methods. The quality of the extracted RNA was assessed by spectrophotometric quantification, A260/A280 purity ratio, RNA Integrity Number (Agilent Bioanalyzer), miRNA quantative real time polymerase chain reaction (qRT-PCR) on two target miRNAs (RNU-24 and miR-16), mRNA quality index by qRT-PCR on the 3' and 5' region of the GAPDH gene, and the PBMC preanalytical score, based on the relative expression levels of the IL8 and EDEM3 coding genes. Results When PAXgene RNA and Tempus blood collection tubes were used following the manufacturers' instructions, there was no statistically or technically significant difference in the output RNA quality attributes. However, the integrity of the RNA extracted from Tempus collection tubes was more sensitive to fill volumes and effective inversion, than to storage temperature, while the integrity of RNA extracted from PAXgene collection tubes was more sensitive to effective inversion and storage temperature than to fill volumes. Conclusions Blood collection tubes with different RNA stabilizers present different robustness to common preanalytical variations.

Asunto(s)

RESUMEN

OBJECTIVE: Studies of mRNA and miRNA expression profiling increasingly use stabilized whole blood. Commercial RNA extraction kits do not provide information about the simultaneous recovery of both mRNA and miRNA. This study evaluated yield, quality, integrity and representation of mRNA and miRNA from whole blood stabilized in Tempus tubes using three RNA extraction kits; two filter-based (Tempus and Norgen) and one bead-based (MagMax; manual vs. semi-automated, and with and without DNase treatment). RESULTS: All RNA extraction kits and methods resulted in similar yields of mRNA (total RNA yield, quality, integrity and representation) whereas there were differences in yields of miRNA. MagMax, either manual or semi-automated, with or without DNase treatment, yielded 1.6-2.2-fold more miRNA than Tempus and Norgen kits. In addition, MagMax and Norgen methods gave greater than 12-fold more and 3.3-fold less enrichment of specific miRNA targets, respectively, in comparison to Tempus extraction reagents. This study identified MagMax kit for simultaneous recovery of both mRNA and miRNA from whole blood collected in Tempus tubes.

Asunto(s)

RESUMEN

OBJECTIVE: We use Tempus blood RNA tubes (Applied Biosystems) during health assessments of American moose (Alces alces spp.) as a minimally invasive means to obtain RNA. Here we describe a novel protocol to additionally isolate high-quality DNA from the supernatant remaining after the RNA isolation methodology. Metrics used to qualify DNA quality included measuring the concentration, obtaining a DNA integrity number from a genomic DNA ScreenTape assay (Agilent), and running the isolated DNA on an agarose gel. RESULTS: Of the 23 samples analyzed, the average DNA concentration was 121 ng/µl (range 4-337 ng/µl) and a genomic DNA ScreenTape assay of seven samples indicated high DNA integrity values for 6 of the 7 samples (range 9.1-9.4 out of 10). Of the DNA sent for genotyping by sequencing, all proved to be of sufficient integrity to yield high-quality next-generation sequence results. We recommend this simple procedure to maximize the yield of both RNA and DNA from blood samples.

Asunto(s)

RESUMEN

We have developed a clinically validated NGS assay that includes tumor, germline and RNA sequencing. We apply this assay to clinical specimens and cell lines, and we demonstrate a clinical sensitivity of 98.4% and positive predictive value of 100% for the clinically actionable variants measured by the assay. We also demonstrate highly accurate copy number measurements and gene rearrangement identification.

RESUMEN

BACKGROUND: The natural history of type 1 diabetes (T1D) is challenging to investigate, especially as pre-diabetic individuals are difficult to identify. Numerous T1D consortia have been established to collect whole blood for gene expression analysis from individuals with or at risk to develop T1D. However, with no universally accepted protocol for their collection, differences in sample processing may lead to variances in the results. Here, we examined whether the choice of blood collection tube and RNA extraction kit leads to differences in the expression of genes that are changed during the progression of T1D, and if these differences could be minimized by measuring gene expression directly from the lysate of whole blood. RESULTS: Microarray analysis showed that the expression of 901 genes is highly influenced by sample processing using the PAXgene versus the Tempus system. These included a significant number of lymphocyte-specific genes and genes whose expression has been reported to differ in the peripheral blood of at-risk and T1D patients compared to controls. We showed that artificial changes in gene expression occur when control and T1D samples were processed differently. The sample processing-dependent differences in gene expression were largely due to loss of transcripts during the RNA extraction step using the PAXgene system. The majority of differences were not observed when gene expression was measured in whole blood lysates prepared from blood collected in PAXgene and Tempus tubes. CONCLUSION: We showed that the gene expression profile of samples processed using the Tempus system is more accurate than that of samples processed using the PAXgene system. Variation in sample processing can result in misleading changes in gene expression. However, these differences can be minimized by measuring gene expression directly in whole blood lysates.

Asunto(s)

RESUMEN

BACKGROUND: More than 50,000 adult and cord blood samples were collected in Tempus tubes and stored at the Norwegian Institute of Public Health Biobank for future use. In this study, we systematically evaluated and compared five blood-RNA isolation protocols: three blood-RNA isolation protocols optimized for simultaneous isolation of all blood-RNA species (MagMAX RNA Isolation Kit, both manual and semi-automated protocols; and Norgen Preserved Blood RNA kit I); and two protocols optimized for large RNAs only (Tempus Spin RNA, and Tempus 6-port isolation kit). We estimated the following parameters: RNA quality, RNA yield, processing time, cost per sample, and RNA transcript stability of six selected mRNAs and 13 miRNAs using real-time qPCR. FINDINGS: Whole blood samples from adults (n = 59 tubes) and umbilical cord blood (n = 18 tubes) samples collected in Tempus tubes were analyzed. High-quality blood-RNAs with average RIN-values above seven were extracted using all five RNA isolation protocols. The transcript levels of the six selected genes showed minimal variation between the five protocols. Unexplained differences within the transcript levels of the 13 miRNA were observed; however, the 13 miRNAs had similar expression direction and they were within the same order of magnitude. Some differences in the RNA processing time and cost were noted. CONCLUSIONS: Sufficient amounts of high-quality RNA were obtained using all five protocols, and the Tempus blood RNA system therefore seems not to be dependent on one specific RNA isolation method.

Asunto(s)

RESUMEN

With this report we aim to make available a standard operating procedure (SOP) developed for RNA stabilization of small blood volumes collected via a finger stick. The anticipation that this procedure may be improved through peer-review and/or readers public comments is another element motivating the publication of this SOP. Procuring blood samples from human subjects can, among other uses, enable assessment of the immune status of an individual subject via the profiling of RNA abundance using technologies such as real time PCR, NanoString, microarrays or RNA-sequencing. It is often desirable to minimize blood volumes and employ methods that are the least invasive and can be practically implemented outside of clinical settings. Finger-stick blood samples are increasingly used for measurement of levels of pharmacological drugs and biological analytes. It is a simple and convenient procedure amenable for instance to field use or self-collection at home using a blood sample collection kit. Such methodologies should also enable the procurement of blood samples at high frequency for health or disease monitoring applications.

Asunto(s)