Looking for a needle in a haystack: de novo phenotypic target identification reveals Hippo pathway-mediated miR-202 regulation of egg production.

Understanding microRNA (miRNA) functions has been hampered by major difficulties in identifying their biological target(s). Currently, the main limitation is the lack of a suitable strategy to identify biologically relevant targets among a high number of putative targets. Here we provide a proof of concept of successful de novo (i.e. without prior knowledge of its identity) miRNA phenotypic target (i.e. target whose de-repression contributes to the phenotypic outcomes) identification from RNA-seq data. Using the medaka mir-202 knock-out (KO) model in which inactivation leads to a major organism-level reproductive phenotype, including reduced egg production, we introduced novel criteria including limited fold-change in KO and low interindividual variability in gene expression to reduce the list of 2853 putative targets to a short list of 5. We selected tead3b, a member of the evolutionarily-conserved Hippo pathway, known to regulate ovarian functions, due to its remarkably strong and evolutionarily conserved binding affinity for miR-202-5p. Deleting the miR-202-5p binding site in the 3' UTR of tead3b, but not of other Hippo pathway members sav1 and vgll4b, triggered a reduced egg production phenotype. This is one of the few successful examples of de novo functional assignment of a miRNA phenotypic target in vivo in vertebrates.

Blood culture quality assurance: findings from a RCPAQAP Key Incident Monitoring and Management Systems (KIMMS) audit of blood culture performance.

Blood cultures (BC) are the gold standard investigation for bloodstream infection. Standards exist for BC quality assurance, but key quality indicators are seldom measured. The Royal College of Pathologists of Australasia Quality Assurance Programs (RCPAQAP) Key Incident Monitoring and Management Systems (KIMMS) invited laboratories for the first time to participate in an audit to determine adult BC positivity rates, contamination rates, sample fill volumes and the proportion received as a single set. The overall aim of the KIMMS audit was to provide laboratories with a mechanism for peer review and benchmarking. Results from 45 laboratories were analysed. The majority of laboratories (n=28, 62%) reported a positivity rate outside the recommended range of 8-15%. Contamination rates ranged from zero (n=5) to 12.5%, with seven laboratories (15%) reporting a contamination rate greater than the recommended 3%. Fifteen laboratories (33%) reported an average fill volume of less than the recommended 8-10 mL per bottle, with 11 laboratories (24%) reporting fill volumes of 5 mL or less whilst 13 (28%) laboratories were not able to provide any fill volume data. Thirteen laboratories (29%) reported that 50% or more of BC were received as single set, and eight (17%) were not able to report this data. This audit highlights there are deficiencies in BC quality measures across laboratories. To support BC quality improvement efforts, RCPAQAP KIMMS will offer a yearly BC quality assurance audit to encourage laboratories to monitor their BC quality performance.

Review of current incidents and risk calculations used in the Royal College of Australasian Pathologists Key Incident Management and Monitoring Systems - a system that could be used by all Australasian medical laboratories, and easily adapted to worldwide use.

INTRODUCTION: The Royal College of Pathologists of Australasia Quality Assurance Programs (RCPAQAP) Key Incident Monitoring and Management Systems (KIMMS) program has found that some existing Quality Indicators are too broad or not well defined. The risk matrix in use does not allow changes in incident Detection or Probability. In 2020, a review was performed: what issues should KIMMS include as Key Incidents and how could risk measurement be improved? MATERIALS AND METHODS: Twenty-seven networked and stand-alone laboratories enrolled in KIMMS during 2020 were surveyed on 45 current and new indicators of risk in the total testing process. They were asked which indicators they considered were significant in causing patient harm. Existing risk matrices in use by members of the KIMMS Advisory Committee laboratories were reviewed regarding their size or structure (3x3 or 5x5) and the descriptions of consequences and probability. RESULTS: Thirteen participants indicated 21 indicators should be monitored, and the KIMMS Advisory committee added a further 13 (11 from the remaining 24 and 2 new). Of the five risk matrices reviewed, all consistently used a 5x5 matrix to estimate Consequences vs Probability of harm. The KIMMS advisory committee added a third parameter to the calculation of Risk, Detectability. CONCLUSION: All 34 pre- and post- indicators should be monitored, covering all aspects of the total testing cycle other than analytical. The risk measurement can be improved by introducing a 5x5 risk matrix to evaluate harm (consequences x probability) and then evaluating risk by adding detectability; risk equals harm x detectability.

C-ECi: a CUBIC-ECi combined clearing method for three-dimensional follicular content analysis in the fish ovary†.

Deciphering mechanisms of oocyte development in the fish ovary still remain challenging, and a comprehensive overview of this process at the level of the organ is still needed. The recent development of optical tissue clearing methods has tremendously boosted the three-dimensional (3D) imaging of large size biological samples that are naturally opaque. However, no attempt of clearing on fish ovary that accumulates extremely high concentration of lipids within oocytes has been reported to date. To face with this ovarian-specific challenge, we combined two existing clearing methods, the nontoxic solvent-based ethyl cinnamate (ECi) method for efficient clearing and the Clear Unobstructed Brain Imaging Cocktails and Computational (CUBIC) method to enhance lipid removal and reduce nonspecific staining. The methyl green fluorescent dye was used to stain nuclei and delineate the follicular structures that include oocytes. Using this procedure (named CUBIC-ECi [C-ECi]), ovaries of both medaka and trout could be imaged in 3D and follicles analyzed. To our knowledge, this is the first procedure elaborated for clearing and imaging fish ovary in 3D. The C-ECi method thus provides an interesting tool for getting precise quantitative data on follicular content in fish ovary and promises to be useful for further developmental and morphological studies.

Changes in error rates in the Australian key incident monitoring and management system program.

INTRODUCTION: The Key incident monitoring and management system program (KIMMS) program collects data for 19 quality indicators (QIs) from Australian medical laboratories. This paper aims to review the data submitted to see whether the number of errors with a higher risk priority number (RPN) have been reduced in preference to those with a lower RPN, and to calculate the cost of these errors. MATERIALS AND METHODS: Data for QIs from 60 laboratories collected through the KIMMS program from 2015 until 2018 were retrospectively reviewed. The results for each QI were averaged for the four-year average and coefficient of variation. To review the changes in QI frequency, the yearly averages for 2015 and 2018 were compared. By dividing the total RPN by 4 and multiplying that number by the cost of recollection of 30 AUD, it was possible to assign the risk cost of these errors. RESULTS: The analysis showed a drop in the overall frequency of incidents (6.5%), but a larger drop in risk (9.4%) over the period investigated. Recollections per year in Australia cost the healthcare industry 27 million AUD. If the RPN data is used, this cost increases to 66 million AUD per year. CONCLUSIONS: Errors with a higher RPN have fallen more than those with lower RPN. The data shows that the errors associated with phlebotomy are the ones that have most improved. Further improvements require a better understanding of the root cause of the errors and to achieve this, work is required in the collection of the data to establish best-practice guidelines.

MiR-202 controls female fecundity by regulating medaka oogenesis.

Female gamete production relies on coordinated molecular and cellular processes that occur in the ovary throughout oogenesis. In fish, as in other vertebrates, these processes have been extensively studied both in terms of endocrine/paracrine regulation and protein expression and activity. The role of small non-coding RNAs in the regulation of animal reproduction remains however largely unknown and poorly investigated, despite a growing interest for the importance of miRNAs in a wide variety of biological processes. Here, we analyzed the role of miR-202, a miRNA predominantly expressed in male and female gonads in several vertebrate species. We studied its expression in the medaka ovary and generated a mutant line (using CRISPR/Cas9 genome editing) to determine its importance for reproductive success with special interest for egg production. Our results show that miR-202-5p is the most abundant mature form of the miRNA and that it is expressed in granulosa cells and in the unfertilized egg. The knock out (KO) of mir-202 gene resulted in a strong phenotype both in terms of number and quality of eggs produced. Mutant females exhibited either no egg production or produced a dramatically reduced number of eggs that could not be fertilized, ultimately leading to no reproductive success. We quantified the size distribution of the oocytes in the ovary of KO females and performed a large-scale transcriptomic analysis approach to identified dysregulated molecular pathways. Together, cellular and molecular analyses indicate that the lack of miR-202 impairs the early steps of oogenesis/folliculogenesis and decreases the number of large (i.e. vitellogenic) follicles, ultimately leading to dramatically reduced female fecundity. This study sheds new light on the regulatory mechanisms that control the early steps of follicular development, including possible targets of miR-202-5p, and provides the first in vivo functional evidence that a gonad-predominant microRNA may have a major role in female reproduction.

Constant Quest for Quality: Digital Cytopathology.

BACKGROUND: Special consideration should be given when creating and selecting cytopathology specimens for digitization to maximize quality. Advances in scanning and viewing technology can also improve whole-slide imaging (WSI) output quality. METHODS: Accumulated laboratory experience with digitization of glass cytopathology slides was collected. RESULTS: This paper describes characteristics of a cytopathology glass slide that can reduce quality on resulting WSI. Important points in the glass cytopathology slide selection process, preparation, scanning, and WSI-editing process that will maximize the quality of the resulting acquired digital image are covered. The paper outlines scanning solutions which have potential to predict issues with a glass cytopathology slide before image acquisition, allowing for adjustment of the scanning approach. WSI viewing solutions that better simulate the traditional microscope experience are also discussed. CONCLUSION: In addition to taking advantage of technical advances, practical steps can taken to maximize quality of cytopathology WSI.

The key incident monitoring and management system - history and role in quality improvement.

BACKGROUND: The determination of reliable, practical Quality Indicators (QIs) from presentation of the patient with a pathology request form through to the clinician receiving the report (the Total Testing Process or TTP) is a key step in identifying areas where improvement is necessary in laboratories. METHODS: The Australasian QIs programme Key Incident Monitoring and Management System (KIMMS) began in 2008. It records incidents (process defects) and episodes (occasions at which incidents may occur) to calculate incident rates. KIMMS also uses the Failure Mode Effects Analysis (FMEA) to assign quantified risk to each incident type. The system defines risk as incident frequency multiplied by both a harm rating (on a 1-10 scale) and detection difficulty score (also a 1-10 scale). RESULTS: Between 2008 and 2016, laboratories participating rose from 22 to 69. Episodes rose from 13.2 to 43.4 million; incidents rose from 114,082 to 756,432. We attribute the rise in incident rate from 0.86% to 1.75% to increased monitoring. Haemolysis shows the highest incidence (22.6% of total incidents) and the highest risk (26.68% of total risk). "Sample is suspected to be from the wrong patient" has the second lowest frequency, but receives the highest harm rating (10/10) and detection difficulty score (10/10), so it is calculated to be the 8th highest risk (2.92%). Similarly, retracted (incorrect) reports QI has the 10th highest frequency (3.9%) but the harm/difficulty calculation confers the second highest risk (11.17%). CONCLUSIONS: TTP incident rates are generally low (less than 2% of observed episodes), however, incident risks, their frequencies multiplied by both ratings of harm and discovery difficulty scores, concentrate improvement attention and resources on the monitored incident types most important to manage.

Making sense of a haemolysis monitoring and reporting system: a nationwide longitudinal multimethod study of 68 Australian laboratory participant organisations.

BACKGROUND: The key incident monitoring and management systems (KIMMS) quality assurance program monitors incidents in the pre- and postanalytical phases of testing in medical laboratories. Haemolysed specimens have been found to be the most frequent preanalytical error and have major implications for patient care. The aims of this study were to assess the suitability of KIMMS for quality reporting of haemolysis and to devise a meaningful method for reporting and monitoring haemolysis. METHODS: A structured survey of 68 Australian KIMMS laboratory participant organisations was undertaken. Quarterly haemolysis reports (2011-2014) were analysed. RESULTS: Among 110 million accessions reported, haemolysis rates varied according to the reporting methods that participants used for assigning accessions (16% of participants reported haemolysis by specimen and 83% reported by episode) and counting haemolysis rejections (61% by specimen, 35% by episode and 3% by test). More than half of the participants (56%) assigned accessions by episode and counted rejections by specimen. For this group, the average haemolysis rate per 100,000 episodes was 177 rejected specimens with the average rate varying from 100 to 233 over time. The majority of participants (91%) determined rejections using the haemolysis index. Two thirds of participants (66%) recorded the haemolysis manually in laboratory information systems. CONCLUSIONS: KIMMS maintains the largest longitudinal haemolysis database in the world. However, as a means of advancing improvements in the quality of the preanalytical laboratory process, there is a need to standardise reporting methods to enable robust comparison of haemolysis rejection rates across participant laboratories.

External Quality Assessment beyond the analytical phase: an Australian perspective.

External Quality Assessment (EQA) is the verification, on a recurring basis, that laboratory results conform to expectations for the quality required for patient care. It is now widely recognised that both the pre- and post-laboratory phase of testing, termed the diagnostic phases, are a significant source of laboratory errors. These errors have a direct impact on both the effectiveness of the laboratory and patient safety. Despite this, Australian laboratories tend to be focussed on very narrow concepts of EQA, primarily surrounding test accuracy, with little in the way of EQA programs for the diagnostic phases. There is a wide range of possibilities for the development of EQA for the diagnostic phases in Australia, such as the utilisation of scenarios and health informatics. Such programs can also be supported through advances in health information and communications technology, including electronic test ordering and clinical decision support systems. While the development of such programs will require consultation and support from the referring doctors, and their format will need careful construction to ensure that the data collected is de-identified and provides education as well as useful and informative data, we believe that there is high value in the development of such programs. Therefore, it is our opinion that all pathology laboratories should strive to be involved in an EQA program in the diagnostic phases to both monitor the diagnostic process and to identify, learn from and reduce errors and near misses in these phases in a timely fashion.

High-resolution 3D imaging of whole organ after clearing: taking a new look at the zebrafish testis.

Zebrafish testis has become a powerful model for reproductive biology of teleostean fishes and other vertebrates and encompasses multiple applications in applied and basic research. Many studies have focused on 2D images, which is time consuming and implies extrapolation of results. Three-dimensional imaging of whole organs recently became an important challenge to better understand their architecture and allow cell enumeration. Several protocols have thus been developed to enhance sample transparency, a limiting step for imaging large biological samples. However, none of these methods has been applied to the zebrafish testis. We tested five clearing protocols to determine if some of them could be applied with only small modifications to the testis. We compared clearing efficiency at both macroscopic and microscopic levels. CUBIC and PACT were suitable for an efficient transparency, an optimal optical penetration, the GFP fluorescence preservation and avoiding meaningful tissue deformation. Finally, we succeeded in whole testis 3D capture at a cellular resolution with both CUBIC and PACT, which will be valuable in a standard workflow to investigate the 3D architecture of the testis and its cellular content. This paves the way for further development of high content phenotyping studies in several fields including development, genetic or toxicology.

Genome-wide identification of novel ovarian-predominant miRNAs: new insights from the medaka (Oryzias latipes).

MicroRNAs (miRNAs) are small, highly conserved non-coding RNAs that play important roles in the regulation of many physiological processes. However, the role of miRNAs in vertebrate oocyte formation (i.e., oogenesis) remains poorly investigated. To gain new insights into the roles of miRNAs in oogenesis, we searched for ovarian-predominant miRNAs. Using a microarray displaying 3,800 distinct miRNAs originating from different vertebrate species, we identified 66 miRNAs that are expressed predominantly in the ovary. Of the miRNAs exhibiting the highest overabundance in the ovary, 20 were selected for further analysis. Using a combination of QPCR and in silico analyses, we identified 8 novel miRNAs that are predominantly expressed in the ovary, including 2 miRNAs (miR-4785 and miR-6352) that exhibit strict ovarian expression. Of these 8 miRNAs, 7 were previously uncharacterized in fish. The strict ovarian expression of miR-4785 and miR-6352 suggests an important role in oogenesis and/or early development, possibly involving a maternal effect. Together, these results indicate that, similar to protein-coding genes, a significant number of ovarian-predominant miRNA genes are found in fish.

Key factors influencing the incidence of hemolysis: A critical appraisal of current evidence.

Hemolysis is a leading cause of pre-analytical laboratory errors. The identification of contributing factors is an important step towards the development of effective practices to reduce and prevent hemolysis. We performed a review of PUBMED, Embase, Medline and CINAHL to identify articles published between January 2000 and August 2016 that identified factors influencing in vitro hemolysis rates. The 40 studies included in this review provide excellent evidence that hemolysis rates are higher in Emergency Departments (EDs), for non-antecubital draws, for specimens drawn using an intravenous catheter compared to venipuncture and for samples transported by pneumatic tube compared to by hand. There is also good evidence that hemolysis rates are higher when specimens are not collected by professional phlebotomists, larger volume specimen tubes are used, specimen tubes are filled less than halfway and tourniquet time is greater than one minute. The results of this review suggest that hospitals and clinical laboratories should consider deploying phlebotomists in EDs, drawing all blood through a venipuncture, using the antecubital region as the optimum blood collection site and transporting specimens by laboratory assistant/other personnel, or if this in not practical, ensuring that pneumatic transport systems are validated, maintained and monitored. Studies also recommend making hemolysis a hospital-wide issue and ensuring high-quality staff training and adherence to standard operating procedures to reduce hemolysis rates. Awareness of the factors that influence hemolysis rates, and adoption of strategies to mitigate these risk factors, is an important step towards creating quality practices to reduce hemolysis rates and improve the quality of patient care.

Current Methods of Haemolysis Detection and Reporting as a Source of Risk to Patient Safety: a Narrative Review.

AIM: Haemolysis has a major impact on patient safety as the need for a replacement specimen increases the risk of injury and infection, delays test results and extends the duration of hospital stays. Consistency of haemolysis detection and reporting can facilitate the generation of benchmark data used to develop quality practices to monitor and reduce this leading cause of pre-analytical laboratory error. This review aims to investigate current methods of haemolysis detection and reporting. METHOD: Due to known heterogeneity and immaturity of the research field, a scoping search was conducted using PUBMED, Embase, Medline and CINAHL. Articles published between 2000 and 2014 that reported haemolysis rates in specimens from the general population were included. RESULTS: Of the 50 studies that met the inclusion criteria, 20 detected haemolysis using the Haemolysis Index (HI), 19 by visual inspection and 13 by undefined methods. There was large intra-study variation in the plasma free haemoglobin level used to establish haemolysis (HI: mean±SD 846±795 mg/L, range 150-3000 mg/L; Visual: 850±436 mg/L, 500-3000 mg/L). Sixteen studies reported the analyte of interest, with only three studies reporting a haemoglobin level at which the specimen would be rejected. CONCLUSION: Despite haemolysis being a frequent and costly problem with a negative impact on patient care, there is poor consistency in haemolysis detection and reporting between studies. Improved consistency would facilitate the generation of benchmark data used to create quality practices to monitor and reduce this leading cause of pre-analytical laboratory error.

Evidence for two distinct waves of epidermal ionocyte differentiation during medaka embryonic development.

BACKGROUND: The fish epidermis contains specific cells, or ionocytes, that are specialized in ion transport and contribute to the osmoregulatory function. Besides the zebrafish model, the medaka (Oryzias latipes) has recently emerged as an important model for osmoregulation studies because it possesses a particularly high adaptability to salinity changes. However, hindering the progress of research on embryonic ionocytes is the lack of a comprehensive view of their developmental dynamic. RESULTS: Using EdU integrations and the foxi3 and NKA markers, we characterized the proliferating progenitors of ionocytes (here called ionoblastes) and we quantified them, along with ionocytes, during embryogenesis. While progenitors of the vitellin zone promptly differentiate in a synchronous manner, progenitors of the lateral zone differentiate progressively and asynchronously. Furthermore, we evidenced that nhe3 is expressed in differentiated ionocytes of both zones, whereas ecac, ncc, and gcm2 are strictly specific of the lateral zone. We also evidenced that the two zones are differentially regulated in distilled water and seawater. CONCLUSIONS: Our data led us to propose a model timeline, which provides evidence for the expansion of two successive and distinct populations of ionocytes. This model opens the way for new studies related to epidermal development, plasticity and osmoregulation ontogeny.

Variation in Laboratory Reporting of Haemolysis - a Need for Harmonisation.

AIM: The purpose of this survey was to determine the cut-offs being used by Australian laboratories using their instrument's Haemolysis Index (HI), whether these cut-offs vary, and at what level of haemolysis (or haemolysis index) did laboratories stop reporting one or more analytes. This was done in response to the large numbers of haemolysed samples reported in the RCPAQAP Key Incident Monitoring and Management System External Quality Assurance program (KIMMS EQA) and lack of information in the literature at the time regarding what to do once a haemolysed sample was identified. As it was known from discussions with laboratory personnel that different instruments reported their HI differently, we asked for the results to be provided in g/L free haemoglobin. METHOD: An electronic survey was conducted with participants enrolled in the RCPA Quality Assurance Programs with a total of 68 laboratories responding to this survey. Some questions attracted a lower level of response. RESULTS: The responses showed a poor understanding of the relationship between HI units and haemoglobin concentration. There was wide variation in the way HI results were reported and thus comparing cut-off values for reporting specific analytes based on the HI was impossible to determine. CONCLUSION: There is a need to harmonise the way laboratories report analytes in the presence of haemolysis. This would involve adopting a uniform definition of HI and a protocol for laboratories to confirm for themselves the level of HI at which each analyte is no longer reported, as this is method dependent and so will vary from laboratory to laboratory.

Myostatin deficiency is associated with an increase in number of total axons and motor axons innervating mouse tibialis anterior muscle.

INTRODUCTION: Myostatin (Mstn) is a secreted protein that acts as a negative regulator of skeletal muscle mass. However, a critical evaluation of neuromuscular aspects of hypertrophied muscles induced by Mstn deficiency has not been done. METHODS: We compared the tibialis anterior muscle-nerve interrelationships in wild-type and Mstn-null mice of both genders by immunohistochemical analyses, which allowed us to count the number of total axons and motor axons and estimate the size of motor units and the innervation ratio of the tibialis anterior muscle (TAm). RESULTS: There was an increase in the number of total axons and motor axons, and higher values in both the motor unit size and the innervation ratio of Mstn-null TAm compared with those of wild-type TAm. CONCLUSIONS: We found that myostatin is involved either directly in the control of neuromuscular interrelationships or indirectly through its effect on muscle size.

AMPK promotes skeletal muscle autophagy through activation of forkhead FoxO3a and interaction with Ulk1.

In skeletal muscle, protein levels are determined by relative rates of protein synthesis and breakdown. The balance between synthesis and degradation of intracellular components determines the overall muscle fiber size. AMP-activated protein kinase (AMPK), a sensor of cellular energy status, was recently shown to increase myofibrillar protein degradation through the expression of MAFbx and MuRF1. In the present study, the effect of AMPK activation by AICAR on autophagy was investigated in muscle cells. Our results show that FoxO3a transcription factor activation by AMPK induces the expression of the autophagy-related proteins LC3B-II, Gabarapl1, and Beclin1 in primary mouse skeletal muscle myotubes and in the Tibialis anterior (TA) muscle. Time course studies reveal that AMPK activation by AICAR leads to a transient nuclear relocalization of FoxO3a followed by an increase of its cytosolic level. Moreover, AMPK activation leads to the inhibition of mTORC1 and its subsequent dissociation of Ulk1, Atg13, and FIP200 complex. Interestingly, we identify Ulk1 as a new interacting partner of AMPK in muscle cells and we show that Ulk1 is associated with AMPK under normal conditions and dissociates from AMPK during autophagy process. Moreover, we find that AMPK phosphorylates FoxO3a and Ulk1. In conclusion, our data show that AMPK activation stimulates autophagy in skeletal muscle cells through its effects on the transcriptional function of FoxO3a and takes part in the initiation of autophagosome formation by interacting with Ulk1. Here, we present new evidences that AMPK plays a crucial role in the fine tuning of protein expression programs that control skeletal muscle mass.