A conserved role for COMA/CENP-H/I/N kinetochore proteins in the spindle checkpoint.

The COMA/CENP-H/I kinetochore complex regulates microtubule dynamics at kinetochores. The complex is also required to generate spindle checkpoint signals in both yeast and human cells under conditions where Aurora B activity is compromised. Our data explain why mammalian cells treated with Aurora inhibitors still have a functional spindle assembly checkpoint (SAC), since the checkpoint signals through CENP-H/I/N. The SAC effect from depleting the CENP-H/I/N complex cannot be explained by a weakened SAC signal, and the complex has no role in the SAC response to paclitaxel. We propose a model to explain the differential response of human cells to nocodazole and paclitaxel.

Droplet Volume Variability and Impact on Digital PCR Copy Number Concentration Measurements.

Digital polymerase chain reaction (dPCR) is increasingly being adopted by reference material producers and metrology institutes for value assignment, and for homogeneity and stability studies of nucleic acid reference materials. A reference method procedure should fulfill several requirements, and the uncertainty and biases should be completely understood. A bias in target concentration when inaccurate droplet volume is used in the droplet dPCR measurement equation has previously been documented. In this study, we characterize both intrawell and interwell droplet volume variability using optical microscopy and determine the impact of these two sources of variability on target concentration estimates. A small optical distortion across the image was measured which, without correction, biased droplet volume measurements. Longitudinal monitoring of interwell droplet volume over 39 weeks using several lots of Mastermix demonstrated a mean droplet volume of 0.786 nL and intermediate precision of 1.7%. The frequency distribution of intrawell droplet volumes varied. Some wells displayed a skewed distribution which resulted in a small bias in estimated target concentration for a simulated dPCR with target concentrations of between 62 and 8000 copies µL-1. The size and direction of this bias was influenced by the distribution pattern of the droplet volumes within the well. The proportion of Mastermix in dPCR mix affected droplet volume. A pipetting error of 10% during mixing of the premix and Mastermix resulted in a 2.6% change in droplet volume and, consequently, a bias in concentration measurements highlighting the advantages of gravimetric preparation of dPCR mixes for high accuracy measurements.

Single swim sessions in C. elegans induce key features of mammalian exercise.

BACKGROUND: Exercise exerts remarkably powerful effects on metabolism and health, with anti-disease and anti-aging outcomes. Pharmacological manipulation of exercise benefit circuits might improve the health of the sedentary and the aging populations. Still, how exercised muscle signals to induce system-wide health improvement remains poorly understood. With a long-term interest in interventions that promote animal-wide health improvement, we sought to define exercise options for Caenorhabditis elegans. RESULTS: Here, we report on the impact of single swim sessions on C. elegans physiology. We used microcalorimetry to show that C. elegans swimming has a greater energy cost than crawling. Animals that swam continuously for 90 min specifically consumed muscle fat supplies and exhibited post-swim locomotory fatigue, with both muscle fat depletion and fatigue indicators recovering within 1 hour of exercise cessation. Quantitative polymerase chain reaction (qPCR) transcript analyses also suggested an increase in fat metabolism during the swim, followed by the downregulation of specific carbohydrate metabolism transcripts in the hours post-exercise. During a 90 min swim, muscle mitochondria matrix environments became more oxidized, as visualized by a localized mitochondrial reduction-oxidation-sensitive green fluorescent protein reporter. qPCR data supported specific transcriptional changes in oxidative stress defense genes during and immediately after a swim. Consistent with potential antioxidant defense induction, we found that a single swim session sufficed to confer protection against juglone-induced oxidative stress inflicted 4 hours post-exercise. CONCLUSIONS: In addition to showing that even a single swim exercise bout confers physiological changes that increase robustness, our data reveal that acute swimming-induced changes share common features with some acute exercise responses reported in humans. Overall, our data validate an easily implemented swim experience as C. elegans exercise, setting the foundation for exploiting the experimental advantages of this model to genetically or pharmacologically identify the exercise-associated molecules and signaling pathways that confer system-wide health benefits.

Interlaboratory Reproducibility of Droplet Digital Polymerase Chain Reaction Using a New DNA Reference Material Format.

Use of droplet digital PCR technology (ddPCR) is expanding rapidly in the diversity of applications and number of users around the world. Access to relatively simple and affordable commercial ddPCR technology has attracted wide interest in use of this technology as a molecular diagnostic tool. For ddPCR to effectively transition to a molecular diagnostic setting requires processes for method validation and verification and demonstration of reproducible instrument performance. In this study, we describe the development and characterization of a DNA reference material (NMI NA008 High GC reference material) comprising a challenging methylated GC-rich DNA template under a novel 96-well microplate format. A scalable process using high precision acoustic dispensing technology was validated to produce the DNA reference material with a certified reference value expressed in amount of DNA molecules per well. An interlaboratory study, conducted using blinded NA008 High GC reference material to assess reproducibility among seven independent laboratories demonstrated less than 4.5% reproducibility relative standard deviation. With the exclusion of one laboratory, laboratories had appropriate technical competency, fully functional instrumentation, and suitable reagents to perform accurate ddPCR based DNA quantification measurements at the time of the study. The study results confirmed that NA008 High GC reference material is fit for the purpose of being used for quality control of ddPCR systems, consumables, instrumentation, and workflow.

Participatory methods for research prioritization in primary care: an analysis of the World Café approach in Ireland and the USA.

Background: There are increasing imperatives for patients and members of the public to engage as partners in identifying health research priorities. The use of participatory methods to engage stakeholders in health care in research prioritization is not commonly reported. Objective: This article analyses the use of World Cafés as a participatory method for research prioritization with marginalized communities in Ireland and the USA. Methods: The principles of purposeful and snowball sampling were followed in both settings and a diverse range of community and health care stakeholders participated (n = 63 Ireland and n = 55 USA). The principles for a classic World Café were employed but there were novel features in each setting as well. Stewart et al.'s (Patients' and clinicians' research priorities. Health Expect 2011; 14: 439-48, conceptual framework for patient engagement was adapted and used to comparatively analyse the strengths and weaknesses of the World Cafés, focusing on agenda setting, engagement with research processes, interactional features and outputs. Results: Design principles for World Cafés were found to align with high-quality patient engagement for research prioritization in both settings. They served to facilitate meaningful collaboration among stakeholder groups in research prioritization (research agenda setting) and explored research priorities (engagement with research). The café ambience, emphasis on hospitality and self-facilitation created an environment for dialogues within and across participating groups (interactional features). There was a commitment to follow-up actions with reference to possible subsequent research (outputs). Conclusions: The World Café is a valuable, participatory, flexible method that can be used with community and health care stakeholders for research prioritization with marginalized communities.

Aberrations in stimulated emission depletion (STED) microscopy.

Like all methods of super-resolution microscopy, stimulated emission depletion (STED) microscopy can suffer from the effects of aberrations. The most important aspect of a STED microscope is that the depletion focus maintains a minimum, ideally zero, intensity point that is surrounded by a region of higher intensity. It follows that aberrations that cause a non-zero value of this minimum intensity are the most detrimental, as they inhibit fluorescence emission even at the centre of the depletion focus. We present analysis that elucidates the nature of these effects in terms of the different polarisation components at the focus for two-dimensional and three-dimensional STED resolution enhancement. It is found that only certain low-order aberration modes can affect the minimum intensity at the Gaussian focus. This has important consequences for the design of adaptive optics aberration correction systems.

Interpreting spatial information and regulating mitosis in response to spindle orientation.

The spindle position checkpoint (SPOC) is a regulatory mechanism that ensures accurate segregation of chromosomes in polarized cells during mitosis. In this issue of Genes & Development, Chan and Amon (pp. 1639-1649) identify a phosphoprotein phosphatase (Rts1-PP2A) as a new member of the checkpoint in budding yeast and define its role in interpreting spatial information during mitosis.

Connecting the microtubule attachment status of each kinetochore to cell cycle arrest through the spindle assembly checkpoint.

Kinetochores generate a signal that inhibits anaphase progression until every kinetochore makes proper attachments to spindle microtubules. This spindle assembly checkpoint (SAC) increases the fidelity of chromosome segregation. We will review the molecular mechanisms by which kinetochores generate the SAC and extinguish the signal after making proper attachments, with the goal of identifying unanswered questions and new research directions. We will emphasize recent breakthroughs in how phosphorylation changes drive the activation and inhibition of the signal. We will also emphasize the dramatic changes in kinetochore structure that occur after attaching to microtubules and how these coordinate SAC function with microtubule attachment status. Finally, we will review the emerging cross talk between the DNA damage response and the SAC.

International Comparison of Enumeration-Based Quantification of DNA Copy-Concentration Using Flow Cytometric Counting and Digital Polymerase Chain Reaction.

Enumeration-based determination of DNA copy-concentration was assessed through an international comparison among national metrology institutes (NMIs) and designated institutes (DIs). Enumeration-based quantification does not require a calibration standard thereby providing a route to "absolute quantification", which offers the potential for reliable value assignments of DNA reference materials, and International System of Units (SI) traceability to copy number 1 through accurate counting. In this study, 2 enumeration-based methods, flow cytometric (FCM) counting and the digital polymerase chain reaction (dPCR), were compared to quantify a solution of the pBR322 plasmid at a concentration of several thousand copies per microliter. In addition, 2 orthogonal chemical-analysis methods based on nucleotide quantification, isotope-dilution mass spectrometry (IDMS) and capillary electrophoresis (CE) were applied to quantify a more concentrated solution of the plasmid. Although 9 dPCR results from 8 laboratories showed some dispersion (relative standard deviation [RSD] = 11.8%), their means were closely aligned with those of the FCM-based counting method and the orthogonal chemical-analysis methods, corrected for gravimetric dilution factors. Using the means of dPCR results, the RSD of all 4 methods was 1.8%, which strongly supported the validity of the recent enumeration approaches. Despite a good overall agreement, the individual dPCR results were not sufficiently covered by the reported measurement uncertainties. These findings suggest that some laboratories may not have considered all factors contributing to the measurement uncertainty of dPCR, and further investigation of this possibility is warranted.

Three-dimensional STED microscopy of aberrating tissue using dual adaptive optics.

When imaging through tissue, the optical inhomogeneities of the sample generate aberrations that can prevent effective Stimulated Emission Depletion (STED) imaging. This is particularly problematic for 3D-enhanced STED. We present here an adaptive optics implementation that incorporates two adaptive optic elements to enable correction in all beam paths, allowing performance improvement in thick tissue samples. We use this to demonstrate 3D STED imaging of complex structures in Drosophila melanogaster brains.

Coma aberrations in combined two- and three-dimensional STED nanoscopy.

Stimulated emission depletion (STED) microscopes, like all super-resolution methods, are sensitive to aberrations. Of particular importance are aberrations that affect the quality of the depletion focus, which requires a point of near-zero intensity surrounded by strong illumination. We present analysis, modeling, and experimental measurements that show the effects of coma aberrations on depletion patterns of two-dimensional (2D) and three-dimensional (3D) STED configurations. Specifically, we find that identical coma aberrations create focal shifts in opposite directions in 2D and 3D STED. This phenomenon could affect the precision of microscopic measurements and has ramifications for the efficacy of combined 2D/3D STED systems.

Nephrectomy for benign disease in the UK: results from the British Association of Urological Surgeons nephrectomy database.

OBJECTIVE: To summarize the practice of UK urologists with regard to nephrectomy for benign disease, documenting the indications, procedural techniques and outcomes. METHODS: All patients undergoing nephrectomy for a benign condition in 2012 were identified from the British Association of Urological Surgeons (BAUS) nephrectomy database. Recorded variables included the technique of surgery, the type of minimally invasive procedure, operating time, blood loss, transfusion rate, conversion rate, intra- and postoperative complications and mortality rate. Cases were also sub-analysed according to their pathologies to determine the differences in complication rate between stone disease, pyelonephritis, non-functioning kidney and other benign lesions. To contextualize procedural complexity, the simple nephrectomy data were compared with those obtained from the BAUS stage T1 radical nephrectomy audit. RESULTS: A total of 1 093 nephrectomies were performed (537 non-functioning kidneys, 142 stone disease, 129 nephrectomies secondary to pyelonephritis and 285 cases with other benign conditions). Of these, 76% were performed laparoscopically. Blood loss >500 mL was noted in 74 cases with a 4.8% blood transfusion rate. The intra- and postoperative complication rates were 5.2 and 11.9%, respectively. Of the 847 minimally invasive procedures, the conversion rate was 5.9%. Patients with stone disease have the highest intra- and postoperative complications (9.9 and 23.9%, respectively) compared with other benign pathologies. The total number of T1 radical nephrectomies performed was 1 095. In comparison with T1 radical nephrectomy, simple nephrectomy carries an increased risk of conversion to an open procedure (1.8 times), a higher rate of blood transfusion (4.8 vs 2.8%), and a higher risk of intra- and postoperative complications (5.2 vs 3.7% and 11.9 vs 10%, respectively). CONCLUSION: The present study reports the largest series of nephrectomies performed for benign disease and the resultant data now support the bespoke preoperative counselling of patients. Furthermore, it confirms the commonly held view that simple nephrectomy can be more difficult than its radical counterpart. The authors suggest that the term 'simple nephrectomy' is changed to 'benign nephrectomy'.

Dynamics of house dust mite transfer in modern clothing fabrics.

BACKGROUND: Clothing is largely presumed as being the mechanism by which house dust mites are distributed among locations in homes, yet little research to date has investigated the capacity with which various clothing fabric types serve as vectors for their accumulation and dispersal. Although previous research has indicated that car seats provide a habitat for mite populations, dynamics involved in the transfer of mites to clothing via car seat material is still unknown. OBJECTIVE: To investigate the dynamics involved in the transfer of house dust mites from car seat material to modern clothing fabrics. METHODS: A total of 480 samples of car seat material were seeded with mites and subjected to contact with plain woven cotton, denim, and fleece. Contact forces equivalent to the mass of a typical adult and child were administered for different durations of contact. RESULTS: Mean transfer efficiencies of mites from car seat material to receiving clothing fabrics ranged from 7.2% to 19.1%. Fabric type, mite condition (live or dead), and the force applied all revealed a significant effect (P < .001 for each variable) on the transfer efficiency of house dust mites from seeded material to receiving fabrics, whereas duration of contact revealed no effect (P = .20). In particular, mean numbers of mites transferred to fleece (compared with denim and plain woven cotton) were greater for each treatment. CONCLUSION: These findings indicate that clothing type can have important implications for the colonization of other biotopes by house dust mites, with potential for affecting an individuals' personal exposure to dust mite allergens.

Validation of DNA methylation biomarkers for diagnosis of acute lymphoblastic leukemia.

BACKGROUND: DNA methylation biomarkers capable of diagnosis and subtyping have been found for many cancers. Fifteen such markers have previously been identified for pediatric acute lymphoblastic leukemia (ALL). Validation of these markers is necessary to assess their clinical utility for molecular diagnostics. Substantial efficiencies could be achieved with these DNA methylation markers for disease tracking with potential to replace patient-specific genetic testing. METHODS: We evaluated DNA methylation of promoter regions of TLX3 (T-cell leukemia homeobox) and FOXE3 (forkhead box E3) in bone marrow biopsies from 197 patients classified as leukemic (n = 95) or clear of the disease (n = 102) by MALDI-TOF. Using a single nucleotide extension assay (methylSABER), we tested 10 bone marrow biopsies collected throughout the course of patient chemotherapy. Using reference materials, diagnostic thresholds and limits of detection were characterized for both methods. RESULTS: Reliable detection of DNA methylation of TLX3 and FOXE3 segregated ALL from those clear of disease with minimal false-negative and false-positive results. The limit of detection with MALDI-TOF was 1000-5000 copies of methylated allele. For methylSABER, the limit of detection was 10 copies of methylated TLX3, which enabled monitoring of minimal residual disease in ALL patients. CONCLUSIONS: Mass spectrometry procedures can be used to regionally multiplex and detect rare DNA methylation events, establish DNA methylation loci as clinically applicable biomarkers for disease diagnosis, and track pediatric ALL.

Unbiased segregation of yeast chromatids in Saccharomyces cerevisiae.

The budding yeast Saccharomyces cerevisiae is characterized by asymmetric cell division and the asymmetric inheritance of spindle components during normal vegetative growth and during certain specialized cell divisions. There has been a longstanding interest in the possibility that yeast chromosomes segregate non-randomly during mitosis and that some of the differences between mother and daughter cells could be explained by selective chromatid segregation. This review traces the history of the experiments to determine if there is biased chromatid segregation in yeast. The special aspects of spindle morphogenesis and behavior in yeast that could accommodate a mechanism for biased segregation are discussed. Finally, a recent experiment demonstrated that yeast chromatids segregate randomly without mother-daughter bias in a common laboratory strain grown under routine laboratory conditions.

DNA methylation ratio variability may impede clinical application of cancer diagnostic markers.

Hypermethylation at promoter regions of tumour suppressor genes is diagnostic for many cancers. Many genomic regions that may be the targets for clinical diagnostic assays have been identified through use of measuring systems reliant on bisulphite conversion, but few of these promising markers are in clinical use. The comparability of a widely used DNA methylation measuring system involving bisulphite conversion was evaluated by supplying three experienced centres with methylated DNA reference material mixtures that were independently prepared and characterised by mass spectrometry and high-pressure liquid chromatography. A replication scheme was designed to evaluate reproducibility of key analytical steps within and between laboratories by regression analysis. In general, methylation was underestimated and methylation ratio values were highly variable. The difference in methylation ratio between CpG sites was the key contributor to variable results. The CpG site effect followed a similar pattern at all centres and at all methylation levels examined indicating that sequence context had a major effect on methylation ratio measurement using the bisulphite conversion process. The magnitude of underestimation combined with the variability of measurements between CpG sites compromises the concept of measuring genomic regional methylation by averaging the methylation ratios of many CpG sites. There were no significant differences in replicate bisulphite conversions or sample work-up and instrument analysis at each centre thus making this technique suitable for comparative intralaboratory investigations. However, it may not be suitable for a routine diagnostic assay without extensive standardisation efforts.

Effect of body mass index on stroke rehabilitation.

OBJECTIVE: To investigate the association between body mass index (BMI) and the functional progress of patients with stroke, admitted to a rehabilitation hospital. DESIGN: A retrospective cohort study. SETTING: A freestanding university rehabilitation hospital stroke unit. PARTICIPANTS: All patients (N=819) admitted to the stroke unit of a rehabilitation hospital during the study. INTERVENTIONS: Not applicable. MAIN OUTCOME MEASURES: The primary study outcome measure was the FIM efficiency of patients by BMI category. RESULTS: For the 819 patients admitted during the observation period, BMI was compared with FIM score changes per day (FIM efficiency). After adjusting for age and sex, the FIM efficiency differed by BMI. The underweight group had the lowest FIM efficiency, followed by the obese and normal-weight subgroups. The overweight group had the highest FIM efficiency (P=.05) when compared with the obese subgroup. CONCLUSIONS: Among patients admitted to an acute rehabilitation hospital for stroke rehabilitation, overweight patients had better functional progress than did patients in the other weight categories.

Novel interactions between actin and the proteasome revealed by complex haploinsufficiency.

Saccharomyces cerevisiae has been a powerful model for uncovering the landscape of binary gene interactions through whole-genome screening. Complex heterozygous interactions are potentially important to human genetic disease as loss-of-function alleles are common in human genomes. We have been using complex haploinsufficiency (CHI) screening with the actin gene to identify genes related to actin function and as a model to determine the prevalence of CHI interactions in eukaryotic genomes. Previous CHI screening between actin and null alleles for non-essential genes uncovered ∼240 deleterious CHI interactions. In this report, we have extended CHI screening to null alleles for essential genes by mating a query strain to sporulations of heterozygous knock-out strains. Using an act1Δ query, knock-outs of 60 essential genes were found to be CHI with actin. Enriched in this collection were functional categories found in the previous screen against non-essential genes, including genes involved in cytoskeleton function and chaperone complexes that fold actin and tubulin. Novel to this screen was the identification of genes for components of the TFIID transcription complex and for the proteasome. We investigated a potential role for the proteasome in regulating the actin cytoskeleton and found that the proteasome physically associates with actin filaments in vitro and that some conditional mutations in proteasome genes have gross defects in actin organization. Whole-genome screening with actin as a query has confirmed that CHI interactions are important phenotypic drivers. Furthermore, CHI screening is another genetic tool to uncover novel functional connections. Here we report a previously unappreciated role for the proteasome in affecting actin organization and function.

Prevalence of comorbid substance use disorders among people with opioid use disorder: A systematic review & meta-analysis.

BACKGROUND: Comorbid substance use disorders (SUDs) among people with opioid use disorder (OUD) contribute to poor clinical outcomes, including overdose and mortality. We present the first systematic review and meta-analysis to estimate the prevalence of specific non-opioid SUDs among people with OUD. METHODS: We searched Embase, PsycINFO, and MEDLINE from 1990 to 2022 for studies that used Diagnostic and Statistical Manual of Mental Disorders (DSM) or International Classification of Diseases (ICD) criteria to assess the prevalence of non-opioid SUDs among individuals with OUD. We used random-effects meta-analyses with 95% Confidence Intervals (CIs) to pool current and lifetime prevalence estimates separately. Meta-regressions and stratified meta-analyses were used to examine differences in prevalence estimates by sample characteristics and methodological factors. RESULTS: Of the 36,971 publications identified, we included data from 194 studies and 77,212 participants with OUD. The prevalence of any comorbid SUD among people with OUD was 59.5% (95%CI 49.1-69.5%) for current non-opioid SUDs, with 72.0% (95%CI 52.5-87.9%) experiencing a comorbid SUD in their lifetime. Of the studies that examined current comorbid SUDs, cocaine use disorder (30.5%, 95%CI 23.0-38.7%) was most common, followed by alcohol (27.1%, 95%CI 24.4- 30.0%), cannabis (22.7%, 95%CI 19.0-26.6%), sedative (16.1%, 95%CI 13.1-19.3%), and methamphetamine (11.4%, 95%CI 6.8-17.1%) use disorders. Substantial heterogeneity (I2>90%) across estimates was observed. Substantial heterogeneity (I2>90%) was observed across estimates, with significant variations in prevalence identified across geographic locations, recruitment settings, and other study-level factors. CONCLUSION: Findings from this study emphasize the importance of comorbid SUD treatment access for people with OUD. Our estimates can inform the provision of treatment and harm reduction strategies for people with OUD and specific subpopulations.