Showing papers by "Translational Research Institute published in 2016"

Quantitation of Apoptosis and Necrosis by Annexin V Binding, Propidium Iodide Uptake, and Flow Cytometry

Abstract: The surface of healthy cells is composed of lipids that are asymmetrically distributed on the inner and outer leaflet of the plasma membrane. One of these lipids, phosphatidylserine (PS), is normally restricted to the inner leaflet of the plasma membrane and is, therefore, only exposed to the cell cytoplasm. However, during apoptosis lipid asymmetry is lost and PS becomes exposed on the outer leaflet of the plasma membrane. Annexin V, a 36-kDa calcium-binding protein, binds to PS; therefore, fluorescently labeled Annexin V can be used to detect PS that is exposed on the outside of apoptotic cells. Annexin V can also stain necrotic cells because these cells have ruptured membranes that permit Annexin V to access the entire plasma membrane. However, apoptotic cells can be distinguished from necrotic cells by co-staining with propidium iodide (PI) because PI enters necrotic cells but is excluded from apoptotic cells. This protocol describes Annexin V binding and PI uptake followed by flow cytometry to detect and quantify apoptotic and necrotic cells.

Synbiotics Easing Renal Failure by Improving Gut Microbiology (SYNERGY): A Randomized Trial

Abstract: Background and objectives The generation of key uremic nephrovascular toxins, indoxyl sulfate (IS), and p-cresyl sulfate (PCS), is attributed to the dysbiotic gut microbiota in CKD. The aim of our study was to evaluate whether synbiotic (pre- and probiotic) therapy alters the gut microbiota and reduces serum concentrations of microbiome–generated uremic toxins, IS and PCS, in patients with CKD. Design, setting, participants, & measurements Predialysis adult participants with CKD (eGFR=10–30 ml/min per 1.73 m2) were recruited between January 5, 2013 and November 12, 2013 to a randomized, double–blind, placebo–controlled, crossover trial of synbiotic therapy over 6 weeks (4-week washout). The primary outcome was serum IS. Secondary outcomes included serum PCS, stool microbiota profile, eGFR, proteinuria-albuminuria, urinary kidney injury molecule-1, serum inflammatory biomarkers (IL-1β, IL-6, IL-10, and TNF-α), serum oxidative stress biomarkers (F2-isoprostanes and glutathione peroxidase), serum LPS, patient-reported health, Gastrointestinal Symptom Score, and dietary intake. A prespecified subgroup analysis explored the effect of antibiotic use on treatment effect. Results Of 37 individuals randomized (age =69±10 years old; 57% men; eGFR=24±8 ml/min per 1.73 m2), 31 completed the study. Synbiotic therapy did not significantly reduce serum IS (−2 μmol/L; 95% confidence interval [95% CI], −5 to 1 μmol/L) but did significantly reduce serum PCS (−14 μmol/L; 95% CI, −27 to −2 μmol/L). Decreases in both PCS and IS concentrations were more pronounced in patients who did not receive antibiotics during the study (n=21; serum PCS, −25 μmol/L; 95% CI, −38 to −12 μmol/L; serum IS, −5 μmol/L; 95% CI, −8 to −1 μmol/L). Synbiotics also altered the stool microbiome, particularly with enrichment of Bifidobacterium and depletion of Ruminococcaceae. Except for an increase in albuminuria of 38 mg/24 h (P=0.03) in the synbiotic arm, no changes were observed in the other secondary outcomes. Conclusion In patients with CKD, synbiotics did not significantly reduce serum IS but did decrease serum PCS and favorably modified the stool microbiome. Large–scale clinical trials are justified.

Analyzing Cell Death by Nuclear Staining with Hoechst 33342.

Abstract: The nuclei of healthy cells are generally spherical, and the DNA is evenly distributed. During apoptosis the DNA becomes condensed, but this process does not occur during necrosis. Nuclear condensation can therefore be used to distinguish apoptotic cells from healthy cells or necrotic cells. Dyes that bind to DNA, such as Hoechst 33342 or 4',6-diamidino-2-phenylindole (DAPI), can be used to observe nuclear condensation. These dyes fluoresce at 461 nm when excited by ultraviolet light and can therefore be visualized using conventional fluorescent microscopes equipped with light sources that emit light at ∼350 nm and filter sets that permit the transmission of light at ∼460 nm. This protocol describes staining and visualization of cells stained with Hoechst 33342, but it can be adapted for staining with DAPI or other dyes.

Small molecule proteostasis regulators that reprogram the ER to reduce extracellular protein aggregation.

Abstract: Newly made proteins must be folded into specific three-dimensional shapes before they can perform their roles in cells. Many proteins are folded in a compartment called the endoplasmic reticulum before being transported to their final location. However, if a cell suddenly needs to make a large number of new proteins, it can overwhelm the endoplasmic reticulum and unfolded proteins may accumulate. The cell responds to this stress by activating the unfolded protein response, which increases the folding capacity of the endoplasmic reticulum to match the demand. However, if the stress persists, then the unfolded protein response instructs the cell to die to protect the rest of the body. A protein called ATF6 is involved in one branch of the unfolded protein response. Endoplasmic reticulum stress causes ATF6 to move from the endoplasmic reticulum to another cell compartment where certain enzymes are able to cut the protein. A fragment of ATF6 then moves to the nucleus of the cell to activate genes needed to increase the cell’s capacity to fold proteins. Errors in protein folding can cause serious diseases in humans and other animals. Drugs that target ATF6 might be able to regulate part of the unfolded protein response to treat these diseases. However, no drugs that act on ATF6 had been identified. Now, two groups of researchers have independently identified small molecules that specifically target ATF6. Plate et al. used a new approach to screen over 600,000 small molecules and identified a small number that could activate ATF6-regulated genes without inducing global endoplasmic reticulum stress. Further experiments tested whether any of these ATF6 drug candidates could prevent the release of incorrectly folded versions of two particular proteins from cells that are associated with types of amyloid disease in humans. One of the small molecules tested effectively reduced the release of these proteins and prevented harmful deposits of the proteins forming in the spaces surrounding cells. In an independent study, Gallagher et al. identified a type of small molecule that can inhibit the activity of ATF6. Together, these findings may lead to further development of new drugs for treating diseases associated with incorrect protein folding in the endoplasmic reticulum.

Measuring Cell Death by Propidium Iodide Uptake and Flow Cytometry.

Abstract: Propidium iodide (PI) is a small fluorescent molecule that binds to DNA but cannot passively traverse into cells that possess an intact plasma membrane. PI uptake versus exclusion can be used to discriminate dead cells, in which plasma membranes become permeable regardless of the mechanism of death, from live cells with intact membranes. PI is excited by wavelengths between 400 and 600 nm and emits light between 600 and 700 nm, and is therefore compatible with lasers and photodetectors commonly available in flow cytometers. This protocol for PI staining can be used to quantitate cell death in most modern research facilities and universities.

Detecting Cleaved Caspase-3 in Apoptotic Cells by Flow Cytometry.

Abstract: Apoptosis is orchestrated by caspases, a family of cysteine proteases that cleave their substrates on the carboxy-terminal side of specific aspartic acid residues. These proteases are generally present in healthy cells as inactive zymogens, but when stimulated they undergo autolytic cleavage to become fully active. They subsequently cleave their substrates at one or two specific sites, which can result in activation, inactivation, relocalization, or remodeling of the substrate. Consequently, many of the cleaved fragments remain intact during apoptosis and can be detected using substrate-specific antibodies. These fragments are most commonly detected by western blotting, which resolves proteins and their fragments based on molecular mass. However, antibodies that only recognize cleaved fragments can be used to specifically label cells in which caspase cleavage has occurred. It is then possible to quantify these cells by flow cytometry. A number of antibodies that specifically recognize caspase-cleaved fragments have been generated, including antibodies that recognize the cleaved form of caspase-3. This caspase is responsible for the majority of proteolysis during apoptosis, and detection of cleaved caspase-3 is therefore considered a reliable marker for cells that are dying, or have died by apoptosis. This protocol outlines the quantification of apoptosis by flow cytometric detection of cleaved caspase-3.

The National Emergency Access Target (NEAT) and the 4-hour rule: time to review the target

Abstract: Objective: We explored the relationship between the National Emergency Access Target (NEAT) compliance rate, defined as the proportion of patients admitted or discharged from emergency departments (EDs) within 4 hours of presentation, and the risk-adjusted in-hospital mortality of patients admitted to hospital acutely from EDs Design, setting and participants: Retrospective observational study of all de-identified episodes of care involving patients who presented acutely to the EDs of 59 Australian hospitals between 1 July 2010 and 30 June 2014 Main outcome measure: The relationship between the risk-adjusted mortality of inpatients admitted acutely from EDs (the emergency hospital standardised mortality ratio [eHSMR]: the ratio of the numbers of observed to expected deaths) and NEAT compliance rates for all presenting patients (total NEAT) and admitted patients (admitted NEAT) Results: ED and inpatient data were aggregated for 125 million ED episodes of care and 116 million inpatient episodes of care A highly significant (P<0001) linear, inverse relationship between eHSMR and each of total and admitted NEAT compliance rates was found; eHSMR declined to a nadir of 73 as total and admitted NEAT compliance rates rose to about 83% and 65% respectively Sensitivity analyses found no confounding by the inclusion of palliative care and/or short-stay patients Conclusion: As NEAT compliance rates increased, in-hospital mortality of emergency admissions declined, although this direct inverse relationship is lost once total and admitted NEAT compliance rates exceed certain levels This inverse association between NEAT compliance rates and in-hospital mortality should be considered when formulating targets for access to emergency care

Risk Factors Associated With Severe Hypoglycemia in Older Adults With Type 1 Diabetes

Abstract: OBJECTIVE Severe hypoglycemia is common in older adults with long-standing type 1 diabetes, but little is known about factors associated with its occurrence. RESEARCH DESIGN AND METHODS A case-control study was conducted at 18 diabetes centers in the T1D Exchange Clinic Network. Participants were ≥60 years old with type 1 diabetes for ≥20 years. Case subjects ( n = 101) had at least one severe hypoglycemic event in the prior 12 months. Control subjects ( n = 100), frequency-matched to case subjects by age, had no severe hypoglycemia in the prior 3 years. Data were analyzed for cognitive and functional abilities, social support, depression, hypoglycemia unawareness, various aspects of diabetes management, C-peptide level, glycated hemoglobin level, and blinded continuous glucose monitoring (CGM) metrics. RESULTS Glycated hemoglobin (mean 7.8% vs. 7.7%) and CGM-measured mean glucose (175 vs. 175 mg/dL) were similar between case and control subjects. More case than control subjects had hypoglycemia unawareness: only 11% of case subjects compared with 43% of control subjects reported always having symptoms associated with low blood glucose levels ( P P = 0.008) and experienced CGM glucose levels P = 0.10). On certain cognitive tests, case subjects scored worse than control subjects. CONCLUSIONS In older adults with long-standing type 1 diabetes, greater hypoglycemia unawareness and glucose variability are associated with an increased risk of severe hypoglycemia. A study to assess interventions to prevent severe hypoglycemia in high-risk individuals is needed.

Body Composition Remodeling and Mortality: The Health Aging and Body Composition Study

Abstract: Background Age-related losses of lean mass and shifts to central adiposity are related to functional decline and may predict mortality and/or explain part of the risk of weight loss. To determine how mortality risk is related to shifts in body composition, changes should be considered in the context of overall weight change. Methods Five-year changes in body composition were assessed with computed tomography (cm2) and dual x-ray absorptiometry (kg) in 869 men and 934 women initially aged 70-79 years. All-cause mortality was monitored for up to 12 years (2002-2003 to September 30, 2014), and risk was assessed using sex-specific Cox models. Results Both men and women lost weight, visceral fat area, thigh muscle area, lean mass, and fat mass (all p < .01) but gained intermuscular thigh fat area (p < .01). There were 995 deaths. After adjustment for total weight change, demographics, and chronic disease, losing thigh muscle area was associated with higher mortality in both men (1.21, 1.08-1.35) and women (1.18, 1.01-1.37, per 9.0cm2) and was especially strong in normal weight (body mass index < 25kg/m2) individuals and those losing weight. Losing intermuscular thigh fat was protective against mortality only in normal weight (0.66, 0.51-0.86) and weight stable men (0.79, 0.66-0.95, per 3.2cm2). Changes in visceral fat area were not associated with mortality. Conclusions Older adults with greater loss of thigh muscle than expected for overall weight change had a higher mortality risk compared to those with relative thigh muscle preservation, suggesting that conservation of muscle mass is important for survival in old age.

Measuring Mitochondrial Transmembrane Potential by TMRE Staining.

Abstract: Adenosine triphosphate (ATP) is the main source of energy for metabolism. Mitochondria provide the majority of this ATP by a process known as oxidative phosphorylation. This process involves active transfer of positively charged protons across the mitochondrial inner membrane resulting in a net internal negative charge, known as the mitochondrial transmembrane potential (ΔΨm). The proton gradient is then used by ATP synthase to produce ATP by fusing adenosine diphosphate and free phosphate. The net negative charge across a healthy mitochondrion is maintained at approximately -180 mV, which can be detected by staining cells with positively charged dyes such as tetramethylrhodamine ethyl ester (TMRE). TMRE emits a red fluorescence that can be detected by flow cytometry or fluorescence microscopy and the level of TMRE fluorescence in stained cells can be used to determine whether mitochondria in a cell have high or low ΔΨm. Cytochrome c is essential for producing ΔΨm because it promotes the pumping the protons into the mitochondrial intermembrane space as it shuttles electrons from Complex III to Complex IV along the electron transport chain. Cytochrome c is released from the mitochondrial intermembrane space into the cytosol during apoptosis. This impairs its ability to shuttle electrons between Complex III and Complex IV and results in rapid dissipation of ΔΨm. Loss of ΔΨm is therefore closely associated with cytochrome c release during apoptosis and is often used as a surrogate marker for cytochrome c release in cells.

Validity and Reliability of Dermoscopic Criteria Used to Differentiate Nevi From Melanoma: A Web-Based International Dermoscopy Society Study

Abstract: Importance The comparative diagnostic performance of dermoscopic algorithms and their individual criteria are not well studied. Objectives To analyze the discriminatory power and reliability of dermoscopic criteria used in melanoma detection and compare the diagnostic accuracy of existing algorithms. Design, Setting, and Participants This was a retrospective, observational study of 477 lesions (119 melanomas [24.9%] and 358 nevi [75.1%]), which were divided into 12 image sets that consisted of 39 or 40 images per set. A link on the International Dermoscopy Society website from January 1, 2011, through December 31, 2011, directed participants to the study website. Data analysis was performed from June 1, 2013, through May 31, 2015. Participants included physicians, residents, and medical students, and there were no specialty-type or experience-level restrictions. Participants were randomly assigned to evaluate 1 of the 12 image sets. Main Outcomes and Measures Associations with melanoma and intraclass correlation coefficients (ICCs) were evaluated for the presence of dermoscopic criteria. Diagnostic accuracy measures were estimated for the following algorithms: the ABCD rule, the Menzies method, the 7-point checklist, the 3-point checklist, chaos and clues, and CASH (color, architecture, symmetry, and homogeneity). Results A total of 240 participants registered, and 103 (42.9%) evaluated all images. The 110 participants (45.8%) who evaluated fewer than 20 lesions were excluded, resulting in data from 130 participants (54.2%), 121 (93.1%) of whom were regular dermoscopy users. Criteria associated with melanoma included marked architectural disorder (odds ratio [OR], 6.6; 95% CI, 5.6-7.8), pattern asymmetry (OR, 4.9; 95% CI, 4.1-5.8), nonorganized pattern (OR, 3.3; 95% CI, 2.9-3.7), border score of 6 (OR, 3.3; 95% CI, 2.5-4.3), and contour asymmetry (OR, 3.2; 95% CI, 2.7-3.7) ( P P Conclusions and Relevance Important dermoscopic criteria for melanoma recognition were revalidated by participants with varied experience. Six algorithms tested had similar but modest levels of diagnostic accuracy, and the interobserver agreement of most individual criteria was poor.

AarF Domain Containing Kinase 3 (ADCK3) Mutant Cells Display Signs of Oxidative Stress, Defects in Mitochondrial Homeostasis and Lysosomal Accumulation

Abstract: Autosomal recessive ataxias are a clinically diverse group of syndromes that in some cases are caused by mutations in genes with roles in the DNA damage response, transcriptional regulation or mitochondrial function. One of these ataxias, known as Autosomal Recessive Cerebellar Ataxia Type-2 (ARCA-2, also known as SCAR9/COQ10D4; OMIM: #612016), arises due to mutations in the ADCK3 gene. The product of this gene (ADCK3) is an atypical kinase that is thought to play a regulatory role in coenzyme Q10 (CoQ10) biosynthesis. Although much work has been performed on the S. cerevisiae orthologue of ADCK3, the cellular and biochemical role of its mammalian counterpart, and why mutations in this gene lead to human disease is poorly understood. Here, we demonstrate that ADCK3 localises to mitochondrial cristae and is targeted to this organelle via the presence of an N-terminal localisation signal. Consistent with a role in CoQ10 biosynthesis, ADCK3 deficiency decreased cellular CoQ10 content. In addition, endogenous ADCK3 was found to associate in vitro with recombinant Coq3, Coq5, Coq7 and Coq9, components of the CoQ10 biosynthetic machinery. Furthermore, cell lines derived from ARCA-2 patients display signs of oxidative stress, defects in mitochondrial homeostasis and increases in lysosomal content. Together, these data shed light on the possible molecular role of ADCK3 and provide insight into the cellular pathways affected in ARCA-2 patients.

Measuring Survival of Adherent Cells with the Colony-Forming Assay

Abstract: Measuring cell death with colorimetric or fluorimetric dyes such as trypan blue and propidium iodide (PI) can provide an accurate measure of the number of dead cells in a population at a specific time; however, these assays cannot be used to distinguish cells that are dying or marked for future death. In many cases it is essential to measure the proliferative capacity of treated cells to provide an indirect measurement of cell death. This can be achieved using the colony-forming assay described here. This protocol specifically applies to measurement of HeLa cells but can be used for most adherent cell lines with limited motility.

Duration of Hemodialysis Following Peritoneal Dialysis Cessation in Australia and New Zealand: Proposal for a Standardized Definition of Technique Failure.

Abstract: ♦ BACKGROUND: Although technique failure is a key outcome in peritoneal dialysis (PD), there is currently no agreement on a uniform definition. We explored different definitions of PD technique failure using data from the Australia and New Zealand Dialysis and Transplant (ANZDATA) Registry. ♦ METHODS: We included 16,612 incident PD patients in Australia and New Zealand from January 1998 to December 2012. Different definitions of technique failure were applied according to the minimum number of days (30, 60, 90, 180, or 365) the patient received hemodialysis after cessation of PD. ♦ RESULTS: Median technique survival varied from 2.0 years with the 30-day definition to 2.4 years with the 365-day definition. For all definitions, the most common causes of technique failure were death, followed by infectious complications. The likelihood of a patient returning to PD within 12 months of technique failure was highest in the 30-day definition (24%), and was very small when using the 180- and 365-day definitions (3% and 0.8%, respectively). Patients whose technique failed due to mechanical reasons were the most likely to return to PD (46% within 12 months using the 30-day definition). ♦ CONCLUSIONS: Both 30- and 180-day definitions have clinical relevance but offer different perspectives with very different prognostic implications for further PD. Therefore, we propose that PD technique failure be defined by a composite endpoint of death or transfer to hemodialysis using both 30-day and 180-day definitions.

Genotoxicity and gene expression modulation of silver and titanium dioxide nanoparticles in mice.

Abstract: Recently, we showed that silver nanoparticles (AgNPs) caused apoptosis, necrosis and DNA strand breaks in different cell models in vitro. These findings warranted analyses of their relevance in vivo. We investigated the genotoxic potential and gene expression profiles of silver particles of nano- (Ag20, 20 nm) and submicron- (Ag200, 200 nm) size and titanium dioxide nanoparticles (TiO2-NPs, 21 nm) in selected tissues from exposed male mice including the gonades. A single dose of 5 mg/kg bw nanoparticles was administered intravenously to male mice derived from C57BL6 (WT) and 8-oxoguanine DNA glycosylase knock-out (Ogg1−/− KO). Testis, lung and liver were harvested one and seven days post-exposure and analyzed for DNA strand breaks and oxidized purines employing the Comet assay with Formamidopyrimidine DNA glycosylase (Fpg) treatment, and sperm DNA fragmentation by the sperm chromatin structure assay (SCSA). Based on an initial screening of a panel of 21 genes, seven genes were selected and their e...

Measuring Cell Death by Trypan Blue Uptake and Light Microscopy.

Abstract: Trypan blue is a colorimetric dye that stains dead cells with a blue color easily observed using light microscopy at low resolution. The staining procedure is rapid and cells can be analyzed within minutes. The number of live (unstained) and dead (blue) cells can be counted using a hemocytometer on a basic upright microscope. Trypan blue staining is therefore a convenient assay for rapidly determining the overall viability of cells in a culture before commencing scientific experimentation, or for quantitating cell death following treatment with any cytotoxic stimuli.

A role for exercise after bariatric surgery

Abstract: Obesity predisposes an individual to develop numerous comorbidities, including type 2 diabetes, and represents a major healthcare issue in many countries worldwide. Bariatric surgery can be an effective treatment option, resulting in profound weight loss and improvements in metabolic health; however, not all patients achieve similar weight loss or metabolic improvements. Exercise is an excellent way to improve health, with well-characterized physiological and psychological benefits. In the present paper we review the evidence to determine whether there may be a role for exercise as a complementary adjunct therapy to bariatric surgery. Objectively measured physical activity data indicate that most patients who undergo bariatric surgery do not exercise enough to reap the health benefits of exercise. While there is a dearth of data on the effects of exercise on weight loss and weight loss maintenance after surgery, evidence from studies of caloric restriction and exercise suggest that similar adjunctive benefits may be extended to patients who perform exercise after bariatric surgery. Recent evidence from exercise interventions after bariatric surgery suggests that exercise may provide further improvements in metabolic health compared with surgery-induced weight loss alone. Additional randomized controlled exercise trials are now needed as the next step to more clearly define the potential for exercise to provide additional health benefits after bariatric surgery. This valuable evidence will inform clinical practice regarding much-needed guidelines for exercise after bariatric surgery.

Single nucleotide polymorphisms in clinics: Fantasy or reality for cancer?

Abstract: Single nucleotide polymorphisms (SNPs) have been classically used for dissecting various human complex disorders using candidate gene studies. During the last decade, large scale SNP analysis i.e. genome-wide association studies (GWAS) have provided an agnostic approach to identify possible genetic loci associated with heterogeneous disease such as cancer susceptibility, prognosis of survival or drug response. Further, the advent of new technologies, including microarray based genotyping as well as high throughput next generation sequencing has opened new avenues for SNPs to be used in clinical practice. It is speculated that the utility of SNPs to understand the mechanisms, biology of variable drug response and ultimately treatment individualization based on the individual’s genome composition will be indispensable in the near future. In the current review, we discuss the advantages and disadvantages of the clinical utility of genetic variants in disease risk-prediction, prognosis, clinical outcome and pharmacogenomics. The lessons and challenges for the utility of SNP based biomarkers are also discussed, including the need for additional functional validation studies.

Characterisation of the gastrointestinal mucosa-associated microbiota: a novel technique to prevent cross-contamination during endoscopic procedures.

Abstract: Background The mucosa-associated microbiota appears to be highly relevant to host-microbe interactions in the gastrointestinal (GI) tract. Thus, precise characterisation of the mucosa-associated microbiota may provide important insights for diagnostic and therapeutic development. However, for technical reasons, mucosal biopsies taken during standard endoscopic procedures are potentially contaminated by GI luminal contents. Aim To develop and validate a biopsy device that minimises contamination during sampling of the mucosa-associated microbiota. Methods A new, encased biopsy forceps was developed, the Brisbane Aseptic Biopsy Device (BABD). This comprises sterile forceps encased by a sheath with a plug at the tip, allowing targeted, aseptic sampling of the mucosa. Matched duodenal biopsies were obtained using the BABD, standard biopsy forceps, and a sterile brush, from patients undergoing upper GI endoscopy for iron deficiency (n = 6). Total genomic deoxyribonucleic acid (gDNA) was extracted from samples and bacterial 16S rRNA gene libraries sequenced to investigate the mucosa-associated microbiota. Results Microbial DNA was recovered from biopsies obtained by the BABD, confirming the presence of a duodenal mucosa-associated microbiota. This microbiota was dominated by the genus Streptococcus, with lower levels of Prevotella, Veillonella and Neisseria. At the individual patient level, substantial differences were observed between matched samples obtained using the different devices. A greater degree of bacterial diversity was observed in samples collected using the standard forceps, indicating the BABD affords collection of samples more representative of the mucosa-associated microbiota, by precluding luminal cross-contamination. Conclusions Cross-contamination can occur when mucosal biopsies are taken during standard endoscopic procedures. Utilising the novel Brisbane Aseptic Biopsy Device can reduce cross-contamination, and it offers improved opportunities to more precisely examine host-mucosa-associated microbiota interactions.

Detection of DNA Fragmentation in Apoptotic Cells by TUNEL

Abstract: Degradation of DNA into oligonucleosomal-sized fragments is a unique event in apoptosis that is orchestrated by caspase-activated DNase. Traditionally, this event is observed by resolving cellular DNA by gel electrophoresis, which results in a characteristic "ladder" pattern. However, this technique is time-consuming and cannot be used to quantitate the number of apoptotic cells in a sample. Terminal dUTP nick-end labeling (TUNEL) of fragmented DNA allows researchers to identify DNA fragmentation at the single-cell level. This method involves the specific addition of fluorescently labeled UTP to the 3'-end of the DNA fragments by terminal deoxynucleotidyl transferase. The TUNEL assay is both fast and sensitive. Here, we describe a protocol in which cells are treated with TUNEL reagent and counterstained with Hoechst 33342. In contrast to TUNEL, which only stains apoptotic cells, Hoechst 33342 stains the DNA of all cells.

Colonic microbiota can promote rapid local improvement of murine colitis by thioguanine independently of T lymphocytes and host metabolism

Abstract: Objective Mercaptopurine (MP) and pro-drug azathioprine are ‘first-line’ oral therapies for maintaining remission in IBD. It is believed that their pharmacodynamic action is due to a slow cumulative decrease in activated lymphocytes homing to inflamed gut. We examined the role of host metabolism, lymphocytes and microbiome for the amelioration of colitis by the related thioguanine (TG). Design C57Bl/6 mice with or without specific genes altered to elucidate mechanisms responsible for TG's actions were treated daily with oral or intrarectal TG, MP or water. Disease activity was scored daily. At sacrifice, colonic histology, cytokine message, caecal luminal and mucosal microbiomes were analysed. Results Oral and intrarectal TG but not MP rapidly ameliorated spontaneous chronic colitis in Winnie mice (point mutation in Muc2 secretory mucin). TG ameliorated dextran sodium sulfate-induced chronic colitis in wild-type (WT) mice and in mice lacking T and B lymphocytes. Remarkably, colitis improved without immunosuppressive effects in the absence of host hypoxanthine (guanine) phosphoribosyltransferase (Hprt)-mediated conversion of TG to active drug, the thioguanine nucleotides (TGN). Colonic bacteria converted TG and less so MP to TGN, consistent with intestinal bacterial conversion of TG to so reduce inflammation in the mice lacking host Hprt. TG rapidly induced autophagic flux in epithelial, macrophage and WT but not Hprt−/− fibroblast cell lines and augmented epithelial intracellular bacterial killing. Conclusions Treatment by TG is not necessarily dependent on the adaptive immune system. TG is a more efficacious treatment than MP in Winnie spontaneous colitis. Rapid local bacterial conversion of TG correlated with decreased intestinal inflammation and immune activation.

Hitchhiker’s Guide to Voxel Segmentation for Partial Volume Correction of In Vivo Magnetic Resonance Spectroscopy

Abstract: Partial volume effects have the potential to cause inaccuracies when quantifying metabolites using proton magnetic resonance spectroscopy (MRS). In order to correct for cerebrospinal fluid content, a spectroscopic voxel needs to be segmented according to different tissue contents. This article aims to detail how automated partial volume segmentation can be undertaken and provides a software framework for researchers to develop their own tools. While many studies have detailed the impact of partial volume correction on proton magnetic resonance spectroscopy quantification, there is a paucity of literature explaining how voxel segmentation can be achieved using freely available neuroimaging packages.

Measuring the DNA Content of Cells in Apoptosis and at Different Cell-Cycle Stages by Propidium Iodide Staining and Flow Cytometry.

Abstract: All cells are created from preexisting cells. This involves complete duplication of the parent cell to create two daughter cells by a process known as the cell cycle. For this process to be successful, the DNA of the parent cell must be faithfully replicated so that each daughter cell receives a full copy of the genetic information. During the cell cycle, the DNA content of the parent cell increases as new DNA is synthesized (S phase). When there are two full copies of the DNA (G2/M phase), the cell splits to form two new cells (G0/G1 phase). As such, cells in different stages of the cell cycle have different DNA contents. The cell cycle is tightly regulated to safeguard the integrity of the cell and any cell that is defective or unable to complete the cell cycle is programmed to die by apoptosis. When this occurs, the DNA is fragmented into oligonucleosomal-sized fragments that are disposed of when the dead cell is removed by phagocytosis. Consequently apoptotic cells have reduced DNA content compared with living cells. This can be measured by staining cells with propidium iodide (PI), a fluorescent molecule that intercalates with DNA at a specific ratio. The level of PI fluorescence in a cell is, therefore, directly proportional to the DNA content of that cell. This protocol describes the use of PI staining to determine the percentage of cells in each phase of the cell cycle and the percentage of apoptotic cells in a sample.

Characterization of cold-induced remodelling reveals depot-specific differences across and within brown and white adipose tissues in mice.

Abstract: Brown and beige adipose tissues dissipate energy in the form of heat via mitochondrial uncoupling protein 1, defending against hypothermia and potentially obesity. The latter has prompted renewed interest in understanding the processes involved in browning to realize the potential therapeutic benefits. To characterize the temporal profile of cold-induced changes and browning of brown and white adipose tissues in mice. Methods: Male C57BL/6J mice were singly housed in conventional cages under cold exposure (4°C) for 1, 2, 3, 4, 5 and 7days. Food intake and body weight were measured daily. Interscapular brown adipose tissue (iBAT), inguinal subcutaneous (sWAT) and epididymal white adipose tissue (eWAT) were harvested for histological, immunohistochemical, gene and protein expression analysis. Results: Upon cold exposure, food intake increased, whilst body weight and adipocyte size were found to be transiently reduced. iBAT mass was found to be increased, whilst sWAT and eWAT were found to be transiently decreased. A combination of morphological, genetic (Ucp-1, Pgc-1I± and Elov13) and biochemical (UCP-1, PPARI³ and aP2) analyses demonstrated the depot-specific remodelling in response to cold exposure. Conclusion: Our results demonstrate the differential responses to cold-induced changes across discrete BAT and WAT depots and support the notion that the effects of short-term cold exposure are achieved by expansion, activation and increasing thermogenic capacity of iBAT, as well as browning of sWAT and, to a lesser extent, eWAT. © 2016 Scandinavian Physiological Society. Published by John Wiley & Sons Ltd

Center-Specific Factors Associated with Peritonitis Risk—A Multi-Center Registry Analysis

Abstract: BackgroundPrevious studies have reported significant variation in peritonitis rates across dialysis centers. Limited evidence is available to explain this variability. The aim of this study was to ...