Influence of DNMT Genotype on Global and Site Specific DNA Methylation Patterns in Neonates and Pregnant Women

This study examines the relationship between common genetic variation within DNA methyltransferase genes and inter-individual variation in DNA methylation. Eleven polymorphisms spanning DNMT1 and DNMT3B were genotyped. Global and gene specific (IGF2, IGFBP3, ZNT5) DNA methylation was quantified by LUMA and bisulfite Pyrosequencing assays, respectively, in neonatal cord blood and in maternal peripheral blood. Associations between maternal genotype and maternal methylation (n ^≈ 333), neonatal genotype and neonatal methylation (n ^≈ 454), and maternal genotype and neonatal methylation (n ^≈ 137) were assessed. The findings of this study provide some support to the hypothesis that genetic variation in DNA methylating enzymes influence DNA methylation at global and gene-specific levels; however observations were not robust to correction for multiple testing. More comprehensive analysis of the influence of genetic variation on global and site specific DNA methylation is warranted.     

Ca2+ Release in Muscle Fibers Expressing R4892W and G4896V Type 1 Ryanodine Receptor Disease Mutants

The large and rapidly increasing number of potentially pathological mutants in the type 1 ryanodine receptor (RyR1) prompts the need to characterize their effects on voltage-activated sarcoplasmic reticulum (SR) Ca²⁺ release in skeletal muscle. Here we evaluated the function of the R4892W and G4896V RyR1 mutants, both associated with central core disease (CCD) in humans, in myotubes and in adult muscle fibers. For both mutants expressed in RyR1-null (dyspedic) myotubes, voltage-gated Ca²⁺ release was absent following homotypic expression and only partially restored following heterotypic expression with wild-type (WT) RyR1. In muscle fibers from adult WT mice, both mutants were expressed in restricted regions of the fibers with a pattern consistent with triadic localization. Voltage-clamp-activated confocal Ca²⁺ signals showed that fiber regions endowed with G4896V-RyR1s exhibited an ∼30% reduction in the peak rate of SR Ca²⁺ release, with no significant change in SR Ca²⁺ content. Immunostaining revealed no associated change in the expression of either α1S subunit (Cav1.1) of the dihydropyridine receptor (DHPR) or type 1 sarco(endo)plasmic reticulum Ca²⁺ ATPase (SERCA1), indicating that the reduced Ca²⁺ release resulted from defective RyR1 function. Interestingly, in spite of robust localized junctional expression, the R4892W mutant did not affect SR Ca²⁺ release in adult muscle fibers, consistent with a low functional penetrance of this particular CCD-associated mutant.     

Tophus burden reduction with pegloticase: results from phase 3 randomized trials and open-label extension in patients with chronic gout refractory to conventional therapy

Introduction

Two replicate randomized, placebo-controlled six-month trials (RCTs) and an open-label treatment extension (OLE) comprised the pegloticase development program in patients with gout refractory to conventional therapy. In the RCTs, approximately 40% of patients treated with the approved dose saw complete response (CR) of at least one tophus. Here we describe the temporal course of tophus resolution, total tophus burden in patients with multiple tophi, tophus size at baseline, and the relationship between tophus response and urate-lowering efficacy.

Methods

Baseline subcutaneous tophi were analyzed quantitatively using computer-assisted digital images in patients receiving pegloticase (8 mg biweekly or monthly) or placebo in the RCTs, and pegloticase in the OLE. Tophus response, a secondary endpoint in the trials, was evaluated two ways. Overall tophus CR was the proportion of patients achieving a best response of CR (without any new/enlarging tophi) and target tophus complete response (TT-CR) was the proportion of all tophi with CR.

Results

Among 212 patients randomized in the RCTs, 155 (73%) had ≥1 tophus and 547 visible tophi were recorded at baseline. Overall tophus CR was recorded in 45% of patients in the biweekly group (P = 0.002 versus placebo), 26% in the monthly group, and 8% in the placebo group after six months of RCT therapy. TT-CR rates at six months were 28%, 19%, and 2% of tophi, respectively. Patients meeting the primary endpoint of sustained urate-lowering response to therapy (responders) were more likely than nonresponders to have an overall tophus CR at six months (54% vs 20%, respectively and 8% with placebo).Both overall tophus CR and TT-CRs increased with treatment duration in the OLE, reaching 70% (39/56) of patients and 55% (132/238) of target tophi after one year of treatment in patients receiving pegloticase during both the RCTs and OLE. At that time point, more tophi had resolved in responders (102/145 or 70% of tophi) than nonresponders (30/93; 32%).

Conclusions

Pegloticase reduced tophus burden in patients with refractory tophaceous gout, especially those achieving sustained urate-lowering. Complete resolution of tophi occurred in some patients by 13 weeks and in others with longer-term therapy.

Trial registrations

{"type":"clinical-trial","attrs":{"text":"NCT00325195","term_id":"NCT00325195"}}NCT00325195, {"type":"clinical-trial","attrs":{"text":"NCT01356498","term_id":"NCT01356498"}}NCT01356498     

Workflow management systems for gene sequence analysis and evolutionary studies – A Review

Post ‘omic’ era has resulted in the development of many primary, secondary and derived databases. Many analytical and visualization bioinformatics tools have been developed to manage and analyze the data available through large sequencing projects. Availability of heterogeneous databases and tools make it difficult for researchers to access information from varied sources and run different bioinformatics tools to get desired analysis done. Building integrated bioinformatics platforms is one of the most challenging tasks that bioinformatics community is facing. Integration of various databases, tools and algorithm is a challenging problem to deal with. This article describes the bioinformatics analysis workflow management systems that are developed in the area of gene sequence analysis and phylogeny. This article will be useful for biotechnologists, molecular biologists, computer scientists and statisticians engaged in computational biology and bioinformatics research.     

Metabolic responses of the South American ornate horned frog (Ceratophrys ornata) to estivation

We examined the metabolic responses of the South American frog, Ceratophrys ornata, to laboratory-induced estivation. Whole-animal and mass-specific oxygen consumption rates (VO₂) did not change during fasting or 56 days of estivation, despite observing significant decreases in body mass. The maintenance of mass-specific metabolic rate at routine levels during estivation suggests that metabolic rate suppression is not a major response to estivation in this species. There was a significant decline in liver glycogen and a loss of adipose tissue mass during estivation, suggesting that both carbohydrate and lipid pathways are used to fuel metabolism during estivation. The activity of pyruvate dehydrogenase, an important regulator of carbohydrate oxidation, and carnitine palmitoyltransferase and 3-hydroxyacyl-CoA dehydrogenase, regulators of lipid oxidation, showed no significant change in activity in liver, heart, and muscle between estivating and active frogs. There was an increase in plasma osmolality, which is characteristic of estivating animals. Overall, our metabolic analysis of estivation in C. ornata indicates that this species does not employ a dramatic suppression metabolic rate to survive dehydration stress and that both endogenous carbohydrates and lipids are used as metabolic fuels.     

Alien futures: What is on the horizon for biological invasions?

Aim

To collect and identify the issues that may affect the future global and local management of biological invasions in the next 20–50 years and provide guidance for the prioritization of actions and policies responding to the management challenges of the future.

Location

Global

Methods

We used an open online survey to poll specialists and stakeholders from around the world as to their opinion on the three most important future issues both globally and at their respective local working level.

Results

The 240 respondents identified 629 global issues that we categorized into topics. We summarized the highest rated topics into five broad thematic areas: (1) environmental change, particularly climate change, (2) the spread of species through trade, (3) public awareness, (4) the development of new technologies to enhance management and (5) the need to strengthen policies. The respondents also identified 596 issues at their respective local working levels. Management, early detection, prevention and funding‐related issues all ranked higher than at the global level. Our global audience of practitioners, policymakers and researchers also elicited topics not identified in horizon scanning exercises led by scientists including potential human health impacts, the need for better risk assessments and legislation, the role of human migration and water management.

Main conclusions

The topic areas identified in this horizon scan provide guidance where future policy priorities for invasive alien species should be set. First, to reduce the magnitude and speed of environmental change and its impacts on biological invasions; second, to restrict the movement of potentially invasive alien species via trade; third, to raise awareness with the general public and empower them to act; and finally, to invest in innovative technologies that can detect and mitigate adverse impacts of introduced species.

     

Effect of Chronic Uremia on the Cell Surface Expression of B7 Family Costimulatory Molecules in an HLA-A2 Transgenic Mouse Model of Chronic Kidney Disease

Uremia due to chronic kidney disease (CKD) in humans is associated with immune dysfunction, increased susceptibility to infections, immune-activation–associated inflammation, and poor responses to vaccines. The pathophysiologic basis of these immune defects is hypothesized to be associated with a wide range of immunologic abnormalities, including an inability to sufficiently express the B7 family (B7-1, CD80; B7-2, CD86) of T-cell costimulatory molecules. However, testing the hypothesis that a state of chronic uremia contributes to attenuated expression of CD80 or CD86 has been difficult because few animal models faithfully recapitulate the immune defects observed in human CKD patients. We used a humanized mouse in a model of surgically induced renal failure and secondary chronic uremia to evaluate the effect of uremia on the expression of these markers. In a manner that resembles the changes observed in CKD patients, surgically induced CKD in mice resulted in decreased costimulatory CD86 expression compared with that in sham-operated controls. Immunodeficiency was functionally demonstrated in this mouse model by documenting an attenuated immune response to a cholera-toxin–based hepatitis B vaccine. This model will be useful for investigating the mechanisms involved in chronic uremia-associated immunodeficiency, poor response to vaccination, and problems associated with immunization of CKD patients.Abbreviations: CKD, chronic kidney disease; CT, cholera toxin; HBsAg, hepatitis B surface antigen; HLA, human leukocyte antigen; Th, T-helper cellThe B7 family of costimulatory molecules is critical in regulating adaptive immune responses and includes B7-1 (CD80) and B7-2 (CD86). These proteins are expressed on lymphoid and nonlymphoid cells and are part of a complex signaling network that includes chemokines, cytokines, adhesion molecules, and other immunoglobulin superfamily members. B7-1 and B7-2 deliver costimulatory or inhibitory signals through interaction with T-cell–associated CD28 or CTLA4 (CD152) molecules.^9,11,18,19 In particular, B7–CD28 ligation is necessary for a robust adaptive immune response to antigen that is presented in context with the MHC and T cell receptor complexes. Without B7 costimulation, T cell activation is compromised and the cell may enter an anergic state.¹³ In addition, active binding of B7, expressed by antigen-presenting cells, to CTLA4 that is expressed on responding T cells inhibits T-cell activation.^12,25 Therefore, any disease that alters the expression or function of B7 proteins has the potential to deregulate adaptive immunity.Uremia secondary to chronic kidney disease (CKD) is a disease that has been associated with reduced B7 expression and defects in innate and adaptive immunity in humans.⁹ Innate and adaptive immune dysfunction in CKD patients is associated with hyperinflammatory conditions, infections, atherosclerosis, and cardiovascular disease.^17,23 Some aspects of this dysfunction include impaired activation of T-lymphocytes, an increased T-helper cell (Th) Th1:Th2 ratio, lymphopenia, and impaired function of antigen-presenting cells.¹⁶ The function of antigen-presenting cells appears compromised in uremic patients through defective expression of B7-2 (CD86) on macrophages and dendritic cells.¹⁰ In contrast to that in human CKD patients, this pathology of reduced B7-2 expression has not previously been investigated in an animal model of uremia, and no model has been identified as having a defect in B7-2 expression.³Animal modeling of CKD is imperative to understand the pathogenesis of the disease. Furthermore, modeling will aid in the design and testing of therapeutic approaches. In the current study we examined the effect of surgically induced chronic uremia on the expression level of B7-1 and B7-2 in spleen cells of humanized B6.Cg-Tg(HLA-A/H2-D)2Enge/J transgenic mice (HLA-A2). We hypothesized that surgical induction of CKD and chronic uremia in HLA-A2 mice would result in the subsequent reduction of expression of B7-2 (that is, increased CD80:CD86 ratio) as compared with that of control mice that underwent sham surgery but did not become uremic. We show that the surgically induced chronic uremia protocol that we established results in a pathologic immune phenotype similar to that reported for immunodeficient humans with CKD, thus suggesting the utility of this approach as a new animal model of CKD.     

Impact of groundwater abstraction on a Banksia woodland, Swan Coastal Plain, Western Australia

Summary The Gnangara Groundwater Mound, centred 38 km north of Perth, Western Australia, is a large, shallow unconfined aquifer that is currently under abstraction as part of the public metropolitan water supply. To investigate the impact of lowering groundwater levels on a Banksia woodland on the Mound, vegetation monitoring near a groundwater abstraction bore (known as P50) began 1 year before becoming operational. In February 1991, 2 years after abstraction commenced, extensive death of the Banksia overstorey was observed within close proximity of the bore, following a short period of high summer temperatures. The site was subsequently revisited and the understorey floristic composition, abundance and vigour of overstorey species resurveyed, and compared with data collected from a site under long‐term monitoring and not currently influenced by abstraction. A lowering of groundwater level by 2.2 m at P50 between the summers of 1990 and 1991, resulting from the cumulative effects of abstraction and below average annual rainfall (low groundwater recharge), coincided with a loss of between 20 and 80% of adults of overstorey species and up to 64% of adults of understorey species within 200 m of the bore. Over a similar time period no significant decreases in the abundance of overstorey or understorey species were recorded in the monitored site not influenced by groundwater abstraction. Of the overstorey species, Holly‐leaf Banksia (Banksia ilicifolia) displayed the greatest susceptibility and lowest net recovery following the abstraction event at P50. The negative impact of groundwater drawdown on Holly‐leaf Banksia populations makes this overstorey species an important indicator of decreasing groundwater levels on the Gnangara Groundwater Mound. Water stress may have been the primary cause of vegetation death in close proximity to the P50 bore, although this would have been exacerbated by extreme summer temperatures (> 45°C) recorded during February 1991. The P50 scenario represents a localized response to an acute drawdown event, in association with other environmental factors, and provides invaluable information on the assessment of groundwater abstraction and poor groundwater recharge events on a Banksia woodland community. However, there are limitations in using the community response at P50 to manage the impact of drawdown events on other plant communities occurring on sandy, shallow aquifers.