Development and validation of creatinine-based estimates of the Glo- Merular Filtration rate equation from Chromium Edta Imaging in the multi-racial Malaysian population

Background Glomerular filtration rate (GFR) is a reliable parameter for assessing kidney function. It is estimated from equations such as Cockcroft–Gault (CG), Modification of Diet in Renal Disease (MDRD), and Chronic Kidney Disease- Epidemiology Collaboration (CKD-EPI). However, these equations were derived using Western population demo- graphic data and had different performances when applied to other populations. Objectives. We developed a new equation (NE) based on the 51Cr EDTA measured GFR that can be used explicitly in the Malaysian multiracial population. Methods This was a cross-sectional study using the Electronic Medical Record (EMR) of pa- tients who underwent 51Cr-EDTA imaging at the Nuclear Medicine Centre, University Malaya Medical Centre (UMMC), from 2013 to 2021. This study had obtained approval from the Medical Research Ethics Committee, UMMC. Results Total data of 209 patients were recruited in this study. 105 were randomised in the development cohort, while 104 were in the validation cohort. A NE was developed based on data in the development cohort and then tested its performance in the validation cohort. The result showed that CKD-EPI had the highest correlation to 51Cr EDTA imaging measured GFR (r-value 0.82), followed by the NE (r-value 0.76). CG had the lowest bias (mean bias of 2.49), followed by the NE (mean bias of 3.52). CKD-EPI had the highest precision in estimating GFR (SD of 22.04ml/min), followed by the NE (SD of 25.05ml/min). CKD-EPI also had the highest accuracy (85.58% in P30 and 100% in P50, followed by MDRD (81.73% in P30 and 96.15% in P50). Conclusion The NE was less accurate than CKD-EPI and MDRD equation but generally has a rel- atively low bias of 3.52 ml/min. The limitation of the small sample size may limit the accuracy of the NE. Future studies with a larger sample size are needed to generate a more robust equation

Evaluation of Five Methods for Total DNA Extraction from Western Corn Rootworm Beetles

Background: DNA extraction is a routine step in many insect molecular studies. A variety of methods have been used to isolate DNA molecules from insects, and many commercial kits are available. Extraction methods need to be evaluated for their efficiency, cost, and side effects such as DNA degradation during extraction. Methodology/Principal Findings: From individual western corn rootworm beetles, Diabrotica virgifera virgifera, DNA extractions by the SDS method, CTAB method, DNAzol reagent, Puregene solutions and DNeasy column were compared in terms of DNA quantity and quality, cost of materials, and time consumed. Although all five methods resulted in acceptable DNA concentrations and absorbance ratios, the SDS and CTAB methods resulted in higher DNA yield (ng DNA vs. mg tissue) at much lower cost and less degradation as revealed on agarose gels. The DNeasy kit was most time-efficient but was the costliest among the methods tested. The effects of ethanol volume, temperature and incubation time on precipitation of DNA were also investigated. The DNA samples obtained by the five methods were tested in PCR for six microsatellites located in various positions of the beetle’s genome, and all samples showed successful amplifications. Conclusion/Significance: These evaluations provide a guide for choosing methods of DNA extraction from western corn rootworm beetles based on expected DNA yield and quality, extraction time, cost, and waste control. The extraction conditions for this mid-size insect were optimized. The DNA extracted by the five methods was suitable for further molecular applications such as PCR and sequencing by synthesis

The epidemiology and natural history of depressive disorders in Hong Kong's primary care

Background: Depressive disorders are commonly managed in primary care and family physicians are ideally placed to serve as central providers to these patients. Around the world, the prevalence of depressive disorders in patients presenting to primary care is between 10-20%, of which around 50% remain undiagnosed. In Hong Kong, many barriers exist preventing the optimal treatment and management of patients with depressive disorders. The pathways of care, the long term outcomes and the factors affecting prognosis of these patients requires closer examination. Methods/Design. The aim of this study is to examine the prevalence, incidence and natural history of depressive disorders in primary care and the factors influencing diagnosis, management and outcomes using a cross-sectional study followed by a longitudinal cohort study. Doctors working in primary care settings across Hong Kong have been invited to participate in this study. On one day each month over twelve months, patients in the doctor's waiting room are invited to complete a questionnaire containing items on socio-demography, co-morbidity, family history, previous doctor-diagnosed mental illness, recent mental and other health care utilization, symptoms of depression and health-related quality of life. Following the consultation, the doctors provide information regarding presenting problem, whether they think the patient has depression, and if so, whether the diagnosis is new or old, and the duration of the depressive illness if not a new diagnosis. If the doctor detects a depressive disorder, they are asked to provide information regarding patient management. Patients who consent are followed up by telephone at 2, 12, 26 and 52 weeks. Discussion. The study will provide information regarding cross-sectional prevalence, 12 month incidence, remission rate, outcomes and factors affecting outcomes of patients with depressive disorders in primary care. The epidemiology, outcomes, pathways of care, predictors for prognosis and service needs for primary care patients with depressive disorders will be described and recommendations made for policy and service planning. © 2011 Chin et al; licensee BioMed Central Ltd.published_or_final_versio

Revisiting the mechanism of coagulation factor XIII activation and regulation from a structure/functional perspective

The activation and regulation of coagulation Factor XIII (FXIII) protein has been the subject of active research for the past three decades. Although discrete evidence exists on various aspects of FXIII activation and regulation a combinatorial structure/functional view in this regard is lacking. In this study, we present results of a structure/function study of the functional chain of events for FXIII. Our study shows how subtle chronological submolecular changes within calcium binding sites can bring about the detailed transformation of the zymogenic FXIII to its activated form especially in the context of FXIIIA and FXIIIB subunit interactions. We demonstrate what aspects of FXIII are important for the stabilization (first calcium binding site) of its zymogenic form and the possible modes of deactivation (thrombin mediated secondary cleavage) of the activated form. Our study for the first time provides a structural outlook of the FXIIIA 2 B 2 heterotetramer assembly, its association and dissociation. The FXIIIB subunits regulatory role in the overall process has also been elaborated upon. In summary, this study provides detailed structural insight into the mechanisms of FXIII activation and regulation that can be used as a template for the development of future highly specific therapeutic inhibitors targeting FXIII in pathological conditions like thrombosis

E2F-1 induces melanoma cell apoptosis via PUMA up-regulation and Bax translocation

BACKGROUND: PUMA is a pro-apoptotic Bcl-2 family member that has been shown to be involved in apoptosis in many cell types. We sought to ascertain whether induction of PUMA plays a crucial role in E2F-1-induced apoptosis in melanoma cells. METHODS: PUMA gene and protein expression levels were detected by real-time PCR and Western blot in SK-MEL-2 and HCT116 cell lines after Ad-E2F-1 infection. Activation of the PUMA promoter by E2F-1 overexpression was detected by dual luciferase reporter assay. E2F-1-induced Bax translocation was shown by immunocytochemistry. The induction of caspase-9 activity was measured by caspase-9 colorimetric assay kit. RESULTS: Up-regulation of the PUMA gene and protein by E2F-1 overexpression was detected by real-time PCR and Western blot analysis in the SK-MEL-2 melanoma cell line. In support of this finding, we found six putative E2F-1 binding sites within the PUMA promoter. Subsequent dual luciferase reporter assay showed that E2F-1 expression could increase the PUMA gene promoter activity 9.3 fold in SK-MEL-2 cells. The role of PUMA in E2F-1-induced apoptosis was further investigated in a PUMA knockout cell line. Cell viability assay showed that the HCT116 PUMA-/- cell line was more resistant to Ad-E2F-1-mediated cell death than the HCT116 PUMA+/+ cell line. Moreover, a 2.2-fold induction of the PUMA promoter was also noted in the HCT116 PUMA+/+ colon cancer cell line after Ad-E2F-1 infection. Overexpression of a truncated E2F-1 protein that lacks the transactivation domain failed to up-regulate PUMA promoter, suggesting that PUMA may be a transcriptional target of E2F-1. E2F-1-induced cancer cell apoptosis was accompanied by Bax translocation from the cytosol to mitochondria and the induction of caspase-9 activity, suggesting that E2F-1-induced apoptosis is mediated by PUMA through the cytochrome C/Apaf-1-dependent pathway. CONCLUSION: Our studies strongly demonstrated that E2F-1 induces melanoma cell apoptosis via PUMA up-regulation and Bax translocation. The signaling pathways provided here will further enhance insights on the mechanisms of E2F-1-induced cancer cell apoptosis as a strategy for cancer therapy

Optimization of growth media components for polyhydroxyalkanoate (PHA) production from organic acids by Ralstonia eutropha

We employed systematic mixture analysis to determine optimal levels of acetate, propionate, and butyrate for cell growth and polyhydroxyalkanoate (PHA) production by Ralstonia eutropha H16. Butyrate was the preferred acid for robust cell growth and high PHA production. The 3-hydroxyvalerate content in the resulting PHA depended on the proportion of propionate initially present in the growth medium. The proportion of acetate dramatically affected the final pH of the growth medium. A model was constructed using our data that predicts the effects of these acids, individually and in combination, on cell dry weight (CDW), PHA content (%CDW), PHA production, 3HV in the polymer, and final culture pH. Cell growth and PHA production improved approximately 1.5-fold over initial conditions when the proportion of butyrate was increased. Optimization of the phosphate buffer content in medium containing higher amounts of butyrate improved cell growth and PHA production more than 4-fold. The validated organic acid mixture analysis model can be used to optimize R. eutropha culture conditions, in order to meet targets for PHA production and/or polymer HV content. By modifying the growth medium made from treated industrial waste, such as palm oil mill effluent, more PHA can be produced.Malaysia. Ministry of Science, Technology and Innovation (MOSTI

Genomic and oncoproteomic advances in detection and treatment of colorectal cancer

<p>Abstract</p> <p>Aims</p> <p>We will examine the latest advances in genomic and proteomic laboratory technology. Through an extensive literature review we aim to critically appraise those studies which have utilized these latest technologies and ascertain their potential to identify clinically useful biomarkers.</p> <p>Methods</p> <p>An extensive review of the literature was carried out in both online medical journals and through the Royal College of Surgeons in Ireland library.</p> <p>Results</p> <p>Laboratory technology has advanced in the fields of genomics and oncoproteomics. Gene expression profiling with DNA microarray technology has allowed us to begin genetic profiling of colorectal cancer tissue. The response to chemotherapy can differ amongst individual tumors. For the first time researchers have begun to isolate and identify the genes responsible. New laboratory techniques allow us to isolate proteins preferentially expressed in colorectal cancer tissue. This could potentially lead to identification of a clinically useful protein biomarker in colorectal cancer screening and treatment.</p> <p>Conclusion</p> <p>If a set of discriminating genes could be used for characterization and prediction of chemotherapeutic response, an individualized tailored therapeutic regime could become the standard of care for those undergoing systemic treatment for colorectal cancer. New laboratory techniques of protein identification may eventually allow identification of a clinically useful biomarker that could be used for screening and treatment. At present however, both expression of different gene signatures and isolation of various protein peaks has been limited by study size. Independent multi-centre correlation of results with larger sample sizes is needed to allow translation into clinical practice.</p

A quantitative systems pharmacology approach, incorporating a novel liver model, for predicting pharmacokinetic drug-drug interactions

All pharmaceutical companies are required to assess pharmacokinetic drug-drug interactions (DDIs) of new chemical entities (NCEs) and mathematical prediction helps to select the best NCE candidate with regard to adverse effects resulting from a DDI before any costly clinical studies. Most current models assume that the liver is a homogeneous organ where the majority of the metabolism occurs. However, the circulatory system of the liver has a complex hierarchical geometry which distributes xenobiotics throughout the organ. Nevertheless, the lobule (liver unit), located at the end of each branch, is composed of many sinusoids where the blood flow can vary and therefore creates heterogeneity (e.g. drug concentration, enzyme level). A liver model was constructed by describing the geometry of a lobule, where the blood velocity increases toward the central vein, and by modeling the exchange mechanisms between the blood and hepatocytes. Moreover, the three major DDI mechanisms of metabolic enzymes; competitive inhibition, mechanism based inhibition and induction, were accounted for with an undefined number of drugs and/or enzymes. The liver model was incorporated into a physiological-based pharmacokinetic (PBPK) model and simulations produced, that in turn were compared to ten clinical results. The liver model generated a hierarchy of 5 sinusoidal levels and estimated a blood volume of 283 mL and a cell density of 193 × 106 cells/g in the liver. The overall PBPK model predicted the pharmacokinetics of midazolam and the magnitude of the clinical DDI with perpetrator drug(s) including spatial and temporal enzyme levels changes. The model presented herein may reduce costs and the use of laboratory animals and give the opportunity to explore different clinical scenarios, which reduce the risk of adverse events, prior to costly human clinical studies