Deterministic modelling and stochastic simulation of biochemical pathways using MATLAB

The analysis of complex biochemical networks is conducted in two popular conceptual frameworks for modelling. The deterministic approach requires the solution of ordinary differential equations (ODEs, reaction rate equations) with concentrations as continuous state variables. The stochastic approach involves the simulation of differential-difference equations (chemical master equations, CMEs) with probabilities as variables. This is to generate counts of molecules for chemical species as realisations of random variables drawn from the probability distribution described by the CMEs. Although there are numerous tools available, many of them free, the modelling and simulation environment MATLAB is widely used in the physical and engineering sciences. We describe a collection of MATLAB functions to construct and solve ODEs for deterministic simulation and to implement realisations of CMEs for stochastic simulation using advanced MATLAB coding (Release 14). The program was successfully applied to pathway models from the literature for both cases. The results were compared to implementations using alternative tools for dynamic modelling and simulation of biochemical networks. The aim is to provide a concise set of MATLAB functions that encourage the experimentation with systems biology models. All the script files are available from www.sbi.uni-rostock.de/ publications_matlab-paper.html.

[Accidental thymic involution in the growing body under the effect of different types of stressors]

Using the quantitative immunohistochemistry, the immunomodulatory effect of different types of stressors (physical and psychoemotional) on the thymus of growing experimental animals was assessed. Sprague-Dawley rats aged 21 day were exposed either to physical (water immersion) or emotional "expectation" stress for 5 hours daily during 7 consecutive days. After the final exposure to stress, animals were sacrificed, thymus was obtained for weighting and was processed for routine histology and immunohistochemistry (CD3, CD8, ED1, PCNA) with subsequent automatic image analysis. The finding obtained have demonstrated severe accidental thymic involution in both groups of experimental animals, which was more prominent under the effect of the physical stressor as compared to "purely" psychoemotional stressor. The major factors of poststress thymic hypoplasia were the increased apoptosis of the cortical thymocytes and inhibition of their proliferation, but not their increased transport to peripheral immune organs.

The obstetric performance of United Kingdom asylum seekers from Somalia: a case-control study and literature review

BACKGROUND

Little published research exists regarding obstetric performance of immigrant women in the United Kingdom. The aim of this study was to evaluate the obstetric performance and fetal outcomes of Somalian women who received prenatal care and requested to deliver at a teaching hospital in North London.

METHOD

This is a case-control study in which consecutive Somalian women were identified as index cases and the subsequent British-born Caucasian women listed in the delivery book served as controls.

RESULTS

69 index and 69 control cases were analyzed. Fifty-five percent of the Somalian women spoke little or no English. Half (50%) had undergone circumcision, the majority being type I WHO classification of female genital circumcision, which did not require significant surgical intervention prior to labor; 13% had cesarean sections, 13% instrumental vaginal deliveries, and 74% had vaginal deliveries. The Somalian women had higher parity (2.35 vs. 1.18) and were more likely to be grand multiparous (9/69 vs. 1/69) compared to controls. Epidural use was less frequent in Somalian women, but otherwise there were no significant differences between the two groups with regard to maternal age, rates of induction of labor, cesarean sections, duration of labor, premature deliveries, instrumental deliveries, and birth weights.

CONCLUSIONS

The demographic characteristics of the Somalian female population appear to exert minimal effect on obstetric and fetal outcomes. This may be due to the increased vigilance exercised by health professionals as well as to the fact that recent arrivals are from more urban and westernized areas in Somalia.

A systems- and signal-oriented approach to intracellular dynamics

A mathematical understanding of regulation, and, in particular, the role of feedback, has been central to the advance of the physical sciences and technology. In this article, the framework provided by systems biology is used to argue that the same can be true for molecular biology. In particular, and using basic modular methods of mathematical modelling which are standard in control theory, a set of dynamic models is developed for some illustrative cell signalling processes. These models, supported by recent experimental evidence, are used to argue that a control theoretical approach to the mechanisms of feedback in intracellular signalling is central to furthering our understanding of molecular communication. As a specific example, a MAPK (mitogen-activated protein kinase) signalling pathway is used to show how potential feedback mechanisms in the signalling process can be investigated in a simulated environment. Such ‘what if’ modelling/simulation studies have been an integral part of physical science research for many years. Using tools of control systems analysis, as embodied in the disciplines of systems biology, similar predictive modelling/simulation studies are now bearing fruit in cell signalling research.

Effect of pH on physiology of Metarhizium anisopliae for production of swainsonine

The effect of pH on the production of swainsonine and fungal morphology at different stages of fermentation of Metarhizium anisopliae was investigated. When no control was applied, the pH of the culture dropped from 6.5 to 3.8 within the first 72 hours and the concentration of swainsonine reached 43.3 mg 1(-1). When the pH was held constant either at the beginning or throughout the fermentation, the maximum recorded swainsonine level was only 8.4 mg 1(-1) corresponding with an increase in the formation of pellets. A late pH control applied after 72 hours, resulted in a swainsonine titer of 45.5 mg 1(-1).

Gentamicin induced dose related alterations in lipid levels and lipid peroxidation in central auditory pathway of the rat

A study was carried out on the effect of gentamicin on the central auditory pathway in rats. Rats were administered graded doses of gentamicin (60 mg, 100 mg and 160 mg/kg b.wt., i.m.) daily for 21 days. Levels of total lipids, phospholipids and cholesterol showed dose related increment in the central auditory pathway. On the other hand, the rate of lipid peroxidation was inhibited in all regions of the central auditory pathway of the rat.

Localisation of the spinal nucleus of the accessory nerve in the rabbit

The spinal nucleus of the accessory nerve (SNA) was localised in eight adult rabbits by a retrograde degeneration technique using thionine as a stain for the Nissl substance. The SNA was found to extend from the caudal one fifth of the medulla oblongata to the cranial one fourth of the sixth cervical segment. In the caudal part of the medulla oblongata, the SNA was located in the dorsal part of the detached ventral grey column. In the first cervical segment, the SNA was dorsolateral to the dorsomedial column and dorsal to the ventromedial column of the ventral grey column. In the cranial part of the second cervical segment, the SNA shifted laterally to the lateral margin of the ventral grey column. After this lateral shift, the SNA was located in the lateral part of the ventral grey column of the second, third and fourth cervical segments. In the fifth and cranial one fourth of the sixth cervical segments, the SNA was not a well defined column of cells but was represented by isolated cells scattered in the ventral part of the ventral grey column between the phrenic nucleus and the ventral border of the grey matter. The total number of chromatolysed cells found in the SNA of the right experimental side varied from 2723 to 3210.

Structures passing through the triangular space of the human upper limb

Structures passing through the triangular space of the human upper limb have been studied in 50 upper limbs from 25 cadavers. In all the specimens used in this study, a branch of the circumflex scapular artery with an accompanying vein was found to pass through this space.

The attachments of the lateral and medial ends of the extensor retinaculum of the human wrist

The attachments of the lateral and medial ends of the extensor retinaculum of the human wrist were observed in 52 human upper limbs (from 26 cadavers) by dissection. In all the specimens used in this study, the lateral end of the retinaculum was found to be attached to the distal part of the anterior border of the radius and its medial end was attached to the styloid process of the ulna, the pisiform and the triquetrum.

Localization of the phrenic nucleus in the spinal cord of the rabbit

The motor fibres of the phrenic nerve arise in the cervical portion of the spinal cord from a group of lower motor neuron cell bodies called the 'phrenic nucleus'. The phrenic nucleus of the rabbit has been located by cutting the right phrenic nerve (phrenicotomy) in the neck and observing retrograde degeneration (chromatolysis) in the cells of the ventral grey horn of the spinal cord 2-4 weeks later. The phrenic nucleus in the rabbit was found to extend from the fourth to the sixth cervical segment. It lay in the caudal half to three fourths of the fourth, the whole of the fifth and the cranial half to two thirds of the sixth segment. The phrenic nucleus in the rabbit is a longitudinal column of cells lying between the ventromedial and the ventrolateral columns of the ventral grey horn of the spinal cord. In the fourth and fifth cervical segments, the phrenic nucleus of the rabbit is dorso-medial to the ventrolateral column and dorsolateral to the ventromedial column. In the sixth segment it is dorsomedial to the ventrolateral column but lateral to the ventromedial column. The total number of chromatolysed cells found in the right phrenic nucleus (after right phrenicotomy in the neck) varied between 1496 and 1754. The chromatolysed cells had a peculiar and characteristic orientation in that in a frontal section they appeared longer than broad with their long axes almost parallel ti the longitudinal axis of the spinal cord.

Prevalence of Metabolic Syndrome in Newly Diagnosed Type 2 Diabetes Mellitus

Background: People with metabolic syndrome are twice as likely to die from, and three times as likely to have a heart attack or stroke compared with people without the syndrome. People with metabolic syndrome have a five-fold greater risk of developing type 2 diabetes. We investigated the prevalence of metabolic syndrome in patients with newly diagnosed diabetes mellitus. Methods: It was a cross sectional study. The study was conducted in Department of Biochemistry, Sylhet MAG Osmani Medical College, Sylhet & Diabetic Hospital, Sylhet. The study was conducted From July 2008 to June 2009 among 200 patients with newly diagnosed type 2 diabetic patients with age >20 years. Along with blood glucose, different components of metabolic syndrome was assessed, i.e. serum triglyceride level, serum HDL level, blood pressure and waist circumference. Results- Prevalence of metabolic syndrome was 73.5% according to NCEP-ATP III criteria, 81.0% according to modified NCEP-ATP III criteria, 82.5% according to modified WHO criteria and 61.0% according to IDF criteria. All variables other than waist hip ratio and fasting blood sugar had statistically significant higher mean values among patients with metabolic syndrome than patients without metabolic syndrome. Conclusion: It may be concluded that prevalence of metabolic syndrome is considerable in newly diagnosed type 2 diabetic patients in our population. The considerable prevalence of metabolic syndrome in our population is implicative of an alarming risk of cardiovascular disease in future. Keywords: Metabolic syndrome; Type II diabetes mellitus. DOI: http://dx.doi.org/10.3329/cardio.v4i1.9385 Cardiovasc. J. 2011; 4(1): 17-25

Complementary and Alternative Medicine in Cardiovascular Care

Complementary and alternative medicine (CAM) refers to a broad set of health care practices that are not part of a country’s own tradition and are not integrated into the dominant health care system. Herbal remedies, dietary supplements, acupuncture, homeopathy, ayurveda, unani, traditional Chinese medicine, prayer, yoga and meditation are the common examples. CAM therapies often represent an enormous area of unregulated and widely practised therapeutics with an inadequate scientific literature. However, there is emerging evidence that some of the CAM therapies are effective in certain clinical conditions. Presently, throughout the world, there is rampant growth of CAM industries, and increasing number of reputed pharmaceutical companies are producing herbals and dietary supplements. Herbal products used for cardiovascular purposes include garlic, hawthorn, ginkgo, horse chestnut and arjun. These substances are often popularly believed to be ‘natural’, hence safe. But adverse reactions including deaths have been reported with some of the CAM products. There is also growing concern for significant drug interaction among commonly used herbals, dietary supplements and cardiovascular drugs. At present, CAM therapies may best be regarded as an adjunct to standard medical care. More scientific research and strict regulation by standard national and international authorities are needed to ensure their efficacy and safety in cardiovascular care. Key words: Complementary and alternative medicine, Herbals, Cardiovascular care. DOI: http://dx.doi.org/10.3329/cardio.v1i1.8211 Cardiovasc. j. 2008; 1(1) : 84-96

Coronary Artery Dissection and Perforation Complicating Percutaneous Coronary Intervention – A Review

After its introduction by Andrew R. Gruentzig in 1977 percutaneous coronary intervention (PCI) is widely utilized in the treatment of symptomatic coronary artery disease. Though it has numerous benefits, serious and potentially life-threatening complications of PCI can occur, including iatrogenic coronary artery dissection and perforation. The incidence of these complications has been augmented by the development of coronary interventional devices intended to remove or ablate tissue. Here we review the classification, incidence, pathogenesis, clinical sequelae and management of coronary artery dissection and perforation in the current era due to PCI. Specifically, the current angiographic classifications of coronary artery dissections and perforations are reviewed. The findings of several recent, registries of PCI-related coronary artery perforations and dissection are summarized. The management of coronary artery dissection and perforation is discussed in details, including the application of newer modalities such as covered stents. Keywords: Percutaneous coronary intervention (PCI); Coronary artery dissection DOI: http://dx.doi.org/10.3329/cardio.v3i2.9198   Cardiovasc. J. 2011; 3(2): 239-247

Study And Analysis Of Stem Cell Therapy And Its Ethical Consideration

The controversy surrounding stem cell research led to an intense debate about ethics. Up until the recent years, the research method mainly focused on Embryonic Stem Cells, which involves taking tissue from an aborted embryo to get proper material to study. This is typically done just days after conception or between the 5th and 9th week. Since then, researchers have moved on to more ethical study methods, such as Induced Pluripotent Stem Cells (iPS). iPS is artificially derived from a non-pluripotent cell, such as adult somatic cells. This is probably an important advancement in stem cell research, since it allows researchers to obtain pluripotent stem cells, which are important in research, without the controversial use of embryos. Nowadays stem cell treatment has been spreaded throughout the world. It has also been grown commercially in developed countries. This paper assesses the stem cell treatment as well as its impact in human life. It also examines specific stem cell therapy market that proves far reaching effect in world economy. Though various organizations have made it as a controversial issue the analysis shows that stem cell treatment has brought positive dimension in human society. A discussion has been made about the ethical issues of stem cell research and therapy; which focus how recent biotechnology and biological understandings of development narrow the debate. It is thought that one day it may be the major key to treat various diseases. DOI: http://dx.doi.org/10.3329/bioethics.v1i3.9631 Bangladesh Journal of Bioethics 2010; 1(3): 22-34