New methods for inferring population dynamics from microbial sequences.

The reduced cost of high throughput sequencing, increasing automation, and the amenability of sequence data for evolutionary analysis are making DNA data (or the corresponding amino acid sequences) the molecular marker of choice for studying microbial population genetics and phylogenetics. Concomitantly, due to the ever-increasing computational power, new, more accurate (and sometimes faster), sequence-based analytical approaches are being developed and applied to these new data. Here we review some commonly used, recently improved, and newly developed methodologies for inferring population dynamics and evolutionary relationships using nucleotide and amino acid sequence data, including: alignment, model selection, bifurcating and network phylogenetic approaches, and methods for estimating demographic history, population structure, and population parameters (recombination, genetic diversity, growth, and natural selection). Because of the extensive literature published on these topics this review cannot be comprehensive in its scope. Instead, for all the methods discussed we introduce the approaches we think are particularly useful for analyses of microbial sequences and where possible, include references to recent and more inclusive reviews.     

New methods for the diagnosis of acute pulmonary embolism

INTRODUCTION: Pulmonary embolism is a high mortality cardiovascular disease, which is difficult to diagnose even today. AIM AND METHOD: In this study the symptoms and the results of diagnostic methods were analysed in 81 patients with acute pulmonary embolism, admitted during a one-year period to Kaposi Mór County Hospital. The patient records were examined with special emphasis on the diagnostic value of novel methods such as D-dimer assay and chest computed tomography scanning along with the routine techniques used in the management of pulmonary embolism. RESULTS: In all patients ECG, in 88% of the cases chest X-ray, in 57% blood gas analysis and in 53% D-dimer assay results were evaluated. 14.8% of the patients died during hospitalisation. The following diagnostic imaging procedures were undertaken: in 80.2% of the cases lung scan, in 59.3% echocardiography and in 8.7% of the cases spiral computed tomography scan were prepared. In 12.3% of all cases thrombolysis proved necessary. The results were compared with data from International Cooperative Pulmonary Embolism Registry Study, which analyses 2454 patient cases. CONCLUSION: It is foreseen that the increasing use of echocardiography, lower limb ultrasound and highly informative spiral computed tomography scanning as an additional means in pulmonary embolism diagnostics may in some cases spare the use of pulmonary scintigraphy.     

New treatment methods for autoimmune thrombocytopenia

--For many years, splenectomy has been considered the only therapy with proven efficacy in patients with relapsed/refractory idiopathic thrombocytopenic purpura (ITP) following corticosteroid therapy. --A broad spectrum of (mostly immunosuppressive) agents are available for patients who fail to respond to splenectomy. However, the risks associated with these agents sometimes outweigh their benefits. --Recently, several new or renewed strategies have been evaluated for chronic refractory ITP. --Short-term therapy with high-dose dexamethasone is an effective alternative to long-term treatment with corticosteroids. --Depletion of B lymphocytes with rituximab, an agent that has an established role in the treatment of non-Hodgkin's lymphoma, also appears to be effective in autoimmune disorders, particularly in ITP. --Although the main problem in ITP is the increased destruction of thrombocytes, stimulation of thrombocyte production with thrombopoietin(TPO)-receptor agonists can increase thrombocyte counts. --Two TPO-receptor agonists, AMG531 and eltrombopag, induce responses in 70-80% of ITP patients and are expected to gain approval for use in ITP soon.     

Development of immunological methods of fertility regulation

Birth control vaccines both would increase the choice of methods open to women and men and additionally would offer specific advantages, including the development of vaccines that are unlikely to disrupt the menstrual cycle or cause the side-effects associated with oral contraceptive (OC) use. For a birth control vaccine to be acceptable for use in human beings, it must meet several criteria: the antigen must be unique to the reproductive target; the antigen must have a fertility-related function that can be blocked by antibody or is susceptible to cell-mediated immunity, and alternatively, the function should be located on a cell that can be lysed by complement; an acceptable level of effectiveness should be achieved by no more than 1 or 2 injections for the primary immunization, with booster injections at intervals of no less than 6-12 months; and the vaccine must undergo sufficient testing in animals to ensure its safety for longterm use. For the vaccine to be widely acceptable, its effects need to be reversible. Before a fertility-regulating vaccine can be envisaged for widespread use in men or women, animal models must be found for thorough testing of toxicity, teratogenicity, effectiveness, duration, and reversibility of immunity and specificity for the target. Theoretically, the mammalian reproductive system is susceptible to immunological intervention at several points. Many reproductive hormones, as well as several antigens could be isolated from the ovum, sperm, embryonic tissue, and fetal tissue, could be candidate targets. Human chorionic gonadotropin (hCG) is a major candidate for vaccine development. The World Health Organization's (WHO) Special Program of Research, Development and Research Training in Human Reproduction, through its Task Force on Vaccines for Fertility Regulation, has been supporting research on a synthetic vaccine directed against the last 37 amino acids of the C-terminal end of the beta hCG molecule. A 2nd approach, being followed by the National Institute of Immunology, New Delhi, and the Population Council, New York, involves developing a vaccine against the entire beta chain of the hCG molecule. A prototype vaccine using the beta subunit of ovine luteinizing hormone emulsified with Freund's complete adjuvant has been studied extensively in female primates by the Population Council, but as yet there is no evidence of acute or chronic health hazards in this heterologous immunization model. The development of a vaccine based on sperm antigens will require considerable basic research. Interference with fertility could occur at several points: during sperm production in the testes, during sperm maturation in the epididymis, or during interaction with the egg in the female reproductive tract. Most research on ovum antigens is directed towards the zona pellucida, the acellular, gelatinous layer surrounding the ovum. It is estimated that vaccines that interfere with sperm function and fertility will be available for human testing by the early 1990s.     

Designing research to study the attributes of fertility regulation methods

A framework for identifying desirable and undesirable attribute of family planning methods in a given culture can be constructed by classifying aspects of the attributes, and then using any of several statistical techniques to analyze the results. Acceptability of a fertility regulation method is a function of the users personality (UP), the perceived attributes of the method (MA), the influence sources (IS), and the communication process (CP). All of these functions interact with each other. Attributes can be classified as objective, which are known and culture-free; subjective, such as perceived effectiveness, risk, convenience, secrecy or pain; and sterotypical, which are associated attributes with no factual basis, such as the belief that IUDs cause cancer. Attributes can be positive or negative. Suggested research designs include weightages of attributes as by popularity; scaling of attributes by importance, by equal-appearing interval, by Q- sort, by summated rating, by semantic difference or by pair-comparison techniques; combinations of attributes; and multivariate analysis of attributes.     

New paradigms in the regulation of bone metabolism

Although multiple hormones and cytokines regulate various aspects of osteoclast formation, the two final effectors, osteoprotegerin (OPG) and its ligand (OPGL/RANKL) have been recently identified. Since then, there have been important advances in the understanding of the molecular mechanisms that regulate the crosstalk between osteoblasts/stromal and hematopoietic osteoclast precursor cells. In this article, we describe the new concepts from the identification of OPG, a protein with potent osteoclastogenesis inhibitory activity, to the isolation of RANKL, a transmembrane ligand expressed on osteoblasts/stromal cells that bind to RANK, a transmembrane receptor on osteoclast cells and its precursors. The interaction between RANK and RANKL triggers a series of mechanisms that result in differentiation, maturation and activation of osteoclasts. OPG inhibits osteoclastogenesis binding to RANKL and blocks its interaction with RANK. Many hormones and cytokines, like PTH and IL-11, act inhibiting production of OPG and stimulating production of RANKL. Contrary to this, estrogens inhibit production of RANKL and RANKL-stimulated osteoclastogenesis. The knowledge of the RANK/RANKL/OPG system and the understanding of osteoclast differentiation and activation has had a great impact on the field of bone metabolism, with new possible treatment strategies for diseases characterized by excessive bone resorption.