Natural products from synthetic biology

DNA sequencing has uncovered microbial secondary metabolic potential that never surfaced in fermentation based screens. Deep and cheap sequencing of a genus such as Streptomyces can rapidly expose hundreds of metabolic genes and operons. Meanwhile, synthetic biologists, in their quest to engineer advanced biofuels, are mastering metabolic engineering. Natural products, a reliable source of new therapeutic leads for many years, have fallen into disfavor with drug discoverers partly because these molecules are rarely available as pure compounds and sourcing is often problematic. The convergence of next generation sequencing and synthetic biology, along with less spectacular progress in analytic technologies such as mass spectroscopy, opens the door to the creation of large, reliable libraries of pure natural products for drug discovery.

Large-scale integrated super-computing platform for next generation virtual drug discovery

Traditional drug discovery starts by experimentally screening chemical libraries to find hit compounds that bind to protein targets, modulating their activity. Subsequent rounds of iterative chemical derivitization and rescreening are conducted to enhance the potency, selectivity, and pharmacological properties of hit compounds. Although computational docking of ligands to targets has been used to augment the empirical discovery process, its historical effectiveness has been limited because of the poor correlation of ligand dock scores and experimentally determined binding constants. Recent progress in super-computing, coupled to theoretical insights, allows the calculation of the Gibbs free energy, and therefore accurate binding constants, for usually large ligand–receptor systems. This advance extends the potential of virtual drug discovery. A specific embodiment of the technology, integrating de novo, abstract fragment based drug design, sophisticated molecular simulation, and the ability to calculate thermodynamic binding constants with unprecedented accuracy, are discussed.

Personnel Security in the Atomic Energy Program

I have attempted to confine this article to an analytic description of the operations of the commission's personnel security program. This program has been analyzed critically and in detail by a number of individuals. I have not attempted to take issue with criticism, for this is not the purpose of a descriptive analysis. I have mentioned those limitations inherent in our program which do not entirely coincide with the traditional methods of due process. These limitations are significant, but, if they are properly exercised in the context of the commission's program, I feel that they are justified.

Mapping human genetic diversity in Asia

Asia harbors substantial cultural and linguistic diversity, but the geographic structure of genetic variation across the continent remains enigmatic. Here we report a large-scale survey of autosomal variation from a broad geographic sample of Asian human populations. Our results show that genetic ancestry is strongly correlated with linguistic affiliations as well as geography. Most populations show relatedness within ethnic/linguistic groups, despite prevalent gene flow among populations. More than 90% of East Asian (EA) haplotypes could be found in either Southeast Asian (SEA) or Central-South Asian (CSA) populations and show clinal structure with haplotype diversity decreasing from south to north. Furthermore, 50% of EA haplotypes were found in SEA only and 5% were found in CSA only, indicating that SEA was a major geographic source of EA populations.

Immunity in the elderly: the role of the thymus

Adjustments to lifestyle including social and medical changes have led to human populations having increased longevity in many countries, producing shifts in the population demographics. Approximately half of the increase in the world's population by 2050 may be accounted for by the prolonged survival of those over the age of 60. It is possible to age in relatively good health, but this is rare and for the majority of individuals, growing old is associated with functional impairment, an increased risk of developing a degenerative condition, an increased susceptibility to disease and an increased risk of death. The ageing human population is one of the most urgent challenges facing us today. Changes in the immune system are considered to have a critical role in the decline seen with age, since many infectious diseases may no longer kill an individual, but may contribute to more subtle overall changes. So the impact of infections in older individuals should not be measured only in terms of direct mortality rates, but also by their contribution to the 'indirect' mortality rate and to changes in the quality of life. Taking a pragmatic approach, we need to understand the drivers for immune decline if we are to consider intervening therapeutically in this process. One of the central drivers to this process is age-linked atrophy of the thymus and reversal of this process may have a considerable role in reversing immune decline.

Minimal residual disease is a significant predictor of treatment failure in non T-lineage adult acute lymphoblastic leukaemia: final results of the international trial UKALL XII/ECOG2993

The predictive value of molecular minimal residual disease (MRD) monitoring using polymerase chain reaction amplification of clone-specific immunoglobulin or T-cell Receptor rearrangements was analysed in 161 patients with non T-lineage Philadelphia-negative acute lymphoblastic leukaemia (ALL) participating in the UK arm of the international ALL trial UKALL XII/Eastern Cooperative Oncology Group (ECOG) 2993. MRD positivity (> or =10(-4)) in patients treated with chemotherapy alone was associated with significantly shorter relapse-free survival (RFS) at several time-points during the first year of therapy. MRD status best discriminated outcome after phase 2 induction, when the relative risk of relapse was 8.95 (2.85-28.09)-fold higher in MRD-positive (> or =10(-4)) patients and the 5-year RFS 15% [95% confidence interval (CI) 0-40%] compared to 71% (56-85%) in MRD-negative (<10(-4)) patients (P = 0.0002) When MRD was detected prior to autologous stem cell transplantation (SCT), a significantly higher rate of treatment failure was observed [5-year RFS 25% (CI 0-55%) vs. 77% (95% CI 54-100%) in MRD-negative/<10(-4), P = 0.01] whereas in recipients of allogeneic-SCT in first complete remission, MRD positivity pre-transplant did not adversely affect outcome. These data provide a rationale for introducing MRD-based risk stratification in future studies for the delineation of those at significant risk of treatment failure in whom intensification of therapy should be evaluated.

A Genomics Approach to Understanding Host Response during Dengue Infection

Dengue infection results in a wide clinical spectrum, ranging from asymptomatic, through fever (DF), to the life threatening complications haemorrhagic fever (DHF) and shock syndrome (DSS). Although we now understand that factors such as repeat infections and the type or magnitude of the host response are important in determining severity, the mechanisms of these actions remain largely unknown. Understanding this host-pathogen interaction may enable outcome prediction and new therapy options. Developments in biology now allow a 'systems approach' to be applied to this problem, utilizing whole genomes of both human and virus, in vitro and in vivo to enable a more complete picture of their interplay to be built up. We have developed a chip-based approach to viral sequencing, to increase efficiency and enable large numbers ofgenomes to be completed, together with a web-based interpretation tool. We have also applied human whole genome expression arrays (24000 genes) to characterize the types of host response made to infection and plan to investigate the role of host variation using human whole genome genetic association studies in the future. These technologies have identified novel host pathways involved in viral replication in vitro, and also host immune responses, such as the interferon signalling pathway, that are influenced by viral sequence. This data will be further refined through interlinking with similar data obtained from a large study of dengue patients, initiated in Singapore, that is able to look at the early host response to infection.

A hybrid computational grid architecture for comparative genomics

Comparative genomics provides a powerful tool for studying evolutionary changes among organisms, helping to identify genes that are conserved among species, as well as genes that give each organism its unique characteristics. However, the huge datasets involved makes this approach impractical on traditional computer architectures leading to prohibitively long runtimes. In this paper, we present a new computational grid architecture based on a hybrid computing model to significantly accelerate comparative genomics applications. The hybrid computing model consists of two types of parallelism: coarse grained and fine grained. The coarse-grained parallelism uses a volunteer computing infrastructure for job distribution, while the fine-grained parallelism uses commodity computer graphics hardware for fast sequence alignment. We present the deployment and evaluation of this approach on our grid test bed for the all-against-all comparison of microbial genomes. The results of this comparison are then used by phenotype--genotype explorer (PheGee). PheGee is a new tool that nominates candidate genes responsible for a given phenotype.

Elucidating the secretion proteome of human embryonic stem cell-derived mesenchymal stem cells

Transplantation of mesenchymal stem cells (MSCs) has been used to treat a wide range of diseases, and the mechanism of action is postulated to be mediated by either differentiation into functional reparative cells that replace injured tissues or secretion of paracrine factors that promote tissue repair. To complement earlier studies that identified some of the paracrine factors, we profiled the paracrine proteome to better assess the relevance of MSC paracrine factors to the wide spectrum of MSC-mediated therapeutic effects. To evaluate the therapeutic potential of the MSC paracrine proteome, a chemically defined serum-free culture medium was conditioned by MSCs derived from human embryonic stem cells using a clinically compliant protocol. The conditioned medium was analyzed by multidimensional protein identification technology and cytokine antibody array analysis and revealed the presence of 201 unique gene products. 86-88% of these gene products had detectable transcript levels by microarray or quantitative RT-PCR assays. Computational analysis predicted that these gene products will significantly drive three major groups of biological processes: metabolism, defense response, and tissue differentiation including vascularization, hematopoiesis, and skeletal development. It also predicted that the 201 gene products activate important signaling pathways in cardiovascular biology, bone development, and hematopoiesis such as Jak-STAT, MAPK, Toll-like receptor, transforming growth factor-beta, and mTOR (mammalian target of rapamycin) signaling pathways. This study identified a large number of MSC secretory products that have the potential to act as paracrine modulators of tissue repair and replacement in diseases of the cardiovascular, hematopoietic, and skeletal tissues. Moreover our results suggest that human embryonic stem cell-derived MSC-conditioned medium has the potency to treat a variety of diseases in humans without cell transplantation.

Survey of psychosocial support provided by UK paediatric oncology centres

AIM

To obtain a comprehensive overview of current patterns of psychosocial support provided by National Health Service (NHS) paediatric oncology treatment centres across the UK.

METHODS

A postal questionnaire was sent to co-ordinators in the UK Children's Cancer Study Group (a professional body that is responsible for the organisation of treatment and management of childhood cancer in the UK) in 21 treatment centres and three separate Teenage Cancer Trus units. A range of psychosocial topics were explored, including ratio of staff providing support to patients; facilities provided for children and families; psychosocial support services such as support groups; information provision; and transition support.

RESULTS

There were many good areas of support provided by centres, but there was also a lack of standard practices and procedures. All centres employed social workers, play specialists, and paediatric oncology outreach nurses, but patient to staff ratios varied across centres. The poorest staff provision was among psychologists, where patient to staff ratios ranged from 132:1 to 1100:1. Written information was standard practice, while provision of other types of information (audiovisual, online) varied; none of the centres provided audio information specifically for children/young people.

CONCLUSION

This variability in practices among centres frequently occurred, as centres rarely had procedures formally agreed or recorded in writing. British government policy currently seeks to develop standards and guidelines of care throughout the National Health Service. This study further demonstrates the importance of standards and the need to agree guidelines for the provision of psychosocial support for children/young people and their families throughout the course of the illness.

Treatment of factor XI inhibitor using recombinant activated factor VIIa

A 30-year-old female with severe factor XI deficiency of 0-2% acquired factor XI inhibitor following many infusions for fresh frozen plasma (FFP) for surgical procedures starting at 4 years of age. Seven months before this inhibitor was diagnosed, surgery was complicated by prolonged bleeding resistant to FFP, requiring epsilon aminocaproic acid (EACA) and surgical packing. The inhibitor was measured at 2.2 Bethesda units, 7 months since the last FFP. The inhibitor was confirmed as specific anti-XI and anti-XIa binding by patient's IgG to immobilized factor XI and factor XIa from whole plasma and purified IgG. For repair of a painful anterior cruciate ligament (ACL) defect she was given recombinant factor VIIa (rVIIa) at 90 mug kg(-1), starting one-half hour preoperatively and continued every 2 h for 8 h when haemostasis was complete. Thereafter the rVIIa was given every 3 h for two doses, and then every 4 h for four doses at which time she was discharged on EACA which was continued for 6 days. There was excellent haemostasis during and following the surgery. There was no evidence of consumptive coagulopathy, with no change in the fibrinogen, platelet count, or D-D dimer; and no increase of platelet factor 4, beta-thromboglobulin, or prothrombin fragment F 1.2. The thrombin-antithrombin complex increased over baseline after 24 h. There was no postoperative deep vein thrombosis or pulmonary embolus. In this patient with a factor XI inhibitor, the recombinant factor VIIa was effective and safe, ensuring adequate haemostasis with no thrombotic complications. This product which was designed for patients with inhibitors to factor VIII or factor IX, and factor VII deficiency, has now been given successfully to four patients with factor XI inhibitors.

Implementing a hospital-based violence-related injury surveillance system--a background to the Jamaican experience

Violence, a leading cause of injuries and death, is recognized as a major public health problem. In 1996, injuries were the second leading cause of hospitalizations in Jamaica. The estimated annual cost of in-patient care for injuries was 11.6 million US dollars. To develop strategies to reduce the impact of violence-related injuries on Jamaican health care resources, the Ministry of Health, Division of Health Promotion and Protection (MOH/DHPP) in collaboration with the Centers for Disease Control and Prevention and the Tropical Metabolic Research Institute, University of the West Indies Mona, designed and implemented a violence-related injury surveillance system (VRISS) at Kingston Public Hospital (KPH). In 1998, the VRISS, based on the International Classification of External Cause of Injury (ICECI), was implemented in the accident and emergency (A&E) department of Jamaica's tertiary care hospital, KPH. VRISS collects demographic, method and circumstance of injury, victim-perpetrator relationship and patient's discharge status data. From 8/1/98 to 7/31/99, data on 6,107 injuries were collected. Injuries occurred primarily among males aged 25-44 years. Most injuries (54%; 3171) were caused by use of a sharp object. Nearly half (49%; 2992) were perpetrated by acquaintances. The majority, 70% (4,252), were the result of a fight or argument and 17% were admitted to the hospital. The VRISS utilized A&E department data to characterize violence-related injuries in Jamaica, a resource-limited environment. These data will be used to guide intervention development to reduce violence-related injuries in Jamaica.

A novel three-dimensional tissue equivalent model to study the combined effects of cyclic mechanical strain and wear particles on the osteolytic potential of primary human macrophages in vitro

The effects of cyclic mechanical strain and challenge with physiologically relevant doses of submicrometre-size polyethylene (PE) particles on the osteolytic potential of primary human mononuclear phagocytes were investigated. Cells were seeded into a three-dimensional tissue matrix and co-cultured with particles (mean size 0.21 microm) at particle volume to cell number ratios of 7.5, 15, 30 and 100 microm3/cell. Matrices were then either cultured statically or subjected to 20 per cent cyclic compressional strain in the 'ComCell' for 16 h prior to the assessment of cell viability and quantification of the pro-inflammatory cytokine tumour necrosis factor alpha (TNFalpha). The MTT (3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazdium bromide) assay was shown to be too insensitive to detect changes in cell viability. However, when quantified by the adenosine triphosphate (ATP) assay, cell viability was demonstrated to be reduced following exposure to cyclic strain. Macrophages cultured in the static three-dimensional tissue equivalent model produced very high levels of TNFalpha in response to submicrometre PE particles at a ratio of 100 microm3/cell. Cyclic strain in the absence of particles gave only a small increase in TNFa production. However, the combined effects of strain and particle stimulation at a ratio of 30 microm3/cell resulted in the secretion of significantly more TNFalpha than was produced by macrophages subjected to strain alone, or the cells-only control. This synergy between cyclic strain and PE particle stimulation was only evident when the volume of particles was reduced below the volume that maximally stimulated cells. These results suggest that while cyclic strain may not be the primary factor responsible for macrophage activation and periprosthetic osteolysis, at low particle load, it may contribute significantly to the osteolytic potential of macrophages in vitro or in vivo.

Neurological and developmental effects of HIV and AIDS in children and adolescents

HIV-related encephalopathy is an important problem in vertically infected children with HIV. Infected infants may manifest early, catastrophic encephalopathy, with loss of brain growth, motor abnormalities, and cognitive dysfunction. Even without evidence of AIDS, infected infants score lower than serorevertors on developmental measures, particularly language acquisition. Children with perinatal or later transfusion-related infection generally are roughly comparable developmentally to their peers until late in their course. Symptoms similar to adult AIDS dementia complex are occasionally seen in adolescents with advanced AIDS, including dementia, bradykinesia, and spasticity. Opportunistic CNS infections such as toxoplasmosis and progressive multifocal leukoencephalopathy are less common in children and adolescents than in adults. Increasing evidence suggests that aggressive antiretroviral treatment may halt or even reverse encephalopathy. Neuroimaging changes may precede or follow clinical manifestations, and include early lenticulostriate vessel echogenicity on cranial ultrasound, calcifying microangiopathy on CT scan, and/or white matter lesions and central atrophy on MRI. Differential diagnosis of neurological dysfunction in an HIV-infected infant includes the effects of maternal substance abuse, other CNS congenital infections, and other causes of early static encephalopathy. Initial entry of HIV into the nervous system occurs very early in infection. The risk of clinical HIV encephalopathy increases with very early age of infection and with high viral loads. Virus is found in microglia and brain derived macrophages, not neurons. The neuronal effect of HIV is probably indirect, with various cytokines implicated. Apoptosis is the presumed mechanism of damage to neurons by HIV.

A review of size and location of ruptured intracranial aneurysms

OBJECTIVE

To review our experience and examine the size at which aneurysms ruptured in our patient population.

METHODS

Patient charts and angiograms for all patients admitted with a diagnosis of subarachnoid hemorrhage to the Thomas Jefferson/Wills Eye Hospital between April 1996 and March 2000 were reviewed.

RESULTS

Of the 362 cases reviewed, definite measurements of the ruptured aneurysm were obtained in 245. The data clearly showed that most ruptured aneurysms presenting to our institution were less than 10 mm in diameter. We found that, regardless of location on the circle of Willis, 85.6% of all aneurysms presenting with rupture were less than 10 mm. Review by location shows that aneurysms of the anterior communicating artery most often presented with rupture at sizes less than 10 mm (94.4%). A large number of ruptured posterior communicating artery aneurysms also presented at sizes less than 10 mm (87.5%). This trend continued for all aneurysm sites in our review. The incidence of subarachnoid hemorrhage in Western countries is estimated at 10 per 100,000 people per year. Recent reports have indicated that aneurysms less than 10 mm in size are unlikely to rupture.

CONCLUSION

We argue that the risk of small aneurysms rupturing is not insignificant, especially those of the anterior communicating artery. Our findings indicate that surgery on unruptured aneurysms should not be predicated on aneurysm size alone.