Thienopyridine-derivatives (ticlopidine, clopidogrel, and prasugrel) are the primary antiplatelet agents. Thrombotic thrombocytopenic purpura (TTP) is a rare drug-associated syndrome, with the thienopyridines being the most common drugs implicated in this syndrome. We reviewed 20 years of information on clinical, epidemiologic, and laboratory findings for thienopyridine-associated TTP. Four, 11, and 11 cases of thienopyridine-associated TTP were reported in the first year of marketing of ticlopidine (1989), clopidogrel (1998), and prasugrel (2010), respectively. As of 2011, the FDA received reports of 97 ticlopidine-, 197 clopidogrel-, and 14 prasugrel-associated TTP cases. Severe deficiency of ADAMTS-13 (a disintegrin and metalloproteinase with a thrombospondin type 1 motif, member 13) was present in 80% and antibodies to 100% of these TTP patients on ticlopidine, 0% of the patients with clopidogrel-associated TTP (p < 0.05), and an unknown percentage of patients with prasugrel-associated TTP. TTP is associated with use of each of the three thienopyridines, although the mechanistic pathways may differ.
thrombotic thrombocytopenic purpura; ticlopidine; clopidogrel; prasugrel; adverse event
While a great deal of research has been performed on the long-term genomic actions of estrogens, their rapid effects and implications for learning and memory are less well characterized. The often conflicting results of estrogenic effects on learning and memory may be due to complex and little understood interactions between genomic and rapid effects. Here, we investigated the effects of low, physiologically relevant, doses of 17β-estradiol on three different learning paradigms that assess social and non-social aspects of recognition memory and spatial memory, during a transcription independent period of memory maintenance. Ovariectomized female CD1 mice were subcutaneously administered vehicle, 1.5 μg/kg, 2 μg/kg, or 3 μg/kg of 17β-estradiol 15 minutes before social recognition, object recognition, or object placement learning. These paradigms were designed to allow the testing of learning effects within 40 min of hormone administration. In addition, using a different set of ovariectomized mice, we examined the rapid effects of 1.5 μg/kg, 2 μg/kg, or 3 μg/kg of 17β-estradiol on CA1 hippocampal dendritic spines. All 17β-estradiol doses tested impacted learning, memory, and CA1 hippocampal spines. 17β-Estradiol improved both social and object recognition, and may facilitate object placement learning and memory. In addition, 17β-estradiol increased dendritic spine density in the stratum radiatum subregion of the CA1 hippocampus, but did not affect dendritic spines in the lacunosum-moleculare, within 40 min of administration. These results demonstrate that the rapid actions of 17β-estradiol have important implications for general learning and memory processes that are not specific for a particular type of learning paradigm. These effects may be mediated by the rapid formation of new dendritic spines in the hippocampus.
estrogens; PPT; DPN; learning and memory; discrimination; hippocampus; Alzheimer's disease; behavioral science; discrimination; DPN; hippocampus; learning and memory; neuroendocrinology; non-genomic; plasticity; PPT
The hypothalamic-pituitary-adrenal (HPA) axis is a major part of the neuroendocrine system in animal responses to stress. It is known that the HPA axis is attenuated at parturition to prevent detrimental effects of glucocorticoid secretion including inhibition of lactation and maternal responsiveness. Luman/CREB3 recruitment factor (LRF) was identified as a negative regulator of CREB3 which is involved in the endoplasmic reticulum stress response. Here, we report a LRF gene knockout mouse line that has a severe maternal behavioral defect. LRF−/− females lacked the instinct to tend pups; 80% of their litters died within 24 h, while most pups survived if cross-fostered. Prolactin levels were significantly repressed in lactating LRF−/− dams, with glucocorticoid receptor (GR) signaling markedly augmented. In cell culture, LRF repressed transcriptional activity of GR and promoted its protein degradation. LRF was found to colocalize with the known GR repressor, RIP140/NRIP1, which inhibits the activity by GR within specific nuclear punctates that are similar to LRF nuclear bodies. Furthermore, administration of prolactin or the GR antagonist RU486 restored maternal responses in mutant females. We thus postulate that LRF plays a critical role in the attenuation of the HPA axis through repression of glucocorticoid stress signaling during parturition and the postpartum period.
Wider use of FDA anti-counterfeit initiatives, limiting pharmaceutical suppliers to reputable distributors, and educating providers and patients about signs of counterfeit drugs can improve the safety of cancer pharmaceuticals.
Counterfeit pharmaceuticals pose risks domestically. Because of their cost, cancer pharmaceuticals are vulnerable. We review findings from a domestic counterfeiting episode involving erythropoietin and outline anticounterfeiting recommendations for policy makers, patients, and health care professionals.
Materials and Methods:
Information was obtained on patients who received counterfeit erythropoietin, its distribution, and criminal investigations into counterfeiting networks. Interview sources included a physician, an attorney, employees of the Florida Department of Health and Human Services and the US Food and Drug Administration's (FDA) Office of Criminal Investigation, manufacturers, and wholesalers. Other sources included the book “Dangerous Doses,” LexisNexis (search terms “counterfeit” and “erythropoietin”) and the FDA database.
Counterfeit product consisted of 2,000 U vials with counterfeit labels denoting 40,000 U. The counterfeiters, in collaboration with a Miami pharmacy, purchased 110,000 erythropoietin 2,000 U vials and affixed counterfeit labels to each vial. Products were then sold via the pharmaceutical “gray market” to wholesalers, then pharmacy chains. Investigations by Florida government officials implicated 17 persons, all of whom were found guilty of trafficking in counterfeit pharmaceuticals. Despite the large size of the operation, the FDA received reports of only 12 patients who had received counterfeit erythropoietin and detailed information for only two individuals. A 17-year-old liver transplant recipient and a 61-year-old patient with breast cancer experienced loss of efficacy after receiving counterfeit erythropoietin.
Wider use of FDA anticounterfeit initiatives, limiting pharmaceutical suppliers to reputable distributors, and educating providers and patients about signs of counterfeit drugs can improve the safety of cancer pharmaceuticals.
Smooth muscle α actin (SMA) is a cytoskeletal protein expressed by mesenchymal and smooth muscle cell types, including mural cells (vascular smooth muscle cells and pericytes). Using Bacterial Artificial Chromosome (BAC) recombineering technology, we generated transgenic reporter mice that express a membrane localized cherry red fluorescent protein (mCherry), driven by the full-length SMA promoter and intronic sequences. We determined that the founders and F1 progeny of five independent lines contain 1-3 copies of the mCherry substituted BAC vector. Furthermore, we characterized the expression of SMA-mCherry in relation to endogenous SMA in the embryo and in adult tissues, and found that the transgenic reporter in each line recapitulated endogenous SMA expression at all time points. We were also able to isolate SMA expressing cells from embryonic tissues using fluorescence activated cell sorting (FACS). We demonstrated that this marker can be combined with other vital fluorescent reporters and it can be used for live imaging of embryonic cardiodynamics. Therefore, these transgenic mice will be useful for isolating live SMA-expressing cells via FACS and for studying the emergence, behavior and regulation of SMA-expressing cells, including vascular smooth muscle cells and pericytes throughout embryonic and postnatal development.
BAC transgenesis; In vivo imaging; Cardiac function; Vascular development; Mesenchymal cell
Competitive effects of younger cohorts on older ones are frequently assumed to be negligible in species where older, larger individuals dominate in pairwise behavioural interactions. Here, we provide field estimates of such competition by recruits on an older age class in Atlantic salmon (Salmo salar), a species where observational studies have documented strong body size advantages which should favour older individuals in direct interactions. By creating realistic levels of spatial variation in the density of underyearling (YOY) recruits over a 1-km stretch of a stream, and obtaining accurate measurements of individual growth rates of overyearlings (parr) from capture–mark–recapture data on a fine spatial scale, we demonstrate that high YOY density can substantially decrease parr growth. Models integrating multiple spatial scales indicated that parr were influenced by YOY density within 16 m. The preferred model suggested parr daily mass increase to be reduced by 39% when increasing YOY density from 0.0 to 1.0 m−2, which is well within the range of naturally occurring densities. Reduced juvenile growth rates will in general be expected to reduce juvenile survival (via increased length of exposure to freshwater mortality) and increase generation times (via increased age at seaward migrations). Thus, increased recruitment can significantly affect the performance of older cohorts, with important implications for population dynamics. Our results highlight that, even for the wide range of organisms that rely on defendable resources, the direction of competition among age classes cannot be assumed a priori or be inferred from behavioural observations alone.
Age structure; Density dependence; Exploitative; Interactive; Inter-cohort competition
Pluripotent stem cell lines have been generated in several domestic animal species; however, these lines traditionally show poor self-renewal and differentiation. Using canine embryonic stem cell (cESC) lines previously shown to have sufficient self-renewal capacity and potency, we generated and compared canine neural stem cell (cNSC) lines derived by lineage selection with epidermal growth factor (EGF) or Noggin along the neural default differentiation pathway, or by directed differentiation with retinoic acid (RA)-induced floating sphere assay. Lineage selection produced large populations of SOX2+ neural stem/progenitor cell populations and neuronal derivatives while directed differentiation produced few and improper neuronal derivatives. Primary canine neural lines were generated from fetal tissue and used as a positive control for differentiation and electrophysiology. Differentiation of EGF- and Noggin-directed cNSC lines in N2B27 with low-dose growth factors (BDNF/NT-3 or PDGFαα) produced phenotypes equivalent to primary canine neural cells including 3CB2+ radial progenitors, MOSP+ glia restricted precursors, VIM+/GFAP+ astrocytes, and TUBB3+/MAP2+/NFH+/SYN+ neurons. Conversely, induction with RA and neuronal differentiation produced inadequate putative neurons for further study, even though appropriate neuronal gene expression profiles were observed by RT-PCR (including Nestin, TUBB3, PSD95, STX1A, SYNPR, MAP2). Co-culture of cESC-derived neurons with primary canine fetal cells on canine astrocytes was used to test functional maturity of putative neurons. Canine ESC-derived neurons received functional GABAA- and AMPA-receptor mediated synaptic input, but only when co-cultured with primary neurons. This study presents established neural stem/progenitor cell populations and functional neural derivatives in the dog, providing the proof-of-concept required to translate stem cell transplantation strategies into a clinically relevant animal model.
The organization and control of polarized growth through the cell cycle of Schizosaccharomyces pombe, a single-celled eukaryote, have been studied extensively. We have investigated the changes in these processes when S. pombe differentiates to form multicellular invasive mycelia and have found striking alterations to the behavior of some of the key regulatory proteins. Cells at the tips of invading filaments are considerably more elongated than cells growing singly and grow at one pole only. The filament tip follows a strict direction of growth through multiple cell cycles. A group of proteins involved in the growth process and actin regulation, comprising Spo20, Bgs4, activated Cdc42, and Crn1, are all concentrated at the growing tip, unlike their distribution at both ends of single cells. In contrast, several proteins implicated in microtubule-dependent organization of growth, including Tea1, Tea4, Mod5, and Pom1, all show the opposite effect and are relatively depleted at the growing end and enriched at the nongrowing end, although Tea1 appears to continue to be delivered to both ends. A third group acting at different stages of the cell cycle, including Bud6, Rga4, and Mid1, localize similarly in filaments and single cells, while Nif1 shows a reciprocal localization to Pom1.
Fifteen million strokes occur worldwide each year with 5 million associated deaths and an additional 5 million people left permanently disabled. In the United States, about 780 000 people suffer a new or recurrent stroke each year. There were an estimated total 5.8 million stroke survivors as of 2008. Mortality from stroke is the third leading cause of death in America following heart disease and cancer. Chest infection may affect up to as many as one-third of stroke patients. This increases the morbidity and mortality of this patient population. Pneumonia causes the highest attributable mortality of all medical complications following stroke. A comprehensive multidisciplinary team approach is required at the hospital level. This requires active administrative commitment and participation. Implementation of evidence-based management strategies can improve outcomes and reduce costs. We sought to review the problem of post-stroke pneumonia and discuss strategies for prevention and intervention.
stroke; pneumonia; aspiration
Background and Case report
Polyarteritis Nodosa (PAN) is a systemic necrotizing vasculitis that affects medium-sized and occasionally involves small arteries leading to the disruption of the internal and external elastic lamina and contribute to the development of aneurysms. Aneurysms develop at bifurcation of major blood vessels; they are prone to thrombosis, rupture and haemorrhage. Retroperitoneal haemorrhage around kidneys was previously reported in patients with PAN. We report a case of massive retroperitoneal bleeding from inferior pancreaticoduodenal artery aneurysm rupture in a 70-year-old female with PAN.
Prognosis of untreated PAN is very poor with 20% 5 year survival rate, therefore early recognition of the disease will prevent catastrophic complications and improves survival.
One hundred twenty-one adult liver transplant recipients were studied for the incidence, risk factors, and morbidity associated with herpesviruses infections after transplantation. The overall incidence of infection was 59% for cytomegalovirus (CMV), 35% for herpes simplex virus (HSV), 25% for Epstein-Barr virus (EBV), and 7% for varicella-zoster virus (VZV). Primary CMV infection occurred in 46% and reactivation CMV infection in 67% of the susceptible recipients. Symptomatic and disseminated CMV diseases were more common when patients developed primary infection (P < .01, for both comparisons). The donor organ appeared to be the only important source of CMV infection in seronegative recipients. The use of OKT3 antibodies was associated with disseminated CMV disease in patients with primary infection (P = .04) but not with reactivation infection (P > .10). Although most HSV infections were oral or genital reactivations, three cases of HSV hepatitis occurred – one was a primary infection. Symptomatic reactivations of HSV were observed in 53% of HSV-seropositive recipients who received OKT3, versus 31% of seropositive recipients who did not receive OKT3 (P = .05).
By dispersing from localized aggregations of recruits, individuals may obtain energetic benefits due to reduced experienced density. However, this will depend on the spatial scale over which individuals compete. Here, we quantify this scale for juvenile Atlantic salmon (Salmo salar) following emergence and dispersal from nests. A single nest was placed in each of ten replicate streams during winter, and information on the individual positions (±1 m) and the body sizes of the resulting young-of-the-year (YOY) juveniles was obtained by sampling during the summer. In six of the ten streams, model comparisons suggested that individual body size was most closely related to the density within a mean distance of 11 m (range 2–26 m). A link between body size and density on such a restricted spatial scale suggests that dispersal from nests confers energetic benefits that can counterbalance any survival costs. For the four remaining streams, which had a high abundance of trout and older salmon cohorts, no single spatial scale could best describe the relation between YOY density and body size. Energetic benefits of dispersal associated with reduced local density therefore appear to depend on the abundance of competing cohorts or species, which have spatial distributions that are less predictable in terms of distance from nests. Thus, given a trade-off between costs and benefits associated with dispersal, and variation in benefits among environments, we predict an evolving and/or phenotypically plastic growth rate threshold which determines when an individual decides to disperse from areas of high local density.
Drift feeding; Density dependence; Natal dispersal; Shadow competition; Suspension feeding
The Atlantic salmon (Salmo salar) is a charismatic anadromous fish of high conservation and economic value. Concerns have been expressed regarding the long-term viability of fisheries throughout the species's distributional range because of abundance variations that cannot currently be explained or predicted. Here, we analyse long-term catch data obtained over a wide geographical range and across a range of spatial subscales to understand more fully the factors that drive population abundance. We use rod catch data from 84 Norwegian rivers over 125 years (1876–2000) and 48 Scottish rivers over 51 years (1952–2002). The temporal correlation in catches is very long-term, with trends persisting over several decades. The spatial correlation is relatively short-range, indicating strong local-scale effects on catch. Furthermore, Scottish salmon populations exhibit recent negative trends in contrast to some more positive trends in Norway—especially in the north.
Atlantic salmon; catches; time series; local effects; regional effects; sea surface temperature
Investigation into the switch between single-celled and filamentous forms of fungi may provide insights into cell polarity, differentiation, and fungal pathogenicity. At the molecular level, much of this investigation has fallen on two closely related budding yeasts, Candida albicans and Saccharomyces cerevisiae. Recently, the much more distant fission yeast Schizosaccharomyces pombe was shown to form invasive filaments after nitrogen limitation (E. Amoah-Buahin, N. Bone, and J. Armstrong, Eukaryot. Cell 4:1287-1297, 2005) and this genetically tractable organism provides an alternative system for the study of dimorphic growth. Here we describe a second mode of mycelial formation of S. pombe, on rich media. Screening of an S. pombe haploid deletion library identified 12 genes required for mycelial development which encode potential transcription factors, orthologues of S. cerevisiae Sec14p and Tlg2p, and the formin For3, among others. These were further grouped into two phenotypic classes representing different stages of the process. We show that galactose-dependent cell adhesion and actin assembly are both required for mycelial formation and mutants lacking a range of genes controlling cell polarity all produce mycelia but with radically altered morphology.
The swine-origin influenza A (H1N1) virus that appeared in 2009 and was first found in human beings in Mexico, is a reassortant with at least three parents. Six of the genes are closest in sequence to those of H1N2 'triple-reassortant' influenza viruses isolated from pigs in North America around 1999-2000. Its other two genes are from different Eurasian 'avian-like' viruses of pigs; the NA gene is closest to H1N1 viruses isolated in Europe in 1991-1993, and the MP gene is closest to H3N2 viruses isolated in Asia in 1999-2000. The sequences of these genes do not directly reveal the immediate source of the virus as the closest were from isolates collected more than a decade before the human pandemic started. The three parents of the virus may have been assembled in one place by natural means, such as by migrating birds, however the consistent link with pig viruses suggests that human activity was involved. We discuss a published suggestion that unsampled pig herds, the intercontinental live pig trade, together with porous quarantine barriers, generated the reassortant. We contrast that suggestion with the possibility that laboratory errors involving the sharing of virus isolates and cultured cells, or perhaps vaccine production, may have been involved. Gene sequences from isolates that bridge the time and phylogenetic gap between the new virus and its parents will distinguish between these possibilities, and we suggest where they should be sought. It is important that the source of the new virus be found if we wish to avoid future pandemics rather than just trying to minimize the consequences after they have emerged. Influenza virus is a very significant zoonotic pathogen. Public confidence in influenza research, and the agribusinesses that are based on influenza's many hosts, has been eroded by several recent events involving the virus. Measures that might restore confidence include establishing a unified international administrative framework coordinating surveillance, research and commercial work with this virus, and maintaining a registry of all influenza isolates.
Pilomatrix carcinoma is the rare malignant counterpart of pilomatrixoma, a skin adnexal tumour originating from hair matrix cells. Pilomatrix carcinoma can arise as a solitary lesion de novo, or through transformation of a pilomatrixoma. Pilomatrixoma was first described erroneously as being of sebaceous gland origin but was later discovered to be derived from hair matrix cells. They are rare, slow growing tumours of the skin found in the lower dermis and subcutaneous fat and are predominantly found in the neck and the scalp. While known to be locally aggressive, no malignant form was thought to exist until it was described relatively recently. Since then, approximately ninety cases of pilomatrix carcinoma have been reported.
We report the case of a 41 year old mentally retarded male who had a longstanding lesion in the left neck for approximately fifteen years previously diagnosed as a pilomatrixoma. He presented with severe headache, falls and visual disturbance and a biopsy showed pilomatrix carcinoma of the occipital region which, on computed tomography ( CT ) invaded the occipital bone, the cerebellum and the left temporal lobe. At his initial presentation he had a craniotomy and subtotal excision of the lesion but received no adjuvant therapy. After an early intracranial recurrence he had further debulking and adjuvant external beam radiotherapy. He has had no further intracranial recurrence after three and a half years of follow-up. Here we present the pathological features of this uncommon tumour.
We report the case of a patient with treated Stage Ia seminoma who was found to have an elevated beta human chorionic gonadotrophin (hCG) on routine follow – up. This instigated restaging and could have lead to commencement of chemotherapy.
The patient was a bodybuilder, and following a negative metastatic work – up, admitted to injecting exogenous beta hCG. This was done to reduce withdrawal symptoms from androgen abuse. The patient remains well eight years post diagnosis.
This case highlights the need for surgical oncologists to conduct vigilant screening of young male patients with a history of testicular germ cell tumours and who may indulge in steroid abuse.
Molecular interaction Information is a key resource in modern biomedical research. Publicly available data have previously been provided in a broad array of diverse formats, making access to this very difficult. The publication and wide implementation of the Human Proteome Organisation Proteomics Standards Initiative Molecular Interactions (HUPO PSI-MI) format in 2004 was a major step towards the establishment of a single, unified format by which molecular interactions should be presented, but focused purely on protein-protein interactions.
The HUPO-PSI has further developed the PSI-MI XML schema to enable the description of interactions between a wider range of molecular types, for example nucleic acids, chemical entities, and molecular complexes. Extensive details about each supported molecular interaction can now be captured, including the biological role of each molecule within that interaction, detailed description of interacting domains, and the kinetic parameters of the interaction. The format is supported by data management and analysis tools and has been adopted by major interaction data providers. Additionally, a simpler, tab-delimited format MITAB2.5 has been developed for the benefit of users who require only minimal information in an easy to access configuration.
The PSI-MI XML2.5 and MITAB2.5 formats have been jointly developed by interaction data producers and providers from both the academic and commercial sector, and are already widely implemented and well supported by an active development community. PSI-MI XML2.5 enables the description of highly detailed molecular interaction data and facilitates data exchange between databases and users without loss of information. MITAB2.5 is a simpler format appropriate for fast Perl parsing or loading into Microsoft Excel.
Viral interference with secretory cargo is a common mechanism for pathogen immune evasion. Selective down regulation of critical immune system molecules such as major histocompatibility complex (MHC) proteins enables pathogens to mask themselves from their host. African swine fever virus (ASFV) disrupts the trans-Golgi network (TGN) by altering the localization of TGN46, an organelle marker for the distal secretory pathway. Reorganization of membrane transport components may provide a mechanism whereby ASFV can disrupt the correct secretion and/or cell surface expression of host proteins. In the study reported here, we used the tsO45 temperature-sensitive mutant of the G protein of vesicular stomatitis virus to show that ASFV significantly reduces the rate at which the protein is delivered to the plasma membrane. This is linked to a general reorganization of the secretory pathway during infection and a specific, microtubule-dependent disruption of structural components of the TGN. Golgin p230 and TGN46 are separated into distinct vesicles, whereupon TGN46 is depleted. These data suggest that disruption of the TGN by ASFV can slow membrane traffic during viral infection. This may be functionally important because infection of macrophages with virulent isolates of ASFV increased the expression of MHC class I genes, but there was no parallel increase in MHC class I molecule delivery to the plasma membrane.
There is intense debate over the potential impact of seal predation on declining salmon stocks in both the Pacific and Atlantic oceans. However, efforts to model such interactions have been constrained by a lack of data on the functional and numerical responses of these predators. Based upon theory, and data from small-scale terrestrial and freshwater systems, a type 3 functional response is expected to best describe predation by generalist pinnipeds. Similarly, theory also predicts that seal numbers should increase with salmon density in rivers following an aggregative response of predator to prey. We tested these predictions by studying the diet and local density of harbour seals in relation to seasonal variations in the abundance of salmonid in a Scottish river system. As predicted, the abundance of seals in the river was directly related to the abundance of returning salmon, and dietary data supported the type 3 functional response to changes in salmonid abundance. These studies provide empirical support for the use of type 3 response in modelling studies.
Phoca vitulina; Salmo spp.; predator–prey relationships
The food intake rate of foragers may be reduced as a result of interference, which may be asymmetric among individuals and occur as a result of intimidation, direct aggression or filtering. It is important to distinguish among these types of interference, because each can have different consequences for individuals, foraging groups and populations. We demonstrate the application of the functional response as a tool for distinguishing between types of interference. We apply the approach to juvenile Atlantic salmon and show that stepwise elimination of interference types is possible from regression analyses of functional responses, identifying filtering as the only effective type of interference in the study environment.
The fission yeast Schizosaccharomyces pombe grows in a single-celled form or can mate and undergo meiosis and sporulation. Here we show that wild-type S. pombe can also differentiate to form elaborately branched hyphae which invade deep into solid medium. Branches appear in the hyphae adjacent to unseparated septa. Electron microscopy reveals unusual multivesicular structures within the hyphae. Nitrogen deprivation appears to be the main stimulus for hyphal growth. No mitogen-activated protein kinase is necessary for the response. Inhibition of cyclic AMP (cAMP) production or signaling prevents the response, and exogenous cAMP promotes it, suggesting that detection of a good carbon source is required for hyphal growth but not for mating.
Most current DNA diagnostic tests for identifying organisms use specific oligonucleotide probes that are complementary in sequence to, and hence only hybridise with the DNA of one target species. By contrast, in traditional taxonomy, specimens are usually identified by 'dichotomous keys' that use combinations of characters shared by different members of the target set. Using one specific character for each target is the least efficient strategy for identification. Using combinations of shared bisectionally-distributed characters is much more efficient, and this strategy is most efficient when they separate the targets in a progressively binary way.
We have developed a practical method for finding minimal sets of sub-sequences that identify individual sequences, and could be targeted by combinations of probes, so that the efficient strategy of traditional taxonomic identification could be used in DNA diagnosis. The sizes of minimal sub-sequence sets depended mostly on sequence diversity and sub-sequence length and interactions between these parameters. We found that 201 distinct cytochrome oxidase subunit-1 (CO1) genes from moths (Lepidoptera) were distinguished using only 15 sub-sequences 20 nucleotides long, whereas only 8–10 sub-sequences 6–10 nucleotides long were required to distinguish the CO1 genes of 92 species from the 9 largest orders of insects.
The presence/absence of sub-sequences in a set of gene sequences can be used like the questions in a traditional dichotomous taxonomic key; hybridisation probes complementary to such sub-sequences should provide a very efficient means for identifying individual species, subtypes or genotypes. Sequence diversity and sub-sequence length are the major factors that determine the numbers of distinguishing sub-sequences in any set of sequences.
IntAct provides an open source database and toolkit for the storage, presentation and analysis of protein interactions. The web interface provides both textual and graphical representations of protein interactions, and allows exploring interaction networks in the context of the GO annotations of the interacting proteins. A web service allows direct computational access to retrieve interaction networks in XML format. IntAct currently contains ∼2200 binary and complex interactions imported from the literature and curated in collaboration with the Swiss-Prot team, making intensive use of controlled vocabularies to ensure data consistency. All IntAct software, data and controlled vocabularies are available at http://www.ebi.ac.uk/intact.