Synthesis of gem-Dimethylcyclopentane-Fused Arenes with Various Topologies via TBD-Mediated Dehydro-Diels-Alder Reaction

The development of efficient methods for the synthesis of substituted polycyclic arenes with various topologies is in high demand due to their excellent electrical and optical properties. In this work, a series of gem-dimethylcyclopentane-fused arenes with more than ten topologies were synthesized via a 1,5,7-Triazabicyclo[4.4.0]dec-5-ene (TBD)-mediated dehydro-Diels-Alder reaction with moderate to good yields. The introduction of the near-planar gem-dimethylcyclopentane moiety not only impacts the molecular conjugative system but also regulates the intermolecular π-π interactions and crystal packing, which are critical for the photoelectric performance of arenes. The photophysical properties, molecular geometry, molecular packing of these compounds, and electrochemical properties were investigated by UV-vis absorption, fluorescence emission spectra, DFT calculations, single-crystal X-ray structure analysis, and cyclic voltammetry study.

[State of the art: Direct oral anticoagulants and transfusion]

Direct oral anticoagulants (DOAC) are indicated for stroke prevention in atrial fibrillation and for the prevention and treatment of venous thromboembolism. As any anticoagulant, they are associated with a bleeding risk. Management of DOAC-induced bleeding is challenging. Idarucizumab, antidote for dabigatran, is currently available and is part of the therapeutic strategy, whereas antidotes for anti-Xa agents are under development. Activated or non-activated prothrombin concentrates are proposed, although their efficacy to reverse DOAC is uncertain. We propose an update on DOAC-associated bleeding management, integrating the availability of idarucizumab and the critical place of DOAC concentration measurements.

[Management of the bleeding risk associated with antiplatelet agents]

Like all antithrombotic drugs, antiplatelet agents expose to a risk of bleeding complications. Clinical research has extensively focused on the efficacy of these drugs to reduce ischemic events. The bleeding risk associated with them was solely considered as an inevitable and acceptable complication. When two new potent P2Y12-receptor inhibitors, prasugrel and ticagrelor, were marketed, the risk of major bleeding increased. These new agents have modified the balance between the absolute risk reduction in ischemic events and the absolute risk increase in bleeding events. This paper is an update on the bleeding risk assessment associated with antiplatelet agents. It discusses the place of platelet function monitoring, and the optimal management of bleeding complications. It addresses the challenging issue of reversal of antiplatelet therapy, focusing especially on ticagrelor, which pharmacodynamics complicate bleeding management.

Multimodal assessment of non-specific hemostatic agents for apixaban reversal

BACKGROUND

Non-specific hemostatic agents, namely activated prothrombin complex concentrate (aPCC), PCC and recombinant activated factor (F) VII (rFVIIa), can be used, off-label, to reverse the effects of FXa inhibitors in the rare cases of severe hemorrhages, as no approved specific antidote is available. We have evaluated the ability of aPCC, PCC and rFVIIa to reverse apixaban.

METHODS

Healthy volunteer whole blood was spiked with therapeutic or supra-therapeutic apixaban concentrations and two doses of aPCC, PCC or rFVIIa. Tests performed included a turbidimetry assay for fibrin polymerization kinetics analysis, scanning electron microscopy for fibrin network structure observation, thrombin generation assay (TGA), thromboelastometry, prothrombin time and activated partial thromboplastin time.

RESULTS

aPCC generated a dense clot constituting thin and branched fibers similar to those of a control without apixaban, increased fibrin polymerization velocity and improved quantitative (endogenous thrombin potential and peak height) as well as latency (clotting and lag times) parameters. Adding PCC also improved the fibrin and increased quantitative parameters, but fibrin polymerization kinetics and latency parameters were not corrected. Finally, rFVIIa improved latency parameters but failed to restore the fibrin network structure, fibrin polymerization velocity and quantitative parameters.

CONCLUSION

aPCC was more effective than PCC or rFVIIa in reversing in vitro the effects of apixaban. aPCC rapidly triggered the development of an apparently normal fibrin network and corrected latency and quantitative parameters, whereas PCC or rFVIIa had only a partial effect.

Inhibition of Ophiognomonia clavigignenti-juglandacearum by Juglans Species Bark Extracts

A rapid and reliable technique is needed for identifying butternut trees (Juglans cinerea) with resistance to butternut canker. We investigated the potential of a bark extract bioassay to detect levels of resistance to Ophiognomonia clavigignenti-juglandacearum (Oc-j), the causal agent of butternut canker. Both reagent grade naphthoquinones and crude bark extracts of Juglans species inhibited germination of Oc-j conidia. A disc diffusion bioassay was used to study the level of inhibition by these bark extracts and results indicated extensive variation within and between butternut and other species of Juglans tested. In many months over a 3 year period, bark from butternut trees selected for apparent disease resistance could be distinguished from that of unselected trees. Inhibition of conidia germination roughly correlated to the level of resistance observed in field inoculations of the trees. Quantification of the naphthoquinone compounds juglone and plumbagin in butternut bark was performed using ultra-high performance liquid chromatography mass spectrometry. While the concentrations of these two compounds varied by month and by individual tree, juglone levels correlated well with the bark extract bioassay in some months. These results suggest that juglone concentration may account in part for the observed range of inhibition observed in the bioassay and variation in canker resistance among selections of butternut field inoculated with Oc-j. The bark extract bioassay described in the following report may have potential use for selecting resistant butternut for conservation and restoration purposes.

Terminal ileum duplication: an unusual case of small bowel obstruction

Duplications of the alimentary tract are uncommon congenital anomalies that usually present during infancy and early childhood. The case of an adolescent presenting with small bowel obstruction secondary to a duplication cyst is presented and the challenges in the management described.

[Are very old patients good candidates for percutaneous coronary intervention? A monocentric retrospective study]

AIM

To determine the feasibility of percutaneous coronary intervention (PCI) in very old patients.

BACKGROUND

The elderly are a growing population with a high prevalence of ischemic heart disease and then subsequent possibility to benefit from coronary interventions.

METHOD

We have conducted a retrospective study using our PCI database since January 2000. Population characteristics, clinical presentation, type of lesions, technical procedure, immediate results and in hospital outcome are compare between patients older than 85 and the other.

RESULTS

Between January 2008 and March 2009, 3130 patients benefit from coronary angioplasty. Among them, 85 patients were older than 85. There were more female in this group (24.7 vs. 14.3%, P=0.007), but no difference in cardiovascular risk profile. The older was more symptomatic (acute coronary syndrome: 59.52 vs. 44%, P=0.004; silent ischemia: 3.6 vs. 25.7%, P=0.000003). The ejection fraction was worse (EF<55%: 29.4 vs. 14.5%, P=0.0001). The lesion was more complex (B2 and C: 67.2 vs. 57.1% P=0.027) and concern more often the left descending artery (85.9 vs. 57.1%, P=0.000001). The technical success was similar in the two groups (93.28 vs. 94.32%, P=0.34) with similar rate of per procedure complications (2.35 vs. 1.5%, P=0.37). Nevertheless, the in-hospital rate mortality was higher in the older patients (7 vs 1.38%, P=0.0014).

CONCLUSION

PCI is safe and safety in very old patients despite significant but acceptable increasing in-hospital mortality due to more severe disease and co morbidities. Further evaluations are necessary in order to edict specific recommendations.

[ST-elevation myocardial infarction in octogerians]

Coronary artery disease is the leading cause of death in developed countries and its incidence and severity is greater among older patients. So, because of the ageing of the population, clinicians will be increasingly confronted in daily practice with managing acute coronary syndrome in extreme old age and high-risk patients. Despite this demographic reality, several large randomized controlled trials evaluating the benefit-risk ratio of invasive versus conservative approach have systematically excluded elderly patients. The extrapolation of evidence-based medicine, initially focused on younger patients, is often contentious in this population and because of the lack of clear and specific recommendations in the elderly, the optimal management of STEMI in octogenarians remains a topic of debate. Elderly patients present unique issues related to the ageing process and multiple comorbid diseases making difficult the extrapolation of evidence obtained on younger demographics. Data from registries seem to support, nevertheless, the benefit of primary revascularization by PCI of the culprit lesion in "selected" octogenarians with a high technical success rate, few complications, acceptable short and long-term mortality rate and quality of life. Obviously, the "ideal octogenarian" doesn't exist and all the old patients are not suitable for an invasive approach. Managing elderly patients requires not only cardiological skills but also geriatric acknowledges and the individualized geriatric assessment is the corner store of the decision process. The aim is to screen for the presence of comorbidities (cognitive disorders, functional decline, anemia, renal insufficiency…), social isolation and existence of an underlying frailty. To conclude, the optimal strategy for the management of STEMI in octogenarians is not univocal: the best approach is the one that offers the greater benefits regard considerations of general health.

Association between human rhinovirus C and severity of acute asthma in children

A new and potentially more pathogenic group of human rhinovirus (HRV), group C (HRVC), has recently been discovered. We hypothesised that HRVC would be present in children with acute asthma and cause more severe attacks than other viruses or HRV groups. Children with acute asthma (n = 128; age 2-16 yrs) were recruited on presentation to an emergency department. Asthma exacerbation severity was assessed, and respiratory viruses and HRV strains were identified in a nasal aspirate. The majority of the children studied had moderate-to-severe asthma (85.2%) and 98.9% were admitted to hospital. HRV was detected in 87.5% and other respiratory viruses in 14.8% of children, most of whom also had HRV. HRVC was present in the majority of children with acute asthma (59.4%) and associated with more severe asthma. Children with HRVC (n = 76) had higher asthma severity scores than children whose HRV infection was HRVA or HRVB only (n = 34; p = 0.018), and all other children (n = 50; p = 0.016). Of the 19 children with a non-HRV virus, 13 had HRV co-infections, seven of these being HRVC. HRVC accounts for the majority of asthma attacks in children presenting to hospital and causes more severe attacks than previously known HRV groups and other viruses.

Home oxygen for children with acute bronchiolitis

A prospective randomised controlled pilot study was performed comparing home oxygen therapy with traditional inpatient hospitalisation for children with acute bronchiolitis. Children aged 3-24 months with acute bronchiolitis, still requiring oxygen supplementation 24 h after admission to hospital, were randomly assigned to receive oxygen supplementation at home with support from "hospital in the home" (HiTH) or to continue oxygen supplementation in hospital. 44 children (26 male, mean age 9.2 months) were recruited (HiTH n = 22) between 1 August and 30 November 2007. Only one child from each group was readmitted to hospital and there were no serious complications. Children in the HiTH group spent almost 2 days less in a hospital bed than those managed as traditional inpatients: HiTH 55.2 h (interquartile range (IQR) 40.3-88.9) versus in hospital 96.9 h (IQR 71.2-147.2) p = 0.001. Home oxygen therapy appears to be a feasible alternative to traditional hospital oxygen therapy in selected children with acute bronchiolitis.

Investigations into the role of ST2 in acute asthma in children

The ST2 gene is a member of the interleukin-1 receptor family and is located on chromosome 2q12, an area of the genome that has been associated with asthma. The soluble product of the ST2 gene, serum ST2 (sST2), has previously been shown to be elevated in adult asthmatic patients. This study investigated the potential role of ST2 in children with acute asthma. Children aged 2-16 years (n = 186) were recruited on presentation with acute asthma in the emergency department. Blood was obtained on presentation and during convalescence. Variables assessed included sST2 levels, a comprehensive assembly of clinical parameters and two polymorphisms in the ST2 gene, -26999G/A, located in the distal promoter region, and ala78glu polymorphism, on exon 3. The A allele of the -26999G/A polymorphism occurred more frequently in asthmatics compared with an unselected control group (P = 0.031). Serum ST2 levels were substantially higher during acute asthma compared with levels after the attack: 0.29 ng/ml (95% confidence interval: 0.23-0.36) and 0.14 ng/ml (0.12-0.17), respectively (P = 0.001) and were inversely related to eosinophil counts during an acute asthma attack (P = 0.002). The -26999AA genotype, as well as the AC haplotype, was associated with asthma severity scores (P = 0.05 and 0.02) compared with the -26999GA and GG genotypes. Serum ST2 levels were not associated with any of the studied genotypes or haplotypes. The observed associations of ST2 genotypes and haplotypes with acute asthma and asthma severity scores as well as the phenotypic differences associated with ST2 polymorphisms suggest that ST2 may play a role in the pathophysiology of asthma.

Anti-bacterial IgE in the antibody responses of house dust mite allergic children convalescent from asthma exacerbation

Background Atopic sensitization to the house dust mite (HDM) is associated with altered antibody responses to the nasopharyngeal colonizing bacterium Haemophilus influenzae and children admitted to the emergency department for asthma exacerbation have reduced IgG responses to HDM allergens.

Objective To investigate anti‐bacterial and anti‐allergen antibody responses during convalescence from asthma exacerbation and differences found in exacerbations associated with and without viral infection.

Results IgE antibodies to the P6 bacterial antigen increased in 60% of sera during convalescence and for many children achieved titres as high as IgE titres to allergens. In contrast IgE anti‐HDM titres declined during convalescence. The anti‐bacterial IgE titres were the same in subjects with and without virus infection while the anti‐HDM IgE declined more rapidly in virus‐infected subjects. IgG titres to the major HDM allergens showed no consistent increase and the overall IgG anti‐HDM titres even declined in subjects without a virus infection. Anti‐bacterial IgG antibodies in contrast to IgE did not change. Patients with frequent episodic or persistent asthma had similar IgE anti‐bacterial titres to patients with infrequent asthma during the acute phase, although they had reduced IgG titres to both the bacteria and the HDM.

Conclusions During the period following an acute exacerbation of asthma there was a marked and specific increase in anti‐bacterial IgE compared with a reduced IgE response to HDM. This provides further support for the concept of T‐helper type 2 responses to bacterial antigens playing a role in asthma pathogenesis.

CD14 C-159T and early infection with Pseudomonas aeruginosa in children with cystic fibrosis

Early acquisition of Pseudomonas aeruginosa is associated with a poorer prognosis in patients with cystic fibrosis. We investigated whether polymorphisms in CD14, the lipopolysaccharide receptor, increase the risk of early infection. Forty-five children with cystic fibrosis were investigated with annual bronchoalveolar lavage (BAL) and plasma sCD14 levels. Plasma sCD14 levels were significantly lower in children from whom P.aeruginosa was subsequently isolated (492.75 microg/ml vs. 1339.43 microg/ml, p = 0.018). Those with the CD14 -159CC genotype had a significantly increased risk of early infection with P.aeruginosa suggesting that CD14 C-159T plays a role in determining the risk of early infection with P.aeruginosa.

Targeting of two signal transduction pathways to different regions of the bacterial cell

Components of bacterial chemosensory pathways which sense via transmembrane receptors have been shown to localize to the cell poles. Many species, however, have operons encoding multiple putative chemosensory pathways, some including putative cytoplasmic receptors. In-genome fusions to single or multiple genes encoding components of two chemosensory pathways in Rhodobacter sphaeroides, cheOp2 and cheOp3, revealed that while sensory transducing proteins associated with transmembrane receptors and encoded on cheOp2 were targeted to the cell poles, the proteins associated with putative cytoplasmic receptors and encoded on cheOp3 were all targeted to a cytoplasmic cluster. No proteins were localized to both sites. These data show that bacteria target components of related pathways to different sites in the cell, presumably preventing direct cross-talk between the different pathways, but allowing a balanced response between extracellular and cytoplasmic signals. It also indicates that there is intracellular organization in bacterial cells, with specific proteins targeted and localized to cytoplasmic regions.

Bedside balloon atrial septostomy on neonatal units

Traditionally, neonates with transposition of the great arteries are immediately transferred to a cardiac centre. Travelling to the bedside to perform a balloon atrial septostomy and allowing the child to remain there for a few days before transfer is safe, effective, and a good use of medical resources.

TlpC, a novel chemotaxis protein in Rhodobacter sphaeroides, localizes to a discrete region in the cytoplasm

TlpC is encoded in the second chemotaxis operon of Rhodobacter sphaeroides. This protein shows some homology to membrane-spanning chemoreceptors of many bacterial species but, unlike these, is essential for R. sphaeroides chemotaxis to all compounds tested. Genomic replacement of tlpC with a C-terminal gfp fusion demonstrated that TlpC localized to a discrete cluster within the cytoplasm. Immunogold electron microscopy also showed that TlpC localized to a cytoplasmic electron-dense region. Correct TlpC-GFP localization depended on the downstream signalling proteins, CheW3, CheW4 and CheA2, and was tightly linked to cell division. Newly divided cells contained a single cluster but, as the cell cycle progressed, a second cluster appeared close to the initial cluster. As elongation continued, these clusters moved apart so that, on septation, each daughter cell contained a single TlpC cluster. The data presented suggest that TlpC is either a cytoplasmic chemoreceptor responding to or integrating global signals of metabolic state or a novel and essential component of the chemotaxis signalling pathway. These data also suggest that clustering is essential for signalling and that a mechanism may exist for targeting and localizing proteins within the bacterial cytoplasm.

CheR- and CheB-dependent chemosensory adaptation system of Rhodobacter sphaeroides

Rhodobacter sphaeroides has multiple homologues of most of the Escherichia coli chemotaxis genes, organized in three major operons and other, unlinked, loci. These include cheA(1) and cheR(1) (che Op(1)) and cheA(2), cheR(2), and cheB(1) (che Op(2)). In-frame deletions of these cheR and cheB homologues were constructed and the chemosensory behaviour of the resultant mutants examined on swarm plates and in tethered cell assays. Under the conditions tested, CheR(2) and CheB(1) were essential for normal chemotaxis, whereas CheR(1) was not. cheR(2) and cheB(1), but not cheR(1), were also able to complement the equivalent E. coli mutants. However, none of the proteins were required for the correct polar localization of the chemoreceptor McpG in R. sphaeroides. In E. coli, CheR binds to the NWETF motif on the high-abundance receptors, allowing methylation of both high- and low-abundance receptors. This motif is not contained on any R. sphaeroides chemoreceptors thus far identified, although 2 of the 13 putative chemoreceptors, McpA and TlpT, do have similar sequences. This suggests that CheR(2) either interacts with the NWETF motif of E. coli methyl-accepting chemotaxis proteins (MCPs), even though its native motif may be slightly different, or with another conserved region of the MCPs. Methanol release measurements show that R. sphaeroides has an adaptation system that is different from that of Bacillus subtilis and E. coli, with methanol release measurable on the addition of attractant but not on its removal. Intriguingly, CheA(2), but not CheA(1), is able to phosphorylate CheB(1), suggesting that signaling through CheA(1) cannot initiate feedback receptor adaptation via CheB(1)-P.

Can we integrate bioinformatics data on the Internet?

The NETTAB (Network Tools and Applications in Biology) 2001 Workshop entitled 'CORBA and XML: towards a bioinformatics-integrated network environment' was held at the Advanced Biotechnology Centre, Genoa, Italy, 17-18 May 2001.

The roles of the multiple CheW and CheA homologues in chemotaxis and in chemoreceptor localization in Rhodobacter sphaeroides

Rhodobacter sphaeroides has multiple homologues of most of the Escherichia coli chemotaxis genes, organized in two major operons and other, unlinked, loci. These include cheA1 and cheW1 (che Op1) and cheA2, cheW2 and cheW3 (che Op2). We have deleted each of these cheA and cheW homologues in-frame and examined the chemosensory behaviour of these strains on swarm plates and in tethered cell assays. In addition, we have examined the effect of these deletions on the polar localization of the chemoreceptor McpG. In E. coli, deletion of either cheA or cheW results in a non-chemotactic phenotype, and these strains also show no receptor clustering. Here, we demonstrate that CheW2 and CheA2 are required for the normal localization of McpG and for normal chemotactic responses under both aerobic and photoheterotrophic conditions. Under aerobic conditions, deletion of cheW3 has no significant effect on McpG localization and only has an effect on chemotaxis to shallow gradients in swarm plates. Under photoheterotrophic conditions, however, CheW3 is required for McpG localization and also for chemotaxis both on swarm plates and in the tethered cell assay. These phenotypes are not a direct result of delocalization of McpG, as this chemoreceptor does not mediate chemotaxis to any of the compounds tested and can therefore be considered a marker for general methyl-accepting chemotaxis protein (MCP) clustering. Thus, there is a correlation between the normal localization of McpG (and presumably other chemoreceptors) and chemotaxis. We propose a model in which the multiple different MCPs in R. sphaeroides are contained within a polar chemoreceptor cluster. Deletion of cheW2 and cheA2 under both aerobic and photoheterotrophic conditions, and cheW3 under photoheterotrophic conditions, disrupts the cluster and hence reduces chemotaxis to any compound sensed by these MCPs.

The ups and downs of protein topology; rapid comparison of protein structure

Protein topology can be described at different levels. At the most fundamental level, it is a sequence of secondary structure elements (a "primary topology string"). Searching predicted primary topology strings against a library of strings from known protein structures is the basis of some protein fold recognition methods. Here a method known as TOPSCAN is presented for rapid comparison of protein structures. Rather than a simple two-letter alphabet (encoding strand and helix), more complex alphabets are used encoding direction, proximity, accessibility and length of secondary elements and loops in addition to secondary structure. Comparisons are made between the structural information content of primary topology strings and encodings which contain additional information ("secondary topology strings"). The algorithm is extremely fast, with a scan of a large domain against a library of more than 2000 secondary structure strings completing in approximately 30 s. Analysis of protein fold similarity using TOPSCAN at primary and secondary topology levels is presented.

Fine tuning bacterial chemotaxis: analysis of Rhodobacter sphaeroides behaviour under aerobic and anaerobic conditions by mutation of the major chemotaxis operons and cheY genes

Rhodobacter sphaeroides chemotaxis is significantly more complex than that of enteric bacteria. Rhodobacter sphaeroides has multiple copies of chemotaxis genes (two cheA, one cheB, two cheR, three cheW, five cheY but no cheZ), controlling a single 'stop-start' flagellum. The growth environment controls the level of expression of different groups of genes. Tethered cell analysis of mutants suggests that CheY(4) and CheY(5) are the motor-binding response regulators. The histidine protein kinase CheA(2) mediates an attractant ('normal') response via CheY(4), while CheA(1) and CheY(5) appear to mediate a repellent ('inverted') response. CheY(3) facilitates signal termination, possibly acting as a phosphate sink, although CheY(1) and CheY(2) can substitute. The normal and inverted responses may be initiated by separate sets of chemoreceptors with their relative strength dependent on growth conditions. Rhodobacter sphaeroides may use antagonistic responses through two chemosensory pathways, expressed at different levels in different environments, to maintain their position in a currently optimum environment. Complex chemotaxis systems are increasingly being identified and the strategy adopted by R.sphaeroides may be common in the bacterial kingdom.

Major depressive illness in women: assessment and treatment in the primary care setting

Depressive illness in women carries with it a tremendous price to the woman's sense of well-being and health. Primary care providers who have frequent and continuous contact with women at risk for developing a depressive disorder are in an excellent position to diagnose and treat depression.

Identification and localization of a methyl-accepting chemotaxis protein in Rhodobacter sphaeroides

Genes coding for a classical membrane spanning chemoreceptor (mcpG) and a response regulator (cheY4) were identified in a region of Rhodobacter sphaeroides DNA unlinked to either of the two previously identified chemosensory operons. Immunogold electron microscopy had shown that the expression of chemoreceptors in R. sphaeroides varies with growth conditions. Using GFP fused to the newly identified McpG, we examined the targeting of this single methyl-accepting chemotaxis protein (MCP) under different growth conditions. The gene encoding the C-terminal McpG-GFP fusion was introduced by homologous recombination into the chromosome, replacing the wild-type gene. The resultant protein localized to the poles of the cell under aerobic, photoheterotrophic and anaerobic dark conditions, demonstrating that this MCP is expressed under all three growth conditions. More protein was always found at one pole than the other. The polar fluorescence increased during the cell cycle, with protein becoming evident at the second pole around the time of septation. At division, each daughter cell had a label at one pole, but the intensity of fluorescence was higher in the daughter cell containing the original labelled pole. McpG localization was not altered in a che Operon 1 deletion strain, lacking CheW1 and CheA1, but a che Operon 2 deletion strain, lacking CheW2, CheW3 and CheA2, showed significantly reduced polar localization. This observation indicates that polar localization of McpG depends on Che proteins encoded by Operon 2, but not homologues encoded by Operon 1.

Using the CATH domain database to assign structures and functions to the genome sequences

The CATH database of protein structures contains approximately 18000 domains organized according to their (C)lass, (A)rchitecture, (T)opology and (H)omologous superfamily. Relationships between evolutionary related structures (homologues) within the database have been used to test the sensitivity of various sequence search methods in order to identify relatives in Genbank and other sequence databases. Subsequent application of the most sensitive and efficient algorithms, gapped blast and the profile based method, Position Specific Iterated Basic Local Alignment Tool (PSI-BLAST), could be used to assign structural data to between 22 and 36 % of microbial genomes in order to improve functional annotation and enhance understanding of biological mechanism. However, on a cautionary note, an analysis of functional conservation within fold groups and homologous superfamilies in the CATH database, revealed that whilst function was conserved in nearly 55% of enzyme families, function had diverged considerably, in some highly populated families. In these families, functional properties should be inherited far more cautiously and the probable effects of substitutions in key functional residues carefully assessed.

LSD1 regulates salicylic acid induction of copper zinc superoxide dismutase in Arabidopsis thaliana

We characterized the accumulation patterns of Arabidopsis thaliana proteins, two CuZnSODs, FeSOD, MnSOD, PR1, PR5, and GST1, in response to various pathogen-associated treatments. These treatments included inoculation with virulent and avirulent Pseudomonas syringae strains, spontaneous lesion formation in the lsd1 mutant, and treatment with the salicylic acid (SA) analogs INA (2,6-dichloroisonicotinic acid) and BTH (benzothiadiazole). The PR1, PR5, and GST1 proteins were inducible by all treatments tested, as expected from previous mRNA blot analysis. The two CuZnSOD proteins were induced by SA analogs and in conjunction with lsd1-mediated spreading cell death. Additionally, LSD1 is a part of a signaling pathway for the induction of the CuZnSOD proteins in response to SA but not in lsd1-mediated cell death. We suggest that the spreading lesion phenotype of lsd1 results from a lack of up-regulation of a CuZnSOD responsible for detoxification of accumulating superoxide before the reactive oxygen species can trigger a cell death cascade.

Managing alcohol-related problems in the primary care setting

Although alcohol-related problems are a significant source of morbidity and mortality in the United States, denial and resistance to treatment by patients and their families make detection challenging. Primary care providers may find it difficult to confront the patient who drinks excessively; however, early intervention can lower morbidity and prevent progressive damage to family and social relationships. Routine alcohol screening of all patients may assist the primary care provider in effectively identifying and treating alcohol abuse. Although abstinence is the primary goal for patients with alcohol-related problems, decreasing intake is also beneficial and may be accomplished with brief primary care interventions. The management of outpatient alcohol detoxification is increasingly provided by primary care providers in managed care environments, but requires careful assessment of the patient's support system, close provider supervision, and appropriate pharmacologic support.

A single backmutation in the human kIV framework of a previously unsuccessfully humanized antibody restores the binding activity and increases the secretion in cos cells

Humanization of rodent mAbs by CDR-grafting (also called "reshaping") is now a standard procedure for reducing immunogenicity and recruiting human effector functions. However, the design of the humanized mAb can sometimes prove circuitous. Attempts were made to humanize L-25, a mouse antibody against the human alpha-4 integrin subunit using the usual protocols. Despite reaching eight backmutations in the light chain, it was not possible to recover the binding activity to the level of the chimeric. In an effort to restore the binding activity, an analysis of the human kappa IV acceptor frameworks was undertaken. This analysis highlighted the Asp at position 9 in framework 1, which although a common amino acid in human kappa IV frameworks, was an unusual residue in mouse kappa frameworks. Backmutating this position to the mouse amino acid completely restored the binding of the humanized antibody and as a by-product also increased the secretion levels in cos cells. Mutating position 9 to the consensus residue for human kappa I also restored the binding and secretion levels although not to the same extent. The resulting humanized antibody had a light chain with only a single backmutation to the mouse sequence.

Fine mapping of the antigen-antibody interaction of scFv215, a recombinant antibody inhibiting RNA polymerase II from Drosophila melanogaster

A bacterially expressed single chain antibody (scFv215) directed against the largest subunit of drosophila RNA polymerase II was analysed. Structure and function of the antigen binding site in scFv215 were probed by chain shuffling and by site-specific mutagenesis. The entire variable region of either the heavy or light chain was replaced by an unrelated heavy or light chain. Both replacements resulted in a total loss of binding activity suggesting that the antigen binding site is contributed by both chains. The functional contributions of each complementarity determining region (CDR) were investigated by site specific mutagenesis of each CDR separately. Mutations in two of the CDRs, CDR1 of light chain and CDR2 of heavy chain, reduced the binding activity significantly. Each of the amino acids in these two CDRs was replaced individually by alanine (alanine walking). Seven amino acid substitutions in the two CDRs were found to reduce the binding activity by more than 50%. The data support a computer model of scFv215 which fits an epitope model based on a mutational analysis of the epitope suggesting an alpha-helical structure for the main contact area.

The CATH Database provides insights into protein structure/function relationships

We report the latest release (version 1.4) of the CATH protein domains database (http://www.biochem.ucl.ac.uk/bsm/cath). This is a hierarchical classification of 13 359 protein domain structures into evolutionary families and structural groupings. We currently identify 827 homologous families in which the proteins have both structual similarity and sequence and/or functional similarity. These can be further clustered into 593 fold groups and 32 distinct architectures. Using our structural classification and associated data on protein functions, stored in the database (EC identifiers, SWISS-PROT keywords and information from the Enzyme database and literature) we have been able to analyse the correlation between the 3D structure and function. More than 96% of folds in the PDB are associated with a single homologous family. However, within the superfolds, three or more different functions are observed. Considering enzyme functions, more than 95% of clearly homologous families exhibit either single or closely related functions, as demonstrated by the EC identifiers of their relatives. Our analysis supports the view that determining structures, for example as part of a 'structural genomics' initiative, will make a major contribution to interpreting genome data.

Effect of microgravity on the development of embryos/larvae and the larval esophageal musculature of the purple starfish, Pisaster ochraceus

Early gastrula stage embryos of the purple starfish, Pisaster ochraceus, were raised for 10 days in microgravity (µG) in an Aquatic Research Facility aboard the space shuttle Endeavour (STS 77). Controls consisted of embryos raised at 1 × g (1G) in flight and embryos raised at 1G on the ground. Experimental organisms and controls were fixed on mission days (MD) 3, 4, 5, 6, and 7 and one sample was returned alive. Comparison of the µG embryos with the 1G in-flight controls and ground controls suggests that there is little difference in size and overall development. Scanning electron microscopic examination of the development of the esophageal musculature showed that the pattern of development and differentiation was normal and was the same in both the in-flight and ground controls. The esophageal muscle cells of specimens returned alive after 10 days in µG contracted normally. Detailed transmission electron microscopic examination of MD 7 embryos revealed a decreased amount of sarcoplasmic reticulum in the µG embryos compared with both MD 7 1G in-flight and ground controls. These results suggest that while exposure to µG may slow muscle differentiation slightly, it has little overall effect on embryos/larvae of up to 7-8 days of development.

Protein folds and functions

BACKGROUND

The recent rapid increase in the number of available three-dimensional protein structures has further highlighted the necessity to understand the relationship between biological function and structure. Using structural classification schemes such as SCOP, CATH and DALI, it is now possible to explore global relationships between protein fold and function, something which was previously impractical.

RESULTS

Using a relational database of CATH data we have generated fold distributions for arbitrary selections of proteins automatically. These distributions have been examined in the light of protein function and bound ligand. Different enzyme classes are not clearly reflected in distributions of protein class and architecture, whereas the type of bound ligand has a much more dramatic effect.

CONCLUSIONS

The availability of structural classification data has enabled this novel overview analysis. We conclude that function at the top level of the EC number enzyme classification is not related to fold, as only a very few specific residues are actually responsible for enzyme activity. Conversely, the fold is much more closely related to ligand type.

Dihydrofolate reductase: a potential drug target in trypanosomes and leishmania

Dihydrofolate reductase has successfully been used as a drug target in the area of anti-cancer, anti-bacterial and anti-malarial chemotherapy. Little has been done to evaluate it as a drug target for treatment of the trypanosomiases and leishmaniasis. A crystal structure of Leishmania major dihydrofolate reductase has been published. In this paper, we describe the modelling of Trypanosoma cruzi and Trypanosoma brucei dihydrofolate reductases based on this crystal structure. These structures and models have been used in the comparison of protozoan, bacterial and human enzymes in order to highlight the different features that can be used in the design of selective anti-protozoan agents. Comparison has been made between residues present in the active site, the accessibility of these residues, charge distribution in the active site, and the shape and size of the active sites. Whilst there is a high degree of similarity between protozoan, human and bacterial dihydrofolate reductase active sites, there are differences that provide potential for selective drug design. In particular, we have identified a set of residues which may be important for selective drug design and identified a larger binding pocket in the protozoan than the human and bacterial enzymes.

Assessment of comparative modeling in CASP2

An assessment is presented for all submissions to the comparative modeling challenge in the 1996 Critical Assessment of Structure Prediction (CASP2). Of the original 12 target structures, 9 were solved prior to the meeting: 8 by X-ray crystallography and 1 by NMR spectroscopy. These targets varied over a large range of difficulty, as assessed by the percentage sequence identity with the principal parent structure, which ranged from 20% up to 85%. The overall quality of the models reflected the similarity of the principal parent. As expected, when the sequence alignment was correct, the core was accurately modeled, with the largest deviations occurring in the loops. Models were built which gave C alpha root-mean-square deviations (RMSDs) compared with the observed structure of < 1 A for targets with high parental similarity; even at 26% sequence identity, the best model structures had C alpha deviations of only 2.2 A. Overall, these deviations are comparable with those observed between the parent structure and the target, but locally there are several examples where the model approaches closer to the target than does the parent. There were three targets below 25% sequence identity, and the models generated for these targets were, in general, significantly less accurate. This principally reflects errors in the alignment which, if systematically shifted, can generate C alpha RMSDs > 18 A. Compared with CASP1, the geometry of the models was significantly improved with no D-amino acids. By far the major contribution to RMSD error was the alignment accuracy, which varied from 100% down to 7% over the range of targets. In the structurally variable regions, global shifts, caused by hinge bending, were the major source of error, giving significantly lower local RMSDs than global RMSDs. In over 50% of these noncore regions, the difference between global and local RMSDs was more than 3 A, and was as high as 10 A for one structurally variable region. For the side chains, the chi 1 RMSDs are strongly correlated with the C alpha RMSDs. For models with C alpha deviations less than 1 A, on average 78.5% of side chains are placed in the correct rotamer, although the chi 1 RMSDs, though clearly better than random, were disappointing at around 46 degrees. As the backbone deviations increased, the side chain placement became less accurate, with an average chi 1 RMSD of 75 degrees on a 1.5-2.5 A C alpha backbone (average 51.4% correct rotamer). Refinement by energy minimization or molecular dynamics made only minor adjustments to improve local geometry and generally made small, but not significant, improvements to the RMSD. In total, 19 groups submitted 62 models (89 coordinate sets) that could be assessed. Most modelers used manual adjustments to sequence alignments and, in general, good alignments were obtained down to 25% sequence identity. The modeling methods ranged from "classical" modeling, involving core building followed by loop and side chain addition, to more sophisticated approaches based on probability distributions, Monte Carlo sampling or distance geometry. For each target, several groups produced equally good models, given the expected errors in the structures (about 0.5 A). No one method came out as clearly superior, although the approaches that inherit directly from the parents generally performed better than the more radical techniques. However, for each target there were some poor models, usually reflecting a poor sequence alignment, and the range of accuracy for each target is therefore large. Fully automated methods are able to perform very well for "easy" targets (85% sequence identity with parent), but when modeling using a distantly related parent, care and expertise, especially in performing the alignment, still appear to be important factors in generating accurate models.

Genetic, structural and functional properties of an IgG DNA-binding monoclonal antibody from a lupus patient with nephritis

Antibodies binding to double-stranded (ds) DNA are strongly associated with renal involvement in patients with systemic lupus erythematosus (SLE). We have generated two new IgG DNA-binding monoclonal antibodies (mAb), RH-14 and DIL-6, from the peripheral blood lymphocytes of two SLE patients with glomerulonephritis using the heteromyeloma cell line CB-F7. RH-14 is an IgG1 lambda antibody which also bound to single-stranded DNA, histones and nucleosomes. DIL-6 is an IgG3 lambda antibody with restricted antigen binding specificity. cDNA encoding the variable regions of the heavy (V(H)) and light (V(L)) chains of RH-14 was sequenced and the antigen binding site of this mAb was computer modelled. Sequence analysis of V(H) and V(L) regions of RH-14 showed that V(H) is derived from germ-line gene V3-7, a member of the V(H)3 family, and V(L) is derived from DPL 11, a member of the V(lambda)2 family. Somatic mutations and basic amino acid residues are identified in the complementarity-determining regions of both V(H) and V(L) regions. The nephritogenic properties of these mAb were analyzed by implanting and growing the hybridoma cells secreting the mAb in the peritoneum of SCID mice. The animals that received the RH-14 hybridoma produced higher levels of proteinuria (3 to > or = 4) (p < 0.001) compared to the groups that received DIL-6 (trace to > or = 1) or CB-F7 (trace). Electron microscopy of kidney sections from all the RH-14-implanted animals showed granular immunoglobulin deposition in the renal glomerular capillaries and mesangium. In this study we have shown for the first time using electron microscopy that a human IgG anti-dsDNA mAb, RH-14, is nephritogenic and that deposition of such an antibody alone is sufficient to induce renal damage.

Two amino acid mutations in an anti-human CD3 single chain Fv antibody fragment that affect the yield on bacterial secretion but not the affinity

Recombinant antibody fragments directed against cell surface antigens have facilitated the development of novel therapeutic agents. As a first step in the creation of cytotoxic immunoconjugates, we constructed a single-chain Fv fragment derived from the murine hybridoma OKT3, that recognizes an epitope on the epsilon-subunit of the human CD3 complex. Two amino acid residues were identified that are critical for the high level production of this scFv in Escherichia coli. First, the substitution of glutamic acid encoded by a PCR primer at position 6 of VH framework 1 by glutamine led to a more than a 30-fold increase in the production of soluble scFv. Second, the substitution of cysteine by a serine in the middle of CDR-H3 additionally doubled the yield of soluble antibody fragment without any adverse effect on its affinity for the CD3 antigen. The double mutant scFv (Q,S) proved to be very stable in vitro: no loss of activity was observed after storage for 1 month at 4 degrees C, while the activity of scFv containing a cysteine residue in CDR-H3 decreased by more than half. The results of production yield, affinity, stability measurements and analysis of three-dimensional models of the structure suggest that the sixth amino acid influences the correct folding of the VH domain, presumably by affecting a folding intermediate, but has no effect on antigen binding.

Structural families in loops of homologous proteins: automatic classification, modelling and application to antibodies

Loop regions of polypeptide in homologous proteins may be classified into structural families. A method is described by which this classification may be performed automatically and "key residue" templates, which may be responsible for the loop adopting a given conformation, are defined. The technique has been applied to the hypervariable loops of antibodies and the results are compared with the previous definition of canonical classes. We have extended these definitions and provide complete sets of structurally determining residues (SDRs) for the observed clusters including the first set of key residues for seven-residue CDR-H3 loops.

Antibody-antigen interactions: contact analysis and binding site topography

We have analysed antigen-contacting residues and combining site shape in the antibody Fv and Fab crystal structures now available from the Protein Data Bank. Antigen-contacting propensities are presented for each antibody residue, allowing a new definition for the complementarity determining regions (CDRs) to be proposed based on observed antigen contacts. Contacts are more common at CDR residues which are located centrally within the combining site; some less central CDR residues are only contacted by large antigens. Non-contacting residues within the CDRs coincide with residues identified by Chothia and co-workers as important in defining "canonical" conformations. An objective means of classifying protein surfaces by gross topography has been developed and applied to the antibody combining site surfaces. The surfaces have been clustered into four topographic classes: concave and moderately concave (mostly hapten binders), ridged (mostly peptide binders) and planar (mostly protein binders). We have determined the topographic classes for ten pairs of complexed and uncomplexed antibody-antigen crystal structures; four change topographic class on complexation. The results will be of use in antibody engineering, antigen docking and in clinical immunology. To demonstrate one application, we show how the data can be used to locate the antigen binding pocket on antibody structures.

Accessing the Kabat antibody sequence database by computer

The Kabat antibody sequence database has for many years been the primary site for depositing sequence information on antibodies and other proteins of immunological interest. The chief drawback of this database has been that it has only been available in the form of a printed book (Kabat et al., Sequences of Proteins of Immunological Interest, 1991). These data have recently become available on the global computer Internet, but no method of searching the data has, as yet, been provided. Here, the development of a specialized database program for accessing the antibody data is described. This database software has been made accessible over the World Wide Web, together with a program which allows a novel antibody sequence to be tested against the Kabat sequence database, to identify unusual features of an antibody sequence which may represent cloning artifacts or sequencing errors.

Functional and modelling studies of the binding of human monoclonal anti-DNA antibodies to DNA

The relationships between the antigen-binding specificities of four human monoclonal anti-DNA antibodies and the structural aspects of the combining sites of two of these were examined. Competition ELISAs were used to examine the reactivities of two IgM MAbs (WRI-176 and RT-79) and two IgG mAbs (D5 and B3) to a wide range of polynucleotides. The mAbs WRI-176 and RT-79 were found to bind predominantly ssDNA, with a preference for poly (dT), whilst D5 and B3 bound components of both ss- and dsDNA, and Z-DNA. The mAb B3 also exhibited a preference for A(T) rich nucleotides. Computer models were generated for the Fv regions of WRI-176 and B3. Models for RT-79 and D5 were not generated as the structure of the long CDR-H3 loops in these mAbs could not be predicted. The B3 combining site contains a groove flanked by three arginines at positions CDR-L1-27A, CDR-L2-54 and CDR-H2-53. Using interactive molecular graphics, B-DNA was docked into the B3 antigen combining site along the plane of the VH/VL interface, whilst Z-DNA was best-fitted at approximately 90 degrees to this direction. The models provide a hypothesis to explain the ability of a single autoantibody to bind two different antigens. In addition, aspects of the base specificity of B3 may be explained. The model of the WRI-176 Fv region revealed a relatively flat surface, on which a large number of hydrophobic and aromatic residues were present. Trp-H52, in particular, is prominent on the surface. This may participate in ssDNA binding through base stacking interactions. The models allow identification of potential targets for site-directed mutagenesis.

Long loops in proteins

In proteins, loop regions which connect secondary structures are generally short (80% are <10 amino acids long). However, long loops, defined here as > or = 10 residues, do occur. Two types of long loop may be distinguished: those which connect adjacent regions of secondary structure ('long-closed') and those which connect distant secondary structures ('long-open'). Only 5% of all loops in proteins fall into the long-open class. Inspection of these unusual long-open loops reveals a higher percentage of proline residues and more helix-helix linkages than expected. Exposure to solvent is similar for long-open and long-closed loops. The role of these loops in protein folding is discussed.

Prediction of hypervariable CDR-H3 loop structures in antibodies

The structure of the most variable antibody hypervariable loop, CDR-H3, has been predicted from amino acid sequence alone. In contrast to other approaches predictions are made for loop lengths up to 17 residues. The predictions have been achieved using artificial neural networks which are trained on a large set of loops from the Brookhaven Protein Databank which have structures similar to CDR-H3. The loop structures are described by the two backbone dihedral angles phi and psi for each residue. For 21 CDR-H3 loops unique to the neural network, the prediction of dihedral angles leads to an average root mean square deviation in the Cartesian coordinates of 2.65 A. The present method, when combined with existing modelling protocols, provides an important addition to the structural prediction of the complementarity determining regions of antibodies.

Breastfeeding: perceived barriers and benefits/enhancers in a rural and urban setting

This study investigated differences in perceived benefits/enhancers and barriers between women who planned to breastfeed, those who were uncertain, and those who did not plan to breastfeed. The volunteers were obtained from rural (60) and urban (82) public health department prenatal clinics. Fifty-three percent of the women were married, the average age was 23 years, 25% had not graduated from high school, 38% were black, and 46% were planning to return to work. The breastfeeding inventory consisted of 13 items to measure benefits and enhancers, 15 to measure barriers, and an open-ended question. Cronbach's alphas for internal consistency for benefits and enhancers and barriers were 0.88 and 0.83 respectively. Analysis of variance found significant differences among the three groups on perceived benefits and barriers. Rural and urban differences existed in perceived benefits/enhancers, but not in perceived barriers. In a multiple discriminant function analysis that included demographic characteristics, the most important predictor of breastfeeding decision was perceived benefits.

MoG: molecular graphics software for the Commodore Amiga

As recently described by Garavelli, the Commodore Amiga 3000 computer is "nearly ideal" for desktop molecular modeling. The chief drawback to date, has been the lack of suitable software. This paper describes a new desktop molecular modeling package, MoG, which is suitable for both research and educational use. The speed of the Amiga 3000 means that MoG competes very favorably with software on IBM-PC machines, and its graphics capabilities allow excellent space-filling representations. The availability of cheap software-compatible home-computer versions of the Amiga places interactive molecular graphics within the reach of many senior high-school students, undergraduates and graduate students.