A subset-oriented algorithm for minimizing the number of steps required for synthesis of cyclic-peptide libraries

Libraries of cyclic peptides are being synthesized using combinatorial chemistry for high throughput screening in the drug discovery process. This paper describes the min_syn_steps.cpp program (available at http://www.imb.uq.edu.au/groups/smythe/tran), which after inputting a list of cyclic peptides to be synthesized, removes cyclic redundant sequences and calculates synthetic strategies which minimize the synthetic steps as well as the reagent requirements. The synthetic steps and reagent requirements could be minimized by finding common subsets within the sequences for block synthesis. Since a brute-force approach to search for optimum synthetic strategies is impractically large, a subset-orientated approach is utilized here to limit the size of the search. (C) 2002 Elsevier Science Ltd. All rights reserved.

Neuronal calcium-binding proteins and schizophrenia

Calcium-binding proteins (CBPs) such as calbindin, parvalbumin and calretinin are used as immunohistochemical markers for discrete neuronal subpopulations. They are particularly useful in identifying the various subpopulations of GABAergic interneurons that control output from prefrontal and cingulate cortices as well as from the hippocampus. The strategic role these interneurons play in regulating output from these three crucial brain regions has made them a focus for neuropathological investigation in schizophrenia. The number of pathological reports detailing subtle changes in these CBP-containing interneurons in patients with schizophrenia is rapidly growing. These proteins however are more than convenient neuronal markers. They confer survival advantages to neurons and can increase the neuron's ability to sustain firing. These properties may be important in the subtle pathophysiology of nondegenerative phenomena such as schizophrenia. The aim of this review is to introduce the reader to the functional properties of CBPs and to examine the emerging literature reporting alterations in these proteins in schizophrenia as well as draw some conclusions about the significance of these findings. (C) 2002 Elsevier Science B.V. All rights reserved.

High irradiance increases organogenesis in friable callus of Caustis blakei Kuk. (Cyperaceae)

Caustis blakei is an attractive cut foliage plant harvested from the wild in Australia and marketed under the name of koala fern. Previous attempts to propagate large numbers of this plant have been unsuccessful. The effect of four light irradiances on organogenesis from compact and friable callus of C. blakei was studied for 21 wk. Both callus types produced numerous primordial shoots but many failed to develop into green plantlets. However, significantly more primordial shoots and green plantlets developed on the friable callus than on the compact callus, and significantly more green plantlets were regenerated under the higher photon irradiances of 200 and 300 mumol m(-2) s(-1) than under the lower irradiances of 100 and 150 mumol m(-2) s(-1). The compact callus produced its maximum number of green plantlets early in the experiment (after 9 wk), while the friable callus continued to produce primordial shoots and green plantlets throughout the period of the experiment, and reached its maximum production of green plantlets at 21 wk under the irradiance of 300 mumol m(-2) s(-1). Organogenesis from friable callus under high irradiance (300 mumol m(-2) s(-1)) offers an efficient propagation method for C. blakei.

Effect of changing data collection parameters on statistical motor unit number estimates

The effect of number of samples and selection of data for analysis on the calculation of surface motor unit potential (SMUP) size in the statistical method of motor unit number estimates (MUNE) was determined in 10 normal subjects and 10 with amyotrophic lateral sclerosis (ALS). We recorded 500 sequential compound muscle action potentials (CMAPs) at three different stable stimulus intensities (10–50% of maximal CMAP). Estimated mean SMUP sizes were calculated using Poisson statistical assumptions from the variance of 500 sequential CMAP obtained at each stimulus intensity. The results with the 500 data points were compared with smaller subsets from the same data set. The results using a range of 50–80% of the 500 data points were compared with the full 500. The effect of restricting analysis to data between 5–20% of the CMAP and to standard deviation limits was also assessed. No differences in mean SMUP size were found with stimulus intensity or use of different ranges of data. Consistency was improved with a greater sample number. Data within 5% of CMAP size gave both increased consistency and reduced mean SMUP size in many subjects, but excluded valid responses present at that stimulus intensity. These changes were more prominent in ALS patients in whom the presence of isolated SMUP responses was a striking difference from normal subjects. Noise, spurious data, and large SMUP limited the Poisson assumptions. When these factors are considered, consistent statistical MUNE can be calculated from a continuous sequence of data points. A 2 to 2.5 SD or 10% window are reasonable methods of limiting data for analysis. Muscle Nerve 27: 320–331, 2003

The first strand transfer reaction of HIV-1 reverse transcription is more efficient in infected cells than in cell-free natural endogenous reverse transcription reactions

Background: In the presence of dNTPs, intact HIV-1 virions are capable of reverse transcribing at least part of their genome, a process known as natural endogenous reverse transcription (NERT). PCR analysis of virion DNA produced by NERT revealed that the first strand transfer reaction (1stST) was inefficient in intact virions, with minus strand (-) strong stop DNA (ssDNA) copy numbers up to 200 times higher than post-1stST products measured using primers in U3 and U5. This was in marked contrast to the efficiency of 1stST observed in single-round cell infection assays, in which (-) ssDNA and U3-U5 copy numbers were indistinguishable. Objectives: To investigate the reasons for the discrepancy in first strand transfer efficiency between intact cell-free virus and the infection process. Study design: Alterations of both NERT reactions and the conditions of cell infection were used to test whether uncoating and/or entry play a role in the discrepancy in first strand transfer efficiency. Results and Conclusions: The difference in 1stST efficiency could not be attributed simply to viral uncoating, since addition of very low concentrations of detergent to NERT reactions removed the viral envelope without disrupting the reverse transcription complex, and these conditions resulted in no improvement in 1stST efficiency. Virus pseudotyped with surface glycoproteins from either vesicular stomatitis virus or amphotrophic murine leukaemia virus also showed low levels of 1stST in low detergent NERT assays and equivalent levels of (-) ssDNA and 1stST in single-round infections of cells, demonstrating that the gp120-mediated infection process did not select for virions capable of carrying out 1stST. These data indicate that a post-entry event or factor may be involved in efficient HIV-1 reverse transcription in vivo. (C) 2002 Elsevier Science B.V. All rights reserved.

Developmental anomalies in the tooth plates and jaw bones of lungfish

Lungfish of the tooth-plated lineage, both fossil and living, may be affected by alterations in the permanent tooth plates and associated jaw bones as they grow. In a few taxa, the unusual structures may be so common that they must be considered as normal for those species, or as a variation of the normal condition. In others the condition is rare, affecting only a few individuals. Variations, or anomalies, may appear in the growing tissues of the lungfish tooth plate at any time in the life cycle, although they usually appear early in development. Once the changes appear, they persist in the dentition. The altered structures include divided or intercalated ridges, short ridge anomaly, changes in the shape, number and position of cusps, pattern loss, and fused ridges or cusps. Criteria used to distinguish alteration from normal conditions are the incidence of the character in the population, the associated changes in the jaw bone, and the position of the altered structure in the tooth plate. The occurrence of similar changes across a wide range of different species suggests that they may have a genetic cause, especially when they are a rare occurrence in most taxa, but common enough to be a part of the normal variation in others. Prevalence of related anomalies throughout the history of the group suggests that dipnoans of the tooth-plated lineage are closely related, despite significant differences in morphology, microstructure, and function of the denfitions.

Alterations in pulmonary vascular function in rats exposed to intermittent hypoxia

Vasoactive agents were examined in arteries from control rats and rats exposed to intermittent hypoxia (10% oxygen; 8 h/day) for 3, 5 or 20 days. Hypoxic rats developed right ventricular hypertrophy after 5 days, but became pulmonary hypertensive (elevated right ventricular systolic pressure; RVSP) only after 20 days. In pulmonary arteries (main and intralobar), responses to acetylcholine and ionomycin (endothelium-dependent vasodilators) were reduced after 20 and 5 days of intermittent hypoxia, whereas contractions to 5-hydroxytryptamine (5-HT) were enhanced (potency increase >10-fold) after 20, 5 and 3 days. Contractions to endothelin-1 and a thromboxane-mimetic, but not Ca-2divided by, were also increased. No changes in vascular function occurred in aorta. Since changes in pulmonary vascular function preceded the increase in RVSP they do not result from, but may contribute to, the development of hypoxia-induced pulmonary hypertension. If similar changes occur in humans, they may be important in conditions characterised by intermittent, as opposed to continuous, hypoxia. (C) 2003 Elsevier B.V. All rights reserved.

Balancing the number and size of sites: An economic approach to the optimal design of cluster samples

The design of randomized controlled trials entails decisions that have economic as well as statistical implications. In particular, the choice of an individual or cluster randomization design may affect the cost of achieving the desired level of power, other things being equal. Furthermore, if cluster randomization is chosen, the researcher must decide how to balance the number of clusters, or sites, and the size of each site. This article investigates these interrelated statistical and economic issues. Its principal purpose is to elucidate the statistical and economic trade-offs to assist researchers to employ randomized controlled trials that have desired economic, as well as statistical, properties. (C) 2003 Elsevier Inc. All rights reserved.

Vitamin C: Effects of exercise and requirements with training

Ascorbic acid or vitamin C is involved in a number of biochemical pathways that are important to exercise metabolism and the health of exercising individuals. This review reports the results of studies investigating the requirement for vitamin C with exercise on the basis of dietary vitamin C intakes, the response to supplementation and alterations in plasma, serum, and leukocyte ascorbic acid concentration following both acute exercise and regular training. The possible physiological significance of changes in ascorbic acid with exercise is also addressed. Exercise generally causes a transient increase in circulating ascorbic acid in the hours following exercise, but a decline below pre-exercise levels occurs in the days after prolonged exercise. These changes could be associated with increased exercise-induced oxidative stress. On the basis of alterations in the concentration of ascorbic acid within the blood, it remains unclear if regular exercise increases the metabolism of vitamin C. However, the similar dietary intakes and responses to supplementation between athletes and nonathletes suggest that regular exercise does not increase the requirement for vitamin C in athletes. Two novel hypotheses are put forward to explain recent findings of attenuated levels of cortisol postexercise following supplementation with high doses of vitamin C.

Histological alterations in liver and testis of Astyanax aff. bimaculatus caused by acute exposition to zinc

This study investigated the effect of acute exposition to zinc (Zn) on histology of the liver and testes of yellow tail lambari (Astyanax aff. bimaculatus). The exposure consisted of six concentrations of Zn (0, 3, 5, 10, 15, and 20 mg/L) for 96 hours of exposure. Fragments of liver and testis were routinely processed and embedded in plastic resin based on glycol methacrylate. Fragments of bones, muscles, liver and testis were dehydrated and digested to quantify the absorption levels of Zn in the tissue. Acute exposure to concentrations above 10mg/L has produced structural changes in the liver and gonads. The changes found in the liver were vascular congestion; decrease of cellular volume; displacement of the hepatocyte nucleus; necrosis; disarrangement of cordon structure; leukocyte infiltrate and vacuolization. The changes found in the gonads were ruptured cyst, delayed development of germ cells, pyknotic nucleus, cell cluster, displacement of cyst wall and vacuolization. The histological changes observed were compatible with the increasing concentration of zinc in environment, compromising liver and reproductive functions, because there was an increase in relative frequency of hepatocytes and reduced sperm production

Genotoxicity biomarkers in occupational to formaldehyde in pathology anatomy laboratories

Formaldehyde (FA) the most simple and reactive of all aldehydes, is a colorless, reactive and readily polymerizing gas at normal temperature. It has a pungent, suffocating odour that is recognized by most human subjects at concentrations below 1ppm. According to the Report on Carcinogens, FA ranks 25th in the overall U.S. chemical production with more than 11 billion pounds (5 million tons) produced each year. Is an important industrial compound that is used in the manufacture of synthetic resins and chemical compounds such as lubricants and adhesives. It has also applications as a disinfectant, preservative and is used in cosmetics. Estimates of the number of persons who are occupationally exposed to FA indicate that, at least at low levels, may occur in a wide variety of industries. The occupational settings with most extensive use of formaldehyde is in the production of resins and in anatomy and pathology laboratories. Several studies reported a carcinogenic effect in humans after inhalation of FA, in particular an increased risk for nasopharyngeal cancer. Nowadays, the International Agency for Research on Cancer (IARC) classifies FA as carcinogenic to humans (group 1), on the basis of sufficient evidence in humans and sufficient evidence in experimental animals. Manifold in vitro studies clearly indicated that FA is genotoxic. FA induced various genotoxic effects in proliferatin cultured mammalian cells. A variety of evidence suggests that the primary DNA alterations after FA exposure are DNA-protein crosslinks. Incomplete repair of DPX can lead to the formation of mutations.

Micronuclei in peripheral blood lymphocytes in formaldehyde occupationally exposed workers

Formaldehyde (CH2O) the most simple and reactive of all aldehydes, is a colorless, reactive and readily polymerizing gas at normal temperature. It has a pungent, suffocating odour that is recognized by most human subjects at concentrations below 1 ppm. According to the Report on Carcinogens, formaldehyde (FA) ranks 25th in the overall U.S. chemical production with more than 11 billion pounds (5 million tons) produced each year. Is an important industrial compound that is used in the manufacture of synthetic resins and chemical compounds such as lubricants and adhesives. It has also applications as a disinfectant, preservative and is used in cosmetics. Estimates of the number of persons who are occupationally exposed to FA indicate that, at least at low levels, may occur in a wide variety of industries. The occupational settings with most extensive use of formaldehyde is in the production of resins and in anatomy and pathology laboratories. Several studies reported a carcinogenic effect in humans after inhalation of FA, in particular an increased risk for nasopharyngeal cancer. Nowadays, the International Agency for Research on Cancer (IARC) classifies FA as carcinogenic to humans (group 1), on the basis of sufficient evidence in humans and sufficient evidence in experimental animals. Manifold in vitro studies clearly indicated that FA is genotoxic. FA induced various genotoxic effects in proliferatin cultured mammalian cells. A variety of evidence suggests that the primary DNA alterations after FA exposure are DNA-protein crosslinks (DPX). Incomplete repair of DPX can lead to the formation of mutations.

Occupational exposure to environmental tobacco smoke in hospitality venues: are genetic- or proteomics-based biomarkers predictive of respiratory diseases?

Environmental tobacco smoke (ETS) is recognized as an occupational hazard in the hospitality industry. Although Portuguese legislation banned smoking in most indoor public spaces, it is still allowed in some restaurants/bars, representing a potential risk to the workers’ health, particularly for chronic respiratory diseases. The aims of this work were to characterize biomarkers of early genetic effects and to disclose proteomic signatures associated to occupational exposure to ETS and with potential to predict respiratory diseases development. A detailed lifestyle survey and clinical evaluation (including spirometry) were performed in 81 workers from Lisbon restaurants. ETS exposure was assessed through the level of PM 2.5 in indoor air and the urinary level of cotinine. The plasma samples were immunodepleted and analysed by 2D-SDSPAGE followed by in-gel digestion and LC-MS/MS. DNA lesions and chromosome damage were analysed innlymphocytes and in exfoliated buccal cells from 19 cigarette smokers, 29 involuntary smokers, and 33 non-smokers not exposed to tobacco smoke. Also, the DNA repair capacity was evaluated using an ex vivo challenge comet assay with an alkylating agent (EMS). All workers were considered healthy and recorded normal lung function. Interestingly, following 2D-DIGE-MS (MALDI-TOF/TOF), 61 plasma proteins were found differentially expressed in ETS-exposed subjects, including 38 involved in metabolism, acute-phase respiratory inflammation, and immune or vascular functions. On the other hand, the involuntary smokers showed neither an increased level of DNA/chromosome damage on lymphocytes nor an increased number of micronuclei in buccal cells, when compared to non-exposed non-smokers. Noteworthy, lymphocytes challenge with EMS resulted in a significantly lower level of DNA breaks in ETS-exposed as compared to non-exposed workers (P<0.0001) suggestive of an adaptive response elicited by the previous exposure to low levels of ETS. Overall, changes in proteome may be promising early biomarkers of exposure to ETS. Likewise, alterations of the DNA repair competence observed upon ETS exposure deserves to be further understood. Work supported by Fundação Calouste Gulbenkian, ACSS and FCT/Polyannual Funding Program.

Estudo mutacional em tumor de Wilms por sequenciação de nova geração

O Tumor de Wilms (TW) é o tumor renal mais comum da infância, com uma incidência de 1 em ~10000 crianças. Esta patologia é de etiologia genética complexa e diversificada. No entanto, cerca de um terço dos doentes apresenta mutações somáticas associadas aos genes WT1, CTNNB1, TP53 e/ou AMER1. Assim, foi desenvolvido um painel de amplicões destes 4 genes para a identificação de mutações num grupo de doentes portugueses com TW, através de uma metodologia baseada na sequenciação de nova geração. As bibliotecas de DNA foram preparadas a partir de amostras de sangue periférico e tumor de 36 doentes com TW e sequenciadas no MiSeq. Foram identificadas alterações somáticas em 7 dos 36 (19,4%) doentes estudados. Conclui-se que a sequenciação de um painel de genes é um método rápido para a deteção de mutações somáticas quando desenhado com cuidado de forma a serem evitados problemas de perda de cobertura.