Alternative splicing enriched cDNA libraries identify breast cancer-associated transcripts

Background: Alternative splicing (AS) is a central mechanism in the generation of genomic complexity and is a major contributor to transcriptome and proteome diversity. Alterations of the splicing process can lead to deregulation of crucial cellular processes and have been associated with a large spectrum of human diseases. Cancer-associated transcripts are potential molecular markers and may contribute to the development of more accurate diagnostic and prognostic methods and also serve as therapeutic targets. Alternative splicing-enriched cDNA libraries have been used to explore the variability generated by alternative splicing. In this study, by combining the use of trapping heteroduplexes and RNA amplification, we developed a powerful approach that enables transcriptome-wide exploration of the AS repertoire for identifying AS variants associated with breast tumor cells modulated by ERBB2 (HER-2/neu) oncogene expression. Results: The human breast cell line (C5.2) and a pool of 5 ERBB2 over-expressing breast tumor samples were used independently for the construction of two AS-enriched libraries. In total, 2,048 partial cDNA sequences were obtained, revealing 214 alternative splicing sequence-enriched tags (ASSETs). A subset with 79 multiple exon ASSETs was compared to public databases and reported 138 different AS events. A high success rate of RT-PCR validation (94.5%) was obtained, and 2 novel AS events were identified. The influence of ERBB2-mediated expression on AS regulation was evaluated by capillary electrophoresis and probe-ligation approaches in two mammary cell lines (Hb4a and C5.2) expressing different levels of ERBB2. The relative expression balance between AS variants from 3 genes was differentially modulated by ERBB2 in this model system. Conclusions: In this study, we presented a method for exploring AS from any RNA source in a transcriptome-wide format, which can be directly easily adapted to next generation sequencers. We identified AS transcripts that were differently modulated by ERBB2-mediated expression and that can be tested as molecular markers for breast cancer. Such a methodology will be useful for completely deciphering the cancer cell transcriptome diversity resulting from AS and for finding more precise molecular markers.

Sedentary subjects have higher PAI-1 and lipoproteins levels than highly trained athletes

Physical exercise protects against the development of cardiovascular disease, partly by lowering plasmatic total cholesterol, LDL-cholesterol and increased HDL-cholesterol levels. In addition, it is now established that reduction plasmatic adiponectin and increased C-reactive protein (CRP) and plasminogen activator inhibitor-1 (PAI-1) levels play a role in the maintenance of an inflammatory state and in the development of cardiovascular disease. This study aimed to examine plasma lipid profile and inflammatory markers levels in individual with sedentary lifestyle and/or highly trained athletes at rest. Methods: Fourteen male subjects (sedentary lifestyle n = 7 and highly trained athletes n = 7) were recruited. Blood samples were collected after an overnight fast (similar to 12 h). The plasmatic lipid profile (Triglycerides, HDL-cholesterol, LDL-cholesterol, total cholesterol, LDL-oxidized and total cholesterol/HDL-c ratio), glucose, adiponectin, C - reactive protein and PAI-1 levels were determined. Results: Total cholesterol, LDL-cholesterol, TG and PAI-1 levels were lower in highly trained athletes group in relation to sedentary subjects (p < 0.01). In addition, we observed a positive correlation between PAI-1 and total cholesterol (r = 0.78; p < 0.0009), PAI-1 and LDL-c (r = 0.69; p < 0.006) and PAI-1 and TG levels (r = 0.56; p < 0.03). The plasma concentration of adiponectin, CRP, glucose, HDL-cholesterol and total cholesterol/HDL-c ratio levels were not different. These results indicate that lifestyle associated with high intensity and high volume exercise induces changes favourable in the lipid profile and PAI-1 levels and may reduce risk cardiovascular diseases.

Missing levels in acoustic resonators

It is shown that the deviations of the experimental statistics of six chaotic acoustic resonators from Wigner-Dyson random matrix theory predictions are explained by a recent model of random missing levels. In these resonatorsa made of aluminum plates a the larger deviations occur in the spectral rigidity (SRs) while the nearest-neighbor distributions (NNDs) are still close to the Wigner surmise. Good fits to the experimental NNDs and SRs are obtained by adjusting only one parameter, which is the fraction of remaining levels of the complete spectra. For two Sinai stadiums, one Sinai stadium without planar symmetry, two triangles, and a sixth of the three-leaf clover shapes, was found that 7%, 4%, 7%, and 2%, respectively, of eigenfrequencies were not detected.

Magnetoconfined levels in a parabolic quantum dot: An analytical solution of a three-dimensional Fock-Darwin problem in a tilted magnetic field

The energy spectrum of an electron confined in a quantum dot (QD) with a three-dimensional anisotropic parabolic potential in a tilted magnetic field was found analytically. The theory describes exactly the mixing of in-plane and out-of-plane motions of an electron caused by a tilted magnetic field, which could be seen, for example, in the level anticrossing. For charged QDs in a tilted magnetic field we predict three strong resonant lines in the far-infrared-absorption spectra.

Supersymmetric and Kaluza-Klein particles multiple scattering in the Earth

Neutrino telescopes with cubic kilometer volumes have the potential to discover new particles. Among them are next to lightest supersymmetric (NLSPs) and next to lightest Kaluza-Klein (NLKPs) particles. Two NLSPs or NLKPs will transverse the detector simultaneously producing parallel charged tracks. The track separation inside the detector can be a few hundred meters. As these particles might propagate a few thousand kilometers before reaching the detector, multiple scattering could enhance the pair separation at the detector. We find that the multiple scattering will alter the separation distribution enough to increase the number of NLKP pairs separated by more than 100 meters (a reasonable experimental cut) by up to 46% depending on the NLKP mass. Vertical upcoming NLSPs will have their separation increased by 24% due to multiple scattering.

Lossless filter for multiple repeats with bounded edit distance

Background: Identifying local similarity between two or more sequences, or identifying repeats occurring at least twice in a sequence, is an essential part in the analysis of biological sequences and of their phylogenetic relationship. Finding such fragments while allowing for a certain number of insertions, deletions, and substitutions, is however known to be a computationally expensive task, and consequently exact methods can usually not be applied in practice. Results: The filter TUIUIU that we introduce in this paper provides a possible solution to this problem. It can be used as a preprocessing step to any multiple alignment or repeats inference method, eliminating a possibly large fraction of the input that is guaranteed not to contain any approximate repeat. It consists in the verification of several strong necessary conditions that can be checked in a fast way. We implemented three versions of the filter. The first is simply a straightforward extension to the case of multiple sequences of an application of conditions already existing in the literature. The second uses a stronger condition which, as our results show, enable to filter sensibly more with negligible (if any) additional time. The third version uses an additional condition and pushes the sensibility of the filter even further with a non negligible additional time in many circumstances; our experiments show that it is particularly useful with large error rates. The latter version was applied as a preprocessing of a multiple alignment tool, obtaining an overall time (filter plus alignment) on average 63 and at best 530 times smaller than before (direct alignment), with in most cases a better quality alignment. Conclusion: To the best of our knowledge, TUIUIU is the first filter designed for multiple repeats and for dealing with error rates greater than 10% of the repeats length.

Sequence-specific electrochemical detection of Alicyclobacillus acidoterrestris DNA using electroconductive polymer-modified fluorine tin oxide electrodes

This study outlines the quantification of low levels of Alicyclobacillus acidoterrestris in pure cultures, since this bacterium is not inactivated by pasteurization and may remain in industrialized foods and beverages. Electroconductive polymer-modified fluorine tin oxide (FTO) electrodes and multiple nanoparticle labels were used for biosensing. The detection of A. acidoterrestris in pure cultures was performed by reverse transcription polymerase chain reaction (RT-PCR) and the sensitivity was further increased by asymmetric nested RT-PCR using electrochemical detection for quantification of the amplicon. The quantification of nested RT-PCR products by Ag/Au-based electrochemical detection was able to detect 2 colony forming units per mL (CFU mL(-1)) of spores in pure culture and low detection and quantification limits (7.07 and 23.6 nM, respectively) were obtained for the target A. acidoterrestris on the electrochemical detection bioassay.

Sequential injection analysis implementing multiple standard additions for As speciation by liquid chromatography and atomic fluorescence spectrometry (SIA-HPLC-AFS)

An analytical procedure for multiple standard additions of arsenic species using sequential injection analysis (SIA) is proposed for their quantification in seafood extracts. SIA presented flexibility for generating multiple specie standards at the ng mL(-1) concentration level by adding different volumes of As(III), As(V), monomethylarsonic (MMA) and dimethylarsinic (DMA) to the sample. The mixed sample plus standard solutions were delivered from SIA to fill the HPLC injection loop. Subsequently, As species were separated by HPLC and analyzed by atomic fluorescence spectrometry (AFS). The proposed system comprised two independently controlled modules, with the HPLC loop acting as the intermediary device. The analytical frequency was enhanced by combining the actions of both modules. While the added sample was flowing through the chromatographic column towards the detection system, the SIA program started performing the standard additions to another sample. The proposed method was applied to spoiled seafood extracts. Detection limits based on 3 sigma for As(III), As(V), MMA and DMA were 0.023, 0.39, 0.45 and 1.0 ng mL(-1), respectively. (C) 2011 Elsevier B.V. All rights reserved.

Evaluation of the use of multiple lines for determination of metals in water by inductively coupled plasma optical emission spectrometry with axial viewing

Inductively coupled plasma optical emission spectrometers (ICP DES) allow fast simultaneous measurements of several spectral lines for multiple elements. The combination of signal intensities of two or more emission lines for each element may bring such advantages as improvement of the precision, the minimization of systematic errors caused by spectral interferences and matrix effects. In this work, signal intensities for several spectral lines were combined for the determination of Al, Cd, Co, Cr, Mn, Pb, and Zn in water. Afterwards, parameters for evaluation of the calibration model were calculated to select the combination of emission lines leading to the best accuracy (lowest values of PRESS-Predicted error sum of squares and RMSEP-Root means square error of prediction). Limits of detection (LOD) obtained using multiple lines were 7.1, 0.5, 4.4, 0.042, 3.3, 28 and 6.7 mu g L(-1) (n = 10) for Al, Cd. Co, Cr, Mn, Pb and Zn, respectively, in the presence of concomitants. On the other hand, the LOD established for the most intense emission line were 16. 0.7, 8.4, 0.074. 23, 26 and 9.6 mu g L(-1) (n = 10) for these same elements in the presence of concomitants. The accuracy of the developed procedure was demonstrated using water certified reference material. The use of multiple lines improved the sensitivity making feasible the determination of these analytes according to the target values required for the current environmental legislation for water samples and it was also demonstrated that measurements in multiple lines can also be employed as a tool to verify the accuracy of an analytical procedure in ICP DES. (C) 2009 Elsevier B.V. All rights reserved.

Forest-related partnerships in Brazilian Amazonia: There is more to sustainable forest management than reduced impact logging

There is more to sustainable forest management than reduced impact logging. Partnerships between multiple actors are needed in order to create the institutional context for good forest governance and sustainable forest management and stimulate the necessary local community involvement. The idea behind this is that the parties would be able to achieve more jointly than on their own by combining assets, knowledge, skills and political power of actors at different levels of scale. This article aims to demonstrate by example the nature and variety of forest-related partnerships in Brazilian Amazonia. Based on the lessons learned from these cases and the authors` experience, the principal characteristics of successful partnerships are described, with a focus on political and socioeconomic aspects. These characteristics include fairly negotiated partnership objectives, the active involvement of the public sector as well as impartial brokers, equitable and cost-effective institutional arrangements, sufficient and equitably shared benefits for all the parties involved, addressing socioeconomic drawbacks, and taking measures to maintain sustainable exploitation levels. The authors argue that, in addition to product-oriented partnerships which focus on sustainable forest management, there is also a need for politically oriented partnerships based on civil society coalitions. The watchdog function of these politically oriented partnerships, their awareness-raising campaigns regarding detrimental policies and practices, and advocacy for good forest governance are essential for the creation of the appropriate legal and political framework for sustainable forest management. (C) 2008 Elsevier B.V. All rights reserved.

Chronic Stress Is Associated with High Cortisol Levels and Emotional Coping Mechanisms in Amnestic Mild Cognitive Impairment

Background/Aims: To investigate the association between cortisol levels, chronic stress and coping in subjects with amnestic-type mild cognitive impairment (aMCI). Methods: Cortisol levels were measured using morning saliva samples from 33 individuals with aMCI and from 41 healthy elderly. Chronic stress was evaluated with the Stress Symptoms List (SSL), whereas coping strategies were assessed using the Jalowiec Coping Scale. Results: aMCI subjects with high SSL scores presented higher cortisol levels (p = 0.045). Furthermore, aMCI subjects who employed emotion-focused coping had higher SSL scores (p = 0.023). Conclusion: The association between increased cortisol secretion, chronic stress and coping strategies may be modulated by the presence or absence of cognitive impairment, where memory deficit awareness constitutes an additional potential factor involved in high stress severity. Copyright (C) 2009 S. Karger AG, Basel

Relationship Between Cortisol Levels and Memory Performance may be Modulated by the Presence or Absence of Cognitive Impairment: Evidence from Healthy Elderly, Mild Cognitive Impairment and Alzheimer`s Disease Subjects

An inverted U-shape function between cortisol levels and memory performance has been reported in studies on both young animals and humans. Yet little is known about this relationship in normal aging or in older subjects with cognitive impairment. This issue is particularly significant since increased levels of cortisol have been reported in Alzheimer`s disease (AD). The present study examined the association between cortisol levels and visual memory performance in healthy subjects as well as in individuals presenting mild cognitive impairment (MCI) or AD. Salivary cortisol was measured in 40 healthy elderly subjects, 31 individuals with amnestic MCI, and 40 subjects with mild probable AD. Memory performance was evaluated using the Brief Cognitive Screening Battery. Higher cortisol levels were associated with better memory performance in healthy elderly (p = 0.005), while higher cortisol levels were correlated with poorer memory performance in MCI subjects (p = 0.011). No correlation between cortisol and memory was found in the AD group (p > 0.05). These results suggest that the relationship between cortisol levels and memory performance in the aging process could vary according to the presence or absence of cognitive impairment.

Heat and exercise acclimation increases intracellular levels of Hsp72 and inhibits exercise-induced increase in intracellular and plasma Hsp72 in humans

In order to verify the effects of heat and exercise acclimation (HA) on resting and exercise-induced expression of plasma and leukocyte heat shock protein 72 (Hsp72) in humans, nine healthy young male volunteers (25.0 +/- 0.7 years; 80.5 +/- 2.0 kg; 180 +/- 2 cm, mean +/- SE) exercised for 60 min in a hot, dry environment (40 +/- 0A degrees C and 45 A +/- 0% relative humidity) for 11 days. The protocol consisted of running on a treadmill using a controlled hyperthermia technique in which the work rate was adjusted to elevate the rectal temperature by 1A degrees C in 30 min and maintain it elevated for another 30 min. Before and after the HA, the volunteers performed a heat stress test (HST) at 50% of their individual maximal power output for 90 min in the same environment. Blood was drawn before (REST), immediately after (POST) and 1 h after (1 h POST) HST, and plasma and leukocytes were separated and stored. Subjects showed expected adaptations to HA: reduced exercise rectal and mean skin temperatures and heart rate, and augmented sweat rate and exercise tolerance. In HST1, plasma Hsp72 increased from REST to POST and then returned to resting values 1 h POST (REST: 1.11 A +/- 0.07, POST: 1.48 A +/- 0.10, 1 h POST: 1.22 A +/- 0.11 ng mL(-1); p < 0.05). In HST2, there was no change in plasma Hsp72 (REST: 0.94 A +/- 0.08, POST: 1.20 A +/- 0.15, 1 h POST: 1.17 A +/- 0.16 ng mL(-1); p > 0.05). HA increased resting levels of intracellular Hsp72 (HST1: 1 A +/- 0.02 and HST2: 4.2 A +/- 1.2 density units, p < 0.05). Exercise-induced increased intracellular Hsp72 expression was observed on HST1 (HST1: REST, 1 A +/- 0.02 vs. POST, 2.9 A +/- 0.9 density units, mean +/- SE, p < 0.05) but was inhibited on HST2 (HST2: REST, 4.2 +/- 1.2 vs. POST, 4.4 +/- 1.1 density units, p > 0.05). Regression analysis showed that the lower the pre-exercise expression of intracellular Hsp72, the higher the exercise-induced increase (R = -0.85, p < 0.05). In conclusion, HA increased resting leukocyte Hsp72 levels and inhibited exercise-induced expression. This intracellular adaptation probably induces thermotolerance. In addition, the non-increase in plasma Hsp72 after HA may be related to lower stress at the cellular level in the acclimated individuals.

Effects of different levels of protein intake and physical training on growth and nutritional status of young rats

This study aimed to investigate the effects of physical training, and different levels of protein intake in the diet, on the growth and nutritional status of growing rats. Newly-weaned Wistar rats (n=48) were distributed into six experimental groups: three of them were subjected to physical swim training (1 h per day. 5 d per week, for 4 wk, after 2 wk of familiarization) and the other three were considered as controls (non-trained). Each pair of groups, trained and non-trained, received diets with a different level of protein in their composition: 14%. 21% or 28%. The animals were euthanized at the end of the training period and the following analyses were performed: proteoglycan synthesis as a biomarker of bone and cartilage growth, IGF-I (insulin-like growth factor-I) assay as a biomarker of growth and nutritional status. total RNA and protein concentration and protein synthesis measured in vivo using a large-dose phenylalanine method. As a main finding, increased dietary protein, combined with physical training, was able to improve neither tissue protein synthesis nor muscle growth. In addition, cartilage and bone growth seem to be deteriorated by the lower and the higher levels of protein intake. Our data allow us to conclude that protein enhancement in the diet, combined with physical exercise, does not stimulate tissue protein synthesis or muscle mass growth. Furthermore, physical training, combined with low protein intake, was not favorable to bone development in growing animals.

Exercise training reduces cardiac angiotensin II levels and prevents cardiac dysfunction in a genetic model of sympathetic hyperactivity-induced heart failure in mice

The role of exercise training (ET) on cardiac renin-angiotensin system (RAS) was investigated in 3-5 month-old mice lacking alpha(2A-) and alpha(2C-)adrenoceptors (alpha(2A)/alpha(2C)ARKO) that present heart failure (HF) and wild type control (WT). ET consisted of 8-week running sessions of 60 min, 5 days/week. In addition, exercise tolerance, cardiac structural and function analysis were made. At 3 months, fractional shortening and exercise tolerance were similar between groups. At 5 months, alpha(2A)/alpha(2C)ARKO mice displayed ventricular dysfunction and fibrosis associated with increased cardiac angiotensin (Ang) II levels (2.9-fold) and increased local angiotensin-converting enzyme activity (ACE 18%). ET decreased alpha(2A)/alpha(2C)ARKO cardiac Ang II levels and ACE activity to age-matched untrained WT mice levels while increased ACE2 expression and prevented exercise intolerance and ventricular dysfunction with little impact on cardiac remodeling. Altogether, these data provide evidence that reduced cardiac RAS explains, at least in part, the beneficial effects of ET on cardiac function in a genetic model of HF.