Statistical modelling of transcript profiles of differentially regulated genes

Background: The vast quantities of gene expression profiling data produced in microarray studies, and the more precise quantitative PCR, are often not statistically analysed to their full potential. Previous studies have summarised gene expression profiles using simple descriptive statistics, basic analysis of variance (ANOVA) and the clustering of genes based on simple models fitted to their expression profiles over time. We report the novel application of statistical non-linear regression modelling techniques to describe the shapes of expression profiles for the fungus Agaricus bisporus, quantified by PCR, and for E. coli and Rattus norvegicus, using microarray technology. The use of parametric non-linear regression models provides a more precise description of expression profiles, reducing the "noise" of the raw data to produce a clear "signal" given by the fitted curve, and describing each profile with a small number of biologically interpretable parameters. This approach then allows the direct comparison and clustering of the shapes of response patterns between genes and potentially enables a greater exploration and interpretation of the biological processes driving gene expression. Results: Quantitative reverse transcriptase PCR-derived time-course data of genes were modelled. "Splitline" or "broken-stick" regression identified the initial time of gene up-regulation, enabling the classification of genes into those with primary and secondary responses. Five-day profiles were modelled using the biologically-oriented, critical exponential curve, y(t) = A + (B + Ct)Rt + ε. This non-linear regression approach allowed the expression patterns for different genes to be compared in terms of curve shape, time of maximal transcript level and the decline and asymptotic response levels. Three distinct regulatory patterns were identified for the five genes studied. Applying the regression modelling approach to microarray-derived time course data allowed 11% of the Escherichia coli features to be fitted by an exponential function, and 25% of the Rattus norvegicus features could be described by the critical exponential model, all with statistical significance of p < 0.05. Conclusion: The statistical non-linear regression approaches presented in this study provide detailed biologically oriented descriptions of individual gene expression profiles, using biologically variable data to generate a set of defining parameters. These approaches have application to the modelling and greater interpretation of profiles obtained across a wide range of platforms, such as microarrays. Through careful choice of appropriate model forms, such statistical regression approaches allow an improved comparison of gene expression profiles, and may provide an approach for the greater understanding of common regulatory mechanisms between genes

Aprotinin reduces cardiac troponin I release and inhibits apoptosis of polymorphonuclear cells during off-pump coronary artery bypass surgery

Objectives: In addition to blood-sparing effects, aprotinin may have cardioprotective and anti-inflammatory effects during cardiopulmonary bypass-assisted cardiac surgery. In this study, the authors examined whether aprotinin had cardioprotective and/or anti-inflammatory effects in patients undergoing off-pump coronary artery bypass grafting. Design: A prospective randomized clinical trial. Setting: University hospital. Participants: Fifty patients were randomized to control (n = 25) or aprotinin treatment (n = 25) groups. Interventions: Aprotinin was given as a loading dose (2 x 10(6) KIU) followed by a continuous infusion at 5 x 10(5) KIU/h until skin closure. Measurements and Main Results: Blood samples for cardiac troponin I; interleukin-6, interleukin-8, and interleukin-10; tumor necrosis factor a; and elastase were taken after anesthesia induction, completion of revascularization, and 6 hours, 12 hours, and 24 hours after revascularization. Blood samples were taken to assess for apoptosis in polymorphonuclear cells. Baseline plasma levels for cardiac troponin I did not differ between groups but were significantly lower in aprotinin-treated patients at the time of revascularization (P = 0.03) and 6 hours (p = 0.004) and 24 hours (p = 0.03) later. Aprotinin significantly reduced apoptosis in polymorphonuclear cells compared with control-treated patients (p = 0.04). There were no differences in plasma cytokine or elastase levels between groups. Conclusions: The authors conclude that aprotinin reduces perioperative cardiac troponin I release and attenuates apoptosis in polymorphonuclear cells but has no significant effects on plasma cytokine levels in patients undergoing off-pump coronary artery bypass graft surgery

Are tibial angles measured with inertial sensors useful surrogates for frontal plane projection angles using 2-dimensional video analysis during single leg squat tasks? A reliability and agreement analysis in elite football (soccer) players

During single leg squats (SLS), tibial angle (TA) quantification using inertial measurement units (IMU) may offer a practical alternative to frontal plane projection angle (FPPA) measurement using 2-dimensional (2D) video analysis. This study determined: (i) the reliability of IMUs and 2D video analysis for TA measurement, and 2D video analysis for FPPA measurement; (ii) the agreement between IMU TA and both 2D video TA and FPPA measurements during single leg squats in elite footballers. 18 players were tested on consecutive days. Absolute TA (ATA) and relative TA (RTA) were measured with IMUs. ATA and FPPA were measured concurrently using 2D video analysis. Within-session reliability for all measurements varied across days (intraclass correlation coefficient (ICC) range=0.27–0.83, standard error of measurement (SEM) range=2.12–6.23°, minimal detectable change (MDC) range=5.87–17.26°). Between-sessions, ATA reliability was good for both systems (ICCs=0.70–0.74, SEMs=1.64–7.53°, MDCs=4.55–7.01°), while IMU RTA and 2D FPPA reliability ranged from poor to good (ICCs=0.39–0.72, SEMs=2.60–5.99°, MDCs=7.20–16.61°). All limits of agreement exceeded a 5° acceptability threshold. Both systems were reliable for between-session ATA, although agreement was poor. IMU RTA and 2D video FPPA reliability was variable. For SLS assessment, IMU derived TAs are not useful surrogates for 2D video FPPA measures in this population

Toll-like receptor variation in the bottlenecked population of the Seychelles warbler: computer simulations see the ‘ghost of selection past’ and quantify the ‘drift debt’

Balancing selection can maintain immunogenetic variation within host populations, but detecting its signal in a post-bottlenecked population is challenging due to the potentially overriding effects of drift. Toll-like receptor genes (TLRs) play a fundamental role in vertebrate immune defence and are predicted to be under balancing selection. We previously characterised variation at TLR loci in the Seychelles warbler (Acrocephalus sechellensis), an endemic passerine that has undergone a historical bottleneck. Five out of seven TLR loci were polymorphic, which is in sharp contrast to the low genome-wide variation observed. However standard population genetic statistical methods failed to detect a contemporary signature of selection at any TLR loci. We examined whether the observed TLR polymorphism could be explained by neutral evolution, simulating the population's demography in the software DIYABC. This showed that the posterior distributions of mutation rates had to be unrealistically high to explain the observed genetic variation. We then conducted simulations with an agent-based model using typical values for the mutation rate, which indicated that weak balancing selection has acted on the three TLR genes. The model was able to detect evidence of past selection elevating TLR polymorphism in the pre-bottleneck populations, but was unable to discern any effects of balancing selection in the contemporary population. Our results show drift is the overriding evolutionary force that has shaped TLR variation in the contemporary Seychelles warbler population, and the observed TLR polymorphisms might be merely the ‘ghost of selection past’. Forecast models predict immunogenetic variation in this species will continue to be eroded in the absence of contemporary balancing selection. Such ‘drift debt’ occurs when a genepool has not yet reached its new equilibrium level of polymorphism, and this loss could be an important threat to many recently bottlenecked populations

Changes in neuropsychological functioning following temporal lobectomy in patients with temporal lobe epilepsy

Purpose: This study was conducted to evaluate the changes in neuropsychological functioning in patients with temporal lobe epilepsy (TLE) after temporal lobe resection. Methods: Fifty-four TLE patients were evaluated before and after surgery using comprehensive neuropsychological tests to assess general intelligence, executive functioning, language, verbal and visual memory, working memory, visuo-spatial ability, attention and motor function. Results: The patients with left TLE showed no impairment of neuropsychological functioning after surgery, with the exception of auditory immediate memory. Furthermore, they showed significant improvement in performance IQ, executive function, working memory, visual memory, attention and psychomotor speed. The patients with right TLE did not show any significant impairment in post-operative neuropsychological functioning. They showed improvements in intellectual and executive functions, language, visual memory, visuo-spatial ability, attention and motor function post-operatively. The patients with hippocampal sclerosis showed greater post-operative improvements than the patients without hippocampal sclerosis regardless of the side. Patients with better pre-operative neuropsychological function had a higher chance of successfully discontinuing all seizure medications after surgery. Discussion: The results of this study suggest that temporal lobectomy does not harm the neuropsychological functioning of patients with intractable TLE and that it improves cognitive functions of the contralateral hemisphere. © 2009 W. S. Maney & Son Ltd

Avian malaria is absent in juvenile colonial herons (Ardeidae) but not Culex pipiens mosquitoes in the Camargue, Southern France

Apicomplexan blood parasites Plasmodium and Haemoproteus (together termed “Avian malaria”) and Leucocytozoon are widespread, diverse vector-transmitted blood parasites of birds, and conditions associated with colonial nesting in herons (Ardeidae) and other waterbirds appear perfect for their transmission. Despite studies in other locations reporting high prevalence of parasites in juvenile herons, juvenile Little Egrets (Egretta garzetta) previously tested in the Camargue, Southern France, had a total absence of malaria parasites. This study tested the hypotheses that this absence was due to insufficient sensitivity of the tests of infection; an absence of infective vectors; or testing birds too early in their lives. Blood was sampled from juveniles of four species shortly before fledging: Little Egret (n = 40), Cattle Egret (Bubulcus ibis; n = 40), Black-crowned Night-Heron (Nycticorax nycticorax, n = 40), and Squacco Heron (Ardeola ralloides; n = 40). Sensitive nested-Polymerase Chain Reaction was used to test for the presence of parasites in both birds and host-seeking female mosquitoes captured around the colonies. No malaria infection was found of in any of the heron species. Four different lineages of Plasmodium were detected in pooled samples of female Culex pipiens mosquitoes, including two in potentially infective mosquitoes. These results confirm that the absence of malaria parasites previously demonstrated in Little Egret is not due to methodological limitations. Although the prevalence of infection in mosquitoes was low, conditions within the colonies were suitable for transmission of Plasmodium. These colonial heron species may have evolved strategies for resisting malaria infection through physiological or behavioral mechanisms

The value of tibial mounted inertial measurement units to quantify running kinetics in elite football (soccer) players. A reliability and agreement study using a research orientated and a clinically orientated system

In elite football, measurement of running kinetics with inertial measurement units (IMUs) may be useful as a component of periodic health examination (PHE). This study determined the reliability of, and agreement between a research orientated IMU and clinically orientated IMU system for initial peak acceleration (IPA) and IPA symmetry index (SI) measurement during running in elite footballers. On consecutive days, 16 participants performed treadmill running at 14kmph and 18kmph. Both IMUs measured IPA and IPA SI concurrently. All measurements had good or excellent within-session reliability (intraclass correlation coefficient (ICC2,1) range = 0.79-0.96, IPA standard error of measurement (SEM) range = 0.19-0.62 g, IPA SI SEM range = 2.50-8.05%). Only the research orientated IMU demonstrated acceptable minimal detectable changes (MDCs) for IPA at 14kmph (range = 7.46-9.80%) and IPA SI at both speeds (range = 6.92-9.21%). Considering both systems, between-session IPA reliability ranged from fair to good (ICC2,1 range = 0.63-0.87, SEM range = 0.51-1.10 g) and poor to fair for IPA SI (ICC2,1 range = 0.32-0.65, SEM range = 8.07-11.18%). All MDCs were >10%. For IPA and SI, the 95% levels of agreement indicated poor between system agreement. Therefore, the use of IMUs to evaluate treadmill running kinetics cannot be recommended in this population as a PHE test to identify prognostic factors for injuries or for rehabilitation purposes

Experimental investigation of aminoacetonitrile formation through the Strecker synthesis in astrophysical-like conditions: reactivity of methanimine (CH2NH), ammonia (NH3), and hydrogen cyanide (HCN)

International audienceAstronomy & Astrophysics Experimental investigation of aminoacetonitrile formation through the Strecker synthesis in astrophysical-like conditions: reactivity of methanimine (CH 2 NH), ammonia (NH 3), and hydrogen cyanide (HCN) ABSTRACT Context. Studing chemical reactivity in astrophysical environments is an important means for improving our understanding of the origin of the organic matter in molecular clouds, in protoplanetary disks, and possibly, as a final destination, in our solar system. Laboratory simulations of the reactivity of ice analogs provide important insight into the reactivity in these environments. Here, we use these experimental simulations to investigate the Strecker synthesis leading to the formation of aminoacetonitrile in astrophysical-like conditions. The aminoacetonitrile is an interesting compound because it was detected in SgrB2, hence could be a precursor of the smallest amino acid molecule, glycine, in astrophysical environments. Aims. We present the first experimental investigation of the formation of aminoacetonitrile NH 2 CH 2 CN from the thermal processing of ices including methanimine (CH 2 NH), ammonia (NH 3), and hydrogen cyanide (HCN) in interstellar-like conditions without VUV photons or particules. Methods. We use Fourier Transform InfraRed (FTIR) spectroscopy to monitor the ice evolution during its warming. Infrared spec-troscopy and mass spectroscopy are then used to identify the aminoacetonitrile formation. Results. We demonstrate that methanimine can react with − CN during the warming of ice analogs containing at 20 K methanimine, ammonia, and [NH + 4 − CN] salt. During the ice warming, this reaction leads to the formation of poly(methylene-imine) polymers. The polymer length depend on the initial ratio of mass contained in methanimine to that in the [NH + 4 − CN] salt. In a methanimine excess, long polymers are formed. As the methanimine is progressively diluted in the [NH + 4 − CN] salt, the polymer length decreases until the aminoacetonitrile formation at 135 K. Therefore, these results demonstrate that aminoacetonitrile can be formed through the second step of the Strecker synthesis in astrophysical-like conditions

The role of TcdB and TccC subunits in secretion of the photorhabdus Tcd toxin complex

The Toxin Complex (TC) is a large multi-subunit toxin encoded by a range of bacterial pathogens. The best-characterized examples are from the insect pathogens Photorhabdus, Xenorhabdus and Yersinia. They consist of three large protein subunits, designated A, B and C that assemble in a 5:1:1 stoichiometry. Oral toxicity to a range of insects means that some have the potential to be developed as pest control technology. The three subunit proteins do not encode any recognisable export sequences and as such little progress has been made in understanding their secretion. We have developed heterologous TC production and secretion models in E. coli and used them to ascribe functions to different domains of the crucial B+C sub-complex. We have determined that the B and C subunits use a secretion mechanism that is either encoded by the proteins themselves or employ an as yet undefined system common to laboratory strains of E. coli. We demonstrate that both the N-terminal domains of the B and C subunits are required for secretion of the whole complex. We propose a model whereby the N-terminus of the C-subunit toxin exports the B+C sub-complex across the inner membrane while that of the B-subunit allows passage across the outer membrane. We also demonstrate that even in the absence of the B-subunit, that the C-subunit can also facilitate secretion of the larger A-subunit. The recognition of this novel export system is likely to be of importance to future protein secretion studies. Finally, the identification of homologues of B and C subunits in diverse bacterial pathogens, including Burkholderia and Pseudomonas, suggests that these toxins are likely to be important in a range of different hosts, including man