Integrated methodologies to study human transcriptional regulation from functional genomics data

Abstract : The human body is composed of a huge number of cells acting together in a concerted manner. The current understanding is that proteins perform most of the necessary activities in keeping a cell alive. The DNA, on the other hand, stores the information on how to produce the different proteins in the genome. Regulating gene transcription is the first important step that can thus affect the life of a cell, modify its functions and its responses to the environment. Regulation is a complex operation that involves specialized proteins, the transcription factors. Transcription factors (TFs) can bind to DNA and activate the processes leading to the expression of genes into new proteins. Errors in this process may lead to diseases. In particular, some transcription factors have been associated with a lethal pathological state, commonly known as cancer, associated with uncontrolled cellular proliferation, invasiveness of healthy tissues and abnormal responses to stimuli. Understanding cancer-related regulatory programs is a difficult task, often involving several TFs interacting together and influencing each other's activity. This Thesis presents new computational methodologies to study gene regulation. In addition we present applications of our methods to the understanding of cancer-related regulatory programs. The understanding of transcriptional regulation is a major challenge. We address this difficult question combining computational approaches with large collections of heterogeneous experimental data. In detail, we design signal processing tools to recover transcription factors binding sites on the DNA from genome-wide surveys like chromatin immunoprecipitation assays on tiling arrays (ChIP-chip). We then use the localization about the binding of TFs to explain expression levels of regulated genes. In this way we identify a regulatory synergy between two TFs, the oncogene C-MYC and SP1. C-MYC and SP1 bind preferentially at promoters and when SP1 binds next to C-NIYC on the DNA, the nearby gene is strongly expressed. The association between the two TFs at promoters is reflected by the binding sites conservation across mammals, by the permissive underlying chromatin states 'it represents an important control mechanism involved in cellular proliferation, thereby involved in cancer. Secondly, we identify the characteristics of TF estrogen receptor alpha (hERa) target genes and we study the influence of hERa in regulating transcription. hERa, upon hormone estrogen signaling, binds to DNA to regulate transcription of its targets in concert with its co-factors. To overcome the scarce experimental data about the binding sites of other TFs that may interact with hERa, we conduct in silico analysis of the sequences underlying the ChIP sites using the collection of position weight matrices (PWMs) of hERa partners, TFs FOXA1 and SP1. We combine ChIP-chip and ChIP-paired-end-diTags (ChIP-pet) data about hERa binding on DNA with the sequence information to explain gene expression levels in a large collection of cancer tissue samples and also on studies about the response of cells to estrogen. We confirm that hERa binding sites are distributed anywhere on the genome. However, we distinguish between binding sites near promoters and binding sites along the transcripts. The first group shows weak binding of hERa and high occurrence of SP1 motifs, in particular near estrogen responsive genes. The second group shows strong binding of hERa and significant correlation between the number of binding sites along a gene and the strength of gene induction in presence of estrogen. Some binding sites of the second group also show presence of FOXA1, but the role of this TF still needs to be investigated. Different mechanisms have been proposed to explain hERa-mediated induction of gene expression. Our work supports the model of hERa activating gene expression from distal binding sites by interacting with promoter bound TFs, like SP1. hERa has been associated with survival rates of breast cancer patients, though explanatory models are still incomplete: this result is important to better understand how hERa can control gene expression. Thirdly, we address the difficult question of regulatory network inference. We tackle this problem analyzing time-series of biological measurements such as quantification of mRNA levels or protein concentrations. Our approach uses the well-established penalized linear regression models where we impose sparseness on the connectivity of the regulatory network. We extend this method enforcing the coherence of the regulatory dependencies: a TF must coherently behave as an activator, or a repressor on all its targets. This requirement is implemented as constraints on the signs of the regressed coefficients in the penalized linear regression model. Our approach is better at reconstructing meaningful biological networks than previous methods based on penalized regression. The method is tested on the DREAM2 challenge of reconstructing a five-genes/TFs regulatory network obtaining the best performance in the "undirected signed excitatory" category. Thus, these bioinformatics methods, which are reliable, interpretable and fast enough to cover large biological dataset, have enabled us to better understand gene regulation in humans.

Brain dysfunctions, psychopathologies, and body image distortions

The major features in eating disorders are a preoccupation with food and its consumption and body dissatisfaction. Diagnostic manuals provide clusters of criteria according to which affected individuals can be categorized into one or other group of eating disorder. Yet, when considering the high proportion of comorbidities and ignoring the content of the symptoms (food, body), the major features seem to yield obsessional-compulsive, addictive, and impulsive qualities. In the present article, we review studies from the neuroscientific literature (mainly lesion studies) on eating disorder, obsessive-compulsive disorder, impulse control disorder, and addiction to investigate the possibility of a wider phenotype that can be related to a common brain network. The literature localizes this network to the right frontal lobe and its connectivities. This network, when dysfunctional, might result in a behavior that favors the preoccupation with particular thoughts, behaviors, anxieties, and uncontrollable urges that are accompanied by little scope for ongoing behavioral adjustments (e.g., impulse control). We reason that this network may turn out to be equally involved in understudied mental conditions of dysfunctional body processing such as muscle dysmorphia, body dysmorphic disorder (including esthetic surgery), and xelomelia. We finally consider previous notions of a wider phenotype approach to current diagnostic practice (using DSM), such as the possibility of a model with a reduced number of diagnostic categories and primary and secondary factors, and to etiological models of mental health conditions.

The building blocks of the full body ownership illusion

Previous work has reported that it is not difficult to give people the illusion of ownership over an artificial body, providing a powerful tool for the investigation of the neural and cognitive mechanisms underlying body perception and self consciousness. We present an experimental study that uses immersive virtual reality (IVR) focused on identifying the perceptual building blocks of this illusion. We systematically manipulated visuotactile and visual sensorimotor contingencies, visual perspective, and the appearance of the virtual body in order to assess their relative role and mutual interaction. Consistent results from subjective reports and physiological measures showed that a first person perspective over a fake humanoid body is essential for eliciting a body ownership illusion. We found that the illusion of ownership can be generated when the virtual body has a realistic skin tone and spatially substitutes the real body seen from a first person perspective. In this case there is no need for an additional contribution of congruent visuotactile or sensorimotor cues. Additionally, we found that the processing of incongruent perceptual cues can be modulated by the level of the illusion: when the illusion is strong, incongruent cues are not experienced as incorrect. Participants exposed to asynchronous visuotactile stimulation can experience the ownership illusion and perceive touch as originating from an object seen to contact the virtual body. Analogously, when the level of realism of the virtual body is not high enough and/or when there is no spatial overlap between the two bodies, then the contribution of congruent multisensory and/or sensorimotor cues is required for evoking the illusion. On the basis of these results and inspired by findings from neurophysiological recordings in the monkey, we propose a model that accounts for many of the results reported in the literature.

Translation and assembly of HLA-DR antigens in Xenopus oocytes injected with mRNA from a human B-cell line.

HLA-DR antigens are polymorphic cell surface glycoproteins, expressed primarily in B lymphocytes and macrophages, which are thought to play an important role in the immune response. Two polypeptide chains, alpha and beta, are associated at the cell surface, and a third chain associates with alpha and beta intracellularly. RNA isolated from the human B-cell line Raji was injected in Xenopus laevis oocytes. Immunoprecipitates of translation products with several monoclonal antibodies revealed the presence of HLA-DR antigens similar to those synthesized in Raji cells. One monoclonal antibody was able to bind the beta chain after dissociation of the three polypeptide chains with detergent. The presence of all three chains was confirmed by two-dimensional gel electrophoresis. The glycosylation pattern of the three chains was identical to that observed in vivo, as evidenced in studies using tunicamycin, an inhibitor of N-linked glycosylation. The presence of alpha chains assembled with beta chains in equimolar ratio was further demonstrated by amino-terminal sequencing. An RNA fraction enriched for the three mRNAs, encoding alpha, beta, and intracellular chains, was isolated. This translation-assembly system and the availability of monoclonal antibodies make it possible to assay for mRNA encoding specific molecules among the multiple human Ia-like antigens.

Different Storing and Processing Conditions of Human Lymphocytes do not Alter P-Glycoprotein Rhodamine 123 Efflux.

P-glycoprotein (Pgp), a protein codified by Multi Drug Resistance (MDR1) gene, has a detoxifying function and might influence the toxicity and pharmacokinetics and pharmacodynamics of drugs. Sampling strategies to improve Pgp studies could be useful to optimize the sensitivity and the reproducibility of efflux assays. This study aimed to compare Pgp expression and efflux activity by measuring Rhodamine123 (Rh123) retention in lymphocytes stored under different conditions, in order to evaluate the potential utility of any of the storing conditions in Pgp functionality. Our results show no change in protein expression of Pgp by confocal studies and Western blotting, nor changes at the mRNA level (qRT-PCR). No differences in Rh123 efflux by Pgp activity assays were found between fresh and frozen lymphocytes after 24 hours of blood extraction, using either of the two Pgp specific inhibitors (VP and PSC833). Different working conditions in the 24 hours post blood extraction do not affect Rh123 efflux. These results allow standardization of Pgp activity measurement in different individuals with different timing of blood sampling and in different geographic areas. _______________

Chromatoid body mediated RNA regulation in mouse male germline

Male germ cell differentiation, spermatogenesis is an exceptional developmental process that produces a massive amount of genetically unique spermatozoa. The complexity of this process along with the technical limitations in the germline research has left many aspects of spermatogenesis poorly understood. Post-meiotic haploid round spermatids possess the most complex transcriptomes of the whole body. Correspondingly, efficient and accurate control mechanisms are necessary to deal with the huge diversity of transcribed RNAs in these cells. The high transcriptional activity in round spermatids is accompanied by the presence of an uncommonly large cytoplasmic ribonucleoprotein granule, called the chromatoid body (CB) that is conjectured to participate in the RNA post-transcriptional regulation. However, very little is known about the possible mechanisms of the CB function. The development of a procedure to isolate CBs from mouse testes was this study’s objective. Anti-MVH immunoprecipitation of cross-linked CBs from a fractionated testicular cell lysate was optimized to yield considerable quantities of pure and intact CBs from mice testes. This protocol produced reliable and reproducible data from the subsequent analysis of CB’s protein and RNA components. We found that the majority of the CB’s proteome consists of RNA-binding proteins that associate functionally with different pathways. We also demonstrated notable localization patterns of one of the CB transient components, SAM68 and showed that its ablation does not change the general composition or structure of the CB. CB-associated RNA analysis revealed a strong accumulation of PIWI-interacting RNAs (piRNAs), mRNAs and long non-coding RNAs (lncRNAs) in the CB. When the CB transcriptome and proteome analysis results were combined, the most pronounced molecular functions in the CB were related to piRNA pathway, RNA post-transcriptional processing and CB structural scaffolding. In addition, we demonstrated that the CB is a target for the main RNA flux from the nucleus throughout all steps of round spermatid development. Moreover, we provided preliminary evidence that those isolated CBs slice target RNAs in vitro in an ATPdependent manner. Altogether, these results make a strong suggestion that the CB functions involve RNA-related and RNA-mediated mechanisms. All the existing data supports the hypothesis that the CB coordinates the highly complex haploid transcriptome during the preparation of the male gametes for fertilization. Thereby, this study provides a fundamental basis for the future functional analyses of ribonucleoprotein granules and offers also important insights into the mechanisms governing male fertility.

Expression of CYP2A3 mRNA and its regulation by 3-methylcholanthrene, pyrazole, and ß-ionone in rat tissues

Cytochrome P450 (CYP) 2A enzymes are involved in the metabolism of numerous drugs and hormones and activate different carcinogens. Human CYP2A6, mouse CYP2A5 and rat CYP2A3 are orthologous enzymes that present high similarity in their amino acid sequence and share substrate specificities. However, different from the human and mouse enzyme, CYP2A3 is not expressed in the rat liver. There are limited data about expression of CYP2A3 in extrahepatic tissues and its regulation by typical CYP inducers. Therefore, the objective of the present study was to analyze CYP2A3 mRNA expression in different rat tissues by RT-PCR, and to study the influence of 3-methylcholanthrene, pyrazole and ß-ionone treatment on its expression. Male Wistar rats were divided into four groups of 5 rats each, and were treated ip for 4 days with 3-methylcholanthrene (25 mg/kg body weight), pyrazole (150 mg/kg body weight), ß-ionone (1 g/kg body weight), or vehicle. Total RNA was extracted from tissues and CYP2A3 mRNA levels were analyzed by semiquantitative RT-PCR. CYP2A3 mRNA was constitutively expressed in the esophagus, lung and nasal epithelium, but not along the intestine, liver, or kidney. CYP2A3 mRNA levels were increased in the esophagus by treatment with 3-methylcholanthrene and pyrazole (17- and 7-fold, respectively), in lung by pyrazole and ß-ionone (3- and 4-fold, respectively, although not statistically significant), in the distal part of the intestine and kidney by 3-methylcholanthrene and pyrazole, and in the proximal part of the intestine by pyrazole. CYP2A3 mRNA was not induced in nasal epithelium, liver or in the middle part of the intestine. These data show that, in the rat, CYP2A3 is constitutively expressed in several extrahepatic tissues and its regulation occurs through a complex mechanism that is essentially tissue specific.

Rapid test for the evaluation of the activity of the prodrug hydroxymethylnitrofurazone in the processing of Trypanosoma cruzi messenger RNAs

No fully effective treatment has been developed since the discovery of Chagas' disease by Carlos Chagas in 1909. Since drug-resistant Trypanosoma cruzi strains are occurring and the current therapy is effectiveness in the acute phase but with various adverse side effects, more studies are needed to characterize the susceptibility of T. cruzi to new drugs. Many natural and/or synthetic substances showing trypanocidal activity have been used, even though they are not likely to be turned into clinically approved drugs. Originally, drug screening was performed using natural products, with only limited knowledge of the molecular mechanism involved in the development of diseases. Trans-splicing, which is unusual RNA processing reaction and occurs in nematodes and trypanosomes, implies the processing of polycistronic transcription units into individual mRNAs; a short transcript spliced leader (SL RNA) is trans-spliced to the acceptor pre-mRNA, giving origin to the mature mRNA. In the present study, permeable cells of T. cruzi epimastigote forms (Y, BOL and NCS strains) were treated to evaluate the interference of two drugs (hydroxymethylnitrofurazone - NFOH-121 and nitrofurazone) in the trans-splicing reaction using silver-stained PAGE analysis. Both drugs induced a significant reduction in RNA processing at concentrations from 5 to 12.5 µM. These data agreed with the biological findings, since the number of parasites decreased, especially with NFOH-121. This proposed methodology allows a rapid and cost-effective screening strategy for detecting drug interference in the trans-splicing mechanism of T. cruzi.

Swimming training down-regulates plasma leptin levels, but not adipose tissue ob mRNA expression

The aim of the present study was to assess the effects of endurance training on leptin levels and adipose tissue gene expression and their association with insulin, body composition and energy intake. Male Wistar rats were randomly divided into two groups: trained (N = 18) and sedentary controls (N = 20). The trained group underwent swimming training for 9 weeks. Leptin and insulin levels, adiposity and leptin gene expression in epididymal and inguinal adipose tissue were determined after training. There were no differences in energy intake between groups. Trained rats had a decreased final body weight (-10%), relative and total body fat (-36 and -55%, respectively) and insulin levels (-55%) compared with controls (P < 0.05). Although trained animals showed 56% lower leptin levels (2.58 ± 1.05 vs 5.89 ± 2.89 ng/mL in control; P < 0.05), no difference in leptin gene expression in either fat depot was demonstrable between groups. Stepwise multiple regression analysis showed that lower leptin levels in trained rats were due primarily to their lower body fat mass. After adjustment for total body fat, leptin levels were still 20% (P < 0.05) lower in exercised rats. In conclusion, nine weeks of swimming training did not affect leptin gene expression, but did lead to a decrease in leptin levels that was independent of changes in body fat.

Estradiol-induced hypophagia is associated with the differential mRNA expression of hypothalamic neuropeptides

Estradiol participates in the control of energy homeostasis, as demonstrated by an increase in food intake and in body weight gain after ovariectomy in rats. In the present study, female Wistar rats (200-230 g, N = 5-15 per group), with free access to chow, were individually housed in metabolic cages. We investigated food intake, body weight, plasma leptin levels, measured by specific radioimmunoassay, and the hypothalamic mRNA expression of orexigenic and anorexigenic neuropeptides, determined by real-time PCR, in ovariectomized rats with (OVX+E) and without (OVX) estradiol cypionate treatment (10 µg/kg body weight, sc, for 8 days). Hormonal and mRNA expression were determined at pre-feeding and 4 h after food intake. OVX+E rats showed lower food intake, less body weight gain and lower plasma leptin levels. In the OVX+E group, we also observed a reduction of neuropeptide Y (NPY), agouti-related protein (AgRP) and cocaine- and amphetamine-regulated transcript (CART) mRNA expression in the arcuate nucleus and a decrease in orexin A in the lateral hypothalamic area (LHA). There was an increase in leptin receptor (LepRb), melanocortin-4 receptor (MC4-R), CART, and mainly corticotropin-releasing hormone (CRH) mRNA in the paraventricular nucleus and LepRb and CART mRNA in the LHA. These data show that hypophagia induced by estradiol treatment is associated with reduced hypothalamic expression of orexigenic peptides such as NPY, AgRP and orexin A, and increased expression of the anorexigenic mediators MC4-R, LepRb and CRH. In conclusion, estradiol decreases food intake, and this effect seems to be mediated by peripheral factors such as leptin and the differential mRNA expression of neuropeptides in the hypothalamus.

The influence of emotional body posture on adults' and 8-year-olds' perception facial expressions

The present set of experiments was designed to investigate the development of children's sensitivity of facial expressions observed within emotional contexts. Past research investigating both adults' and children's perception of facial expressions has been limited primarily to the presentation of isolated faces. During daily social interactions, however, facial expressions are encountered within contexts conveying emotions (e.g., background scenes, body postures, gestures). Recently, research has shown that adults' perception of facial expressions is influenced by these contexts. When emotional faces are shown in incongruent contexts (e.g., when an angry face is presented in a context depicting fear) adults' accuracy decreases and their reaction times increase (e.g., Meeren et a1. 2005). To examine the influence of emotional body postures on children's perception of facial expressions, in each of the experiments in the current study adults and 8-year-old children made two-alternative forced choice decisions about facial expressions presented in congruent (e.g., a face displayed sadness on a body displaying sadness) and incongruent (e.g., a face displaying fear on a body displaying sadness) contexts. Consistent with previous studies, a congruency effect (better performance on congruent than incongruent trials) was found for both adults and 8-year-olds when the emotions displayed by the face and body were similar to each other (e.g., fear and sad, Experiment l a ) ; the influence of context was greater for 8-year-olds than adults for these similar expressions. To further investigate why the congruency effect was larger for children than adults in Experiment 1 a, Experiment 1 b was conducted to examine if increased task difficulty would increase the magnitude of adults' congruency effects. Adults were presented with subtle facial and despite successfully increasing task difficulty the magnitude of the. congruency effect did not increase suggesting that the difference between children's and adults' congruency effects in Experiment l a cannot be explained by 8-year-olds finding the task difficult. In contrast, congruency effects were not found when the expressions displayed by the face and body were dissimilar (e.g., sad and happy, see Experiment 2). The results of the current set of studies are examined with respect to the Dimensional theory and the Emotional Seed model and the developmental timeline of children's sensitivity to facial expressions. A secondary aim of the series of studies was to examine one possible mechanism underlying congruency effe cts-holistic processing. To examine the influence of holistic processing, participants completed both aligned trials and misaligned trials in which the faces were detached from the body (designed to disrupt holistic processing). Based on the principles of holistic face processing we predicted that participants would benefit from misalignment of the face and body stimuli on incongruent trials but not on congruent trials. Collectively, our results provide some evidence that both adults and children may process emotional faces and bodies holistically. Consistent with the pattern of results for congruency effects, the magnitude of the effect of misalignment varied with the similarity between emotions. Future research is required to further investigate whether or not facial expressions and emotions conveyed by the body are perceived holistically.

Studies on new processing aids and other compounding ingredients in special purpose rubbers

In the first part of the study we probed the effectiveness of rice bran oil as a multipurpose compounding ingredient for nitrile (NBR) and chloroprene (CR) rubbers. This oil has already been successfully employed in the compounding of NR and SBR in this laboratory.In this context we thought it worthwhile to try this oil in the polar rubbers viz, NBR and CR also. The principle of like dissolves like as applicable to solvents is equally applicable while selecting a plasticiser, elastomer combination. Because of the compatibility considerations polar plasticisers are preferred for polar rubbers like NBR and CR. Although plasticisation is a physical phenomenon and no chemical reaction is involved, the chemical structure of plasticisers determines how much physical attraction there is between the rubber and the plasticiser. In this context it is interesting to note that the various fatty acids present in rice bran oil have a long paraffinic chain, characteristic of waxes, with an acid group at the end of the molecule. The paraffinic end of the molecule contributes lubricating effects and limits compatibility whereas the acid end group contributes some polarity and is also chemically reactive. Because of absorption of acid group on the surface of pigments, these acids will have active pigment wetting characteristics also. These factors justifies the role of rice bran oil as a co-activator and lubricating agent for NBR and CR. In fact in our study we successfully replaced stearic acid as co-activator and aromatic oillDOP as processing aid for CR and NBR with rice bran oil.This part of the study has got special significance in the fact that rubber industry now heavily depends on petroleum industry for process oils. The conventional process oils like aromatic, naphthenic and paraffinic oils are increasingly becoming costlier, as its resources in nature are fast depleting. Moreover aromatic process oils are reported to be carcinogenic because of the presence of higher levels of polycyclic aromatic compounds in these oils.As a result of these factors, a great amount research is going on world over for newer processing aids which are cost effective, nontoxic and performanance wise at par with the conventional ones used in the rubber industry. Trials with vegetable oils in this direction is worth trying.Antioxidants are usually added to the rubber compound to minimise ageing effects from heat, light, oxygen etc. As rice bran oil contains significant amount of tocopherols and oryzanol which are natural antioxidants, we replaced a phenolic antioxidant like styrenated phenol (SP) from the compound recipe of both the rubbers with RBO and ascertained whether this oil could function in the role of antioxidant as well.Preparation and use of epoxidised rice bran oil as plasticiser has already been reported.The crude rice bran oil having an iodine value of 92 was epoxidised in this laboratory using peracetic acid in presence of sulphuric acid as catalyst. The epoxy content of the epoxidised oil was determined volumetrically by treating a known weight of the oil with excess HCI and back titrating the residual HCI with standard alkali solution. The epoxidised oil having an epoxy content of 3.4% was tried in the compounding of NBR and CR as processing aids. And results of these investigations are also included in this chapter. In the second part of the study we tried how RBO/ERBO could perform when used as a processing aid in place of aromatic oil in the compounding of black filled NRCR blends. Elastomers cannot have all the properties required for a particular applications, so it is common practice in rubber industry to blend two elastomers to have desired property for the resulting blend.In this RBO/ERBO was tried as a processing aid for plasticisation, dispersion of fillers, and vulcanisation of black filled NR-CR blends.Aromatic oil was used as a control. The results of our study indicate that these oils could function as a processing aid and when added together with carbon black function as a cure accelerator also.PVC is compatible with nitrile rubber in all proportions, provided NBR has an acrylonitrile content of 25 to 40%. Lower or higher ACN content in NBR makes it incompatible with PVC.PVC is usually blended with NBR at high temperatures. In order to reduce torque during mixing, additional amounts of plasticisers like DOP are added. The plasticiser should be compatible both with PVC and NBR so as to get a homogeneous blend. Epoxidised soyaben oil is reported to have been used in the compounding of PVC as it can perfonn both as an efficient plasticiser and heat stabilizer.At present DOP constitute the largest consumed plasticiser in the PVC compounding. The migration of this plasticiser from food packaging materials made of PVC poses great health hazards as this is harmful to human body. In such a scenario we also thought it worthwhile to see whether DOP could be replaced by rice bran oil in the compounding of NBR-PVC blends Different blends of NBR-PVC were prepared with RBO and were vulcanized using sulphur and conventional accelerators. The various physical and mechanical properties of the vulcanisates were evaluated and compared with those prepared with DOP as the control plasticiser. Epoxidised rice bran oil was also tried as plasticiser for the preparation of NBR-PVC blends. A comparison of the processability and cure characteristics of the different blends prepared with DOP and ERBO showed that ERBO based blends have better processability and lower cure time values. However the elastographic maximum torque values are higher for the DOP based blends. Almost all of the physical properties evaluated are found to be slightly better for the DOP based blends over the ERBO based ones. However a notable feature of the ERBO based blends is the better percentage retention of elongation at break values after ageing over the DOP based blends. The results of these studies using rice bran oil and its epoxidised variety indicated that they could be used as efficient plasticisers in place of DOP and justifies their role as novel, nontoxic, and cheap plasticisers for NBR-PVC blends.

Prevalence and distribution of Salmonella serotypes in marketed broiler chickens and processing environment in Coimbatore City of southern India

Broiler chicken is gaining popularity among the consumers of India. Since poultry is recognised as a leading food vehicle for Salmonella contamination, the prevalence and distribution of Salmonella serotypes in broiler chickens and processing environments of retail outlets has been studied. In the present study 214 samples of broiler chicken and 311 environmental samples from cage were analysed for the presence of Salmonella. Of the various body parts of live chicken analysed prevalence varied from 1.4% in cloacca to 6.9% in crop region. Environmental samples from the cage showed higher prevalence of Salmonella ranging from0 to 16.67%. Apart from Salmonella enteritidis, which was the predominant Salmonella serotype in the chickens as well as in the environmental samples, other serotypes such as S. bareilly, S. cerro, S. mbandaka and S. moladewere also encountered. The results of the research calls for strict hygiene standards for retail broiler chicken processing outlets

Meat yield and quality of Tanzania Shorthorn Zebu cattle finished on molasses/maize grain with agro-processing by-products in 90 days feedlot period

This study was conducted to evaluate the effects of feeding molasses or maize grain with agro-processing by-products on yield and quality of meat from Tanzania shorthorn zebu (TSZ) cattle. Forty five steers aged 2.5 to 3.0 years with 200 +/- 5.4 kg body weight were allocated into five dietary treatments namely hominy feed with molasses (HFMO), rice polishing with molasses (RPMO), hominy feed with maize meal (HFMM), rice polishing with maize meal (RPMM) and maize meal with molasses (MMMO). Ad libitum amount of each dietary treatment and hay were offered to nine steers for 90 days. Cooking loss (CL) and Warner Bratzler shear force (WBSF) values were determined on M. longissimus thoracis et lumborum aged for 3, 6, 9 and 12 days. Steers fed on HFMO diet had higher (P < 0.05) nutrient intake (86.39 MJ/d energy; 867 g/d CP), weight gain (919 g/d) and half carcass weight (75.8 kg) than those fed other diets. Meat of steers from all diets was tender with average WBSF values of 47.9 N cm^(−2). The CL (22.0 +/- 0.61%) and WBSF (53.4 +/- 0.70 N cm^(−2)) were highest in meat aged for 3 days followed by 6, 9 and 12 days. WBSF values for meat aged for 9 and 12 days from steers fed HFMO and RPMM diets were similar and lower than those on other dietary treatments x aging periods. Overall, molasses and hominy feed can be used to replace maize meal in feedlot finishing diets to spare its use in animal feeds.

Face processing in humans is compatible with a simple shape-based model of vision

Understanding how the human visual system recognizes objects is one of the key challenges in neuroscience. Inspired by a large body of physiological evidence (Felleman and Van Essen, 1991; Hubel and Wiesel, 1962; Livingstone and Hubel, 1988; Tso et al., 2001; Zeki, 1993), a general class of recognition models has emerged which is based on a hierarchical organization of visual processing, with succeeding stages being sensitive to image features of increasing complexity (Hummel and Biederman, 1992; Riesenhuber and Poggio, 1999; Selfridge, 1959). However, these models appear to be incompatible with some well-known psychophysical results. Prominent among these are experiments investigating recognition impairments caused by vertical inversion of images, especially those of faces. It has been reported that faces that differ "featurally" are much easier to distinguish when inverted than those that differ "configurally" (Freire et al., 2000; Le Grand et al., 2001; Mondloch et al., 2002) ??finding that is difficult to reconcile with the aforementioned models. Here we show that after controlling for subjects' expectations, there is no difference between "featurally" and "configurally" transformed faces in terms of inversion effect. This result reinforces the plausibility of simple hierarchical models of object representation and recognition in cortex.