Virtual models of the HLA class I antigen processing pathway

Antigen recognition by cytotoxic CD8 T cells is dependent upon a number of critical steps in MHC class I antigen processing including proteosomal cleavage, TAP transport into the endoplasmic reticulum, and MHC class 1 binding. Based on extensive experimental data relating to each of these steps there is now the capacity to model individual antigen processing steps with a high degree of accuracy. This paper demonstrates the potential to bring together models of individual antigen processing steps, for example proteosome cleavage, TAP transport, and MHC binding, to build highly informative models of functional pathways. In particular, we demonstrate how an artificial neural network model of TAP transport was used to mine a HLA-binding database so as to identify H LA-binding peptides transported by TAP. This integrated model of antigen processing provided the unique insight that HLA class I alleles apparently constitute two separate classes: those that are TAP-efficient for peptide loading (HLA-B27, -A3, and -A24) and those that are TAP-inefficient (HLA-A2, -B7, and -B8). Hence, using this integrated model we were able to generate novel hypotheses regarding antigen processing, and these hypotheses are now capable of being tested experimentally. This model confirms the feasibility of constructing a virtual immune system, whereby each additional step in antigen processing is incorporated into a single modular model. Accurate models of antigen processing have implications for the study of basic immunology as well as for the design of peptide-based vaccines and other immunotherapies. (C) 2004 Elsevier Inc. All rights reserved.

Fermentative production of hydrogen from cassava processing wastewater by Clostridium acetobutylicum

This work reports on the effect of initial substrate concentration on COD consumption, pH, and H(2) production during cassava processing wastewater fermentation by Clostridium acetobutylicum ATCC 824. Five initial COD wastewater concentrations, namely 5.0, 7.5, 10.7, 15.0, and 30.0 g/L, were used. The results showed that higher substrate concentrations (30.0 and 15.0 COD/L) led to lower H(2) yield as well as less efficient substrate conversion into H(2). On the other hand, initial COD concentrations of 10.7, 7.5 and 5 g/L furnished 1.34, 1.2 and 2.41 mol H(2)/mol glucose, with efficiency of glucose conversion into H(2) of 34, 30, and 60% (mol/mol), respectively. These results demonstrate that cassava processing wastewater, a highly polluting effluent, can be successfully employed as substrate for H(2) production by C acetobutylicum at lower COD concentrations. (C) 2011 Elsevier Ltd. All rights reserved.

Snakes and kittens in the grass: No evidence for preferential processing of fear-relevant animals in visual search

Ohman and colleagues provided evidence for preferential processing of pictures depicting fear-relevant animals by showing that pictures of snakes and spiders are found faster among pictures of fiowers and mushrooms than vice versa and that the speed of detecting fear-relevant animals was not affected by set size whereas the speed of detecting fiowers/mushrooms was. Experiment 1 replicated this finding. Experiment 2, however, found similar search advantages when pictures of cats and horses or of wolves and big cats were to be found among pictures of flowers and mushrooms. Moreover, Experiment 3, in a within subject comparison, failed to find faster identification of snakes and spiders than of cats and horses among flowers and mushrooms. The present findings seem to indicate that previous reports of preferential processing of pictures of snakes and spiders in a visual search task may reflect a processing advantage for animal pictures in general rather than fear-relevance.

Why fear snakes and spiders? Evidence for a learning-based account of fear-relevant stimulus-processing

Fear-relevant stimuli, such as snakes, spiders and heights, preferentially capture attention as compared to nonfear-relevant stimuli. This is said to reflect an encapsulated mechanism whereby attention is captured by the simple perceptual features of stimuli that have evolutionary significance. Research, using pictures of snakes and spiders, has found some support for this account; however, participants may have had prior fear of snakes and spiders that influenced results. The current research compared responses of snake and spider experts who had little fear of snakes and spiders, and control participants across a series of affective priming and visual search tasks. Experts discriminated between dangerous and nondangerous snakes and spiders, and expert responses to pictures of nondangerous snakes and spiders differed from those of control participants. The current results dispute that stimulus fear relevance is based purely on perceptual features, and provides support for the role of learning and experience.

Soil mineral genesis and distribution in a saline lake landscape of the Pantanal Wetland, Brazil

The origin of the saline lakes in the Pantanal wetland has been classically attributed to processes occurring in past periods. However, recent studies have suggested that saline water is currently forming from evaporative concentration of fresh water, which is provided annually by seasonal floods. Major elements (Ca, Mg, K) and alkalinity appear to be geochemically controlled during the concentration of waters and may be involved in the formation of carbonates and clay minerals around the saline lakes. The mineralogy of soils associated with a representative saline lake was investigated using XRD, TEM-EDS, and ICP-MS in order to identify the composition and genesis of the secondary minerals suspected to be involved in the control of major elements. The results showed that Ca, Mg, and K effectively undergo oversaturation and precipitation as the waters become more saline. These elements are incorporated in the authigenically formed carbonates, smectites, and micas surrounding the saline lake. The control of Ca occurs by precipitation of calcite and dolomite in nodules while Mg and K are mainly involved in the neoformation of Mg-smectites (stevensitic and saponitic minerals) and, probably, iron-enriched micas (ferric-illite) in surface and subsurface horizons. Therefore, our study confirms that the salinity of Pantanal, historically attributed to inheritance from former regimes, has a contribution of current processes. (C) 2009 Elsevier B.V. All rights reserved.

Individual differences in motivated social cognition: The case of self-serving information processing

Three experiments examined the hypothesis that people show consistency in motivated social cognitive processing across self-serving domains. Consistent with this hypothesis, Experiment 1 revealed that people who rated a task at which they succeeded as more important than a task at which they failed also cheated on a series of math problems, but only when they could rationalize their cheating as unintentional. Experiment 2 replicated this finding and demonstrated that a self-report measure of self-deception did not predict this rationalized cheating. Experiment 3 replicated Experiments 1 and 2 and ruled out several alternative explanations. These experiments suggest that people who show motivated processing in ego-protective domains also show motivated processing in extrinsic domains. These experiments also introduce a new measurement procedure for differentiating between intentional versus rationalized cheating.

Visuospatial processing and the function of prefrontal-parietal networks in autism spectrum disorders: a functional MRI study

Objective: Individuals with autism spectrum disorders typically have normal visuospatial abilities but impaired executive functioning, particularly in abilities related to working memory and attention. The aim of this study was to elucidate the functioning of frontoparietal networks underlying spatial working memory processes during mental rotation in persons with autism spectrum disorders. Method: Seven adolescent males with normal IQ with an autism spectrum disorder and nine age- and IQ-matched male comparison subjects underwent functional magnetic resonance imaging scans while performing a mental rotation task. Results: The autism spectrum disorders group showed less activation in lateral and medial premotor cortex, dorsolateral prefrontal cortex, anterior cingulate gyrus, and caudate nucleus. Conclusions: The finding of less activation in prefrontal regions but not in parietal regions supports a model of dysfunction of frontostriatal networks in autism spectrum disorders.

Processing of mutated human proinsulin to mature insulin in the non-endocrine cell line, CHO

Heterologous genes encoding proproteins, including proinsulin, generally produce mature protein when expressed in endocrine cells while unprocessed or partially processed protein is produced in non-endocrine cells. Proproteins, which are normally processed in the regulated pathway restricted to endocrine cells, do not always contain the recognition sequence for cleavage by furin, the endoprotease specific to the constitutive pathway, the principal protein processing pathway in non-endocrine cells. Human proinsulin consists of B-Chain-C-peptide-A-Chain and cleavage at the B/C and C/A junctions is required for processing. The B/C, but not the C/A junction, is recognised and cleaved in the constitutive pathway. We expressed a human proinsulin and a mutated proinsulin gene with an engineered furin recognition sequence at the C/A junction and compared the processing efficiency of the mutant and native proinsulin in Chinese Hamster Ovary cells. The processing efficiency of the mutant proinsulin was 56% relative to 0.7% for native proinsulin. However, despite similar levels of mRNA being expressed in both cell lines, the absolute levels of immunoreactive insulin, normalized against mRNA levels, were 18-fold lower in the mutant proinsulin-expressing cells. As a result, there was only a marginal increase in absolute levels of insulin produced by these cells. This unexpected finding may result from preferential degradation of insulin in non-endocrine cells which lack the protection offered by the secretory granules found in endocrine cells.

Centrifugal processing of cell debris and inclusion bodies from recombinant Escherichia coli

The settling characteristics of cell debris and inclusion bodies prior to, and following, fractionation in a disc-stack centrifuge were measured using Cumulative Sedimentation Analysis (CSA) and Centrifugal Disc photosedimentation (CDS). The impact of centrifuge feedrate and repeated homogenisation on both cell debris and inclusion body collection efficiency was investigated. Increasing the normalised centrifuge feedrate (Q/Sigma) from 1.32 x 10(-9) m s(-1) to 3.97 x 10(-9) m s(-1) leads to a 36% increase in inclusion body paste purity. Purity may also be improved by repeated homogenisation. Increasing the number of homogeniser passes results in smaller cell debris size whilst leaves inclusion body size unaltered. At a normalised centrifuge feedrate of 2.65 x 10(-9) m s(-1), increasing the number of homogeniser passes from two (2) to ten (10) improved overall inclusion body paste purity by 58%. Grade-efficiency curves for both the cell debris and inclusion bodies have also been generated in this study. The data are described using an equation developed by Mannweiler (1989) with parameters of k = 0.15-0.26 and n = 2.5-2.6 for inclusion bodies, and k = 0.12-0.14 and n = 2.0-2.2 for cell debris. This is the first accurate experimentally-determined grade efficiency curve for cell debris. Previous studies have simply estimated debris grade efficiency curves using an approximate debris size distribution and grade efficiency curves determined with 'ideal particles' (e.g. spherical PVA particles). The findings of this study may be used to simulate and optimise the centrifugal fractionation of inclusion bodies from cell debris.

Bone mineral apparent density in juvenile dermatomyositis: the role of lean body mass and glucocorticoid use

Objective: To analyse bone mineral density (BMD) in juvenile dermatomyositis (JDM) and its possible association with body composition, disease activity, duration of disease, glucocorticoid (GC) use, and biochemical bone parameters, including osteoprotegerin (OPG) and receptor activator of nuclear factor B (RANKL). Methods: Twenty girls with JDM and 20 controls matched for gender and age were selected. Body composition and BMD were analysed by dual-energy X-ray absorptiometry (DXA) and bone mineral apparent density (BMAD) was calculated. Duration of disease, cumulative GC, and GC pulse therapy use were determined from medical records. Disease activity and muscle strength were measured by the Disease Activity Score (DAS), the Childhood Myositis Assessment Scale (CMAS), and the Manual Muscle Test (MMT). Inflammatory and bone metabolism parameters were also analysed. OPG and RANKL were measured in patients and controls using an enzyme-linked immunosorbent assay (ELISA). Results: A lower BMAD in the femoral neck (p< 0.001), total femur (p< 0.001), and whole body (p=0.005) was observed in JDM patients compared to controls. Body composition analysis showed a lower lean mass in JDM compared to controls (p=0.015), but no difference was observed with regard to fat mass. A trend of lower serum calcium was observed in JDM (p=0.05), whereas all other parameters analysed, including OPG and RANKL, were similar. Multiple linear regression analysis revealed that, in JDM, lean mass (p< 0.01) and GC pulse therapy use (p< 0.05) were independent factors for BMAD in the hip region. Conclusions: This study has identified low lean mass and GC pulse therapy use as the major factors for low hip BMAD in JDM patients.

Primary antiphospholipid syndrome in premenopausal women: low vitamin D, high fat mass and maintained bone mineral mass

The aim of this study was to analyze vitamin D levels and their association with bone mineral density and body composition in primary antiphospholipid syndrome. For this cross-sectional study 23 premenopausal women with primary antiphospholipid syndrome (Sapporo criteria) and 23 age- and race-matched healthy controls were enrolled. Demographic, anthropometric, clinical and laboratorial data were collected using clinical interview and chart review. Serum 25-hydroxyvitamin D levels, parathormone, calcium and 24-hour urinary calcium were evaluated in all subjects. Bone mineral density and body composition were studied by dual X-ray absorptiometry. The mean age of patients and controls was 33 years. Weight (75.61 [20.73] vs. 63.14 [7.34] kg, p=0.009), body mass index (29.57 [7.17] vs. 25.35 [3.37] kg, p=0.014) and caloric ingestion (2493 [1005.6] vs. 1990 [384.1] kcal/day, p=0.03) were higher in PAPS than controls. All PAPS were under oral anticoagulant with INR within therapeutic range. Interestingly, biochemical bone parameters revealed lower levels of 25-hydroxyvitamin D [21.64 (11.26) vs. 28.59 (10.67) mg/dl, p=0.039], serum calcium [9.04 (0.46) vs. 9.3 (0.46) mg/dl, p=0.013] and 24-hour urinary calcium [106.55 (83.71) vs. 172.92 (119.05) mg/d, p=0.027] in patients than in controls. Supporting these findings, parathormone levels were higher in primary antiphospholipid syndrome than in controls [64.82 (37.83) vs. 44.53 (19.62) pg/ml, p=0.028]. The analysis of osteoporosis risk factors revealed that the two groups were comparable (p>0.05). Lumbar spine, femoral neck, total femur and whole body bone mineral density were similar in both groups (p>0.05). Higher fat mass [28.51 (12.93) vs. 20.01 (4.68) kg, p=0.005] and higher percentage of fat [36.08 (7.37) vs. 31.23 (4.64)%, p=0.010] were observed in PAPS in comparison with controls; although no difference was seen regarding lean mass. In summary, low vitamin D in primary antiphospholipid syndrome could be secondary to higher weight and fat mass herein observed most likely due to adipocyte sequestration. This weight gain may also justify the maintenance of bone mineral density even with altered biochemical bone parameters. Lupus (2010) 19, 1302-1306.

Mild head injury and speed of information processing: A prospective study of professional rugby league players

The sensitivity of several short tests of speed of information processing to the effects of mild head injury in rugby league football was investigated. The measures used were the Symbol Digit Modalities Test, the Digit Symbol Substitution Test, and the Speed of Comprehension Test. Two studies were conducted, the first to examine the effect of practice, the second to determine sensitivity to cognitive impairment immediately following injury. The first study established alternate form equivalence and demonstrated that performance on the Speed of Comprehension and Digit Symbol Substitution tests improved with practice, whereas the Symbol Digit Modalities test remained stable. A second study of 10 players who subsequently sustained mild head injuries showed that measures of speed of information processing were sensitive to impairment in the postacute phase, whereas an untimed task of word recognition (Spot-the-Word) was not. Speed of Comprehension was more sensitive to postinjury impairment than either the Digit Symbol Substitution or Symbol Digit Modalities tests. A repeated baseline assessment before injury using the higher score to reflect a player's potential, allowed measurement of impaired performance on sensitive tests.

Enhancing the phonological processing skills of children with specific reading disability

The present study evaluated the benefits of phonological processing skills training for children with persistent reading difficulties. Children aged between 9-14 years, identified as having a specific reading disability, participated in the study. In a series of three experiments, pedagogical issues related to length of training time, model of intervention and severity of readers' phonological processing skills deficit prior to intervention, were explored. The results indicated that improvement in poor readers' phonological processing skills led to a dramatic improvement in their reading accuracy and reading comprehension performance. Increasing the length of training time significantly improved transfer effects to the reading process. Children with particularly severe phonological processing skill deficits benefited from art extended training period, and both individual and group intervention models for phonological processing training proved successful. Implications for speech and language therapists are discussed.

The Saskatchewan Pediatric Bone Mineral Accrual Study: Bone mineral acquisition during the growing years

To investigate bone mineral accretion in growing children, the Saskatchewan Pediatric Bone Mineral Accrual Study was initiated in 1991. The study involves the collection of dietary and physical activity information along with anthropometric growth and maturity measurements every 6 months and dual-energy X-ray absorptiometer (DXA) bone scans of the whole body, AP lumbar spine and proximal femur taken annually, The study has now finished its 6th year and 68 males and 72 females from an original sample of 228 elementary schoolchildren are still involved, To investigate how bone mineral at clinically important sites proceeds in relation to maturation we developed distance and velocity growth curves for height and bone mineral content (BMC) for the AP lumbar spine, the femoral neck and the whole body, In both boys and girls, over 35% of total body and AP spine bone mineral and over 27% of the bone mineral at the femoral neck was laid down during the 4-year adolescent period surrounding peak linear growth velocity. The clinical significance of these values can be appreciated by consideration of the fact that as much bone mineral will be laid down during these 4 adolescent growing years as most people will lose during all of adult life.

Bone mineral and calcium accretion during puberty

We measured bone mineral content (BMC) and estimated calcium accretion in children to provide insight into dietary calcium requirements during growth. Anthropometric measurements were done semiannually and whole-body BMC was measured annually by dual-energy X-ray absorptiometry for 4 y in 228 children (471 scans in 113 boys and 507 scans in 115,girls). Mean values for BMC, skeletal area, and height were calculated for 1-y age groups from 9.5 to 19.5 y of age. Cross-sectional analysis of the pooled data gave peak height velocity and peak BMC velocity (PBMCV) and the ages at which these occurred (13.3 y in boys and 11.4 y in girls). PBMCV did not peak until 1.2 y after peak height velocity in boys and 1.6 y after peak height velocity in girls. Within 3 y on either side of PBMCV, boys had consistently higher BMC and BMC velocity compared with girls and the discrepancy increased steadily through puberty. Three years before PBMCV, BMC Values in girls were 69% of those in boys; 3 y after peak height velocity this proportion fell to 51%. PBMCV was 320 g/y in boys and 240 g/y in girls. Under the assumption that bone mineral is 32.2% calcium, these values corresponded to a daily calcium retention of 282 mg in boys and 212 mg in girls. Individual Values could be much greater. In one boy in a group of six subjects for whom there were enough data for individual analysis through puberty, PBMCV was 555 g Ca/y or 490 mg Ca/d. Such high skeletal demands for calcium require large dietary calcium intakes and such requirements may not be met immediately in some children.