NetMHCpan,a method for MHC class I binding prediction beyond humans

Binding of peptides to major histocompatibility complex (MHC) molecules is the single most selective step in the recognition of pathogens by the cellular immune system. The human MHC genomic region (called HLA) is extremely polymorphic comprising several thousand alleles, each encoding a distinct MHC molecule. The potentially unique specificity of the majority of HLA alleles that have been identified to date remains uncharacterized. Likewise, only a limited number of chimpanzee and rhesus macaque MHC class I molecules have been characterized experimentally. Here, we present NetMHCpan-2.0, a method that generates quantitative predictions of the affinity of any peptide–MHC class I interaction. NetMHCpan-2.0 has been trained on the hitherto largest set of quantitative MHC binding data available, covering HLA-A and HLA-B, as well as chimpanzee, rhesus macaque, gorilla, and mouse MHC class I molecules. We show that the NetMHCpan-2.0 method can accurately predict binding to uncharacterized HLA molecules, including HLA-C and HLA-G. Moreover, NetMHCpan-2.0 is demonstrated to accurately predict peptide binding to chimpanzee and macaque MHC class I molecules. The power of NetMHCpan-2.0 to guide immunologists in interpreting cellular immune responses in large out-bred populations is demonstrated. Further, we used NetMHCpan-2.0 to predict potential binding peptides for the pig MHC class I molecule SLA-1*0401. Ninety-three percent of the predicted peptides were demonstrated to bind stronger than 500 nM. The high performance of NetMHCpan-2.0 for non-human primates documents the method’s ability to provide broad allelic coverage also beyond human MHC molecules. The method is available at . Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

High level expression of human endostatin in Pichia pastoris using a synthetic gene construct

Endostatin, a 20-kDa C-terminal fragment derived from type XVIII collagen, is a potent angiogenesis inhibitor and an antitumor factor. To improve the production of recombinant human endostatin on increasing demand in clinical practice, we constructed an artificial gene encoding its mature peptide sequence in human collagen XVIII. The synthetic gene consisted of 20 codons in preference in methylotropic yeast—Pichia pastoris and was cloned into expression vector pPICZαA; and the recombinant protein was expressed in P. pastoris strain SMD1168 and purified to near homogeneity using heparin affinity chromatography. The amount of expressed recombinant protein in cultural media using described strategy was 80 mg/l in shake flask cultivation and 435 mg/l in high-density bioreactor fermentation. Methylthiazolium assay demonstrated that human endostatin expressed in P. pastoris using artificial synthetic gene of preference in P. pastoris was able to inhibit the acidic fibroblast growth factor-induced proliferation of endothelial cells in vitro.     

Effect of diet and mating status on ovarian development and oviposition in the polyphagous predator Macrolophus caliginosus (Heteroptera: Miridae)

The mirid bug Macrolophus caliginosus is commercially reared on eggs of Ephestia kuehniella, constituting an effective but expensive factitious food. Artificial diets can decrease the rearing costs of this natural enemy, but developing and evaluating an artificial diet is a very time-consuming activity. In the current study, development and reproduction of M. caliginosus on two artificial diets based on egg yolk were investigated. The artificial diets resulted in longer development and lower adult weights, but survival was comparable with that of control insects fed E. kuehniella eggs. Reproductive potential of the predator reared on factitious and artificial foods was assessed using a dissection method. The influence of nymphal food on fecundity was less important than that of adult food. Adults fed E. kuehniella eggs had a preoviposition period of about 4 days, whereas adults offered only plant material started laying eggs about 7 days after emergence. Ovarian scores at day 7 were higher for females fed E. kuehniella eggs than for those given access only to a tobacco leaf. Ovarian scores were not significantly affected by mating status. In a final test, a parallel comparison of two methods for assessing reproductive response to diet was made. Here, adult couples were offered one of four diets: E. kuehniella eggs, one of two artificial diets or no food. Half of the females were dissected and the other half was held for determining lifetime oviposition. Females fed E. kuehniella eggs had superior ovarian scores and laid more eggs than those fed either artificial diet or those given no extra food. A good correlation (r = 0.97) was obtained between ovarian scores and oviposition data, indicating that dissecting females after 1 week provides a reliable estimate of fecundity as affected by diet quality. Rapid reproductive assessments as used in the current study will help to increase the rate of development of artificial diets and may contribute to more cost effective production methods for augmentative biological control agents.     

Innate versus adaptive immunity in sticklebacks: evidence for trade-offs from a selection experiment

In vertebrates, the immune system consists of two arms of different characteristics: the innate and the acquired immune response. Parasites that are only shortly exposed to the immune system are most efficiently attacked by fast, constitutive innate immune mechanisms. Here, we experimentally selected within four fish families for high innate resistance versus susceptibility of three-spined sticklebacks (Gasterosteus aculeatus) against infection with the eye-fluke (Diplostomum pseudospathacaeum), a parasite whose metacercariae are protected from the immune system within the eye lens. We predicted that in families with high susceptibility, the adaptive immune system would be upregulated when challenged with infection. In accordance, we found that MHC class IIB expression is increased by approximately 50% in those lines selected for higher parasite load (i.e. low innate response). This suggests extensive genetic correlations between innate and adaptive immune system and/or crosstalk between both lines of defense. An efficient, specific innate immune response might reduce overall activation of the immune system and potentially alleviate associated effects of immunopathology.     

Development of an efficient method for screening microorganisms by using symbiotic association between <Emphasis Type="Italic">Nasutitermes takasagoensis</Emphasis> and intestinal microorganisms

Screening method of microorganisms that utilized the symbiotic association between insect (Nasutitermes takasagoensis: Nt) and intestinal microorganisms was developed. The existence of desired microorganisms that grew by degrading difficult-to-degrade materials in the gut was detected using survivability of Nt as an indicator. The desired microorganisms were isolated from the survived Nt. It was thought that guts of Nt behave as continuous culture systems whereby microorganisms that cannot degrade diet components are washed out, whereas those that can degrade it are retained and concentrated in the gut. About 60% of Nt fed with phenol artificial diet (PAD) died within 7 days, while 4% of termites survived for 9 days. The structure of intestinal microorganisms of the survived Nt fed with PAD differed from the bacterial communities obtained from enrichment culture (which contained phenol) of wood-feeding Nt. Relatively high colonies (650-times) were detected in the gut of Nt fed on phenol artificial diet compared with those obtained when Nt was fed on wood. Seven denaturing gradient gel electrophoresis (DGGE) bands were detected from gut of wood-feeding Nt, whereas 11 DGGE-bands were detected from that of phenol-feeding Nt. Out of 11 DGGE-bands, 5 of them were sequenced, and bacterial species including phenol-degrading bacteria were identified.     

建立“人工面神经技术”恢复周围性面瘫兔的闭眼功能

目的：建立“人工面神经技术”以恢复单侧周围性面瘫兔的眼轮匝肌闭眼功能,为周围性面瘫提供一种新的治疗手段。方法：制备单侧周围性面瘫兔,建立健侧眼轮匝肌肌电信号采集、中枢信号处理模式识别、患侧电流刺激眼轮匝肌系统。当健侧眼轮匝肌采集的肌电信号经信号识别、提取以及电脑分析判断,符合其闭眼刺激阈值时,即对人工电刺激器发出指令,由刺激电极直接作用于惠侧眼轮匝肌,引起眼睑完全闭合。结果：以最小电流刺激患侧眼轮匝肌,引起眼睑完全闭合。刺激方式为正负矩形波,电流强度为0．30～0．50mA。结论：利用可植入式微机电技术,在单侧周围性面瘫模型建立“人工面神经反射弧”,恢复患侧眼轮匝肌闭眼收缩,可维持双侧闭眼功能的对称性和同步性。     

Estimating biofilm reaction kinetics using hybrid mechanistic-neural network rate function model

This work describes an alternative method for estimation of reaction rate of a biofilm process without using a model equation. A first principles model of the biofilm process is integrated with artificial neural networks to derive a hybrid mechanistic-neural network rate function model (HMNNRFM), and this combined model structure is used to estimate the complex kinetics of the biofilm process as a consequence of the validation of its steady state solution. The performance of the proposed methodology is studied with the aid of the experimental data of an anaerobic fixed bed biofilm reactor. The statistical significance of the method is also analyzed by means of the coefficient of determination (R²) and model efficiency (ME). The results demonstrate the effectiveness of HMNNRFM for estimating the complex kinetics of the biofilm process involved in the treatment of industry wastewater.     

Personal reflections on the nature of intelligence in humans and machines

Computers, the human mind, and social systems have common problems of inadequate memory and insufficient data manipulation speed. In each of these domains, information compression techniques have evolved to reduce storage and processing needs. Among the techniques for information compression, coding of information in procedures stands out as exceptionally powerful. Procedural information coding also gives rise to behavior that may be defined as intelligent. It is found in the human mind, in machines and in social systems. Its use in human thought is aided by language development which promotes regular review of abstract procedures. A practical consequence of better understanding of procedural information coding is the possibility of training people to exhibit greater mental capacity, a controversial possibility. This paper explores the impact of data processing resource limitations, data compression and procedural thinking in men and machines.     

Contrast-enhanced versus non-enhanced three-dimensional echocardiography of left ventricular volumes

Background In three-dimensional echocardiography (3DE), individual endocardial trabeculae are not clearly visible necessitating left ventricular (LV) volumes to be measured by tracing the innermost endocardial contour. Ultrasound contrast agents aim to improve endocardial definition, but may delineate the outermost endocardial contour by filling up intertrabecular space. Although measurement reproducibility may benefit, there may be a significant influence on absolute LV volume measurements. Methods Twenty patients with a recent myocardial infarction and good ultrasound image quality underwent 3DE using the TomTec Freehand method before and during continuous intravenous contrast infusion. LV volumes were measured offline using TomTec Echo-Scan software. Results The use of contrast enhancement increased end-diastolic (110±35 vs. 144±53 ml; p<0.01) and end-systolic volume measurements (68±31 vs. 87±45 ml; p<0.01) significantly compared with non-contrast; the ejection fraction remained unchanged (40±13 vs. 41±14%, p=NS). Measurement reproducibility did not improve significantly, however. Conclusion Volumes measured by 3DE are significantly larger when ultrasound contrast is used. Possibly, intertrabecular space comprises a substantial part of the LV cavity. In the presence of an adequate apical acoustic window, ultrasound contrast does not improve LV volume measurement reproducibility. (Neth Heart J 2008;16:47-52.)     

Non-coordinate expression of collagen mRNAs during carbon monoxide-induced cardiac hypertrophy

Collagen gene expression during volume overload-induced cardiac hypertrophy was investigated in adult male rats. Hypertrophy of the left ventricle (22%) and right ventricle (37%) occurred following 27 days continuous exposure to 700 ppm carbon monoxide; hematocrit increased nearly 47%. To examine potential cellular and molecular control of restructuring in the heart, we investigated the expression of two specific procollagen mRNAs for collagen types which have different structural-functional roles [Type I (alpha-1) & Type IV]. Type I (interstitial) mRNA levels increased at least 100% relative to controls within 3 days of initial exposure to 700ppm CO, then declined afterwards; type IV(basement membrane) mRNA levels increased more modestly at first, and increased further afterwards. The ratio of type I/type IV RNA's also increased initially, then later declined, with the greatest differences in the relative responses of type I and IV mRNAs seen in the right ventricle. These data suggest that types I and IV collagen mRNA expression is not coordinately expressed during this type of volume overload-induced hypertrophy in rat heart.