Domain libraries: Synthetic diversity for de novo design of antibody V-regions

A completely synthetic gene library encoding the variable light (VL) immunoglobulin domains has been constructed in vitro. The library was constructed by assembling a set of six oligodeoxyribonucleotides (oligos) using the polymerase chain reaction (PCR). Three out of the six overlapping oligonucleotides were synthesized with randomized complementarity determining regions (CDR) with the codon pattern, (NNS)_n, where N is any of the four nucleotides (nt) and n is the number of codons with variation in the CDR. The framework regions, taken from the D1.3 anti-lysozyme antibody (Ab), were kept intact. Overlapping regions of approx. 20 nt, together with two additional flanking primers carrying the desired restriction sites, allowed the construction of a library in one single PCR reaction. The VL library was cloned into the phage display vector pEXmide3, and ten randomly picked clones were sequenced. These sequences exhibited complete diversity in all the three CDR and the codons for five canonical amino acid (aa) residues were kept intact and identified. Seven clones contained the full-length gene for the VL domain while deletions were observed in three clones. The restricted use of nt at the third position successfully avoided the stop codons TGA and TAA, whereas the stop codon TAG is read as Gln in an amber suppressor strain. We call this synthetic Ab diversity Domain Library, and it represents an example of syntheticlibraries with extensive, multiple randomized sequences. The use of Domain Libraries opens up the possibility for design in Ab engineering, e.g., additional CDR regions can be added or their length varied. Furthermore, the use of synthetic gene libraries, constructed with the Domain Library strategy, is not limited to the construction of synthetic Ab fragments, but can be used in the design of other types of proteins.     

Dependence on cations for the binding activity of lectins as determined by affinity electrophoresis

The metal ion content of eighteen different lectins was determined. The lectins were demetallized and the binding activity of native and demetallized forms were investigated using non-denaturing polyacrylamide affinity gel electrophoresis. The binding activities of all lectins were dependent on their metal ion content; when the cations were removed the lectins lost their carbohydrate binding activity. There was a marked difference in the strength with which lectins bind divalent cations.     

盐生植物角果碱蓬种子二型性对环境的适应策略

角果碱蓬(Suaeda corniculata)是藜科一年生盐生植物, 在我国分布于北方盐碱滩涂和盐碱荒漠地区。角果碱蓬具有棕色和黑色两种异型体种子(简称棕色和黑色种子)。对采自内蒙古鄂托克前旗盐渍化生境的角果碱蓬二型种子的形态、休眠和萌发特性开展对比研究, 测定了二型种子休眠和萌发行为对温度、光照和盐分(NaCl)的响应, 以揭示盐生植物异型种子对温带盐漠生境的适应对策。结果表明: (1)二型性种子在大小、种皮特性和结实比例方面有显著差异。与黑色种子相比, 棕色种子个体较大, 种皮透水性强。黑色种子与棕色种子的结实比例约为5.6 : 1。(2)新成熟的棕色种子的萌发对各温度梯度和光照条件不敏感, 萌发率较高(84%-100%); 而新成熟的黑色种子萌发率较低(8%-78%), 萌发对光照敏感。(3)黑色种子具有浅度生理休眠, 种皮划破、赤霉素处理和低温层积均可有效地提高种子的萌发率。(4)二型种子萌发对土壤盐分的胁迫具有不同的响应。与黑色种子相比, 棕色种子对盐分胁迫不敏感, 在较高的盐分浓度下仍有较高的萌发率, 低温层积处理能够降低黑色种子对盐胁迫的敏感性, 有效地提高种子的初始萌发率、萌发恢复率和最终萌发率。角果碱蓬二型种子不同的形态、休眠和萌发特性, 提高了该物种在高度异质性生境中的适合度, 对种群成功地适应温带盐漠环境具有重要的意义。     

荷木树干CO_2释放通量与木质部液流和CO_2浓度的关系

采用红外气体分析仪,于2008年10月17-19日连续3个昼夜原位监测了荷木的树干CO_2释放通量、树干温度、木质部液流密度和CO_2浓度.结果表明:树干CO_2释放通量(EA)日变化呈S形曲线,不同径级间差异显著.EA与树干温度呈显著幂函数关系(0.24

Abstract：

By using a Li-820 infra-red CO_2 gas analyzer, an in situ measurement of Schima super-ba stem CO_2 efflux was conducted for three consecutive days from 17 to 19 October 2008. In the meantime, the stem temperature, xylem sap efflux density, and xylem CO_2 concentration were measured. The stem CO_2 efflux had a diurnal variation of "S" pattern, and differed significantly with stem diameter. There was a significant exponential relationship between stem CO_2 efflux and stem temperature (0. 24 < R~2 < 0. 78). The temperature coefficient (b) and regression coeffi-cient (R~2) were higher at nighttime than at daytime, and the Q_(10) value ranged from 2. 01 to 2. 79. The stem CO_2 efflux correlated significantly with the xylem CO_2 concentration, and the best regression curve was cubic (R~2= 0. 48). Excluding the effects of stem temperature, the stem CO_2 efflux showed a significant negative correlation with xylem sap flux density (r =-0.462). Therefore, only using simple temperature function to estimate stem CO_2 efflux would yield a significant error, and xylem sap flux should be taken into consideration in the stem CO_2 emux estimation.     

Attovial‐based antibody nanoarrays

Antibody array‐based technology is a powerful emerging tool in proteomics, but to enable global proteome analysis, antibody array layouts with even higher density has to be developed. To this end, we have further developed the first generation of a nanoarray platform, based on attoliter‐sized vials, attovials, which we have characterized and used for the detection of complement factor C1q in human serum samples. Finally, we demonstrated proof‐of‐concept for individual functionalization of the attovials with a recombinant antibody.     

The presence of serum anti-Ascaris lumbricoides IgE antibodies and of Trichuris trichiura infection are risk factors for wheezing and/or atopy in preschool-aged Brazilian children

Background

The elucidation of factors that trigger the development of transient wheezing in early childhood may be an important step toward understanding the pathogenesis of asthma and other allergic diseases later in life. Transient wheezing has been mainly attributed to viral infections, although sensitisation to aeroallergens and food allergens may occur at an early age. In developing countries, intestinal helminthic infections have also been associated with allergy or atopy-related disorders.

Objective

The aim of this study was to explore the association of Trichuris trichiura and Ascaris lumbricoides infections with wheezing and atopy in early childhood.

Study design

A cross-sectional study using a Portuguese-language ISAAC phase I questionnaire, adapted for preschool-aged children, nested in a cohort study of childhood diarrhoea, was conducted on 682 children. Two faecal samples per child were examined for the presence of intestinal helminthic infection. IgE antibodies against three allergenic preparations (Dermatophagoides pteronyssinus, Blomia tropicalis and common child food), as well as against A. lumbricoides antigens, were measured in a sub-sample of these children, whose parents allowed the procedure. Atopy was defined by the presence of levels of serum IgE antibodies ≥0.35 kU/L against at least one of the three tested allergenic preparations.

Results

Active T. trichiura infection but not A. lumbricoides infection was positively associated with wheezing in the total studied children population [adjusted OR = 2.60; CI = 1.54;4.38] and in the atopic children sub-population [adjusted OR = 3.07; CI = 1.00;9.43]. The association with atopy was also positive and statistically significant only in the brute analysis [OR = 2.13; CI = 1.03;4.40]. Anti-A. lumbricoides IgE antibodies, but not current A. lumbricoides infection, were positively associated with wheezing in atopic children [adjusted OR = 2.01; CI = 1.00;4.50] and in non-atopic children [adjusted OR = 3.07; CI = 1.13;8.35] and it was also associated with atopy [adjusted OR = 7.29; CI = 3.90; 13.4]. On the other hands, reports of wheezing were not significantly associated with atopy.

Conclusions

These data corroborate previous studies showing that wheezing is predominantly associated with infection in early childhood and shows that anti-A. lumbricoides IgE antibodies, but not active Ascaris infections, are associated with wheezing and atopy. Additionally, the data demonstrate that T. trichiura infection may play a role in the pathogenesis of atopic wheezing in early childhood.     

Spatial prediction of malaria prevalence in an endemic area of Bangladesh

Background

Malaria is a major public health burden in Southeastern Bangladesh, particularly in the Chittagong Hill Tracts region. Malaria is endemic in 13 districts of Bangladesh and the highest prevalence occurs in Khagrachari (15.47%).

Methods

A risk map was developed and geographic risk factors identified using a Bayesian approach. The Bayesian geostatistical model was developed from previously identified individual and environmental covariates (p < 0.2; age, different forest types, elevation and economic status) for malaria prevalence using WinBUGS 1.4. Spatial correlation was estimated within a Bayesian framework based on a geostatistical model. The infection status (positives and negatives) was modeled using a Bernoulli distribution. Maps of the posterior distributions of predicted prevalence were developed in geographic information system (GIS).

Results

Predicted high prevalence areas were located along the north-eastern areas, and central part of the study area. Low to moderate prevalence areas were predicted in the southwestern, southeastern and central regions. Individual age and nearness to fragmented forest were associated with malaria prevalence after adjusting the spatial auto-correlation.

Conclusion

A Bayesian analytical approach using multiple enabling technologies (geographic information systems, global positioning systems, and remote sensing) provide a strategy to characterize spatial heterogeneity in malaria risk at a fine scale. Even in the most hyper endemic region of Bangladesh there is substantial spatial heterogeneity in risk. Areas that are predicted to be at high risk, based on the environment but that have not been reached by surveys are identified.

     

One-step fractionation of complex proteomes enables detection of low abundant analytes using antibody-based microarrays

Antibody-based microarray is a novel technology with great promise within high-throughput proteomics. The tremendous complexity of all proteomes will, however, pose major technological challenges, especially when targeting low-abundant analytes that remains to be resolved. In this paper, we have shown that antibody microarrays readily could be used for screening of low-abundant low molecular weight analytes in complex proteomes by optimizing the sample format. Focused antibody microarrays, based on human recombinant single-chain Fv anti-cytokine antibodies on Ni2+-NTA functionalized glass slides or black polymer Maxisorp substrates, and crude cell supernatants from activated dendritic cells, containing low levels of secreted cytokines, was used for evaluation. The proteome was pre-fractionated based on size in a simple one-step procedure using centrifugal filter devices of various molecular weight cutoffs. The results showed that the generation of a nondiluted low molecular weight (LMW) fraction, corresponding to less than 2% of the original protein content, was critical for the successful screening of cytokines in the sub pg/mL range. The reduced complexity of the LMW fraction significantly improved the assay sensitivity, by improving the fluorescent tagging step and/or reducing the nonspecific binding to the substrates.