The coupling hypothesis: why genome scans may fail to map local adaptation genes

Genomic scans of multiple populations often reveal marker loci with greatly increased differentiation between populations. Often this differentiation coincides in space with contrasts in ecological factors, forming a genetic-environment association (GEA). GEAs imply a role for local adaptation, and so it is tempting to conclude that the strongly differentiated markers are themselves under ecologically based divergent selection, or are closely linked to loci under such selection. Here, we highlight an alternative and neglected explanation: intrinsic (i.e. environment-independent) pre- or post-zygotic genetic incompatibilities rather than local adaptation can be responsible for increased differentiation. Intrinsic genetic incompatibilities create endogenous barriers to gene flow, also known as tension zones, whose location can shift over time. However, tension zones have a tendency to become trapped by, and therefore to coincide with, exogenous barriers due to ecological selection. This coupling of endogenous and exogenous barriers can occur easily in spatially subdivided populations, even if the loci involved are unlinked. The result is that local adaptation explains where genetic breaks are positioned, but not necessarily their existence, which can be best explained by endogenous incompatibilities. More precisely, we show that (i) the coupling of endogenous and exogenous barriers can easily occur even when ecological selection is weak; (ii) when environmental heterogeneity is fine-grained, GEAs can emerge at incompatibility loci, but only locally, in places where habitats and gene pools are sufficiently intermingled to maintain linkage disequilibria between genetic incompatibilities, local-adaptation genes and neutral loci. Furthermore, the association between the locally adapted and intrinsically incompatible alleles (i.e. the sign of linkage disequilibrium between endogenous and exogenous loci) is arbitrary and can form in either direction. Reviewing results from the literature, we find that many predictions of our model are supported, including endogenous genetic barriers that coincide with environmental boundaries, local GEA in mosaic hybrid zones, and inverted or modified GEAs at distant locations. We argue that endogenous genetic barriers are often more likely than local adaptation to explain the majority of Fst-outlying loci observed in genome scan approaches - even when these are correlated to environmental variables.     

Historical introgression and the role of selective vs. neutral processes in structuring nuclear genetic variation (AFLP) in a circumpolar marine fish, the capelin (Mallotus villosus)

The capelin (Mallotus villosus) is a widespread marine fish species for which previous work has identified geographically distinct mtDNA clades, the frontiers of which are well within adult and larval dispersal capabilities. Here, we use AFLPs to test for the presence of nuclear gene flow among clades. In addition, we evaluate genetic structuring within one clade, the Northwest Atlantic (NWA). We found that each of the mtDNA clades corresponds with a unique nuclear DNA genetic cluster. Within the NWA clade, we detected individuals with small but significant amounts of genetic ancestry from other clades, likely due to historical introgression. Further support for historical introgression comes from analyses of variance in locus-specific differentiation, which support introgression between some clades and divergence without gene flow between others. Within the NWA, we identified two genetic clusters that correspond to sites in geographically adjacent areas. However, these clusters differ primarily at 'outlier' loci, and a genetic subdivision (K=2) was not supported by genetic clustering programs using neutral loci. Significant neutral F(ST) differentiation was found only between sites that otherwise differed at outlier loci. Thus, these populations may be in the initial stages of 'isolation by adaptation'. These results suggest strong between-clade reproductive isolation despite opportunities for gene flow and support the hypothesis that selection can contribute to divergence in otherwise 'open' systems.     

Investigation of protein induction in tumour vascular targeted strategies by MALDI MSI

Characterising the protein signatures in tumours following vascular-targeted therapy will help determine both treatment response and resistance mechanisms. Here, mass spectrometry imaging and MS/MS with and without ion mobility separation have been used for this purpose in a mouse fibrosarcoma model following treatment with the tubulin-binding tumour vascular disrupting agent, combretastatin A-4-phosphate (CA-4-P). Characterisation of peptides after in situ tissue tryptic digestion was carried out using Matrix-Assisted Laser Desorption/Ionisation-Mass Spectrometry (MALDI-MS) and Matrix-Assisted Laser Desorption/Ionisation-Ion Mobility Separation-Mass Spectrometry Imaging (MALDI IMS-MSI) to observe the spatial distribution of peptides. Matrix-Assisted Laser Desorption/Ionisation-Ion Mobility Separation-Tandem Mass Spectrometry (MALDI-IMS-MS/MS) of peaks was performed to elucidate any pharmacological responses and potential biomarkers. By taking tumour samples at a number of time points after treatment gross changes in the tissue were indicated by changes in the signal levels of certain peptides. These were identified as arising from haemoglobin and indicated the disruption of the tumour vasculature. It was hoped that the use of PCA-DA would reveal more subtle changes taking place in the tumour samples however these are masked by the dominance of the changes in the haemoglobin signals.     

In vivo imaging of the airway wall in asthma: fibered confocal fluorescence microscopy in relation to histology and lung function

Background

Airway remodelling is a feature of asthma including fragmentation of elastic fibres observed in the superficial elastin network of the airway wall. Fibered confocal fluorescence microscopy (FCFM) is a new and non-invasive imaging technique performed during bronchoscopy that may visualize elastic fibres, as shown by in vitro spectral analysis of elastin powder. We hypothesized that FCFM images capture in vivo elastic fibre patterns within the airway wall and that such patterns correspond with airway histology. We aimed to establish the concordance between the bronchial elastic fibre pattern in histology and FCFM. Second, we examined whether elastic fibre patterns in histology and FCFM were different between asthmatic subjects and healthy controls. Finally, the association between these patterns and lung function parameters was investigated.

Methods

In a cross-sectional study comprising 16 subjects (8 atopic asthmatic patients with controlled disease and 8 healthy controls) spirometry and bronchoscopy were performed, with recording of FCFM images followed by endobronchial biopsy at the airway main carina. Elastic fibre patterns in histological sections and FCFM images were scored semi-quantitatively. Agreement between histology and FCFM was analysed using linearly weighted kappa κ_w.

Results

The patterns observed in histological sections and FCFM images could be divided into 3 distinct groups. There was good agreement between elastic fibre patterns in histology and FCFM patterns (κ_w 0.744). The semi-quantitative pattern scores were not different between asthmatic patients and controls. Notably, there was a significant difference in post-bronchodilator FEV₁ %predicted between the different patterns by histology (p = 0.001) and FCFM (p = 0.048), regardless of asthma or atopy.

Conclusion

FCFM captures the elastic fibre pattern within the airway wall in humans in vivo. The association between post-bronchodilator FEV₁ %predicted and both histological and FCFM elastic fibre patterns points towards a structure-function relationship between extracellular matrix in the airway wall and lung function.

Trial registration

Netherlands Trial Register NTR1306     

甲钴胺联合高能激光治疗带状疱疹疗效观察及护理体会

目的:探讨甲钴胺联合高能激光治疗带状疱疹疗效及护理方法。方法:自2008年1月至2010年3月入院的81例带状疱疹患者分为两组,治疗组予甲钴胺、单磷酸阿糖腺苷和高能激光联合治疗并配合精心护理,对照组仅予单磷酸阿糖腺苷治疗,两组均在治疗第10天时观察症状及体征的变化。患者出院后随访半年。结果:治疗组与对照组有效率分别为90.2%和56.4%,差异有统计学意义(P<0.05)。治疗组与对照组的止疱时间(1.4±1.1天vs2.6±1.3天)、结痂时间(5.4±1.4天vs8.1±1.5天)和止痛时间(3.0±1.6天vs 5.8±3.3天),以及治疗后两组患者直观模拟尺评分结果(2.95±1.45 vs 3.97±1.85)差异有统计学意义(P<0.05)。随访半年结果治疗组出现后遗神经痛较对照组少(P<0.05)。结论:甲钴胺联合高能激光治疗带状疱疹并配合精心护理有利于取得良好的临床治疗效果。     

激光微束在两种鱼受精卵上打孔技术研究

在埃及胡子鲶和苏氏芒鲶两种鱼受精卵上,用脉冲ＹＡＧ激光微束打孔技术,成功地导入了外源指示剂和用激光微束打过孔的受精卵孵化出了仔鱼,为今后激光微束打孔植入外源基因和针类转基因研究做了一些有意义的探索工作。     

激光照射茶树花药培养及其过氧化物酶同工酶的分析

Ｈｅ－Ｎｅ和ＣＯ２激光对茶树花药培养的药裂率和出愈率的影响,既有促进作用,也有抑制作用。按出愈率和愈伤组织生长状况的序列：Ｈｅ－Ｎｅ：２０Ｊ／ｃｍ＾２〉ＣＫ〉Ｈｅ－Ｎｅ：３０Ｊ／ｃｍ＾２〉ＣＯ２：３５．４Ｊ／ｃｍ＾２。对Ｈｅ－Ｎｅ激光照射花药及其愈伤组织的过氧化物酶同工酶分析,主要表现在弱酶带的变化上,无规律差异。     

Probability of detecting disease-associated single nucleotide polymorphisms in case-control genome-wide association studies

Some case-control genome-wide association studies (CCGWASs) select promising single nucleotide polymorphisms (SNPs) by ranking corresponding p-values, rather than by applying the same p-value threshold to each SNP. For such a study, we define the detection probability (DP) for a specific disease-associated SNP as the probability that the SNP will be "T-selected," namely have one of the top T largest chi-square values (or smallest p-values) for trend tests of association. The corresponding proportion positive (PP) is the fraction of selected SNPs that are true disease-associated SNPs. We study DP and PP analytically and via simulations, both for fixed and for random effects models of genetic risk, that allow for heterogeneity in genetic risk. DP increases with genetic effect size and case-control sample size and decreases with the number of nondisease-associated SNPs, mainly through the ratio of T to N, the total number of SNPs. We show that DP increases very slowly with T, and the increment in DP per unit increase in T declines rapidly with T. DP is also diminished if the number of true disease SNPs exceeds T. For a genetic odds ratio per minor disease allele of 1.2 or less, even a CCGWAS with 1000 cases and 1000 controls requires T to be impractically large to achieve an acceptable DP, leading to PP values so low as to make the study futile and misleading. We further calculate the sample size of the initial CCGWAS that is required to minimize the total cost of a research program that also includes follow-up studies to examine the T-selected SNPs. A large initial CCGWAS is desirable if genetic effects are small or if the cost of a follow-up study is large.     

Mapping of the interleukin-10/interleukin-10 receptor combining site.

The discontinuous interleukin-10(IL-10)/interleukin-10 receptor (IL-10R) combining site was mapped using sets of overlapping peptides derived from both binding partners bound to continuous cellulose membranes. Low affinity binding of single regions of the discontinuous contact sites on IL-10 and IL-10R could be identified due to (1) high peptide density on the membrane support, (2) incubation with high protein concentrations, (3) indirect immunodetection of the ligates after electrotransfer onto polyvinylene difluoride membranes, and (4) use of highly overlapping peptide scans of different length (6-mers and 15-mers). The single binding regions identified for each protein species are separated in the protein sequences, but form continuous areas on the surface of IL-10 (X-ray structure) and IL-10R (computer model). Furthermore, four epitopes of neutralizing anti-IL-10 and anti-IL-10R antibodies were mapped and overlap with these binding regions. Soluble peptides (15- to 19-mers) each spanning one of the three identified IL-10-derived receptor binding regions displayed no significant affinity to IL-10R as expected, whereas a peptide (35-mer) comprising two of these regions had considerably higher binding activity. The data are consistent with a previously published computer model of the IL-10/IL-10R complex. This approach should be generally applicable for the mapping of non-linear protein-protein contact sites.     

He-Ne激光对小麦属间杂交影响的研究

1988年以来,作者采用He-Ne激光辐照黑麦花粉与杂交相结合的新方法,对小麦属间杂交(普通小麦×黑麦)进行了研究,获得了较好的效应.试验采用随机区组排列,重复三次,单粒条播.辐照方法,采用He-Ne激光分别以100秒、200秒、300秒辐照三个黑麦品种的花粉,与普通小麦授粉,配制成9个(普通小麦×黑麦)属间杂交组合.所得结果,采用方差分析、新复极差测验法,测定了组合与对照组合相比的差异显著性,也测定了各组合间相互比较的差异显著性.激光辐照小麦属间杂交所获种子的结实率极显著高于对照,为113.52～341.60%.籽粒千粒重和饱满度均超过对照,分别为84.07～295.43%、30.30～127.27%,差异均极显著.L1代籽粒出苗率和植株成活率分别比对照提高58.18～83.06%、41.35～87.78%,差异达到极显著水平.He-Ne激光的诱变作用,在于促进了小麦属间杂交的可交配性,提高了杂交籽粒的结实率,改善了籽粒的饱满度,提高了籽粒的千粒重,因而促进了杂种种子的出苗率和成活率.并且,在L1代植株中均获得了染色体自然加倍的双二倍体即小黑麦种子.现已获得L1～L8代的小黑麦后代材料和稳定株系.高科技的激光诱变育种,为小麦属间杂交育种工作开辟了新的简便途径.