Combination of meta-analysis and graph clustering to identify prognostic markers of ESCC

Esophageal squamous cell carcinoma (ESCC) is one of the most malignant gastrointestinal cancers and occurs at a high frequency rate in China and other Asian countries. Recently, several molecular markers were identified for predicting ESCC. Notwithstanding, additional prognostic markers, with a clear understanding of their underlying roles, are still required. Through bioinformatics, a graph-clustering method by DPClus was used to detect co-expressed modules. The aim was to identify a set of discriminating genes that could be used for predicting ESCC through graph-clustering and GO-term analysis. The results showed that CXCL12, CYP2C9, TGM3, MAL, S100A9, EMP-1 and SPRR3 were highly associated with ESCC development. In our study, all their predicted roles were in line with previous reports, whereby the assumption that a combination of meta-analysis, graph-clustering and GO-term analysis is effective for both identifying differentially expressed genes, and reflecting on their functions in ESCC.     

Effect of epistasis and linkage on fixation probability in three-locus models: an ancestral recombination-selection graph approach

We study the probability of ultimate fixation of a single new mutant arising in an individual chosen at random at a locus linked to two other loci carrying previously arisen mutations. This is done using the Ancestral Recombination-Selection Graph (ARSG) in a finite population in the limit of a large population size, which is also known as the Ancestral Influence Graph (AIG). An analytical expansion of the fixation probability with respect to population-scaled recombination rates and selection intensities is obtained. The coefficients of the expansion are expressed in terms of the initial state of the population and the epistatic interactions among the selected loci. Under the assumption of weak selection at tightly linked loci, the sign of the leading term, which depends on the signs of epistasis and initial linkage disequilibrium, determines whether an increase in recombination rates increases the chance of ultimate fixation of the new mutant. If mutants are advantageous, this is the case when epistasis is positive or null and the initial linkage disequilibrium is negative, which is an expected state in a finite population under directional selection. Moreover, this is also the case for a neutral mutant modifier coding for higher recombination rates if the same conditions hold at the selected loci. Under the same conditions, deleterious mutants are disfavored for ultimate fixation and neutral modifiers for higher recombination rates still favored. The recombination rates between the modifier locus and the selected loci do not come into play in the leading terms of the approximation for the fixation probability, but they do in higher-order terms.     

Using Pareto optimality to explore the topology and dynamics of the human connectome

Graph theory has provided a key mathematical framework to analyse the architecture of human brain networks. This architecture embodies an inherently complex relationship between connection topology, the spatial arrangement of network elements, and the resulting network cost and functional performance. An exploration of these interacting factors and driving forces may reveal salient network features that are critically important for shaping and constraining the brain''s topological organization and its evolvability. Several studies have pointed to an economic balance between network cost and network efficiency with networks organized in an ‘economical’ small-world favouring high communication efficiency at a low wiring cost. In this study, we define and explore a network morphospace in order to characterize different aspects of communication efficiency in human brain networks. Using a multi-objective evolutionary approach that approximates a Pareto-optimal set within the morphospace, we investigate the capacity of anatomical brain networks to evolve towards topologies that exhibit optimal information processing features while preserving network cost. This approach allows us to investigate network topologies that emerge under specific selection pressures, thus providing some insight into the selectional forces that may have shaped the network architecture of existing human brains.     

A sublethal dose of thiamethoxam causes a reduction in xylem feeding by the bird cherry-oat aphid (Rhopalosiphum padi), which is associated with dehydration and reduced performance

The active ingestion of xylem sap by aphids is hypothesised to be an important mechanism for rehydration. When starved bird cherry-oat aphids (Rhopalosiphum padi) were allowed to feed on wheat (Triticum aestivum) treated with a sublethal dose of the xylem-mobile neonicotinoid thiamethoxam, analysis of feeding behaviours using the electrical penetration graph revealed a reduction in xylem feeding that was reversed on removal of the toxin. To test the importance of xylem-feeding behaviour as a rehydration mechanism, the effects of the sublethal dose of thiamethoxam on aphid water content, honeydew excretion, growth and fecundity were investigated. Body water contents of starved R. padi feeding on wheat treated with thiamethoxam were significantly reduced compared to aphids feeding on wheat treated with distilled water (74.5 ± 0.23 and 75.6 ± 0.18%, respectively). In addition, the sublethal dose of thiamethoxam had detrimental effects on aphid performance. At reproductive maturity, aphids that had been born on wheat treated with thiamethoxam were significantly smaller (as measured by body plan area; 1.07 ± 0.03 mm²), lighter (0.31 ± 0.04 mg) and less fecund (2.85 ± 0.36 nymphs/day) than aphids born on wheat treated with distilled water (1.87 ± 0.02 mm², 0.72 ± 0.03 mg, 11.28 ± 0.58 nymphs/day, respectively). Regardless of whether the observed impairment of xylem feeding is due to a neurotoxic or an antifeedant effect, these results have important implications for commercial crop protection as the behaviour-modifying effects of the sublethal dose of thiamethoxam may change the efficacy of this pesticide throughout the growing season.     

矿物油处理对马铃薯长管蚜定向和取食行为的影响（英文）

大田和实验室研究均表明矿物油的施用可有效降低蚜虫对非持久性病毒的传播。我们分别于矿物油喷施马铃薯植株24 h和7 d后,调查其对马铃薯长管蚜Macrosiphum euphorbiae行为的影响;采用暗室生测法调查了蚜虫对处理的植物挥发性化合物的反应;采用刺探电位技术（EPG）评价了矿物油处理对蚜虫取食行为的影响。结果表明：矿物油处理导致植物对寄主的引诱作用失效,这种效果至少持续24 h。矿物油处理马铃薯植株24 h和7 d后,蚜虫对处理植株的取食行为发生改变。开始记录至第1次刺探所需时间降低,但只在处理7 d后显著降低,提示矿物油处理有助于蚜虫口针的穿刺。然而,流涎阶段以及韧皮部汁液吸食阶段（摄食阶段）显著缩短。本研究中观察到的蚜虫行为的改变不能充分解释施用矿物油的大田中为什么出现7 d 的保护作用,因此可能还存在其他的机制。     

Role of host‐plant selection in resistance of wild Solanum species to Macrosiphum euphorbiae and Myzus persicae

Damage to potatoes by Macrosiphum euphorbiae (Thomas) and Myzus persicae (Sulzer) (both Hemiptera: Aphididae) can be controlled through plant resistance. We used ethological experiments and electric penetration graph (EPG) analysis to evaluate the role of host selection in the previously assessed resistance levels of Solanum accessions: Solanum circaeifolium Bitter subsp. capsicibaccatum (Cárdenas) (PI210036), S. chomatophilum Bitter (PI243340 and PI310990), S. okadae Hawkes & Hjert. (PI458367), S. oplocense Hawkes (PI473368), S. pinnatisectum Dunal (PI186553), S. polyadenium Greenm. (PI230463), S. tarijense Hawkes (PI414150), and S. trifidum Correll (PI255538), to M. euphorbiae and M. persicae. Through multivariate analysis, we grouped behavioural variables into factors, which we related to host selection behaviours, and then evaluated whether factors varied between each accession and the susceptible S. tuberosum. None of the factors obtained by ethological experiments differed among accessions. Four of six and three of five factors obtained through EPG varied among accessions for M. euphorbiae and M. persicae, respectively, and were used to suggest resistance characteristics. The resistance to M. persicae of both S. chomatophilum accessions was associated with pathway activity disturbance. Solanum tarijense and S. polyadenium resistance to M. persicae resulted from leaf surface characteristics, which may be trichomes. Solanum oplocense and S. trifidum resistance to M. euphorbiae resulted from the wound response system, whereas S. pinnatisectum resistance may stem from nutritionally unbalanced or toxic phloem sap. Solanum polyadenium resistance to M. euphorbiae was phloem‐based. Solanum circaeifolium ssp. capsicibaccatum resistance to M. persicae, and the resistance of PI243340 S. chomatophilum and S. tarijense to M. euphorbiae were not related to host selection and therefore were presumably due to physiologically active compounds.     

Mi‐mediated aphid resistance in tomato: tissue localization and impact on the feeding behavior of two potato aphid clones with differing levels of virulence

The Mi‐1.2 gene in tomato, Solanum lycopersicum L. (Solanaceae), confers resistance against several herbivores, including the potato aphid, Macrosiphum euphorbiae (Thomas) (Hemiptera: Sternorrhyncha: Aphididae) and the sweetpotato whitefly, Bemisia tabaci (Gennadius) (Hemiptera: Sternorrhyncha: Aleyrodidae). Previous studies on the tissue localization of resistance have given varying results; whitefly resistance was attributed to factors localized in the mesophyll or epidermis, whereas aphid resistance was attributed to factors localized in the phloem. Our study utilizes the direct current electrical penetration graph (DC‐EPG) technique to compare aphid feeding behavior on resistant (Mi‐1.2+) and susceptible (Mi‐1.2?) tomato plants. This study also compares the impact of resistance on the feeding behavior of two aphid clones that vary in their virulence, or their ability to survive and reproduce on resistant plants. Previous work had shown that the avirulent WU11 clone is almost completely inhibited by resistance, whereas the semi‐virulent WU12 clone can colonize resistant hosts. Here, DC‐EPG analysis shows that both aphid clones take longer to initiate cell sampling and to establish a confirmed sieve element phase on resistant plants than on susceptible hosts, and have shorter ingestion periods on resistant plants. However, the magnitude of these deterrent effects is far less for the semi‐virulent clone than for the avirulent aphids. In particular, the WU12 clone is less sensitive to factors that limit sieve element ingestion, showing shorter non‐probe duration and rapidly establishing sustained phloem ingestion on resistant plants when compared to the WU11 clone. We conclude that, in addition to previously described factors in the phloem that inhibit ingestion, Mi‐mediated aphid resistance also involves factors (possibly in the mesophyll and/or epidermis) that delay initiation of phloem salivation, and that act in the intercellular spaces to deter the first cell sampling. Furthermore, the relative effectiveness of these components of resistance differs among insect populations.     

Global architecture of metabolite distributions across species and its formation mechanisms

Living organisms produce metabolites of many types via metabolic reactions. Especially, flavonoids, a type of secondary metabolite, of plant species are interesting examples. Since plant species are believed to have specific flavonoids that were formed response to diverse environments, elucidation of the design principles of metabolite distributions across plant species is important for understanding metabolite diversity and plant evolution. In our previous study, we found heterogeneous connectivity in metabolite distribution, and proposed a simple model to explain the possible origin of heterogeneous connectivity. In this paper, we determine additional structural properties of metabolite distribution among families that are analogous analogy with plant–animal mutualistic networks: nested structure and modular structure. An earlier model representative of these structural properties in bipartite relationships was established on the basis of the traits of elements and external factors. However, we found that the architecture of metabolite distribution could be explained by simple evolutionary processes without trait-based mechanisms by comparing our model and the earlier model. Our model provided a better qualitative and quantitative prediction of nested and modular structures in addition to heterogeneous connectivity. This finding implies an alternative possible origin of these structural properties, and suggests the mechanisms underlying establishment metabolite distributions across plant species are simpler than expected.     

禾谷缢管蚜在三个小麦品种上取食行为的EPG比较

应用刺探电位图谱（EPG）技术对禾谷缢管蚜Rhopalosiphum padi在不同小麦品种(Ww2730、小偃22和Batis)苗期的取食行为进行了比较研究。结果表明：在小偃22上蚜虫开始取食的第1次刺探时间最晚,且持续时间最短;在Ww2730上取食受到机械阻力的个体最多,且出现F波的几率和持续时间最长;两品种上蚜虫在木质部主动摄取汁液（G波）花费的时间最长。 在Batis上,蚜虫口针第1次到达韧皮部时需要分泌较多水溶性唾液(E1波),但随后只需分泌较少的水溶性唾液就可以成功取食,而且被动吸食韧皮部汁液的时间（E2波）最长。蚜虫口针在到达小偃22韧皮部取食之前,出现多次的口针试探、回撤,并且多次、多量分泌水溶性唾液（E1波）;虽然蚜虫在小偃22上口针最先到达韧皮部,但被动吸食韧皮部汁液的时间（E2波）最短。由此得出结论：小偃22表皮部、韧皮部存在阻碍禾谷缢管蚜取食的物理和生化因素; 禾谷缢管蚜在Ww2730取食遇到更多的是细胞间机械阻力; Batis是较感蚜的品种。