Three-way interaction model with switching mechanism as an effective strategy for tracing functionally-related genes

Introduction: Identification of functionally-related genes is an important step in understanding biological systems. The most popular strategy to infer functional dependence is to study pairwise correlations between gene expression levels. However, certain functionally-related genes may have a low expression correlation due to their nonlinear interactions. The use of a three-way interaction (3WI) model with switching mechanism (SM) is a relatively new strategy to trace functionally-related genes. The 3WI model traces the dynamic and nonlinear nature of the co-expression relationship of two genes by introducing their link to the expression level of a third gene.

Areas covered: In this paper, we reviewed a variety of existing methods for tracing the 3WIs. Furthermore, we provide a comprehensive review of the previous biological studies based on 3WI models.

Expert commentary: Comparison of features of these methods indicates that the modified liquid association algorithm has the best efficiency for tracing 3WI between others. The limited number of biological studies based on the 3WI suggests that high computational demand of the available algorithms is a major challenge to apply this approach for analyzing high-throughput omics data.     

One‐Step In Situ Formation of N‐doped Carbon Nanosheet 3D Porous Networks/TiO2 Hybrids with Ultrafast Sodium Storage

In spite of the satisfactory advancement in preparing TiO₂‐based hybrid structures, most methods rely on additional template‐based multistep reactions for engineering the given structure. Herein, a unique self‐template and in situ recrystallization strategy is explored to synthesize uniform flowerlike multicompositional structures of nitrogen‐doped porous carbon nanosheet networks immobilizing TiO₂ nanoparticles (TiO₂∩NPCSs) via a self‐prepared single precursor and subsequent thermal treatment. Depending on the unique coordination ability of 2,4‐dihydroxybenzoic acid with metal ions under alkaline conditions to form a flowerlike network, a self‐produced single precursor can be achieved. Careful investigations of the self‐prepared precursor reveal a high practicability of the present synthetic scheme. Because of the novel structural and compositional features, these TiO₂∩NCSN flowers indicate superior sodium storage properties when evaluated as anodes for sodium‐ion batteries. Impressively, the TiO₂∩NCSN flowers deliver high reversible capacities of 152 mAh g^?1 at 2C for 3000 cycles and 114 mAh g^?1 at 10C for 10000 cycles, as well as an ultrahigh rate capability up to 50C with a capacity of 101 mAh g^?1. The facile method could stimulate further capability in precise construction of complex architectures with complicated compositions for different device applications.     

超快速反应聚合物光纤氧测定装置及其用于活体动物机械通气下动脉血氧分压连续动态变化的初步实验报告*

目的: 我们在中国尝试使用超快反应聚合物光纤氧感受器置入整体活体动物动脉血管,再通过光电转换测定系统以记录活体动物颈动脉PO₂（PaO₂）连续动态的快速变化,为完善整体整合生理学理论体系中循环参与呼吸调控和呼吸循环代谢一体化调控提供实验依据。方法: ①超快反应氧感受器制作、性能及其测定系统标定：在实验室加热总长2 m光纤的远端5 mm部分,拉动直到它成锥形尖端,清洁并干燥后,将1 mm锥形光纤尖端浸涂到发光体掺杂聚合物溶液中,在溶剂快速蒸发同时将其缓慢抽出来形成氧气感测尖端,室温干燥24 h。对完成制作的感受器进行性能标定,并于第37日重复标定。②动物实验：在潍坊医学院实验室对山羊全麻气管插管氧气机械通气下,切皮暴露双颈动脉和左侧股动脉,分别把超快反应氧传感器直接插入动脉中,通过光导纤维、激发与检测Y型光纤耦合器经光电转换连接到个人电脑,实现机械通气下活体山羊颈动脉PaO₂的连续动态反应,主要分析PaO₂的呼吸间波浪式交替升降和肺-颈动脉时间延迟。结果: 该置入式超快反应氧传感器在液相的响应时间为100 ms。活体山羊实验40%~60%氧气机械通气心率和血压稳定,左和右颈动脉PaO₂随着呼吸机的吸气和呼气呈现波浪式上升和下降的呼吸交替现象,幅度高达15 mmHg;左侧股动脉位置记录的信息噪音显著干扰PaO₂变化。肺-颈动脉时间延迟是在吸气和呼气开始后1.5~1.7 s左侧和右侧颈动脉PaO₂都开始上升和下降;即肺通气开始后3次心跳,左心室可把肺毛细血管后动脉化的肺静脉血液送到外周化学感受器位置中断吸气切换为呼气和中断呼气切换为吸气,如此实现吸呼周而复始。结论: 活体动物置入动脉的超快反应氧传感器及其测定系统可测定PaO₂生理性波浪式变化,能为整体整合生理学医学新理论体系中解释吸气和呼气相互切换的机制提供实验依据。     

Array CGH analysis of a cohort of Russian patients with intellectual disability

The use of array comparative genomic hybridization (array CGH) as a diagnostic tool in molecular genetics has facilitated the identification of many new microdeletion/microduplication syndromes (MMSs). Furthermore, this method has allowed for the identification of copy number variations (CNVs) whose pathogenic role has yet to be uncovered. Here, we report on our application of array CGH for the identification of pathogenic CNVs in 79 Russian children with intellectual disability (ID). Twenty-six pathogenic or likely pathogenic changes in copy number were detected in 22 patients (28%): 8 CNVs corresponded to known MMSs, and 17 were not associated with previously described syndromes. In this report, we describe our findings and comment on genes potentially associated with ID that are located within the CNV regions.     

DNA bending facilitates the error‐free DNA damage tolerance pathway and upholds genome integrity

DNA replication is sensitive to damage in the template. To bypass lesions and complete replication, cells activate recombination‐mediated (error‐free) and translesion synthesis‐mediated (error‐prone) DNA damage tolerance pathways. Crucial for error‐free DNA damage tolerance is template switching, which depends on the formation and resolution of damage‐bypass intermediates consisting of sister chromatid junctions. Here we show that a chromatin architectural pathway involving the high mobility group box protein Hmo1 channels replication‐associated lesions into the error‐free DNA damage tolerance pathway mediated by Rad5 and PCNA polyubiquitylation, while preventing mutagenic bypass and toxic recombination. In the process of template switching, Hmo1 also promotes sister chromatid junction formation predominantly during replication. Its C‐terminal tail, implicated in chromatin bending, facilitates the formation of catenations/hemicatenations and mediates the roles of Hmo1 in DNA damage tolerance pathway choice and sister chromatid junction formation. Together, the results suggest that replication‐associated topological changes involving the molecular DNA bender, Hmo1, set the stage for dedicated repair reactions that limit errors during replication and impact on genome stability.     

Partner switching can favour cooperation in a biological market

Intraspecific cooperation and interspecific mutualisms can be promoted by mechanisms that reduce the frequency with which cooperative organisms are exploited by unhelpful partners. One such mechanism consists of changing partners after interacting with an uncooperative individual. I used McNamara et al.'s (Nature, 451, 2008, 189) partner switching model as a framework to examine whether this mechanism can select for increased cooperative investment by house sparrows (Passer domesticus) collaborating to rear offspring; previous research on this species has shown that substantial cooperative investments by both pair members are required to achieve high pay‐offs from collaborating. I found that the poorer the outcome of a breeding attempt relative to the number of eggs the female invested, the greater the likelihood of partner switching. The incidence of partner switching changed seasonally, with peak switching coinciding with an increase in the number of alternative partners available to females. After females switched partners, their breeding outcomes rose to match those of females that remained with the same partner; this was not the case for males that switched partners. Consistent with the model's prediction, males in stable partnerships achieved over 25% higher than average reproductive success, which was attributable to both persistently good breeding outcomes and their older partners' high fecundity. These results provide empirical support for the hypothesis that partner switching favours increased cooperative investment levels, and they demonstrate that variation in the relative value of by‐product benefits can enhance that process.     

超声波辅助抽提法在孔雀石绿分子印迹固相萃取中的应用

采用沉淀聚合法制备孔雀石绿分子印迹聚合物(MG-MIPs),以洗脱效率及吸附量为指标,考察超声波辅助抽提法对MIPs中MG洗脱效果及吸附性能的影响,通过扫描电镜观察MIPs的表面形态,并对其吸附性能进行研究。结果表明:模板分子MG在超声30 min、超声10次、料液比m(MG-MIPs)∶V(甲醇-乙酸溶液)为1∶10(g/m L)、温度为25℃、超声功率为270 W的条件下,洗脱效果最好,MIPs在固相萃取柱中的吸附效率较高,达到198μg/g。     

Ngadju kala: Australian Aboriginal fire knowledge in the Great Western Woodlands

Indigenous fire knowledge offers significant benefits for ecosystem management and human livelihoods, but is threatened worldwide because of disruption of customary practices. In Australia, the historical prevalence and characteristics of Aboriginal burning are intensely debated, including arguments that Aboriginal burning was frequent across the continent. Frequent burning is supported by contemporary Aboriginal knowledge and practice in some regions, but in southern Australia evidence is typically limited to historical and ecological records. Towards characterizing Aboriginal fire regimes in southern Australia, we collaborated with Ngadju people from the globally significant Great Western Woodlands in south‐western Australia to document their fire knowledge. We used workshops, site visits, interviews and occupation mapping to aid knowledge sharing. Consistent with the established significance of Aboriginal fire in Australia, planned fires were important in Ngadju daily life and land management. However, Ngadju use of fire was characterized by its selectivity rather than its ubiquity. Specifically, Ngadju described only highly targeted planned burning across extensive eucalypt woodlands and sandplain shrublands. By contrast, frequent planned burning was described for resource‐rich landscape elements of more restricted extent (granite outcrop vegetation, grasslands and coastal scrub). Overall, Ngadju fires are likely to have resulted in subtle but purposeful direct effects on the vegetation and biota. However the extent to which they collectively constrained large, intense wildfires remains unclear. Ngadju demonstrated a predictive knowledge of the ecological consequences of burning, including attention to fine‐scale needs of target organisms, and application of diverse fire regimes. These are consistent with the recently proposed concept that Aboriginal burning was guided by ‘templates’ targeting different resources, although diverse regimes predominantly reflect edaphically driven vegetation patterns rather than template‐driven use of fire to create resource diversity. We conclude that Ngadju fire knowledge fills an important gap in understanding Aboriginal fire regimes in southern Australia, highlighting a novel balance between frequent and constrained use of fire.     

TGF‐β1 improves mucosal IgA dysfunction and dysbiosis following intestinal ischaemia–reperfusion in mice

Intestinal ischaemia/reperfusion (I/R) severely disrupts gut barriers and leads to high mortality in the critical care setting. Transforming growth factor (TGF)‐β1 plays a pivotal role in intestinal cellular and immune regulation. However, the effects of TGF‐β1 on intestinal I/R injury remain unclear. Thus, we aimed to investigate the effects of TGF‐β1 on gut barriers after intestinal I/R and the molecular mechanisms. Intestinal I/R model was produced in mice by clamping the superior mesenteric artery for 1 hr followed by reperfusion. Recombinant TGF‐β1 was intravenously infused at 15 min. before ischaemia. The results showed that within 2 hrs after reperfusion, intestinal I/R disturbed intestinal immunoglobulin A class switch recombination (IgA CSR), the key process of mucosal IgA synthesis, and resulted in IgA dysfunction, as evidenced by decreased production and bacteria‐binding capacity of IgA. Meanwhile, the disruptions of intestinal microflora and mucosal structure were exhibited. Transforming growth factor‐β1 activated IgA CSR as evidenced by the increased activation molecules and IgA precursors. Strikingly, TGF‐β1 improved intestinal mucosal IgA dysfunction, dysbiosis and epithelial damage at the early stage after reperfusion. In addition, SB‐431542, a specific inhibitor of activating mothers against decapentaplegic homologue (SMAD) 2/3, totally blocked the inductive effect of TGF‐β1 on IgA CSR and almost abrogated the above protective effects on intestinal barriers. Taken together, our study demonstrates that TGF‐β1 protects intestinal mucosal IgA immunity, microbiota and epithelial integrity against I/R injury mainly through TGF‐β receptor 1/SMAD 2/3 pathway. Induction of IgA CSR may be involved in the protection conferred by TGF‐β1.