Phylogenetic revision of Agapophytinae subf.n. (Diptera: Therevidae) based on molecular and morphological evidence

Agapophytinae subf.n. is a highly diverse lineage of Australasian Therevidae, comprising eight described and two new genera: Agapophytus Guérin‐Méneville, Acupalpa Kröber, Acraspisa Kröber, Belonalys Kröber, Bonjeania Irwin & Lyneborg, Parapsilocephala Kröber, Acatopygia Kröber, Laxotela Winterton & Irwin, Pipinnipons gen.n. and Patanothrix gen.n. A genus‐level cladistic analysis of the subfamily was undertaken using sixty‐eight adult morphological characters and c. 1000 base pairs of the elongation factor‐1α (EF‐1α) protein coding gene. The morphological data partition produced three most parsimonious cladograms, whereas the molecular data partition gave a single most parsimonious cladogram, which did not match any of the cladograms found in the morphological analysis. The level of congruence between the data partitions was determined using the partition homogeneity test (HT_F) and Wilcoxon signed ranks test. Despite being significantly incongruent in at least one of the incongruence tests, the partitions were combined in a simultaneous analysis. The combined data yielded a single cladogram that was better supported than that of the individual partitions analysed separately. The relative contributions of the data partitions to support for individual nodes on the combined cladogram were investigated using Partitioned Bremer Support. The level of support for many nodes on the combined cladogram was non‐additive and often greater than the sum of support for the respective nodes on individual partitions. This synergistic interaction between incongruent data partitions indicates a common phylogenetic signal in both partitions. It also suggests that criteria for partition combination based solely on incongruence may be misleading. The phylogenetic relationships of the genera are discussed using the combined data. A key to genera of Agapophytinae is presented, with genera diagnosed and figured. Two new genera are described: Patanothrix with a new species (Pat. skevingtoni) and Pat. wilsoni (Mann) transferred from Parapsilocephala, and Pipinnipons with a new species (Pip. kroeberi). Pipinnipons fascipennis (Kröber) is transferred from Squamopygia Kröber and Pip. imitans (Mann) is transferred from Agapophytus. Agapophytus bicolor (Kröber) is transferred from Parapsilocephala. Agapophytus varipennis Mann is synonymised with Aga. queenslandi Kröber and Aga. flavicornis Mann is synonymised with Aga. pallidicornis (Kröber).     

Toward more comprehensive environmental impact assessments: interlinked global models of LCIA and IAM applicable to this century

The International Journal of Life Cycle Assessment - Despite the long-standing demand for research on dynamic lifecycle assessment (LCA) for policymaking, only a few studies have addressed this...     

Comprehensive landscape and interference of clonal haematopoiesis mutations for liquid biopsy: A Chinese pan-cancer cohort

Tumour-derived DNA found in the plasma of cancer patients provides the probability to detect somatic mutations from circulating cell-free DNA (cfDNA) in plasma samples. However, clonal hematopoiesis (CH) mutations affect the accuracy of liquid biopsy for cancer diagnosis and treatment. Here, we integrated landscape of CH mutations in 11,725 pan-cancer patients of Chinese and explored effects of CH on liquid biopsies in real-world. We first identified 5933 CHs based on panel sequencing of matched DNA of white blood cell and cfDNA on 301 genes for 5100 patients, in which CH number of patients had positive correlation with their diagnosis age. We observed that canonical genes related to CH, including DNMT3A, TET2, ASXL1, TP53, ATM, CHEK2 and SF3B1, were dominant in the Chinese cohort and 13.29% of CH mutations only appeared in the Chinese cohort compared with the Western cohort. Analysis of CH gene distribution bias indicated that CH tended to appear in genes with functions of tyrosine kinase regulation, PI3K-Akt signalling and TP53 activity, suggesting unfavourable effects of CH mutations in cancer patients. We further confirmed effect of driver genes carried by CH on somatic mutations in liquid biopsy of cancer patients. Forty-eight actionable somatic mutations in 17 driver genes were considered CH genes in 92 patients (1.80%) of the Chinese cohort, implying potential impacts of CH on clinical decision-making. Taken together, this study exhibits strong evidence that gene mutations from CH interfere accuracy of liquid biopsies using cfDNA in cancer diagnosis and treatment in real-world.     

Broadening the versatility of lentiviral vectors as a tool in nucleic acid research via genetic code expansion

With the aim of broadening the versatility of lentiviral vectors as a tool in nucleic acid research, we expanded the genetic code in the propagation of lentiviral vectors for site-specific incorporation of chemical moieties with unique properties. Through systematic exploration of the structure–function relationship of lentiviral VSVg envelope by site-specific mutagenesis and incorporation of residues displaying azide- and diazirine-moieties, the modifiable sites on the vector surface were identified, with most at the PH domain that neither affects the expression of envelope protein nor propagation or infectivity of the progeny virus. Furthermore, via the incorporation of such chemical moieties, a variety of fluorescence probes, ligands, PEG and other functional molecules are conjugated, orthogonally and stoichiometrically, to the lentiviral vector. Using this methodology, a facile platform is established that is useful for tracking virus movement, targeting gene delivery and detecting virus–host interactions. This study may provide a new direction for rational design of lentiviral vectors, with significant impact on both basic research and therapeutic applications.     

Ring1a/b polycomb proteins regulate the mesenchymal stem cell niche in continuously growing incisors

Rodent incisors are capable of growing continuously and the renewal of dental epithelium giving rise to enamel-forming ameloblasts and dental mesenchyme giving rise to dentin-forming odontoblasts and pulp cells is achieved by stem cells residing at their proximal ends. Although the dental epithelial stem cell niche (cervical loop) is well characterized, little is known about the dental mesenchymal stem cell niche. Ring1a/b are the core Polycomb repressive complex1 (PRC1) components that have recently also been found in a protein complex with BcoR (Bcl-6 interacting corepressor) and Fbxl10. During mouse incisor development, we found that genes encoding members of the PRC1 complex are strongly expressed in the incisor apical mesenchyme in an area that contains the cells with the highest proliferation rate in the tooth pulp, consistent with a location for transit amplifying cells. Analysis of Ring1a(-/-);Ring1b(cko/cko) mice showed that loss of Ring1a/b postnatally results in defective cervical loops and disturbances of enamel and dentin formation in continuously growing incisors. To further characterize the defect found in Ring1a(-/-);Ring1b(cko/cko) mice, we demonstrated that cell proliferation is dramatically reduced in the apical mesenchyme and cervical loop epithelium of Ring1a(-/-);Ring1b(cko/cko) incisors in comparison to Ring1a(-/-);Ring1b(fl/fl)cre- incisors. Fgf signaling and downstream targets that have been previously shown to be important in the maintenance of the dental epithelial stem cell compartment in the cervical loop are downregulated in Ring1a(-/-);Ring1b(cko/cko) incisors. In addition, expression of other genes of the PRC1 complex is also altered. We also identified an essential postnatal requirement for Ring1 proteins in molar root formation. These results show that the PRC1 complex regulates the transit amplifying cell compartment of the dental mesenchymal stem cell niche and cell differentiation in developing mouse incisors and is required for molar root formation.     

温敏核不育小麦可育花药和败育花药发育观察

对温敏核不育小麦百农不育系（Bainong sterility,BNS）的可育和不育花药结构进行对比观察。在减数分裂期、小孢子早期和小孢子晚期,可育花药与不育花药的结构相同。小孢子分裂形成二胞花粉后,可育花粉中随着大液泡的分解,细胞质内含物增加,其中出现一些颗粒状物质。不育花药中,小孢子也可分裂形成二胞花粉,但营养细胞的大液泡不分解,细胞质也不增加,最终花粉中的细胞质消失,花粉败育。该种温敏核不育小麦的花粉败育时间发生在二胞花粉早期,可能和其大液泡没有适时分解有关。花粉败育时间的确定为进一步深入研究该种雄性不育小麦的败育机制打下了基础。     

A multiple kernel density clustering algorithm for incomplete datasets in bioinformatics

Background

While there are a large number of bioinformatics datasets for clustering, many of them are incomplete, i.e., missing attribute values in some data samples needed by clustering algorithms. A variety of clustering algorithms have been proposed in the past years, but they usually are limited to cluster on the complete dataset. Besides, conventional clustering algorithms cannot obtain a trade-off between accuracy and efficiency of the clustering process since many essential parameters are determined by the human user’s experience.

Results

The paper proposes a Multiple Kernel Density Clustering algorithm for Incomplete datasets called MKDCI. The MKDCI algorithm consists of recovering missing attribute values of input data samples, learning an optimally combined kernel for clustering the input dataset, reducing dimensionality with the optimal kernel based on multiple basis kernels, detecting cluster centroids with the Isolation Forests method, assigning clusters with arbitrary shape and visualizing the results.

Conclusions

Extensive experiments on several well-known clustering datasets in bioinformatics field demonstrate the effectiveness of the proposed MKDCI algorithm. Compared with existing density clustering algorithms and parameter-free clustering algorithms, the proposed MKDCI algorithm tends to automatically produce clusters of better quality on the incomplete dataset in bioinformatics.

     

苹果园中凹唇壁蜂和紫壁蜂的生态位比较研究

本文对凹唇壁蜂Osmia excavata Alfken和紫壁蜂O.jacoti Cockerell的时间、空间、营养和筑巢生态位进行了研究。结果表明,在苹果园内人工释放和管理条件下,两种壁蜂在不同的资源序列上具有不同的生态位宽度、生态位重叠和不同程度的竞争关系。其中在营养上的竞争最为激烈,生态位重叠值和种间竞争系数分别高达0.9690和0.9994。日活动时间生态位竞争次之,其重叠值和种间竞争系数分别为0.7960和0.9350;时间生态位(季节)和空间生态位重叠值则分别为0.6500和0.6710,种间竞争系数为0.8213和0.8234;并且在人工巢管的选择上竞争性最小,生态位重叠值仅为0.4930,种间竞争系数为0.6052。凹唇壁蜂在营养生态位和时间生态位上较高的专一性均表现出其比紫壁蜂对苹果传粉作用更为显著。紫壁蜂在苹果开花后期的传粉作用较强。     

20‐HETE synthesis inhibition attenuates traumatic brain injury–induced mitochondrial dysfunction and neuronal apoptosis via the SIRT1/PGC‐1α pathway: A translational study

Objectives20‐hydroxyeicosatetraenoic acid (20‐HETE) is a metabolite of arachidonic acid catalysed by cytochrome P450 enzymes and plays an important role in cell death and proliferation. We hypothesized that 20‐HETE synthesis inhibition may have protective effects in traumatic brain injury (TBI) and investigated possible underlying molecular mechanisms.Materials and methodsNeurologic deficits, and lesion volume, reactive oxygen species (ROS) levels and cell death as assessed using immunofluorescence staining, transmission electron microscopy and Western blotting were used to determine post‐TBI effects of HET0016, an inhibitor of 20‐HETE synthesis, and their underlying mechanisms.ResultsThe level of 20‐HETE was found to be increased significantly after TBI in mice. 20‐HETE synthesis inhibition reduced neuronal apoptosis, ROS production and damage to mitochondrial structures after TBI. Mechanistically, HET0016 decreased the Drp1 level and increased the expression of Mfn1 and Mfn2 after TBI, indicating a reversal of the abnormal post‐TBI mitochondrial dynamics. HET0016 also promoted the restoration of SIRT1 and PGC‐1α in vivo, and a SIRT1 activator (SRT1720) reversed the downregulation of SIRT1 and PGC‐1α and the abnormal mitochondrial dynamics induced by 20‐HETE in vitro. Furthermore, plasma 20‐HETE levels were found to be higher in TBI patients with unfavourable neurological outcomes and were correlated with the GOS score.ConclusionsThe inhibition of 20‐HETE synthesis represents a novel strategy to mitigate TBI‐induced mitochondrial dysfunction and neuronal apoptosis by regulating the SIRT1/PGC‐1α pathway.