Multiomic Metabolic Enrichment Network Analysis Reveals Metabolite–Protein Physical Interaction Subnetworks Altered in Cancer

Metabolism is recognized as an important driver of cancer progression and other complex diseases, but global metabolite profiling remains a challenge. Protein expression profiling is often a poor proxy since existing pathway enrichment models provide an incomplete mapping between the proteome and metabolism. To overcome these gaps, we introduce multiomic metabolic enrichment network analysis (MOMENTA), an integrative multiomic data analysis framework for more accurately deducing metabolic pathway changes from proteomics data alone in a gene set analysis context by leveraging protein interaction networks to extend annotated metabolic models. We apply MOMENTA to proteomic data from diverse cancer cell lines and human tumors to demonstrate its utility at revealing variation in metabolic pathway activity across cancer types, which we verify using independent metabolomics measurements. The novel metabolic networks we uncover in breast cancer and other tumors are linked to clinical outcomes, underscoring the pathophysiological relevance of the findings.     

Highly specialized Cretaceous beetle parasitoids (Ripiphoridae) identified with optimized visualization of microstructures

Extremely miniaturized longipedes insects (body length c. 0.3 mm) embedded in two pieces of Cretaceous amber from Myanmar are described and interpreted. Using inverted fluorescence and light microscopy for detailed analysis of microstructures, the inclusions were identified as primary larvae of the beetle family Ripiphoridae, subfamily Ripidiinae. While the structure of thoracic and abdominal segments including appendages corresponds well with the groundplan known in recent members of Ripidiinae, a curved prosternal ridge with prominent spines (each c. 5 μm), the reduced condition of stemmata and antennae and the lack of sharp mandibles are unique features within the entire family, apparently apomorphies of the longipedes larvae. A sinuate prosternal edge with a dense row of spines (prosternoctenidium) might be homologous with ‘head ctenidia’ in some previously described miniaturized conicocephalate larvae, but further investigation is needed. The morphological differences between the head of longipedes larvae and extant Ripidiinae are interpreted as adaptations to different groups of hosts and life strategies. Palaeoethology of the longipedes larvae is briefly discussed. In addition, the systematic placement of conicocephalate larvae from Canadian, Myanmar and Russian Cretaceous ambers, already interpreted by various authors as primary instars within Coleopterida (assigned to either Strepsiptera or to the coleopteran Tenebrionoidea: Ripiphoridae), is discussed.     

Expression of mouse metallothionein-I gene confers cadmium resistance in transgenic tobacco plants

Transgenic tobacco plants containing a mouse metallothionein-I (MT-I) gene fused to the cauliflower mosaic virus 35S (CaMV 35S) promoter and nopaline synthase (nos) polyadenylation site were obtained by transforming tobacco leaf discs with an Agrobacterium tumefaciens strain carrying the chimaeric gene. Transformants were directly selected and rooted on medium containing cadmium and kanamycin. A total of 49 individual transgenic tobacco plants were regenerated. Among them 20% showed a very high expression level and their growth was unaffected by up to 200 M cadmium, whereas the growth of control plants was severely affected leaf chlorosis occurred on medium containing only 10 M cadmium. The concentration of MT-I in leaves of control and transgenic tobacco was determined with Cd/haemoglobin saturation assay, a polarographic method and western blotting. In addition, seeds from self-fertilized transgenic plants were germinated on medium containing toxic levels of cadmium and scored for tolerance/susceptibility to this heavy metal. The ratio of tolerant to susceptible plants was 3:1 indicating that the metallothionein gene is inherited as a single locus.     

金属螯合亲和层析纯化金属硫蛋白

将二价铜离子螯合在Chelating Sepharose Fast Flow凝胶上制成亲和层析柱,锌诱导兔肝和镉诱导小鼠肝经匀浆、乙醇处理后上柱,用pH4.0的醋酸盐缓冲液平衡,再用pH5.2不同浓度的醋酸盐缓冲液分别洗脱,可得两个金属硫蛋白(MT)洗脱峰,经确定先后为MT-2和MT-1.分离方法比传统的凝胶过滤-离子交换法简单、省时,适于实验室规模分离纯化.     

α-Domain of human metallothionein IA can bind to metals in transgenic tobacco plants

We have introduced a genetically marked Dissociation transposable element (Ds ^HPT ) into tomato (Lycopersicon esculentum) by Agrobacterium tumefaciens-mediated transformation. Probes for the flanking regions of the T-DNA and transposed Ds ^HPT elements were obtained with the inverse polymerase chain reaction (IPCR) technique and used in RFLP linkage analyses. The RFLP map location of 11 T-DNAs carrying Ds ^HPT was determined. The T-DNAs are distributed on 7 of the 12 tomato chromosomes. To explore the feasibility of gene tagging strategies in tomato using Ds ^HPT , we examined the genomic distribution of Ds ^HPT receptor sites relative to the location of two different, but very closely linked, T-DNA insertion sites. After crosses with plants expressing Ac transposase, the hygromycin phosphotransferase (HPT) marker on the Ds element and the excision markers β-glucuronidase (GUS) and Basta resistance (BAR) facilitated the identification of plants bearing germinally transposed Ds ^HPT elements. RFLP mapping of 21 transposed Ds ^HPT elements originating from the two different T-DNA insertions revealed distinct patterns of reintegration sites.     

尕海湿地草甸土退化过程土壤氮矿化演变特征

氮矿化是生态系统循环的重要环节之一,影响着生态系统功能和氮素生物地球化学循环,因此研究高寒湿地退化过程中土壤氮矿化演变特征,对揭示气候变化和人为活动干扰背景下的湿地土壤氮素循环过程具有重要意义。以尕海湿地4种不同退化梯度(未退化、轻度退化、中度退化、重度退化)土壤为研究对象,采用野外树脂芯原位培养方法,通过对植物生长季不同生长阶段(生长初期、生长盛期、枯萎期)土壤氮素矿化作用研究,分析湿地退化演替过程中土壤氮矿化时空变化特征及其与土壤环境因子和酶活性之间的关系。结果表明：尕海湿地退化对土壤氮矿化过程有显著抑制作用,与未退化(0.143 mg kg^-1 d^-1)相比,轻度退化、中度退化、重度退化的土壤净氮矿化速率分别减小了0.018 mg kg^-1 d^-1、0.025 mg kg^-1 d^-1、0.020 mg kg^-1 d^-1;随着退化程度加剧,土壤净氨化速率逐渐减小或者不变,而净硝化速率却增大。随时间推移,各退化...     

A meta-analysis on morphological,physiological and biochemical responses of plants with PGPR inoculation under drought stress

Plant growth-promoting rhizobacteria (PGPR) can help plants to resist drought stress. However, the mechanisms of how PGPR inoculation affect plant status under drought remain incompletely understood. We performed a meta-analysis of plant response to PGPR inoculation by compiling data from 57 PGPR-inoculation studies, including 2, 387 paired observations on morphological, physiological and biochemical parameters under drought and well-watered conditions. We compare the PGPR effect on plants performances among different groups of controls and treatments. Our results reveal that PGPR enables plants to restore themselves from drought-stressed to near a well-watered state, and that C4 plants recover better from drought stress than C3 plants. Furthermore, PGPR is more effective underdrought than well-watered conditions in increasing plant biomass, enhancing photosynthesis and inhibiting oxidant damage, and the responses of C4 plants to the PGPR effect was stronger than that of C3 plants under drought conditions. Additionally, PGPR belonging to different taxa and PGPR with different functional traits have varying degrees of drought-resistance effects on plants. These results are important to improve our understanding of the PGPR beneficial effects on enhanced drought-resistance of plants.     

Comparative Transcriptome Analyses Reveal Genes Related to Spine Development in Cucumber (<i>Cucumis sativus</i>)

Fruit spine is an important quality trait of cucumber. To better understand the molecular basis of cucumber spine development and function, RNA-Seq was performed to identify differentially expressed genes (DEGs) in fruit spines of different development stages, namely, 8 days before anthesis (SpBA8), anthesis (SpA) and 8 days after anthesis (SpAA8). Stage-wise comparisons obtained 2,259 (SpBA8 vs. SpA), 4,551 (SpA vs. SpAA8), and 5,290 (SpBA8 vs. SpAA8) DEGs. All the DEGs were classified into eight expression clusters by trend analysis. Among these DEGs, in addition to the Mict, Tril, CsTTG1, CsMYB6, NS, and Tu genes that have been reported to regulate fruit spine formation, we found that the CsHDG11, CsSCL8, CsSPL8, CsZFP6 and CsZFP8 may also be involved in spine development in cucumber. Our study provides a theoretical basis for further research on molecular mechanisms of spine development in cucumber.     

通过和玉米杂交诱导硬粒小麦单倍体

硬粒小麦（Ｔｒｉｔｉｃｕｍ ｄｕｒｕｍ Ｄｅｓｆ．）ＤＲ１４７授以超甜玉米（Ｚｅａ ｍ ａｙｓ Ｌ．） ｓｓ ７７００的花粉后,在８３．４％ 的柱头上观察到花粉萌发及花粉管长入胚囊,有９．９％ 的子房发生了卵细胞的单受精,１．９％ 的子房发生了中央细胞的单受精,３２．７％ 的子房发生了双受精。尽管双受精后可同时形成胚和胚乳,但胚乳往往发育迟缓,甚至败育。硬粒小麦×玉米形成的杂合子核型高度不稳定,在最初的几次细胞分裂中,来自父本玉米的染色体逐步被排除,最后形成硬粒小麦单倍体胚。在授以玉米花粉４ ｈ 后用１００ ｐｐｍ ２,４－Ｄ溶液浸蘸硬粒小麦穗部,可以有效地促进幼胚在缺乏胚乳或胚乳败育情况下的生长和发育。授粉９—１３ ｄ 后由５３３个硬粒小麦子房解剖出２５个胚,得胚率为４．７％ 。通过幼胚拯救获得１１棵正常植株,植株获得率为２．１％ 。根尖细胞染色体计数表明,它们为单倍体（２ｎ＝ ２ｘ＝ １４）。