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.     

Real Time Measures of Prestin Charge and Fluorescence during Plasma Membrane Trafficking Reveal Sub-Tetrameric Activity

Prestin (SLC26a5) is the outer hair cell integral membrane motor protein that drives cochlear amplification, and has been described as an obligate tetramer. We studied in real time the delivery of YFP-prestin to the plasma membrane of cells from a tetracycline-inducible cell line. Following the release of temperature block to reinstate trans Golgi network delivery of the integral membrane protein, we measured nonlinear capacitance (NLC) and membrane fluorescence during voltage clamp. Prestin was delivered exponentially to the plasma membrane with a time constant of less than 10 minutes, with both electrical and fluorescence methods showing high temporal correlation. However, based on disparity between estimates of prestin density derived from either fluorescence or NLC, we conclude that sub-tetrameric forms of prestin contribute to our electrical and fluorescence measures. Thus, in agreement with previous observations we find that functional prestin is not an obligate tetramer.     

主养青鱼池塘生态系统能量转换率的研究

1985—1987年对苏州市郊区主养青鱼池塘生态系统的能量转换率进行了分析。结果表明,主养青鱼净产7.5、11.25、15t/ha 3个产量级型池塘青鲤团头鲂产出能占养鱼总产出能的比例分别为82.49、78.03、79.34％;总投入能(太阳辐射能+辅助能)转移到鱼的总产出能转换率分别为0.19、0.24、0.31％;太阳辐射能转移到毛和净初级生产力的能量转换率分别为0.76、0.90、0.96％和0.61、0.72、0.77％;净初级生产力转移到滤食性鱼净产量的能量转换率分别为4.02、4.63、5.27％;辅助能转移到鱼净产量的能量转换率分别为12.20、11.33。11.74％。在3个产量级型池塘中,以15t/ha产量级的能量转换率为最佳型。     

皖南、赣北奥陶纪笔石立体标本形成环境的初步研究*

皖南、赣东北和赣西北地区奥陶纪笔石地层发育良好,笔石化石丰富。宁国组和胡乐组均为笔石相地层,但笔石的保存特点并不相同。立体保存的黄铁矿化笔石标本主要见于宁国组,而胡乐组的笔石几乎均为薄膜标本。在比较宁国组和胡乐组在岩性、颜色、化石、矿物和元素等方面的特点后发现,两者有较明显的差异。这表明宁国组和胡乐组形成时的环境是不同的,前者为弱还原环境,后者为较强的还原环境,而在研究区内影响笔石体立体保存的主要因素为还原环境和较高的铁含量。在还原环境下,铁可呈Fe~(2+)存在,笔石体内含有硫,死亡后经降解作用可生成H_2S;H_2S和Fe~(2+)结合可使笔石体黄铁矿化,从而使笔石体硬化而呈立体保存下来。宁国组的铁含量明显高于胡乐组,这似可以解释宁国组产有较多笔石立体标本的原因。     

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.     

声学指数在城市森林鸟类多样性评估中的应用

鸣声是鸟类之间进行沟通和传递信息的重要方式,这为通过声学监测评估鸟类多样性提供了独特的机会。利用声学指数快速评估生物多样性是一种新兴的调查方法,但城市森林中的复杂声环境可能会导致声学指数的指示结果出现偏差。为了解声学指数在城市森林中应用的可行性,本研究在北京市东郊森林公园设置了50个矩阵式调查样点,于2021年4–6月每月进行1次鸟类传统观测和同步鸣声采集,通过比较两种方法的结果来探究声学监测的有效性。采用Spearman相关分析和广义线性混合模型评估6个常用声学指数与鸟类丰富度和多度的关系,并衡量了每个指数的性能。结果表明:(1)本研究共记录到鸟类10目23科35种,通过声学监听识别的总物种数与传统鸟类观测相等,但具体鸟种存在差异;(2)不同月份间声学指数与鸟类丰富度和多度的相关性有明显差别,声学复杂度指数(ACI)和标准化声景差异指数(NDSI)优于其他指数,是评估鸟类多样性的关键变量;(3)声学指数对鸟类多度的预测能力(R²m=0.32,R2c=0.80)要高于丰富度(R²m=0.12,R2c=0.18)。声学指数为快速评估生物多样性提...     

High-resolution mapping of the S and Z loci of Phalaris coerulescens.

Self incompatibility (SI) in Phalaris coerulescens is gametophytically determined by two unlinked multi allelic loci (S and Z). Neither the S nor Z genes have yet been cloned. As part of a map-based cloning strategy, high-resolution maps of the S and Z regions were generated from distorted segregating populations using RFLP probes from wheat, barley, oat, and Phalaris. The S locus was delimited to 0.26 cM with two boundary markers (Xwg811 and Xpsr168) and cosegregated with Xbm2 and Xbcd762. Xbcd266 was the closest marker linked to Z (0.9 cM). A high level of colinearity in the S and Z regions was found in both self-incompatible and -compatible species. The S locus was localized to the subcentromere region of chromosome 1 and the Z locus to the long arm end of chromosome 2. Several rice BAC clones orthologous to the S and Z locus regions were identified. This opens the possibility of using the rice genome sequence data to generate more closely linked markers and identify SI candidate genes. These results add further support to the conservation of gene order in the S and Z regions of the grass genomes.     

Developmental control of xylem hydraulic resistances and vulnerability to embolism in Fraxinus excelsior L.: impacts on water relations

The freezing tolerance of many plants, such as pea (Pisum sativum),is increased by exposure to low temperature or abscisic acidtreatment, although the physiological basis of this phenomenonis poorly understood. The freezing tolerance of pea shoot tips,root tips, and epicotyl tissue was tested after cold acclimationat 2C, dehydration/rehydration, applications of 10^–4M abscisic acid (ABA), and deacclimation at 25C. Tests wereconducted using the cultivar ‘Alaska’, an ABA-deficientmutant ‘wil’, and its ‘wildtype’. Freezinginjury was determined graphically as the temperature that caused50% injury (T₅₀) from electrical conductivity. Endogenous ABAwas measured using an indirect enzyme-linked immunosorbant assay,and novel proteins were detected using 2-dimensional polyacrylamidegel electrophoresis. The maximum decrease in T₅₀ for root tissuewas 1C for all genotypes, regardless of treatment. For ‘Alaska’shoot tips and epicotyl tissue, exogenous ABA increased thefreezing tolerance by –1.5 to –4.0C, while coldtreatment increased the freezing tolerance by –7.5 to–14.8C. Cold treatment increased the freezing toleranceof shoot tips by –9 and –15C for ‘wil’and ‘wild-type’, respectively. Cold acclimationincreased endogenous ABA concentrations in ‘Alaska’shoot tips and epicotyls 3- to 4-fold. Immunogold labeling increasednoticeably in the nucleus and cytoplasm of the epicotyl after7 d at 2C and was greatest after 30 d at the time of maximumfreezing tolerance and soluble ABA concentration. Cold treatmentinduced the production of seven, three, and two proteins inshoot, epicotyl, and root tissue of ‘Alaska’, respectively.In ‘Alaska’ shoot tissue, five out of seven novelproteins accumulated in response to both ABA and cold treatment.However, only a 24 kDa protein was produced in ‘wil’and ‘wild-type’ shoot and epicotyl tissues aftercold treatment. Abscisic acid and cold treatment additivelyincreased the freezing tolerance of pea epicotyl and shoot tissuesthrough apparently independent mechanisms that both resultedin the production of a 24 kDa protein. Key words: Pisum sativum, cold acclimation, immuno-localization