A novel ATM‐dependent checkpoint defect distinct from loss of function mutation promotes genomic instability in melanoma

Melanomas have high levels of genomic instability that can contribute to poor disease prognosis. Here, we report a novel defect of the ATM‐dependent cell cycle checkpoint in melanoma cell lines that promotes genomic instability. In defective cells, ATM signalling to CHK2 is intact, but the cells are unable to maintain the cell cycle arrest due to elevated PLK1 driving recovery from the arrest. Reducing PLK1 activity recovered the ATM‐dependent checkpoint arrest, and over‐expressing PLK1 was sufficient to overcome the checkpoint arrest and increase genomic instability. Loss of the ATM‐dependent checkpoint did not affect sensitivity to ionizing radiation demonstrating that this defect is distinct from ATM loss of function mutations. The checkpoint defective melanoma cell lines over‐express PLK1, and a significant proportion of melanomas have high levels of PLK1 over‐expression suggesting this defect is a common feature of melanomas. The inability of ATM to impose a cell cycle arrest in response to DNA damage increases genomic instability. This work also suggests that the ATM‐dependent checkpoint arrest is likely to be defective in a higher proportion of cancers than previously expected.     

Decoupled genomic elements and the evolution of partner quality in nitrogen‐fixing rhizobia

Understanding how mutualisms evolve in response to a changing environment will be critical for predicting the long‐term impacts of global changes, such as increased N (nitrogen) deposition. Bacterial mutualists in particular might evolve quickly, thanks to short generation times and the potential for independent evolution of plasmids through recombination and/or HGT (horizontal gene transfer). In a previous work using the legume/rhizobia mutualism, we demonstrated that long‐term nitrogen fertilization caused the evolution of less‐mutualistic rhizobia. Here, we use our 63 previously isolated rhizobium strains in comparative phylogenetic and quantitative genetic analyses to determine the degree to which variation in partner quality is attributable to phylogenetic relationships among strains versus recent genetic changes in response to N fertilization. We find evidence of distinct evolutionary relationships between chromosomal and pSym genes, and broad similarity between pSym genes. We also find that nifD has a unique evolutionary history that explains much of the variation in partner quality, and suggest MoFe subunit interaction sites in the evolution of less‐mutualistic rhizobia. These results provide insight into the mechanisms behind the evolutionary response of rhizobia to long‐term N fertilization, and we discuss the implications of our results for the evolution of the mutualism.     

Signaling Dynamics Control Cell Fate in the Early Drosophila Embryo

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Energetic implications of floodplain wetland restoration strategies for waterfowl

Modifications of the Illinois River and associated tributaries have resulted in altered hydrologic cycles and persistent river‐floodplain connections during the growing season that frequently impede the establishment of hydrophytic vegetation and have reduced value for migratory waterfowl and other waterbirds. To help guide floodplain restoration, we compared energetic carrying capacity for waterfowl in two wetland complexes along the Illinois River under different management regimes during 2012–2015. The south pool of Chautauqua National Wildlife Refuge (CNWR) was seasonally flooded due to a partial river connection and managed for moist‐soil vegetation. Emiquon Preserve was hydrologically isolated from the Illinois River by a high‐elevation levee and managed as a semipermanently flooded emergent marsh. Semipermanent emergent marsh management at Emiquon Preserve produced 5,495 energetic use‐days (EUD)/ha for waterfowl and other waterbirds across wetland cover types and years, and seasonal moist‐soil management at CNWR produced 6,199 EUD/ha in one of 4 years. At Emiquon Preserve, the aquatic bed cover type produced 9,660 EUD/ha, followed by 5,261 EUD/ha in moist‐soil, 1,398 EUD/ha in persistent emergent, 1,185 EUD/ha in hemi‐marsh, and 12 EUD/ha in open water cover types. At CNWR, the annual grass and sedge cover type produced 7,031 EUD/ha, followed by 5,618 EUD/ha in annual broadleaf and 1,305 EUD/ha in perennial grass cover types. Restoration of floodplain wetlands in isolation from frequent flood pulses during the growing season can produce hemi‐marsh and aquatic bed vegetation communities that provide high‐quality habitat for waterfowl and which have been mostly eliminated from large river systems in the Midwest, U.S.A.     

基于Agent模型的生态公平指数构建与模拟

伴随着社会经济的发展,社会公平逐渐成为热点话题。社会公平问题不但体现在社会现象上,还对生态系统起着重要的影响。通过构建资本交换自主体模型,模拟社会财富分配动态过程,可观测资本交换熵指数变化情况,从而解释熵增原理。除此以外,不同系统的最终状态能达到的最大熵指数不同,用熵增原理与本文构建的最大熵指数模型可以对系统的生态公平进行纵向或横向评价。构建的资本交换熵模型也可以证明最大熵原理,同时,财富集中的现象将会使生态环境的选择权完全交予富人群体,影响可持续发展。     

The 2-oxoacid dehydrogenase multi-enzyme complex of the archaeon Thermoplasma acidophilum - recombinant expression, assembly and characterization

The aerobic archaea possess four closely spaced, adjacent genes that encode proteins showing significant sequence identities with the bacterial and eukaryal components comprising the 2-oxoacid dehydrogenase multi-enzyme complexes. However, catalytic activities of such complexes have never been detected in the archaea, although 2-oxoacid ferredoxin oxidoreductases that catalyze the equivalent metabolic reactions are present. In the current paper, we clone and express the four genes from the thermophilic archaeon, Thermoplasma acidophilum, and demonstrate that the recombinant enzymes are active and assemble into a large (M(r) = 5 x 10(6)) multi-enzyme complex. The post-translational incorporation of lipoic acid into the transacylase component of the complex is demonstrated, as is the assembly of this enzyme into a 24-mer core to which the other components bind to give the functional multi-enzyme system. This assembled complex is shown to catalyze the oxidative decarboxylation of branched-chain 2-oxoacids and pyruvate to their corresponding acyl-CoA derivatives. Our data constitute the first proof that the archaea possess a functional 2-oxoacid dehydrogenase complex.     

Protein partners in the life history of activated fibroblast growth factor receptors

Fibroblast growth factor receptors (FGFRs) are a family of four transmembrane (TM) receptor tyrosine kinases (RTKs) which bind to a large family of fibroblast growth factor (FGF) ligands with varying affinity and specificity. FGFR signaling regulates many physiological and pathological processes in development and tissue homeostasis. Understanding FGFR signaling processes requires the identification of partner proteins which regulate receptor function and biological outputs. In this study, we employ an epitope-tagged, covalently dimerized, and constitutively activated form of FGFR1 to identify potential protein partners by MS. By this approach, we sample candidate FGFR effectors throughout the life history of the receptor. Functional classification of the partners identified revealed specific subclasses involved in protein biosynthesis and folding; structural and regulatory components of the cytoskeleton; known signaling effectors and small GTPases implicated in endocytosis and vesicular trafficking. The kinase dependency of the interaction was determined for a subset of previously unrecognized partners by coimmunoprecipitation, Western blotting, and immunocytochemistry. From this group, the small GTPase Rab5 was selected for functional interrogation. We show that short hairpin (sh) RNA-mediated depletion of Rab5 attenuates the activation of the extracellular-regulated kinase (ERK) 1/2 pathway by FGFR signaling. The strategic approach adopted in this study has revealed bona fide novel effectors of the FGFR signaling pathway.     

Chronic vs. short-term acute O3 exposure effects on nocturnal transpiration in two Californian oaks

We tested the effect of daytime chronic moderate ozone (O3) exposure, short-term acute exposure, and both chronic and acute O3 exposure combined on nocturnal transpiration in California black oak and blue oak seedlings. Chronic O3 exposure (70 ppb for 8 h/day) was implemented in open-top chambers for either 1 month (California black oak) or 2 months (blue oak). Acute O3 exposure (approximately 1 h in duration during the day, 120-220 ppb) was implemented in a novel gas exchange system that supplied and maintained known O3 concentrations to a leaf cuvette. When exposed to chronic daytime O3 exposure, both oaks exhibited increased nocturnal transpiration (without concurrent O3 exposure) relative to unexposed control leaves (1.8x and 1.6x, black and blue oak, respectively). Short-term acute and chronic O3 exposure did not further increase nocturnal transpiration in either species. In blue oak previously unexposed to O3, short-term acute O3 exposure significantly enhanced nocturnal transpiration (2.0x) relative to leaves unexposed to O3. California black oak was unresponsive to (only) short-term acute O3 exposure. Daytime chronic and/or acute O3 exposures can increase foliar water loss at night in deciduous oak seedlings.