丛枝菌根真菌影响作物非生物胁迫耐受性的研究进展

土壤中存在着大量不同种类的微生物资源,土壤微生物能够与自然界中的大多数植物密切合作,其中丛枝菌根真菌(arbuscular mycorrhizal fungi,AMF)起着十分重要的作用。近年来,对于AMF的研究越来越多。AMF是存在于土壤中的重要真菌之一,是土壤中的菌根真菌菌丝与高等植物营养根系形成的一种联合体。AMF可以与陆地上90%左右的植物根系形成共生体,通过在植物根系形成重要的“丛枝菌根”结构而为植物提供更多的养分。为了了解接种AMF对作物生长过程中耐受一些非生物胁迫(如干旱、极端温度、重金属污染、盐分、不利的土壤pH变化等)性能方面的影响,基于之前接种AMF对养分胁迫下玉米生长影响的研究,在扩大作物品种的基础上,通过查阅大量文献,结合试验研究及对前人和近年来关于AMF的一些最新研究进展,获得了具有实践性意义的新发现：AMF与植物共生有助于植物生长,可以改善植物的营养状况,并且可以保护植物免受各种非生物环境胁迫的影响。由此可以得出结论：AMF通过各种机制改善植物生长状况,提高作物抗逆性,为作物增产、农民增收创造了福利,并且避免了由于肥料过量施用导致的一些污染环境问题。本文主要综述了接种AMF在各种非生物环境胁迫(干旱、极端温度、重金属污染、盐分、不利的土壤pH变化等)条件下对植株生长和发育的有利影响,并对目前存在的不足和今后研究的重点提出几点建议。     

Automatic morphological subtyping reveals new roles of caspases in mitochondrial dynamics

Morphological dynamics of mitochondria is associated with key cellular processes related to aging and neuronal degenerative diseases, but the lack of standard quantification of mitochondrial morphology impedes systematic investigation. This paper presents an automated system for the quantification and classification of mitochondrial morphology. We discovered six morphological subtypes of mitochondria for objective quantification of mitochondrial morphology. These six subtypes are small globules, swollen globules, straight tubules, twisted tubules, branched tubules and loops. The subtyping was derived by applying consensus clustering to a huge collection of more than 200 thousand mitochondrial images extracted from 1422 micrographs of Chinese hamster ovary (CHO) cells treated with different drugs, and was validated by evidence of functional similarity reported in the literature. Quantitative statistics of subtype compositions in cells is useful for correlating drug response and mitochondrial dynamics. Combining the quantitative results with our biochemical studies about the effects of squamocin on CHO cells reveals new roles of Caspases in the regulatory mechanisms of mitochondrial dynamics. This system is not only of value to the mitochondrial field, but also applicable to the investigation of other subcellular organelle morphology.     

Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma genes Online)

Background

An adequate and expressive ontological representation of biological organisms and their parts requires formal reasoning mechanisms for their relations of physical aggregation and containment.

Results

We demonstrate that the proposed formalism allows to deal consistently with "role propagation along non-taxonomic hierarchies", a problem which had repeatedly been identified as an intricate reasoning problem in biomedical ontologies.

Conclusion

The proposed approach seems to be suitable for the redesign of compositional hierarchies in (bio)medical terminology systems which are embedded into the framework of the OBO (Open Biological Ontologies) Relation Ontology and are using knowledge representation languages developed by the Semantic Web community.     

Overview of BioCreative II gene normalization

Background:

The goal of the gene normalization task is to link genes or gene products mentioned in the literature to biological databases. This is a key step in an accurate search of the biological literature. It is a challenging task, even for the human expert; genes are often described rather than referred to by gene symbol and, confusingly, one gene name may refer to different genes (often from different organisms). For BioCreative II, the task was to list the Entrez Gene identifiers for human genes or gene products mentioned in PubMed/MEDLINE abstracts. We selected abstracts associated with articles previously curated for human genes. We provided 281 expert-annotated abstracts containing 684 gene identifiers for training, and a blind test set of 262 documents containing 785 identifiers, with a gold standard created by expert annotators. Inter-annotator agreement was measured at over 90%.

Results:

Twenty groups submitted one to three runs each, for a total of 54 runs. Three systems achieved F-measures (balanced precision and recall) between 0.80 and 0.81. Combining the system outputs using simple voting schemes and classifiers obtained improved results; the best composite system achieved an F-measure of 0.92 with 10-fold cross-validation. A 'maximum recall' system based on the pooled responses of all participants gave a recall of 0.97 (with precision 0.23), identifying 763 out of 785 identifiers.

Conclusion:

Major advances for the BioCreative II gene normalization task include broader participation (20 versus 8 teams) and a pooled system performance comparable to human experts, at over 90% agreement. These results show promise as tools to link the literature with biological databases.

     

Introducing meta-services for biomedical information extraction

We introduce the first meta-service for information extraction in molecular biology, the BioCreative MetaServer (BCMS; http://bcms.bioinfo.cnio.es/). This prototype platform is a joint effort of 13 research groups and provides automatically generated annotations for PubMed/Medline abstracts. Annotation types cover gene names, gene IDs, species, and protein-protein interactions. The annotations are distributed by the meta-server in both human and machine readable formats (HTML/XML). This service is intended to be used by biomedical researchers and database annotators, and in biomedical language processing. The platform allows direct comparison, unified access, and result aggregation of the annotations.     

Clinicopathologic features and outcomes following surgery for pancreatic adenosquamous carcinoma

Background

The use of diagnostic ¹⁸F-fluorodeoxyglucose (¹⁸F-FDG) positron emission tomography/computed tomography (PET/CT) imaging for the staging, restaging, and treatment monitoring of melanoma patients has become a well-recognized standard of care. It plays a key role in detecting sites of occult disease and is widely utilized in the medical and surgical planning of such patients. In the current report, we describe an innovative multimodality approach of perioperative ¹⁸F-FDG PET/CT imaging, intraoperative ¹⁸F-FDG handheld gamma probe detection, and intraoperative ultrasound for tumor localization and verification of resection of all sites of hypermetabolic tumor foci in a case of occult recurrent metastatic melanoma.

Case presentation

This report discusses a case of occult recurrent metastatic melanoma, isolated to three separate sites within the subcutaneous tissues of the left thigh region, which was not clinically apparent but was found on diagnostic restaging whole body ¹⁸F-FDG PET/CT scan utilizing an intravenous injection of 14.8 mCi ¹⁸F-FDG. Then, on the day of surgery, the patient received an intravenous injection of 12.8 mCi ¹⁸F-FDG. A multimodality approach of intraoperative handheld gamma probe detection, intraoperative ultrasound tumor localization, specimen PET/CT imaging, and postoperative PET/CT imaging was utilized for accomplishing and verifying the excision of all three sites of occult recurrent metastatic melanoma within the left thigh region.

Conclusion

This innovative multimodality approach of perioperative ¹⁸F-FDG PET/CT imaging, intraoperative ¹⁸F-FDG handheld gamma probe detection, and intraoperative ultrasound is promising combined technology for aiding in tumor localization and verification of excision and may ultimately impact positively upon long-term outcome of selected patients.     

组蛋白变异体HIST2H2BE通过上调p 21表达诱导细胞衰老

已知组蛋白变异体在基因转录调控、DNA修复以及凋亡等过程中起着重要作用。但组蛋白变异体在细胞衰老中的作用尚不清楚。本研究证明,组蛋白变异体HIST2H2BE可上调p 21的表达,影响细胞的衰老进程。基因芯片、半定量RT-PCR以及Real-time PCR揭示,HIST2H2BE在衰老细胞中表达升高,且其表达具有衰老特异性。在年轻成纤维细胞中过表达HIST2H2BE,可显著减少EdU掺入细胞的百分率,升高细胞衰老标志物SA-β-gal活性以及p 21的表达,提示HIST2H2BE具有细胞衰老调节作用。此外,利用siRNA抑制p 21表达,可明显衰减HIST2H2BE活化SA-β-gal。以上结果显示,组蛋白变异体HIST2H2BE是一个重要的衰老调节蛋白质,其对细胞衰老的调节依赖于p 21。该研究结果为深入探讨染色质结构改变在细胞衰老中的作用提供了新线索。     

Synthesis and cytotoxic, anti-inflammatory, and anti-oxidant activities of 2',5'-dialkoxylchalcones as cancer chemopreventive agents

In an effort to develop novel anti-tumor, or cancer chemopreventive agents, a series of 2',5'-dialkoxylchalcones were prepared by Claisen-Schmidt condensation of appropriate acetophenones with suitable aromatic aldehyde. In vitro screening revealed low micromolar activity (IC(50)) against several human cancer cell lines. Selective compound 10 induced an accumulation of A549 cells in the G(2)/M phase arrest which was well correlated with inhibitory activity against tubulin polymerization. Cytotoxic compounds 3 and 12 showed significant inhibitory effects on NO production in lipopolysaccharide (LPS)-activated RAW 264.7 macrophage-like cells while cytotoxic compound 10 revealed potent inhibitory effect on TNF-alpha formation in RAW 264.7 cells in response to LPS. Compounds 3 and 10 also showed significant inhibitory effects on xanthine oxidase. The present results suggested that compounds 3 and 10 were potential to be served as cancer chemopreventive agents.     

Design, synthesis and cytotoxic effect of hydroxy- and 3-alkylaminopropoxy-9,10-anthraquinone derivatives

In previous paper, we have reported the synthesis and the cytotoxic effect of 1,3-dihydroxy-9,10-anthraquinone derivatives. For further design of more potent compounds, a new series of 1-hydroxy-3-(3-alkylaminopropoxy)-9,10-anthraquinones and 3-(3-alkylaminopropoxy)-9,10-anthraquinones have been synthesized. The cytotoxicity of synthetic compounds were evaluated against human Hep G2, Hep 3B and HT-29 cells. Almost all compounds indicated significant inhibitory activity against Hep G2, Hep 3B and HT-29 cell lines in vitro. Compound 5 exhibited selective cytotoxicity against Hep G2 in a concentration-dependent manner with ED50 value of 1.23 +/- 0.05 microM. Structure-activity analysis revealed that most of the 1-hydroxy-3-(3-alkylamino-2-hydroxypropoxy)-9,10-anthraquinone showed stronger cytotoxic effects than those of 1-hydroxy-3- or 3-(3-alkylaminopropoxy)-9,10-anthraquinones against Hep 3B cell line in vitro. A sub-G1 cell stage and DNA fragmentation in MCF-7 cells were significantly observed after 72 h incubation with selective compound 16. The results show that 16 causes cell death by apoptosis.