端粒和端粒酶的发现及其生物学意义

2009年的诺贝尔生理学或医学奖授予了美国加州大学旧金山分校的Elizabeth H．Blackburn、约翰霍普金斯大学的Carol W．Greider以及哈佛医学院的Jack W．Szostak三位科学家,肯定他们在发现端粒以及端粒酶保护染色体末端方面所做出的贡献。端粒以及端粒酶的发现历经近半个世纪,追溯起端粒和端粒酶的整个发现过程,却是耐人寻味,给人启发。端粒是真核生物中位于染色体末端的DNA和蛋白质的复合物,它对于维持基因组的完整性以及染色体的稳定性都有着至关重要的作用。端粒DNA可以被一种特化的称为“端粒酶”的逆转录酶延伸。端粒长度的维持以及端粒结构的稳定在细胞衰老、癌症发生以及干细胞全能性自我更新能力维持等生命过程中都起重要作用。     

APC senses cell-cell contacts and moves to the nucleus upon their disruption.

The adenomatous polyposis coli (APC) tumor suppressor protein is involved in the Wnt/wingless pathway, modulating beta-catenin activity. We report the development of a highly specific, chemically synthesized oligobody (oligonucleotide-based synthetic antibody), directed against the N-terminal region of APC. Using this reagent, we found that within 16 h of disrupting HT-29 cell-cell contacts by harvesting cells with trypsin/EDTA treatment and replating, APC was translocated from the cytoplasm to the nucleus. Five days after plating the cells, when the cells had returned to their normal confluent phenotype and cell-cell contacts were reestablished, APC returned to the cytoplasm. These results suggest that APC functions as part of a "sensor" system, and responds to the loss of cell-cell contacts by moving to the nucleus, and returning to the cytoplasm when the contacts are fully restored.     

Coyote senses in predation: Environmental influences on their relative use

The purpose of this study was to determine the relative importance of vision, audition, and olfaction to coyotes (Canis latrans) hunting under various environmental conditions. The time durations for four coyotes to locate rabbits within a large outdoor enclosure were determined, with the visual, auditory, and olfactory stimuli emitted by the rabbits blocked individually, in pairs, and altogether. Visual stimuli were eliminated by conducting the tests only during sub-threshold nocturnal conditions. Auditory stimuli were eliminated by killing the rabbits immediately prior to a test. Olfactory stimuli were eliminated by inducing anosmia in each coyote through irrigation of the nasal mucosa with a 10% zinc sulphate solution. The relative importance of these three senses in decreasing order was concluded to be: vision, olfaction, and audition.     

TRPs in our senses

In the last decade, studies of transient receptor potential (TRP) channels, a superfamily of cation-conducting membrane proteins, have significantly extended our knowledge about the molecular basis of sensory perception in animals. Due to their distinct activation mechanisms and biophysical properties, TRP channels are highly suited to function in receptor cells, either as receptors for environmental or endogenous stimuli or as molecular players in signal transduction cascades downstream of metabotropic receptors. As such, TRP channels play a crucial role in many mammalian senses, including touch, taste and smell. Starting with a brief survey of sensory TRP channels in invertebrate model systems, this review covers the current state of research on TRP channel function in the classical mammalian senses and summarizes how modulation of TRP channels can tune our sensations.     

EBIMed--text crunching to gather facts for proteins from Medline

To allow efficient and systematic retrieval of statements from Medline we have developed EBIMed, a service that combines document retrieval with co-occurrence-based analysis of Medline abstracts. Upon keyword query, EBIMed retrieves the abstracts from EMBL-EBI's installation of Medline and filters for sentences that contain biomedical terminology maintained in public bioinformatics resources. The extracted sentences and terminology are used to generate an overview table on proteins, Gene Ontology (GO) annotations, drugs and species used in the same biological context. All terms in retrieved abstracts and extracted sentences are linked to their entries in biomedical databases. We assessed the quality of the identification of terms and relations in the retrieved sentences. More than 90% of the protein names found indeed represented a protein. According to the analysis of four protein-protein pairs from the Wnt pathway we estimated that 37% of the statements containing such a pair mentioned a meaningful interaction and clarified the interaction of Dkk with LRP. We conclude that EBIMed improves access to information where proteins and drugs are involved in the same biological process, e.g. statements with GO annotations of proteins, protein-protein interactions and effects of drugs on proteins. AVAILABILITY: Available at http://www.ebi.ac.uk/Rebholz-srv/ebimed     

Finding relevant references to genes and proteins in Medline using a Bayesian approach

MOTIVATION: Mining the biomedical literature for references to genes and proteins always involves a tradeoff between high precision with false negatives, and high recall with false positives. Having a reliable method for assessing the relevance of literature mining results is crucial to finding ways to balance precision and recall, and for subsequently building automated systems to analyze these results. We hypothesize that abstracts and titles that discuss the same gene or protein use similar words. To validate this hypothesis, we built a dictionary- and rule-based system to mine Medline for references to genes and proteins, and used a Bayesian metric for scoring the relevance of each reference assignment. RESULTS: We analyzed the entire set of Medline records from 1966 to late 2001, and scored each gene and protein reference using a Bayesian estimated probability (EP) based on word frequency in a training set of 137837 known assignments from 30594 articles to 36197 gene and protein symbols. Two test sets of 148 and 150 randomly chosen assignments, respectively, were hand-validated and categorized as either good or bad. The distributions of EP values, when plotted on a log-scale histogram, are shown to markedly differ between good and bad assignments. Using EP values, recall was 100% at 61% precision (EP=2 x 10(-5)), 63% at 88% precision (EP=0.008), and 10% at 100% precision (EP=0.1). These results show that Medline entries discussing the same gene or protein have similar word usage, and that our method of assessing this similarity using EP values is valid, and enables an EP cutoff value to be determined that accurately and reproducibly balances precision and recall, allowing automated analysis of literature mining results. .     

Resolving the first steps to multicellularity

Multicellular life has evolved many times, yet each origin requires free cells to integrate unselfishly into a higher-level individual. How can such transitions evolve? In a new paper, Herron and Michod investigate the recent origins of multicellularity in colonial algae. Their phylogenetic reconstructions provide a striking dissection of early steps, and altruistic traits are at the crux of it. Key evolutionary reversals are also revealed, where cellular selfishness might have thwarted multicellular integration.     

Olfaction and taste senses in sturgeon behaviour

Olfaction is one of the fundamental senses for spawning and feeding behaviour in sturgeons. The olfactory spectra of free amino acids affecting behaviour in sturgeon species of the family Acipenseridae are narrow and similar. The threshold concentrations for effective amino acids (glycine and L-alanine) are 1 μM The taste spectra are highly species specific, especially for the oral taste modality. There is a good correlation between the responses of extra-oral and oral taste systems within the same species. The extra-oral taste system is more sensitive and has a wider effective spectrum than the oral system. The extra-oral taste system develops more rapidly than oral taste system during sturgeon ontogenesis.     

植物组织RNA提取的难点及对策

酚类化合物、多糖、蛋白质和未知次级代谢产物是影响植物组织ＲＮＡ提取的几个主要干扰因素。本文对它们在植物ＲＮＡ提取过程中的干扰作用、现象以及消除它们的一些方法进行了综述。     

ADAM: another database of abbreviations in MEDLINE

MOTIVATION: Abbreviations are an important type of terminology in the biomedical domain. Although several groups have already created databases of biomedical abbreviations, these are either not public, or are not comprehensive, or focus exclusively on acronym-type abbreviations. We have created another abbreviation database, ADAM, which covers commonly used abbreviations and their definitions (or long-forms) within MEDLINE titles and abstracts, including both acronym and non-acronym abbreviations. RESULTS: A model of recognizing abbreviations and their long-forms from titles and abstracts of MEDLINE (2006 baseline) was employed. After grouping morphological variants, 59 405 abbreviation/long-form pairs were identified. ADAM shows high precision (97.4%) and includes most of the frequently used abbreviations contained in the Unified Medical Language System (UMLS) Lexicon and the Stanford Abbreviation Database. Conversely, one-third of abbreviations in ADAM are novel insofar as they are not included in either database. About 19% of the novel abbreviations are non-acronym-type and these cover at least seven different types of short-form/long-form pairs. AVAILABILITY: A free, public query interface to ADAM is available at http://arrowsmith.psych.uic.edu, and the entire database can be downloaded as a text file.     

The opportunistic human pathogen Acinetobacter baumannii senses and responds to light

Light is a ubiquitous environmental signal that many organisms sense and respond to by modulating their physiological responses accordingly. While this is an expected response among phototrophic microorganisms, the ability of chemotrophic prokaryotes to sense and react to light has become a puzzling and novel issue in bacterial physiology, particularly among bacterial pathogens. In this work, we show that the opportunistic pathogen Acinetobacter baumannii senses and responds to blue light. Motility and formation of biofilms and pellicles were observed only when bacterial cells were incubated in darkness. In contrast, the killing of Candida albicans filaments was enhanced when they were cocultured with bacteria under light. These bacterial responses depend on the expression of the A. baumannii ATCC 17978 A1S_2225 gene, which codes for an 18.6-kDa protein that contains an N-terminal blue-light-sensing-using flavin (BLUF) domain and lacks a detectable output domain(s). Spectral analyses of the purified recombinant protein showed its ability to sense light by a red shift upon illumination. Therefore, the A1S_2225 gene, which is present in several members of the Acinetobacter genus, was named blue-light-sensing A (blsA). Interestingly, temperature plays a role in the ability of A. baumannii to sense and respond to light via the BlsA photoreceptor protein.     

Search filters for finding prognostic and diagnostic prediction studies in Medline to enhance systematic reviews

Background

The interest in prognostic reviews is increasing, but to properly review existing evidence an accurate search filer for finding prediction research is needed. The aim of this paper was to validate and update two previously introduced search filters for finding prediction research in Medline: the Ingui filter and the Haynes Broad filter.

Methodology/Principal Findings

Based on a hand search of 6 general journals in 2008 we constructed two sets of papers. Set 1 consisted of prediction research papers (n = 71), and set 2 consisted of the remaining papers (n = 1133). Both search filters were validated in two ways, using diagnostic accuracy measures as performance measures. First, we compared studies in set 1 (reference) with studies retrieved by the search strategies as applied in Medline. Second, we compared studies from 4 published systematic reviews (reference) with studies retrieved by the search filter as applied in Medline. Next – using word frequency methods – we constructed an additional search string for finding prediction research. Both search filters were good in identifying clinical prediction models: sensitivity ranged from 0.94 to 1.0 using our hand search as reference, and 0.78 to 0.89 using the systematic reviews as reference. This latter performance measure even increased to around 0.95 (range 0.90 to 0.97) when either search filter was combined with the additional string that we developed. Retrieval rate of explorative prediction research was poor, both using our hand search or our systematic review as reference, and even combined with our additional search string: sensitivity ranged from 0.44 to 0.85.

Conclusions/Significance

Explorative prediction research is difficult to find in Medline, using any of the currently available search filters. Yet, application of either the Ingui filter or the Haynes broad filter results in a very low number missed clinical prediction model studies.