 | .reports |
For a comprehensive review of the most interesting recent articles published in the biological sciences, visit Faculty of 1000 Biology, an online literature awareness tool published by BioMed Central. Faculty of 1000 Biology systematically highlights exciting recent publications on the basis of recommendations of a faculty of well over 1,000 of the world's leading researchers. |
|
| Faculty Comments |
|
|
| Faculty Member |
Comments |
William Martin
Heinrich-Heine-Universitat Dusseldorf, Germany
PLANT BIOLOGY
 New Finding
|
This is a landmark analysis of plant mitochondrial genome sequences that sets the record straight on several important points regarding previously inferred mitochondrion-to-nucleus gene transfers in plants. There have been prominent claims for massive lateral gene transfers (LGT) of plant mtDNA based on Southern hydridizations, implicating almost patterns of gene presence and absence in plant mtDNA seemingly inexplicable without invoking LGT. The present paper shows that the Southern screens for presence or absence of genes in mtDNA has led to erroneous conclusions in the case of tobacco. Thus, more caution is needed when interpreting Southern hydridizations as an indicator of nuclear or mitochondrial localization of plant genes.
Evaluated 4 Jan 2005 |
|
|
|
| Faculty Comments |
|
|
| Faculty Member |
Comments |
Rolf Apweiler
EMBL Outstation Hinxton (EBI), United Kingdom
GENOMICS & GENETICS
 Tech Advance
|
This paper describes an open-source system for analyzing, storing, and validating proteomics information derived from tandem mass spectrometry; a potentially important component in the struggle to make data from proteomics experiments available in a standardized way for broad dissemination by the scientific community. There has been considerable discussion as to how data from proteomics experiments can be standardized for broad dissemination and about the best methods for validating results of statistical analyses that constitute the final mapping of a list of tandem mass spectra to a list of protein sequences in a proteomics experiment. In response to this, the authors have designed a database schema to serve as both an extension and a simplification of the HUPO Proteomics Standards Initiative (PSI) idea of Minimal Standards for the Annotation of a Proteomics Experiment (MIAPE), for the purpose of validating observed protein coverage and peptide fragmentation data. The design goal of the schema was to create a database which could be used both on its own to provide answers to queries as well as to serve as an index to experimental information stored in XML documents. It is based on a combination of data analysis servers, a user interface, and a relational database. The database was designed to store the minimum amount of information necessary to search and retrieve data obtained from the publicly available data analysis servers.
Evaluated 4 Jan 2005 |
|
|
|
| Faculty Comments |
|
|
| Faculty Member |
Comments |
Brent Iverson
University of Texas, United States of America
CHEMICAL BIOLOGY
Tech Advance
|
A new library of fluorogenic alpha-chloroacetamide based activity probes was developed in order to map the enzymatic activities of proteomes. Optimized probe sets were used to analyze lean and obese strains of mice, leading to the identification of hydroxypyruvate reductase as being upregulated in the obese strain. This study offers a new paradigm in how enymatic activity, not RNA levels, can be mapped directly to identify important factors associated with disease states.
Evaluated 4 Jan 2005 |
|
|
|
| Faculty Comments |
|
|
| Faculty Member |
Comments |
Leonie Ringrose
University of Heidelberg, Germany
DEVELOPMENTAL BIOLOGY
Tech Advance
|
This paper stands out among the multitude of recent published methods for microRNA target prediction, because it provides a thorough statistical rationale for evaluating the significance of target predictions. Furthermore the prediction method is the only software currently available in a web-server format (http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/). Because microRNAs are short, and hybridise imperfectly to their target mRNAs, a huge number of binding sites is possible. This makes accurate microRNA target prediction very difficult. The authors provide an elegant new time-efficient algorithm ('RNAhybrid'), and in addition describe several statistical methods that aid in separating the wheat from the chaff. These include normalisation of binding energies according to target length, microRNA specific statistics, and correction for statistical dependences between orthologous target genes. This rigourous statistical approach pays off: the authors not only correctly predict known and tested microRNA targets in Drosophila, they also predict targets that had been identified experimentally, but had escaped detection by other prediction methods. This lends conviction to the other new targets predicted in this study, and to the sober reevaluation of previously published target predictions. The ready availability of the software should encourage biologists to adopt RNAhybrid as the method of choice for predicting microRNA targets.
Evaluated 4 Jan 2005 |
|
|
|
| Faculty Comments |
|
|
| Faculty Member |
Comments |
Mark D. Adams
Case Western Reserve University, United States of America
GENOMICS & GENETICS
New Finding
|
This paper demonstrates that (lack of) polymorphism among individuals of a species can be used to define functionally important genome regions. This is similar to the 'phylogenetic shadowing' approach developed by this group {1}, but more generally applicable because related species at an appropriate phylogenetic distance are not required. {1} Boffelli et al. Science 2003, 299:1391-4 [PMID:12610304].
Evaluated 4 Jan 2005 |
|
|
|
|
Exceptional
Recommended
Must Read