This page lists the papers that have been featured as "Paper[s] of the Day[s]" in the BioCurious lobby. This information can also be downloaded as a BibTeX file, updated approximately weekly. The "Paper of the Day" choices are currently run by Tristan Eversole; for additional information, comments, or suggestions, contact him. Updates currently occur on Mondays, Wednesdays, and Fridays— help with the rest of the week would be greatly appreciated.

Although I will try to pick papers of general interest to the Biocurious members and the mailing list, these selections necessarily reflect my own interests and biases and do not represent Biocurious itself. On the other hand, it would be unwise to assume that I agree with every point of view I select. —T. E.

Techniques: Genetics: Microbiology: Other:

Papers by Category:

Evolutionary Biology:

• LaBarbera. Why the Wheels Won't Go. The American Naturalist (1983) vol. 121 (3) pp. 395-408

The scarcity of rotating systems in nature is a function primarily of the limited utility of such systems in natural environments; constraints intrinsic to biological systems (such as physiological problems of nutrient supply) are of secondary importance. In aquatic environments, rotating systems are advantageous only at low Reynolds numbers; in terrestrial environments, rotating systems are feasible as a form of transportation only on relatively flat, open terrain and become less useful as the size of the rotating element decreases. Prokaryotic flagella are popularly believed to be the only rotating system in nature, but dung beetles and tumbleweeds also use such systems for transportation. Whenever rotating systems are a feasible mode of transportation, organisms have evolved that use these systems. 

• Kirkwood and Austad. Why do we age?. Nature (2000) vol. 408 (6809) pp. 233-8

The evolutionary theory of ageing explains why ageing occurs, giving valuable insight into the mechanisms underlying the complex cellular and molecular changes that contribute to senescence. Such understanding also helps to clarify how the genome shapes the ageing process, thereby aiding the study of the genetic factors that influence longevity and age-associated diseases. 

Techniques:

• Chalfie et al. Green fluorescent protein as a marker for gene expression. Science (New York, NY) (1994) vol. 263 (5148) pp. 802-5

A complementary DNA for the Aequorea victoria green fluorescent protein (GFP) produces a fluorescent product when expressed in prokaryotic (Escherichia coli) or eukaryotic (Caenorhabditis elegans) cells. Because exogenous substrates and cofactors are not required for this fluorescence, GFP expression can be used to monitor gene expression and protein localization in living organisms. 

• Nikolaou et al. VeSTIS: A Versatile Semi-Automatic Taxon Identification System from Digital Images.  (2010)

In this work we present a flexible Open Source software platform for training classifiers capable of identifying the taxonomy of a specimen from digital images. We demonstrate the performance of our system in a pilot study, building a feed-forward artificial neural network to effectively classify five different species of marine annelid worms of the class Polychaeta. We also discuss on the extensibility of the system, and its potential uses either as a research tool or in assisting routine taxon identification procedures. 

Note: As far as I can tell, this software no longer exists. 

• Casiraghi et al. DNA barcoding: a six-question tour to improve users' awareness about the method. Briefings in bioinformatics (2010) vol. 11 (4) pp. 440-53

DNA barcoding is a recent and widely used molecular-based identification system that aims to identify biological specimens, and to assign them to a given species. However, DNA barcoding is even more than this, and besides many practical uses, it can be considered the core of an integrated taxonomic system, where bioinformatics plays a key role. DNA barcoding data could be interpreted in different ways depending on the examined taxa but the technique relies on standardized approaches, methods and analyses. The existing reference towards a common way to treat DNA barcoding data, analyses and results is the Barcode of Life Data Systems. However, the scientific community has produced in the recent years a number of alternative methods to manage barcoding data. The present work starts from this point, because users should be aware of the consequences their choices produce on the results. Despite the fact that a strict standardization is the essence of DNA barcoding, we propose a tour of six questions to improve the users' awareness about the method, the correct use of concepts and alternative tools provided by scientific community. 

• Hull et al. Defrosting the digital library: bibliographic tools for the next generation web. PLoS Computational Biology (2008) vol. 4 (10) pp. e1000204

Many scientists now manage the bulk of their bibliographic information electronically, thereby organizing their publications and citation material from digital libraries. However, a library has been described as "thought in cold storage," and unfortunately many digital libraries can be cold, impersonal, isolated, and inaccessible places. In this Review, we discuss the current chilly state of digital libraries for the computational biologist, including PubMed, IEEE Xplore, the ACM digital library, ISI Web of Knowledge, Scopus, Citeseer, arXiv, DBLP, and Google Scholar. We illustrate the current process of using these libraries with a typical workflow, and highlight problems with managing data and metadata using URIs. We then examine a range of new applications such as Zotero, Mendeley, Mekentosj Papers, MyNCBI, CiteULike, Connotea, and HubMed that exploit the Web to make these digital libraries more personal, sociable, integrated, and accessible places. We conclude with how these applications may begin to help achieve a digital defrost, and discuss some of the issues that will help or hinder this in terms of making libraries on the Web warmer places in the future, becoming resources that are considerably more useful to both humans and machines. 

Genetics:

• Chan et al. Refactoring bacteriophage T7. Molecular systems biology (2005) vol. 1 pp. 2005.0018

Natural biological systems are selected by evolution to continue to exist and evolve. Evolution likely gives rise to complicated systems that are difficult to understand and manipulate. Here, we redesign the genome of a natural biological system, bacteriophage T7, in order to specify an engineered surrogate that, if viable, would be easier to study and extend. Our initial design goals were to physically separate and enable unique manipulation of primary genetic elements. Implicit in our design are the hypotheses that overlapping genetic elements are, in aggregate, nonessential for T7 viability and that our models for the functions encoded by elements are sufficient. To test our initial design, we replaced the left 11,515 base pairs (bp) of the 39,937 bp wild-type genome with 12,179 bp of engineered DNA. The resulting chimeric genome encodes a viable bacteriophage that appears to maintain key features of the original while being simpler to model and easier to manipulate. The viability of our initial design suggests that the genomes encoding natural biological systems can be systematically redesigned and built anew in service of scientific understanding or human intention. 

• Evans et al. Genomics. Deflating the genomic bubble. Science (New York, NY) (2011) vol. 331 (6019) pp. 861-2. No abstract. 

• Gerstein et al. What is a gene, post-ENCODE? History and updated definition. Genome Research (2007) vol. 17 (6) pp. 669-81

While sequencing of the human genome surprised us with how many protein-coding genes there are, it did not fundamentally change our perspective on what a gene is. In contrast, the complex patterns of dispersed regulation and pervasive transcription uncovered by the ENCODE project, together with non-genic conservation and the abundance of noncoding RNA genes, have challenged the notion of the gene. To illustrate this, we review the evolution of operational definitions of a gene over the past century--from the abstract elements of heredity of Mendel and Morgan to the present-day ORFs enumerated in the sequence databanks. We then summarize the current ENCODE findings and provide a computational metaphor for the complexity. Finally, we propose a tentative update to the definition of a gene: A gene is a union of genomic sequences encoding a coherent set of potentially overlapping functional products. Our definition side-steps the complexities of regulation and transcription by removing the former altogether from the definition and arguing that final, functional gene products (rather than intermediate transcripts) should be used to group together entities associated with a single gene. It also manifests how integral the concept of biological function is in defining genes. 

Microbiology:

• Shapiro. Thinking about bacterial populations as multicellular organisms. Annual Review of Microbiology (1998) vol. 52 pp. 81-104

It has been a decade since multicellularity was proposed as a general bacterial trait. Intercellular communication and multicellular coordination are now known to be widespread among prokaryotes and to affect multiple phenotypes. Many different classes of signaling molecules have been identified in both Gram-positive and Gram-negative species. Bacteria have sophisticated signal transduction networks for integrating intercellular signals with other information to make decisions about gene expression and cellular differentiation. Coordinated multicellular behavior can be observed in a variety of situations, including development of E. coli and B. subtilis colonies, swarming by Proteus and Serratia, and spatially organized interspecific metabolic cooperation in anaerobic bioreactor granules. Bacteria benefit from multicellular cooperation by using cellular division of labor, accessing resources that cannot effectively be utilized by single cells, collectively defending against antagonists, and optimizing population survival by differentiating into distinct cell types. 

Other:

• Polanyi. The republic of science: Its political and economic theory. Minerva (2000) vol. 38 (1) pp. 1-21. No abstract.

• Rowe et al. CheapStat: An Open-Source, "Do-It-Yourself" Potentiostat for Analytical and Educational Applications. PLoS ONE (2011) vol. 6 (9) pp. e23783

Although potentiostats are the foundation of modern electrochemical research, they have seen relatively little application in resource poor settings, such as undergraduate laboratory courses and the developing world. One reason for the low penetration of potentiostats is their cost, as even the least expensive commercially available laboratory potentiostats sell for more than one thousand dollars. An inexpensive electrochemical workstation could thus prove useful in educational labs, and increase access to electrochemistry-based analytical techniques for food, drug and environmental monitoring. With these motivations in mind, we describe here the CheapStat, an inexpensive (<$80), open-source (software and hardware), hand-held potentiostat that can be constructed by anyone who is proficient at assembling circuits. This device supports a number of potential waveforms necessary to perform cyclic, square wave, linear sweep and anodic stripping voltammetry. As we demonstrate, it is suitable for a wide range of applications ranging from food- and drug-quality testing to environmental monitoring, rapid DNA detection, and educational exercises. The device's schematics, parts lists, circuit board layout files, sample experiments, and detailed assembly instructions are available in the supporting information and are released under an open hardware license. 

• Cyranoski et al. Education: The PhD factory. Nature (2011) vol. 472 (7343) pp. 276-9. No Abstract.

• Kareiva. Ominous trends in nature recreation. Proceedings Of The National Academy Of Sciences Of The United States Of America (2008) vol. 105 (8) pp. 2757-8. No abstract.

• Greene. Organisms in nature as a central focus for biology. Trends in ecology & evolution (Personal edition) (2005) vol. 20 (1) pp. 23-7

Theories summarize science, tell us what to measure when we test hypotheses, and help us study nature better. Nevertheless, organisms themselves embody genetics, development, morphology, physiology and behavior, and they are the units of populations, communities and ecosystems. Biologists seek to understand organisms, their diversification and environmental relationships--not theories and experiments per se--and discoveries of new organisms and new facts about organisms reset the research cycles of hypothesis testing that underlie conceptually progressive science. I argue here that recent disagreements about the fate of natural history are thus more apparent than real and should not distract us from addressing important issues. The conservation of biodiversity requires factual knowledge of particular organisms, yet we know little or nothing about most species, and organismal diversity is often poorly represented in biological education. Accordingly, I urge those who are especially concerned with teaching and conservation to seek increased financial and curricular support for descriptive natural history, which is so fundamental to many of the applied facets of biology. 

• Page. Organisms in nature as a central focus for biology. Trends in ecology & evolution (Personal edition) (2005) vol. 20 (7) pp. 361-2. Response to Greene.