Two Years Later: Journals Are Not Yet Enforcing the ARRIVE Guidelines on Reporting Standards for Pre-Clinical Animal Studies

There is growing concern that poor experimental design and lack of transparent reporting contribute to the frequent failure of pre-clinical animal studies to translate into treatments for human disease. In 2010, the Animal Research: Reporting of In Vivo Experiments (ARRIVE) guidelines were introduced to help improve reporting standards. They were published in PLOS Biology and endorsed by funding agencies and publishers and their journals, including PLOS, Nature research journals, and other top-tier journals. Yet our analysis of papers published in PLOS and Nature journals indicates that there has been very little improvement in reporting standards since then. This suggests that authors, referees, and editors generally are ignoring guidelines, and the editorial endorsement is yet to be effectively implemented.     

The PLOS ONE Synthetic Biology Collection: Six Years and Counting

Since it was launched in 2006, PLOS ONE has published over fifty articles illustrating the many facets of the emerging field of synthetic biology. This article reviews these publications by organizing them into broad categories focused on DNA synthesis and assembly techniques, the development of libraries of biological parts, the use of synthetic biology in protein engineering applications, and the engineering of gene regulatory networks and metabolic pathways. Finally, we review articles that describe enabling technologies such as software and modeling, along with new instrumentation. In order to increase the visibility of this body of work, the papers have been assembled into the PLOS ONE Synthetic Biology Collection (www.ploscollections.org/synbio). Many of the innovative features of the PLOS ONE web site will help make this collection a resource that will support a lively dialogue between readers and authors of PLOS ONE synthetic biology papers. The content of the collection will be updated periodically by including relevant articles as they are published by the journal. Thus, we hope that this collection will continue to meet the publishing needs of the synthetic biology community.     

What Can Article-Level Metrics Do for You?

Article-level metrics (ALMs) provide a wide range of metrics about the uptake of an individual journal article by the scientific community after publication. They include citations, usage statistics, discussions in online comments and social media, social bookmarking, and recommendations. In this essay, we describe why article-level metrics are an important extension of traditional citation-based journal metrics and provide a number of example from ALM data collected for PLOS Biology.The scientific impact of a particular piece of research is reflected in how this work is taken up by the scientific community. The first systematic approach that was used to assess impact, based on the technology available at the time, was to track citations and aggregate them by journal. This strategy is not only no longer necessary—since now we can easily track citations for individual articles—but also, and more importantly, journal-based metrics are now considered a poor performance measure for individual articles [1],[2]. One major problem with journal-based metrics is the variation in citations per article, which means that a small percentage of articles can skew, and are responsible for, the majority of the journal-based citation impact factor, as shown by Campbell [1] for the 2004 Nature Journal Impact Factor. Figure 1 further illustrates this point, showing the wide distribution of citation counts between PLOS Biology research articles published in 2010. PLOS Biology research articles published in 2010 have been cited a median 19 times to date in Scopus, but 10% of them have been cited 50 or more times, and two articles [3],[4] more than 300 times. PLOS Biology metrics are used as examples throughout this essay, and the dataset is available in the supporting information (Data S1). Similar data are available for an increasing number of other publications and organizations.Open in a separate windowFigure 1Citation counts for PLOS Biology articles published in 2010.Scopus citation counts plotted as a probability distribution for all 197 PLOS Biology research articles published in 2010. Data collected May 20, 2013. Median 19 citations; 10% of papers have at least 50 citations.Scientific impact is a multi-dimensional construct that can not be adequately measured by any single indicator [2],[5],[6]. To this end, PLOS has collected and displayed a variety of metrics for all its articles since 2009. The array of different categorised article-level metrics (ALMs) used and provided by PLOS as of August 2013 are shown in Figure 2. In addition to citations and usage statistics, i.e., how often an article has been viewed and downloaded, PLOS also collects metrics about: how often an article has been saved in online reference managers, such as Mendeley; how often an article has been discussed in its comments section online, and also in science blogs or in social media; and how often an article has been recommended by other scientists. These additional metrics provide valuable information that we would miss if we only consider citations. Two important shortcomings of citation-based metrics are that (1) they take years to accumulate and (2) citation analysis is not always the best indicator of impact in more practical fields, such as clinical medicine [7]. Usage statistics often better reflect the impact of work in more practical fields, and they also sometimes better highlight articles of general interest (for example, the 2006 PLOS Biology article on the citation advantage of Open Access articles [8], one of the 10 most-viewed articles published in PLOS Biology).Open in a separate windowFigure 2Article-level metrics used by PLOS in August 2013 and their categories.Taken from [10] with permission by the authors.A bubble chart showing all 2010 PLOS Biology articles (Figure 3) gives a good overview of the year''s views and citations, plus it shows the influence that the article type (as indicated by dot color) has on an article''s performance as measured by these metrics. The weekly PLOS Biology publication schedule is reflected in this figure, with articles published on the same day present in a vertical line. Figure 3 also shows that the two most highly cited 2010 PLOS Biology research articles are also among the most viewed (indicated by the red arrows), but overall there isn''t a strong correlation between citations and views. The most-viewed article published in 2010 in PLOS Biology is an essay on Darwinian selection in robots [9]. Detailed usage statistics also allow speculatulation about the different ways that readers access and make use of published literature; some articles are browsed or read online due to general interest while others that are downloaded (and perhaps also printed) may reflect the reader''s intention to look at the data and results in detail and to return to the article more than once.Open in a separate windowFigure 3Views vs. citations for PLOS Biology articles published in 2010.All 304 PLOS Biology articles published in 2010. Bubble size correlates with number of Scopus citations. Research articles are labeled green; all other articles are grey. Red arrows indicate the two most highly cited papers. Data collected May 20, 2013.When readers first see an interesting article, their response is often to view or download it. By contrast, a citation may be one of the last outcomes of their interest, occuring only about 1 in 300 times a PLOS paper is viewed online. A lot of things happen in between these potential responses, ranging from discussions in comments, social media, and blogs, to bookmarking, to linking from websites. These activities are usually subsumed under the term “altmetrics,” and their variety can be overwhelming. Therefore, it helps to group them together into categories, and several organizations, including PLOS, are using the category labels of Viewed, Cited, Saved, Discussed, and Recommended (Figures 2 and ​and4,4, see also [10]).Open in a separate windowFigure 4Article-level metrics for PLOS Biology.Proportion of all 1,706 PLOS Biology research articles published up to May 20, 2013 mentioned by particular article-level metrics source. Colors indicate categories (Viewed, Cited, Saved, Discussed, Recommended), as used on the PLOS website.All PLOS Biology articles are viewed and downloaded, and almost all of them (all research articles and nearly all front matter) will be cited sooner or later. Almost all of them will also be bookmarked in online reference managers, such as Mendeley, but the percentage of articles that are discussed online is much smaller. Some of these percentages are time dependent; the use of social media discussion platforms, such as Twitter and Facebook for example, has increased in recent years (93% of PLOS Biology research articles published since June 2012 have been discussed on Twitter, and 63% mentioned on Facebook). These are the locations where most of the online discussion around published articles currently seems to take place; the percentage of papers with comments on the PLOS website or that have science blog posts written about them is much smaller. Not all of this online discussion is about research articles, and perhaps, not surprisingly, the most-tweeted PLOS article overall (with more than 1,100 tweets) is a PLOS Biology perspective on the use of social media for scientists [11].Some metrics are not so much indicators of a broad online discussion, but rather focus on highlighting articles of particular interest. For example, science blogs allow a more detailed discussion of an article as compared to comments or tweets, and journals themselves sometimes choose to highlight a paper on their own blogs, allowing for a more digestible explanation of the science for the non-expert reader [12]. Coverage by other bloggers also serves the same purpose; a good example of this is one recent post on the OpenHelix Blog [13] that contains video footage of the second author of a 2010 PLOS Biology article [14] discussing the turkey genome.F1000Prime, a commercial service of recommendations by expert scientists, was added to the PLOS Article-Level Metrics in August 2013. We now highlight on the PLOS website when any articles have received at least one recommendation within F1000Prime. We also monitor when an article has been cited within the widely used modern-day online encyclopedia, Wikipedia. A good example of the latter is the Tasmanian devil Wikipedia page [15] that links to a PLOS Biology research article published in 2010 [16]. While a F1000Prime recommendation is a strong endorsement from peer(s) in the scientific community, being included in a Wikipedia page is akin to making it into a textbook about the subject area and being read by a much wider audience that goes beyond the scientific community. PLOS Biology is the PLOS journal with the highest percentage of articles recommended in F1000Prime and mentioned in Wikipedia, but there is only partial overlap between the two groups of articles because they focus on different audiences (Figure 5). These recommendations and mentions in turn show correlations with other metrics, but not simple ones; you can''t assume, for example, that highly cited articles are more likely to be recommended by F1000Prime, so it will be interesting to monitor these trends now that we include this information.Open in a separate windowFigure 5 PLOS Biology articles: sites of recommendation and discussion.Number of PLOS Biology research articles published up to May 20, 2013 that have been recommended by F1000Prime (red) or mentioned in Wikipedia (blue).With the increasing availability of ALM data, there comes a growing need to provide tools that will allow the community to interrogate them. A good first step for researchers, research administrators, and others interested in looking at the metrics of a larger set of PLOS articles is the recently launched ALM Reports tool [17]. There are also a growing number of service providers, including Altmetric.com [18], ImpactStory [19], and Plum Analytics [20] that provide similar services for articles from other publishers.As article-level metrics become increasingly used by publishers, funders, universities, and researchers, one of the major challenges to overcome is ensuring that standards and best practices are widely adopted and understood. The National Information Standards Organization (NISO) was recently awarded a grant by the Alfred P. Sloan Foundation to work on this [21], and PLOS is actively involved in this project. We look forward to further developing our article-level metrics and to having them adopted by other publishers, which hopefully will pave the way to their wide incorporation into research and researcher assessments.     

An open science pathway for drug marketing authorization—Registered drug approval

Florian Naudet and co-authors propose a pathway involving registered criteria for evaluation and approval of new drugs.

Publisher’s note: This Perspective is one of the two winning Essays of the “Reimagine biomedical research for a healthier future” Essay challenge, launched by the Health Research Alliance in partnership with PLOS. This publication is coordinated with that of the other winning Essay in PLOS Biology. The competition was intended to spark a discussion around the future of biomedical research; publication does not imply endorsement from HRA or PLOS.

     

On testing structural identifiability by a simple scaling method: Relying on scaling symmetries can be misleading

A recent paper published in PLOS Computational Biology [1] introduces the Scaling Invariance Method (SIM) for analysing structural local identifiability and observability. These two properties define mathematically the possibility of determining the values of the parameters (identifiability) and states (observability) of a dynamic model by observing its output. In this note we warn that SIM considers scaling symmetries as the only possible cause of non-identifiability and non-observability. We show that other types of symmetries can cause the same problems without being detected by SIM, and that in those cases the method may lead one to conclude that the model is identifiable and observable when it is actually not.     

Distributions of beta sheets in proteins with application to structure prediction

We recently developed the Rosetta algorithm for ab initio protein structure prediction, which generates protein structures from fragment libraries using simulated annealing. The scoring function in this algorithm favors the assembly of strands into sheets. However, it does not discriminate between different sheet motifs. After generating many structures using Rosetta, we found that the folding algorithm predominantly generates very local structures. We surveyed the distribution of beta-sheet motifs with two edge strands (open sheets) in a large set of non-homologous proteins. We investigated how much of that distribution can be accounted for by rules previously published in the literature, and developed a filter and a scoring method that enables us to improve protein structure prediction for beta-sheet proteins. Proteins 2002;48:85-97.     

On the Limitations of Using Ribosomal Genes as References for the Study of Codon Usage: A Rebuttal

In a recent paper published in PLOS ONE, Wang et al. challenge our finding that the identity of optimal codons in different genomes follows a set of clear rules. Here we provide a rebuttal of their paper and demonstrate that the results of our original PLOS Genetics paper stand. This provides us with an opportunity to bring up an aspect of how codon usage has been studied that should be of general interest. The Wang et al. study, as well as many other studies, used ribosomal genes as a reference set for the study of patterns of codon usage. We discuss here the assumptions that are made in order to justify using ribosomal genes to study codon bias, suggest that this practice can at times be problematic, and discuss its limitations.     

Protein structure prediction using sparse NOE and RDC restraints with Rosetta in CASP13

Computational methods that produce accurate protein structure models from limited experimental data, for example, from nuclear magnetic resonance (NMR) spectroscopy, hold great potential for biomedical research. The NMR-assisted modeling challenge in CASP13 provided a blind test to explore the capabilities and limitations of current modeling techniques in leveraging NMR data which had high sparsity, ambiguity, and error rate for protein structure prediction. We describe our approach to predict the structure of these proteins leveraging the Rosetta software suite. Protein structure models were predicted de novo using a two-stage protocol. First, low-resolution models were generated with the Rosetta de novo method guided by nonambiguous nuclear Overhauser effect (NOE) contacts and residual dipolar coupling (RDC) restraints. Second, iterative model hybridization and fragment insertion with the Rosetta comparative modeling method was used to refine and regularize models guided by all ambiguous and nonambiguous NOE contacts and RDCs. Nine out of 16 of the Rosetta de novo models had the correct fold (global distance test total score > 45) and in three cases high-resolution models were achieved (root-mean-square deviation < 3.5 å). We also show that a meta-approach applying iterative Rosetta + NMR refinement on server-predicted models which employed non-NMR-contacts and structural templates leads to substantial improvement in model quality. Integrating these data-assisted refinement strategies with innovative non-data-assisted approaches which became possible in CASP13 such as high precision contact prediction will in the near future enable structure determination for large proteins that are outside of the realm of conventional NMR.     

Construction and Characterization of T7 Bacteriophages Harboring Apidaecin-Derived Sequences

The global spread of multi- and pan-resistant bacteria has triggered research to identify novel strategies to fight these pathogens, such as antimicrobial peptides and, more recently, bacteriophages. In a proof-of-concept study, we have genetically modified lytic T7Select phages targeting Escherichia coli Rosetta by integrating DNA sequences derived from the proline-rich antimicrobial peptide, apidaecin. This allowed testing of our hypothesis that apidaecins and bacteriophages can synergistically act on phage-sensitive and phage-resistant E. coli cells and overcome the excessive cost of peptide drugs by using infected cells to express apidaecins before cell lysis. Indeed, the addition of the highly active synthetic apidaecin analogs, Api802 and Api806, to T7Select phage-infected E. coli Rosetta cultures prevented or delayed the growth of potentially phage-resistant E. coli Rosetta strains. However, high concentrations of Api802 also reduced the T7Select phage fitness. Additionally, plasmids encoding Api802, Api806, and Api810 sequences transformed into E. coli Rosetta allowed the production of satisfactory peptide quantities. When these sequences were integrated into the T7Select phage genome carrying an N-terminal green fluorescent protein (GFP-) tag to monitor the expression in infected E. coli Rosetta cells, the GFP–apidaecin analogs were produced in reasonable quantities. However, when Api802, Api806 and Api810 sequences were integrated into the T7Select phage genome, expression was below detection limits and an effect on the growth of potentially phage-resistant E. coli Rosetta strains was not observed for Api802 and Api806. In conclusion, we were able to show that apidaecins can be integrated into the T7Select phage genome to induce their expression in host cells, but further research is required to optimize the engineered T7Select phages for higher expression levels of apidaecins to achieve the expected synergistic effects that were visible when the T7Select phages and synthetic Api802 and Api806 were added to E. coli Rosetta cultures.     

Neues aus der Paläoneurologie

Progress in paleontological brain research is demonstrated by giving some examples of recent discoveries which illustrate the various possibilities of studies in this field. An enlarged English text, with details and figures of the specimens cited, will be published in the Proceedings of the 3rd International Conference of Neurobiologists.     

Collection Overview: Ten Years of Wonderful Open Access Science

To mark our tenth Anniversary at PLOS Biology, we are launching a special, celebratory Tenth Anniversary PLOS Biology Collection which showcases 10 specially selected PLOS Biology research articles drawn from a decade of publishing excellent science. It also features newly commissioned articles, including thought-provoking pieces on the Open Access movement (past and present), on article-level metrics, and on the history of the Public Library of Science. Each research article highlighted in the collection is also accompanied by a PLOS Biologue blog post to extend the impact of these remarkable studies to the widest possible audience.As we celebrate 10 years of PLOS Biology, 10 years of the Public Library of Science, and 10 years of strong advocacy and trail-blazing for the Open Access movement, we mustn''t forget the real star of the show – the fantastic science that we''ve published.It''s hard to cast one''s mind back 10 years and recall the scepticism with which open access publishing was initially received. A key concern at the time was that the model would be tainted with the stigma of “vanity publishing,” and that this model, in which the author pays to publish, is incompatible with integrity, editorial rigour, and scientific excellence. As also discussed in the accompanying editorial [1], the sheer quality of the science that has appeared in PLOS Biology has been vital for dispelling this myth.Our tenth anniversary provides us with a great opportunity to celebrate all of the 1800 or so research articles published in PLOS Biology since our launch in 2003. Unable to showcase each one in turn, we turned to our Editorial Board to help us pick the top 10 research articles to feature in a special Tenth Anniversary PLOS Biology Collection (www.ploscollections.org/Biology10thAnniversary). During the month of October, we will also publish a PLOS Biologue blog post (http://blogs.plos.org/biologue/) for each of these selected research articles, trying to capture and convey what it is about them that the staff editors, the editorial board, and the authors feel is special.By now, you''re probably wondering which papers we selected. The selection is detailed in Box 1, with links to each article. If you haven''t read these articles before, we urge you to read them now and to judge for yourself. As Editorial Board Member Steve O''Rahilly put it, “I think a common theme in many of the best PLOS Biology papers is that they are rich in data that is analysed very carefully and self-critically and presented without hype. However the conclusions are important for the biological community and their insights are likely to stand the test of time.”As well as publishing research articles, PLOS Biology has a thriving Magazine section that has hosted scientific and policy debates, aired polemical and provocative views, celebrated scientific lives in obituaries, reviewed interesting books, and explored unsolved mysteries. One example of how this section has triggered productive community debate is Rosie Redfield''s Perspective on how genetics should be taught to undergraduates [2]. Yet we don''t seek just to provoke debate, but also to enlighten; take a moment to read Georgina Mace''s editorial on the current issues and debates in the sustainability sciences [3]. We also try to break down barriers between fields [4] and to promote public engagement with science [5],[6].We feel strongly that our role doesn''t end with publishing the research article itself. Instead, we aim to unpackage the fascinating discoveries published in PLOS Biology by commissioning articles that explain the significance and impact of the research we publish to audiences of varying expertise. These companion articles range from Primers, which are written by experts who contextualise research articles for those in the field; to Synopses, which are written by science writers who digest an article for our wider readership of biologists; and finally, to PLOS Biologue blog posts, which distil research discoveries for a more general scientifically engaged public. We also use social media to bring these findings to the attention of a global online audience.Of course, the continued success of PLOS Biology doesn''t rest solely on the amazing research we''ve already published; it also hinges on the ground-breaking science we strive to publish in the future. Maintaining the high quality of the biology that we publish is of vital importance to us, not least because, as Editorial Board Member Robert Insall reflects, “What I like about PLOS Biology is that it avoids other journals'' fixation on fashion and the biggest names. This means the papers PLOS Biology is publishing now will last longer and mean more in a generation''s time.”

Box 1. Research Articles Featured in the Tenth Anniversary PLOS Biology Collection

Our Editorial Board Members helped us select 10 articles from the great science published during PLOS Biology''s first decade to feature in our Tenth Anniversary Collection. Please access these articles from the list below and from our Collection page. To read the PLOS Biologue blog posts that accompany them, please go to http://blogs.plos.org/biologue/ for more information.Carmena J et al. (2003) Learning to Control a BrainMachine Interface for Reaching and Grasping by Primates  Primer: Current Approaches to the Study of Movement Control  Synopsis: Retraining the Brain to Recover Movement Brennecke J et al. (2004) Principles of MicroRNA–Target Recognition  Synopsis: Seeds of Destruction: Predicting How microRNAs Choose Their Target Voight BF et al. (2005) A Map of Recent Positive Selection in the Human Genome  Synopsis: Clues to Our Past: Mining the Human Genome for Signs of Recent Selection Palmer C et al. (2007) Development of the Human Infant Intestinal Microbiota  Synopsis: Microbes Colonize a Baby''s Gut with Distinction Levy S et al. (2007) The Diploid Genome Sequence of an Individual Human  Synopsis: A New Human Genome Sequence Paves the Way for Individualized Genomics Illingworth R et al. (2008) A Novel CpG Island Set Identifies Tissue-Specific Methylation at Developmental Gene Loci Silva J et al. (2008) Promotion of Reprogramming to Ground State Pluripotency by Signal Inhibition  Synopsis: A Shortcut to Immortality: Rapid Reprogramming with Tissue Cells Coppé J-P et al. (2008) Senescence-Associated Secretory Phenotypes Reveal Cell-Nonautonomous Functions of Oncogenic RAS and the p53 Tumor Suppressor Shu X et al. (2011) A Genetically Encoded Tag for Correlated Light and Electron Microscopy of Intact Cells, Tissues, and Organisms Bonds MH et al. (2012) Disease Ecology, Biodiversity, and the Latitudinal Gradient in Income  Synopsis: Which Came First: Burden of Infectious Disease or Poverty?     

The PyRosetta Toolkit: A Graphical User Interface for the Rosetta Software Suite

The Rosetta Molecular Modeling suite is a command-line-only collection of applications that enable high-resolution modeling and design of proteins and other molecules. Although extremely useful, Rosetta can be difficult to learn for scientists with little computational or programming experience. To that end, we have created a Graphical User Interface (GUI) for Rosetta, called the PyRosetta Toolkit, for creating and running protocols in Rosetta for common molecular modeling and protein design tasks and for analyzing the results of Rosetta calculations. The program is highly extensible so that developers can add new protocols and analysis tools to the PyRosetta Toolkit GUI.     

斑马鱼基因ATF4多克隆抗体的制备

ATF4是含有bZIP结构域的ATF／CREB转录因子家族成员,对胚胎的发育以及细胞的增殖、分化有重要的调节作用。制备ATF4的多克隆抗体对于研究其在斑马鱼心脏发育过程中的作用有重要的意义。研究首先通过生物信息学方法,选择ATF4基因中特异性强、具亲水性的一段核苷酸序列（1017bp）,通过PCR扩增,将片段重组到原核表达载体pET-28a,然后转化入Rosetta菌株中。经测序鉴定正确后,用IPTG诱导表达融合蛋白,以该融合蛋白免疫小鼠,获得ATF4多克隆抗鼠血清。对该多抗血清抗体进行验证,具有很好特异性和较高效价,可以用作Western—blotting、免疫印迹等试验分析。     

Canadian contributions to research on neglected tropical diseases

BackgroundThe World Health Organization’s (WHO) Neglected Tropical Disease (NTD) Road Map for 2021–2030 was recently endorsed by all member states at the World Health Assembly in November 2020. Although only 3 of the 20 NTDs are endemic in Canada (i.e., echinococcosis, rabies, and scabies), the Canadian research community has contributed to advancing the knowledge base of all 20 NTDs. Previous research comprehensively detailed Canadian research on 11 NTDs between 1950 and 2010 using a network analysis approach. The specific objective of the present analysis was to update the publication record over the last decade (2010–2019) to include all 20 NTDs.Materials and methodsA bibliometric analysis was conducted in Scopus and Web of Science databases (for English or French articles published between January 1, 2010 and December 31, 2019) using appropriate search terms for each of the 20 NTDs and where at least 1 of the authors had a Canadian institution address. A 21st search was added to include publications including multiple NTDs or a discussion of NTDs in general. Following assessment of inclusion and exclusion criteria, 2 reviewers independently screened all abstracts, with discordant observations rereviewed to arrive at an agreement. Duplicates were removed.ResultsA total of 1,790 publications were retrieved (1,738 with a disease–specific NTD focus and 52 with a general NTD focus, resulting in 1,659 unique publications), giving an average of over 160 articles per year. Over 80% were classified as full–length research articles. The top 3 journals in terms of frequency were PLOS Neglected Tropical Diseases, PLOS ONE, and the American Journal of Tropical Medicine and Hygiene. Authors’ institutions were from all Canadian provinces. While all 20 NTDs were addressed in these publications, the 5 most commonly studied were leishmaniasis, dengue fever and chikungunya, Chagas disease, soil–transmitted helminthiases, and rabies.ConclusionsCanadian researchers across the country have contributed to the evidence base of all 20 NTDs, publishing an average of over 160 publications per year between 2010 and 2019. As WHO NTD Road Map 2021–2030 rolls out globally, the Canadian research community, in collaboration with its partners and in solidarity with people living in vulnerable circumstances in endemic regions worldwide, is well positioned to meet future research challenges so that the goal of eliminating the disease burden attributable to NTDs can be achieved.     

An overview of methods for the detection and observation of arbuscular mycorrhizal fungi in roots†

One of the most cited papers in arbuscular mycorrhizal (AM) research was published by Phillips and Hayman in 1970 describing an easy standard method to stain AM fungi (AMF) in roots. Since then, a number of other methods (destructive–non-destructive; vital–non-vital) on how to visualize AMF in roots have been published. Our review provides an overview on present techniques used to visualize AMF in roots and gives recommendations on their use. We hope that the present review will help the readers to choose an appropriate method to visualize AMF in roots for their specific experimental set-up.     

Current topics in organogenesis and gametogenesis

At the 49(th) Annual Drosophila Research Conference from April 3-8, 2008 in San Diego there were eight talks and over ninety posters in the section on Organogenesis and Gametogenesis. These covered a wide range of topics within the two broad categories of organ-specific stem cells (including germ cells) and organ-specific developmental programs. Here we discuss eleven of these presentations describing current research into the formation of the gonad, intestine, trachea, muscle and leg joint. The new insights presented advance our understanding of the molecular events that underlie interactions between stem cells and their niches as well as mechanisms underlying tissue-specific differentiation programs.     

High-level production of bacillus subtilis glycine oxidase by fed-batch cultivation of recombinant Escherichia coli Rosetta (DE3)

A fed-batch process for the high cell density cultivation of Escherichia coli Rosetta (DE3) and the production of the recombinant protein glycine oxidase (GOX) from Bacillus subtilis was developed. GOX is a deaminating enzyme that shares substrate specificity with d-amino acid oxidase and sarcosine oxidase and has great biotechnological potential. The B. subtilis gene coding for GOX was expressed in E. coli Rosetta under the strong inducible T7 promotor of the pET28a vector. Exponential feeding based on the specific growth rate and a starvation period for acetate utilization was used to control cell growth, acetate production, and reconsumption and glucose consumption during fed-batch cultivation. Expression of GOX was induced at three different cell densities (20, 40, and 60 g . L(-1)). When cells were induced at intermediate cell density, the amount of GOX produced was 20 U . g(-1) cell dry weight and 1154 U . L(-1) with a final intracellular protein concentration corresponding to approximately 37% of the total cell protein concentration. These values were higher than those previously published for GOX expression and also represent a drastic decrease of 26-fold in the cost of the culture medium.     

Synopsis of the International Gap Junction Conference in Elsinore, Denmark August 5-9, 2007

This synopsis covers the main results and conclusions from the platform presentations during the International Gap Junction Conference. More detailed information is provided in the mini reviews on controversial scientific issues, short reports of research results and conference abstracts published in this issue of Cell Communication and Adhesion.