VirB2 and VirB5 proteins: specialized adhesins in bacterial type-IV secretion systems?

Many type-IV secretion systems (T4SSs) of plant and human pathogens assemble a pilus used to inject virulence molecules (effectors) into host target cells. The T4SS of Agrobacterium tumefaciens consists of VirB1-VirB11 and VirD4 proteins. Whether targeting of T4SSs to the host requires a T4SS-adhesin that specifically engages host receptors for delivery of effectors has, until recently, remained unclear. Recent data of Agrobacterium and Helicobacter indicate that two classes of T4SS components, VirB2 and VirB5, might function as adhesins that mediate host-cell targeting through binding to specific host receptors. Here, we discuss this important issue and recent progress in the field.     

Otd/Crx,a dual regulator for the specification of ommatidia subtypes in the Drosophila retina

Comparison between the inputs of photoreceptors with different spectral sensitivities is required for color vision. In Drosophila, this is achieved in each ommatidium by the inner photoreceptors R7 and R8. Two classes of ommatidia are distributed stochastically in the retina: 30% contain UV-Rh3 in R7 and blue-Rh5 in R8, while the remaining 70% contain UV-Rh4 in R7 and green-Rh6 in R8. We show here that the distinction between the rhodopsins expressed in the two classes of ommatidia depends on a series of highly conserved homeodomain binding sites present in the rhodopsin promoters. The homeoprotein Orthodenticle acts through these sites to activate rh3 and rh5 in their specific ommatidial subclass and through the same sites to prevent rh6 expression in outer photoreceptors. Therefore, Otd is a key player in the terminal differentiation of subtypes of photoreceptors by regulating rhodopsin expression, a function reminiscent of the role of one of its mammalian homologs, Crx, in eye development.     

Long‐term decline despite conservation efforts questions Eurasian Stone‐curlew population viability in intensive farmlands

Agricultural intensification over the past decades has led to a generalized decline in farmland biodiversity. Farmland birds are particularly exposed to rapid changes in habitat and reduced food resources or availability. Understanding how farmland specialists can be preserved and their populations enhanced are major challenges for this century. Based on a long‐term (19‐year) study of a Eurasian Stone‐curlew Burhinus oedicnemus population, we estimated the demographic parameters, including clutch size, egg volume, hatching success, survival rate and apparent population size. Demographic rates found for this French population were, on average, comparable to those found elsewhere in Europe. However, all demographic parameters showed negative trends, including a dramatic decline in the local population (26% decline over 14 years) and a 10% decline in adult survival rate over 11 years. Such a long‐term decline, despite on‐going conservation efforts, calls into question the overall sustainability of arable Stone‐curlew populations. We infer some of the possible causes of this decline, in particular food shortage, and discuss how this pattern could be reversed through conservation measures applicable at very large spatial scales.     

Seasonal variation and the immune response: a fish perspective

The environment in which an animal lives affects the physiology and psychology of that animal. The greater the distance from the equator the more profound this influence becomes, as the environment becomes more variable over the years. Temperature, photoperiod, precipitation and other environmental conditions, which are directly or indirectly controlled by the season, can affect an animal. It is becoming apparent that these conditions may impact on the immune system, and this can affect animal health. This review looks at the known mechanisms for transducing environmental cues and how these can affect immune parameters and function. The main focus is fish, especially in relation to aquaculture and the associated disease risks. Work on other animal classes is included for comparison.     

Do-it-yourself biology: challenges and promises for an open science and technology movement

The do-it-yourself biology (DIYbio) community is emerging as a movement that fosters open access to resources permitting modern molecular biology, and synthetic biology among others. It promises in particular to be a source of cheaper and simpler solutions for environmental monitoring, personal diagnostic and the use of biomaterials. The successful growth of a global community of DIYbio practitioners will depend largely on enabling safe access to state-of-the-art molecular biology tools and resources. In this paper we analyze the rise of DIYbio, its community, its material resources and its applications. We look at the current projects developed for the international genetically engineered machine competition in order to get a sense of what amateur biologists can potentially create in their community laboratories over the coming years. We also show why and how the DIYbio community, in the context of a global governance development, is putting in place a safety/ethical framework for guarantying the pursuit of its activity. And finally we argue that the global spread of DIY biology potentially reconfigures and opens up access to biological information and laboratory equipment and that, therefore, it can foster new practices and transversal collaborations between professional scientists and amateurs.     

HPLC Measurement of the DNA Oxidation Biomarker, 8-oxo-7,8-dihydro-2’-deoxyguanosine,in Cultured Cells and Animal Tissues

Oxidative stress is associated with many physiological and pathological processes, as well as xenobiotic metabolism, leading to the oxidation of biomacromolecules, including DNA. Therefore, efficient detection of DNA oxidation is important for a variety of research disciplines, including medicine and toxicology. A common biomarker of oxidatively damaged DNA is 8-oxo-7,8-dihydro-2''-deoxyguanosine (8-oxo-dGuo; often erroneously referred to as 8-hydroxy-2''-deoxyguanosine (8-OH-dGuo or 8-oxo-dG)). Several protocols for 8-oxo-dGuo measurement by high pressure liquid chromatography with electrochemical detection (HPLC-ED) have been described. However, these were mainly applied to purified DNA treated with pro-oxidants. In addition, due to methodological differences between laboratories, mainly due to differences in analytical equipment, the adoption of published methods for detection of 8-oxo-dGuo by HPLC-ED requires careful optimization by each laboratory. A comprehensive protocol, describing such an optimization process, is lacking. Here, a detailed protocol is described for the detection of 8-oxo-dGuo by HPLC-ED, in DNA from cultured cells or animal tissues. It illustrates how DNA sample preparation can be easily and rapidly optimized to minimize undesirable DNA oxidation that can occur during sample preparation. This protocol shows how to detect 8-oxo-dGuo in cultured human alveolar adenocarcinoma cells (i.e., A549 cells) treated with the oxidizing agent KBrO₃, and from the spleen of mice exposed to the polycyclic aromatic hydrocarbon dibenzo(def,p)chrysene (DBC, formerly known as dibenzo(a,l)pyrene, DalP). Overall, this work illustrates how an HPLC-ED methodology can be readily optimized for the detection of 8-oxo-dGuo in biological samples.     

Microbial Contents of Vacuum Cleaner Bag Dust and Emitted Bioaerosols and Their Implications for Human Exposure Indoors

Vacuum cleaners can release large concentrations of particles, both in their exhaust air and from resuspension of settled dust. However, the size, variability, and microbial diversity of these emissions are unknown, despite evidence to suggest they may contribute to allergic responses and infection transmission indoors. This study aimed to evaluate bioaerosol emission from various vacuum cleaners. We sampled the air in an experimental flow tunnel where vacuum cleaners were run, and their airborne emissions were sampled with closed-face cassettes. Dust samples were also collected from the dust bag. Total bacteria, total archaea, Penicillium/Aspergillus, and total Clostridium cluster 1 were quantified with specific quantitative PCR protocols, and emission rates were calculated. Clostridium botulinum and antibiotic resistance genes were detected in each sample using endpoint PCR. Bacterial diversity was also analyzed using denaturing gradient gel electrophoresis (DGGE), image analysis, and band sequencing. We demonstrated that emission of bacteria and molds (Penicillium/Aspergillus) can reach values as high as 1E5 cell equivalents/min and that those emissions are not related to each other. The bag dust bacterial and mold content was also consistent across the vacuums we assessed, reaching up to 1E7 bacterial or mold cell equivalents/g. Antibiotic resistance genes were detected in several samples. No archaea or C. botulinum was detected in any air samples. Diversity analyses showed that most bacteria are from human sources, in keeping with other recent results. These results highlight the potential capability of vacuum cleaners to disseminate appreciable quantities of molds and human-associated bacteria indoors and their role as a source of exposure to bioaerosols.