DNA sequence homology between attB-related sites of Corynebacterium diphtheriae, Corynebacterium ulcerans, Corynebacterium glutamicum, and the attP side of γ-Cornephage

Chromosomal restriction fragments of Corynebacterium ulcerans and C. diphtheriae, containing an integration site for corynephages of the beta family, show homology on Southern blots. Homologous DNA in also found in the soil isolate C. glutamicum, although this strain is not susceptible to beta-corynephages. Three of these DNA fragments, one for each bacterial strain, and a fragment of gamma-corynephage DNA previously shown to contain the phage integration site, were cloned and sequenced. Alignment of the 3 bacterial sequences shows a very high degree of homology in a stretch of ca 120 nucleotides, whereas the rest of the sequences is generally non-homologous. Within this common bacterial portion, a segment of ca. 96 nucleotides (core sequence) is also highly homologous to the phage sequence. The first half (ca. 50 bp) of the core sequence is identical in all aligned sequences whereas the second half, which is largely occupied by a stem-and-loop structure, contains point mutations peculiar to each clone. The described sequences are likely to be involved in phage integration/excision processes.     

Revisiting Street Intersections Using Slot-Based Systems

Since their appearance at the end of the 19th century, traffic lights have been the primary mode of granting access to road intersections. Today, this centuries-old technology is challenged by advances in intelligent transportation, which are opening the way to new solutions built upon slot-based systems similar to those commonly used in aerial traffic: what we call Slot-based Intersections (SIs). Despite simulation-based evidence of the potential benefits of SIs, a comprehensive, analytical framework to compare their relative performance with traffic lights is still lacking. Here, we develop such a framework. We approach the problem in a novel way, by generalizing classical queuing theory. Having defined safety conditions, we characterize capacity and delay of SIs. In the 2-road crossing configuration, we provide a capacity-optimal SI management system. For arbitrary intersection configurations, near-optimal solutions are developed. Results theoretically show that transitioning from a traffic light system to SI has the potential of doubling capacity and significantly reducing delays. This suggests a reduction of non-linear dynamics induced by intersection bottlenecks, with positive impact on the road network. Such findings can provide transportation engineers and planners with crucial insights as they prepare to manage the transition towards a more intelligent transportation infrastructure in cities.     

ECOLOGICAL AND EVOLUTIONARY IMPLICATIONS OF CARBON ALLOCATION IN MARINE PHYTOPLANKTON AS A FUNCTION OF NITROGEN AVAILABILITY: A FOURIER TRANSFORM INFRARED SPECTROSCOPY APPROACH1

An imbalance in the cellular C:N ratio may appreciably affect C allocation in algal cells. The consequences of these rearrangements of cellular pools on cell energetics, ecological fitness, and evolutionary trajectories are little known, although they are expected to be substantial. We investigated the fate of C in 11 microalgae cultured semicontinuously at three [NO₃^?] and constant pCO₂. We developed a new computational method for the semiquantitative use of Fourier transform infrared (FTIR) spectroscopy data for the determination of macromolecular composition. No obvious relationship was observed between the taxonomy and the allocation strategies adopted by the 11 species considered in this study. Not all species responded to a lower N availability by accumulating lipids or carbohydrates: Dunaliella parva W. Lerche and Thalassiosira pseudonana Hasle et Heimdal were homeostatic with respect to organic cell composition. A hyperbolic dependence of the lipid concentration from cell volume was observed. The level of reduction of organic constituents of green algae was parabolically related to size and was modulated in response to changes in N availability; the same was not true for the species bearing a “red” chloroplast. The above observations are discussed with respect to phytoplankton species composition and palatability for grazers, oleogenesis, and overall cell energetics.     

β-Glucan Induces Reactive Oxygen Species Production in Human Neutrophils to Improve the Killing of Candida albicans and Candida glabrata Isolates from Vulvovaginal Candidiasis

Vulvovaginal candidiasis (VVC) is among the most prevalent vaginal diseases. Candida albicans is still the most prevalent species associated with this pathology, however, the prevalence of other Candida species, such as C. glabrata, is increasing. The pathogenesis of these infections has been intensely studied, nevertheless, no consensus has been reached on the pathogenicity of VVC. In addition, inappropriate treatment or the presence of resistant strains can lead to RVVC (vulvovaginal candidiasis recurrent). Immunomodulation therapy studies have become increasingly promising, including with the β-glucans. Thus, in the present study, we evaluated microbicidal activity, phagocytosis, intracellular oxidant species production, oxygen consumption, myeloperoxidase (MPO) activity, and the release of tumor necrosis factor α (TNF-α), interleukin-8 (IL-8), IL-1β, and IL-1Ra in neutrophils previously treated or not with β-glucan. In all of the assays, human neutrophils were challenged with C. albicans and C. glabrata isolated from vulvovaginal candidiasis. β-glucan significantly increased oxidant species production, suggesting that β-glucan may be an efficient immunomodulator that triggers an increase in the microbicidal response of neutrophils for both of the species isolated from vulvovaginal candidiasis. The effects of β-glucan appeared to be mainly related to the activation of reactive oxygen species and modulation of cytokine release.     

Junk or functional DNA? ENCODE and the function controversy

In its last round of publications in September 2012, the Encyclopedia Of DNA Elements (ENCODE) assigned a biochemical function to most of the human genome, which was taken up by the media as meaning the end of ‘Junk DNA’. This provoked a heated reaction from evolutionary biologists, who among other things claimed that ENCODE adopted a wrong and much too inclusive notion of function, making its dismissal of junk DNA merely rhetorical. We argue that this criticism rests on misunderstandings concerning the nature of the ENCODE project, the relevant notion of function and the claim that most of our genome is junk. We argue that evolutionary accounts of function presuppose functions as ‘causal roles’, and that selection is but a useful proxy for relevant functions, which might well be unsuitable to biomedical research. Taking a closer look at the discovery process in which ENCODE participates, we argue that ENCODE’s strategy of biochemical signatures successfully identified activities of DNA elements with an eye towards causal roles of interest to biomedical research. We argue that ENCODE’s controversial claim of functionality should be interpreted as saying that 80 % of the genome is engaging in relevant biochemical activities and is very likely to have a causal role in phenomena deemed relevant to biomedical research. Finally, we discuss ambiguities in the meaning of junk DNA and in one of the main arguments raised for its prevalence, and we evaluate the impact of ENCODE’s results on the claim that most of our genome is junk.     

Cities through the Prism of People’s Spending Behavior

Scientific studies of society increasingly rely on digital traces produced by various aspects of human activity. In this paper, we exploit a relatively unexplored source of data–anonymized records of bank card transactions collected in Spain by a big European bank, and propose a new classification scheme of cities based on the economic behavior of their residents. First, we study how individual spending behavior is qualitatively and quantitatively affected by various factors such as customer’s age, gender, and size of his/her home city. We show that, similar to other socioeconomic urban quantities, individual spending activity exhibits a statistically significant superlinear scaling with city size. With respect to the general trends, we quantify the distinctive signature of each city in terms of residents’ spending behavior, independently from the effects of scale and demographic heterogeneity. Based on the comparison of city signatures, we build a novel classification of cities across Spain in three categories. That classification exhibits a substantial stability over different city definitions and connects with a meaningful socioeconomic interpretation. Furthermore, it corresponds with the ability of cities to attract foreign visitors, which is a particularly remarkable finding given that the classification was based exclusively on the behavioral patterns of city residents. This highlights the far-reaching applicability of the presented classification approach and its ability to discover patterns that go beyond the quantities directly involved in it.     

A Rapid Protocol of Crude RNA/DNA Extraction for RT-qPCR Detection and Quantification of 'Candidatus Phytoplasma prunorum'

Many efforts have been made to develop a rapid and sensitive method for phytoplasma and virus detection. Taking our cue from previous works, different rapid sample preparation methods have been tested and applied to Candidatus Phytoplasma prunorum (‘Ca. P. prunorum’) detection by RT-qPCR. A duplex RT-qPCR has been optimized using the crude sap as a template to simultaneously amplify a fragment of 16S rRNA of the pathogen and 18S rRNA of the host plant. The specific plant 18S rRNA internal control allows comparison and relative quantification of samples. A comparison between DNA and RNA contribution to qPCR detection is provided, showing higher contribution of the latter. The method presented here has been validated on more than a hundred samples of apricot, plum and peach trees. Since 2013, this method has been successfully applied to monitor ‘Ca. P. prunorum’ infections in field and nursery. A triplex RT-qPCR assay has also been optimized to simultaneously detect ‘Ca. P. prunorum’ and Plum pox virus (PPV) in Prunus.     

Did sulfate availability facilitate the evolutionary expansion of chlorophyll a+c phytoplankton in the oceans?

During the Mesozoic Era, dinoflagellates, coccolithophorids and diatoms became prominent primary producers in the oceans, succeeding an earlier biota in which green algae and cyanobacteria had been proportionally more abundant. This transition occurred during an interval marked by increased sulfate concentration in seawater. To test whether increasing sulfate availability facilitated the evolutionary transition in marine phytoplankton, the cyanobacterium Synechococcus sp., the green alga Tetraselmis suecica and three algae containing chlorophyll a+c (the diatom Thalassiosira weissflogii, the dinoflagellate Protoceratium reticulatum and the coccolithophorid Emiliania huxleyi) were grown in media containing 1, 5, 10, 20, or 30 mm SO(4) (2-) . The cyanobacterium and the green alga showed no growth response to varying [SO(4) (2-) ]. By contrast, the three chlorophyll a+c algae showed improved growth with higher [SO(4) (2-) ], but only up to 10 mm. The chlorophyll a+c algae, but not the green alga or cyanobacterium, also showed lower C:S with higher [SO(4) (2-) ]. When the same experiment was repeated in the presence of a ciliate predator (Euplotes sp.), T. suecica and T. weissflogii increased their specific growth rate in most treatments, whereas the growth rate of Synechococcus sp. was not affected or decreased in the presence of grazers. In a third experiment, T. suecica, T. weissflogii, P. reticulatum and Synechococcus sp. were grown in conditions approximating modern, earlier Paleozoic and Proterozoic seawater. In these treatments, sulfate availability, nitrogen source, metal availability and Pco(2) varied. Monospecific cultures exhibited their highest growth rates in the Proterozoic treatment. In mixed culture, T. weissflogii outgrew other species in modern seawater and T.suecica outgrew the others in Paleozoic water. Synechococcus sp. grew best in Proterozoic seawater, but did not outgrow eukaryotic species in any treatment. Collectively, our results suggest that secular increase in seawater [SO(4) (2-) ] may have facilitated the evolutionary expansion of chlorophyll a+c phytoplankton, but probably not to the exclusion of other biological and environmental factors.     

Chiral tetrahydroquinoline derivatives as potent anti-hyperalgesic agents in animal models of sustained inflammation and chronic neuropathic pain

Chiral tetrahydroquinoline derivatives have been prepared by an asymmetric Mannich-type condensation reaction using commercially available vinyloxyethylsilane and a N-arylimino R-(+)-t-butyl lactate ester, in the presence of a catalytic amount of metal triflates as Lewis acids. This synthetic approach gave rise to the target aldehyde intermediate in moderate facial diastereoselectivity and in high chemical yield. This efficient route enabled to scale up the synthesis of an orally bioavailable glycine antagonist showing outstanding in vivo anti-hyperalgesic activity in different animal models of sustained inflammation and chronic neuropathic pain.