Information is Specific to Life

Analyses of bacterial genomes suggest that horizontal genetic transfer was an important process in the acquisition of new functions. Models of bacterial diversification are explored in detail in this chapter. Although the rate of horizontal transfer in Escherichia coli is substantial, and potentially useful information has been delivered in the form of selfish operons, it is clear that bacterial genomes are not growing ever larger in size; it is also clear that particular bacterial strains exhibit a definable set of metabolic capabilities and certainly do not perform every biochemical function possible. The acquired sequences—when they are maintained by natural selection and show signs of amelioration—must provide a selectable function that contributes to cellular fitness, few point mutation changes are likely to improve cellular fitness. For this reason, acquired genes are more likely to contribute to the long-term evolution of bacterial species than are point mutations. Both mutational processes and horizontal genetic transfer have allowed diversity of bacterial species in soils to arise from the common ancestor of all known life. If the roles of horizontal genetic transfer and chromosomal deletion are considered in shaping the composition of bacterial chromosomes, we can see that the mode of genome evolution has strong implications for how bacteria diversify. More recent work examining the role played by laterally transferred genes in lineage diversification concluded that the acquisition of laterally acquired genes (like the cob operons in Salmonella) was the initiating event leading to genetic isolation between bacterial species.

Streptococcus pneumoniae is an important global pathogen that causes bacterial pneumonia, sepsis and meningitis. Beta-lactam antibiotics are the first-line treatment for pneumococcal disease, however, their effectiveness is hampered by beta-lactam resistance facilitated by horizontal genetic transfer (HGT) with closely related species. Although interspecies HGT is known to occur among the species of the genus Streptococcus , the rates and effects of HGT between Streptococcus pneumoniae and its close relatives involving the penicillin binding protein (pbp) genes remain poorly understood. Here we applied the fastGEAR tool to investigate interspecies HGT in pbp genes using a global collection of whole-genome sequences of Streptococcus mitis , Streptococcus oralis and S. pneumoniae . With these data, we established that pneumococcal serotypes 6A, 13, 14, 16F, 19A, 19F, 23F and 35B were the highest-ranking serotypes with acquired pbp fragments. S. mitis was a more frequent pneumococcal donor of pbp fragments and a source of higher pbp nucleotide diversity when compared with S. oralis . Pneumococci that acquired pbp fragments were associated with a higher minimum inhibitory concentration (MIC) for penicillin compared with pneumococci without acquired fragments. Together these data indicate that S. mitis contributes to reduced β-lactam susceptibility among commonly carried pneumococcal serotypes that are associated with long carriage duration and high recombination frequencies. As pneumococcal vaccine programmes mature, placing increasing pressure on the pneumococcal population structure, it will be important to monitor the influence of antimicrobial resistance HGT from commensal streptococci such as S. mitis .

Activation of retroviruses in normal cells can induce tumors and a wide array of cancers contains retrovirus-like particles. The potential role of these endogenous retroviruses in the development and progression of tumors has been discussed in many studies. However the effects of retrovirus insertion into cancer cells have not yet been fully examined. In this study, we explore genetic material transfer either between retrovirus-transduced prostate cancer PC3 cells or between PC3 cells and their host environment through extracellular vesicles (EV) and virus-like particles. For these purposes, we transduced PC3 cells with either GFP-encoding retrovirus or with m-cherry-encoding lentivirus. Co-incubation of GFP-expressing cells with m-cherry-expressing cells for 72h yielded yellow PC3 cells. Yellow cells were also observed in the experiments where lentiviral m-cherry expressing PC3 cells were cultured with tissue culture medium from retrovirus GFP expressing PC3 cells. These results indicated that horizontal genetic information transfer involves neither fusion nor contact between the cells. Since incubation of the retrovirus GFP-expressing PC3 cells with the medium from the lentivirus m-cherry expressing PC3 cells, did not yield yellow cells the genetic material transfer requires retrovirus insertion in PC3 cells. Using Western blot and Q-PCR, we found the exosomes from the medium generated by retrovirus GFP expressing PC3 cells to carry human endogenous retroviral proteins syncytin 1 and 2 and contain RNAs encoding these proteins. Exosomes from the lentivirus m-cherry expressing PC3 cells had lower protein expression of Syncytin 1&2 than exosomes from retrovirus GFP expressing PC3 cells. Application of Syncytin 1 or 2 antibodies to the medium generated by or co-cultured retrovirus GFP expressing PC3 and lentivirus m-cherry expressing PC3 cells suppressed horizontal transfer of the genetic information from retrovirus GFP expressing PC3 cells to other cells. The specific mechanisms by which retroviral transduction and syncytins control the generation of a GFP-encoding pseudotyped retrovirus or EV and the delivery of their content, as well as the role of the virus/EV-mediated horizontal genetic material transfer between prostate cancer cells and between prostate cancer and their microenvironment remain to be clarified. Citation Format: Berna Uygur, Leonid Chernomordik. Retrovirus insertion induces syncytin mediated exosomes delivery in prostate cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5340. doi:10.1158/1538-7445.AM2017-5340

Event Abstract Back to Event Mapping the cardiomagnetic field with 19 room temperature second-order gradiometers Antoine Weis1*, Georg Bison2, Natascia Castagna1, Adrian Hofer1, Paul Knowles1, Jean-Luc Schenker1 and Malgorzata Kasprzak1 1 University of Fribourg, Switzerland 2 Friedrich-Schiller-University, Biomagnetic Center, Germany Objective: Optically pumped atomic magnetometers (LOPM) have become competitive with the well-established SQUID technology for recording biomagnetic fields. Since our first demonstration in 2003 [1] that a single gradiometer of two laser optically-pumped atomic magnetometers (LOPM) can be used for MCG mapping, we have struggled to develop multisensor arrays for recording field maps in clinically adapted measurement times. Methods: The field sensing element is a room-temperature Cs vapor contained in paraffin-coated cells [2]. The LOPM combines optical pumping by resonant laser light, rf-driven magnetic resonance, and laser readout to measure the magnetic field via spin precession. Digital phase detectors are used to either lock the field to the rf drive, or vice-versa. Coils permit feedback stabilization of the field in each sensor. With a set of feedback loops we have made 19 second order gradiometers (19+3+3 sensors in three planes) operated in an Al shielding room. RESULTS: The system has been successfully used [3] for recording heart field maps of more than 20 healthy subjects. Measurements on cardiac patients are in preparation and results shall be presented. Conclusion: We have demonstrated that a multisensor arrangement of laser pumped atomic magnetometers can be used for the simultaneous recording of cardiomagnetic field maps at 19 grid points in less than 2 minutes.

The Origins of Ecological Diversity in Prokaryotes

Phenotypic and genomic characterization of Pseudomonas putida ITEM 17297 spoiler of fresh vegetables: Focus on biofilm and antibiotic resistance interaction

More than two decades ago, experiments on the ribonuclease susceptibility of different RNAs led to the realization that uninterrupted tracts of polyadenylic acid (poly[A]) are present within eukaryotic messenger RNAs (Lim and Canellakis 1970; Darnell et al. 1971a,b; Edmonds et al. 1971; Kates 1971; Lee et al. 1971). It is now well recognized that almost all mRNAs whose biosynthesis originates within nuclei contain a 3′ poly(A) tail. Poly(A) sequences are not encoded within genes (Philipson et al. 1971; Birnboim et al. 1973; Jacobson et al. 1974) but are added to nascent pre-mRNAs in a processing reaction that involves site-specific cleavage and subsequent polyadenylation. The site of cleavage is determined by a highly conserved AAUAAA sequence usually 5–30 nucleotides 5′ to the site and by other less well-conserved sequences 3′, and sometimes 5′, to the site. Cleavage and polyadenylation are dependent on poly(A) polymerase and several other factors that impart specificity and processivity to the reaction. For reviews on the sequence and factor requirements of polyadenylation, see Wickens (1990), Proudfoot (1991), Wahle and Keller (1992), and Manley and Proudfoot (1994). Pulse-chase experiments demonstrated that a large fraction of newly synthesized nuclear poly(A) was conserved in cytoplasmic mRNA (Puckett et al. 1975). These experiments provided early support for the notion that heterogeneous nuclear RNA (hnRNA) was the precursor to mRNA and also forced the conclusion that at least one function of poly(A) must be cytoplasmic. Evidence that the latter conclusion had merit is presented in this chapter, where I consider the...

A model of senescence as the piecewise loss of control over transcription

The relationship of the DNA sequences from which polyribosomal messenger RNA (mRNA) and heterogeneous nuclear RNA (NRNA) of mouse L cells are transcribed was investigated by means of hybridization kinetics and thermal denaturation of the hybrids. Hybridization was performed in formamide solutions at DNA excess. Under these conditions most of the hybridizing mRNA and NRNA react at values of Dot (DNA concentration multiplied by time) expected for RNA transcribed from the nonrepeated or rarely repeated fraction of the genome. However, a fraction of both mRNA and NRNA hybridize at values of Dot about 10,000 times lower, and therefore must be transcribed from highly redundant DNA sequences. The fraction of NRNA hybridizing to highly repeated sequences is about 1.7 times greater than the corresponding fraction of mRNA. The hybrids formed by the rapidly reacting fractions of both NRNA and mRNA melt over a narrow temperature range with a midpoint about 11°C below that of native L cell DNA. This indicates that these hybrids consist of partially complementary sequences with approximately 11% mismatching of bases. Hybrids formed by the slowly reacting fraction of NRNA melt within 4°–6°C of native DNA, indicating very little, if any, mismatching of bases. Hybrids of the slowly reacting components of mRNA, formed under conditions of sufficiently low RNA input, have a high thermal stability, similar to that observed for hybrids of the slowly reacting NRNA component. However, when higher inputs of mRNA are used, hybrids are formed which have a strikingly lower thermal stability. This observation can be explained by assuming that there is sufficient similarity among the relatively rare DNA sequences coding for mRNA so that under hybridization conditions, in which these DNA sequences are not truly in excess, reversible hybrids exhibiting a considerable amount of mispairing are formed. The fact that a comparable phenomenon has not been observed for NRNA may mean that there is less similarity among the relatively rare DNA sequences coding for NRNA than there is among the rare sequences coding for mRNA.

30] Purification of messenger RNA and heterogeneous nuclear RNA containing poly(A) sequences

Relative occurrence of polyadenylic acid sequences in messenger and heterogeneous nuclear RNA of L cells as determined by poly (U)-hydroxylapatite chromatography

The role of melanocortins and cytokines in human adipose tissue and adipocytes

THE presence of polyadenylic acid (poly(A)) tracts in both the heterogeneous nuclear RNA (HnRNA) and polysomal messenger RNA of eukaryotic cells indicates that the high molecular weight HnRNA is the precursor of polysomal mRNA1–3. At least two features of HnRNA, double stranded regions4 and small segments of polyuridylic acid5, seem to be absent from polysomal mRNA. These data and previous observations on the metabolism of HnRNA in vivo6–10 suggest that HnRNA is cleaved and only a selected portion(s) transported to the cytoplasm as functional mRNA.

This thesis deals with recurrent neural networks, a particular class of artificial neural networks which can learn a generative model of input sequences. The input is mapped, through a feedback loop and a non-linear activation function, into a hidden state, which is then projected into the output space, obtaining either a probability distribution or the new input for the next time-step. This work consists mainly of two parts: a theoretical study for helping the understanding of recurrent neural networks framework, which is not yet deeply investigated, and their application to non-linear prediction problems, since recurrent neural networks are really powerful models suitable for solving several practical tasks in different fields. For what concerns the theoretical part, we analyse the weaknesses of state-of-the-art models and tackle them in order to improve the performance of a recurrent neural network. Firstly, we contribute in the understanding of the dynamical properties of a recurrent neural network, highlighting the close relation between the definition of stable limit cycles and the echo state property of an echo state network. We provide sufficient conditions for the convergence of the hidden state to a trajectory, which is uniquely determined by the input signal, independently of the initial states. This may help extend the memory of the network and increase the design options for the network. Moreover, we develop a novel approach to address the main problem in training recurrent neural networks, the so-called vanishing gradient problem. Our new method allows us to train a very simple recurrent neural network, making the gradient not to vanish even after many time-steps. Exploiting the singular value decomposition of the vanishing factors in the gradient and random matrices theory, we find that the singular values have to be confined in a narrow interval and derive conditions about their root mean square value. Then, we also improve the efficiency of the training of a recurrent neural network, defining a new method for speeding up this process. Thanks to a least square regularization, we can initialize the parameters of the network, in order to set them closer to the minimum and running fewer epochs of classical training algorithms. Moreover, it is also possible to completely train the network with our initialization method, running more iterations of it without losing in performance with respect to classical training algorithms. Finally, it is also possible to use it as a real-time learning algorithm, adjusting the parameters to the new data through one iteration of our initialization. In the last part of this thesis, we apply recurrent neural networks to non-linear prediction problems. We consider prediction of numerical sequences, estimating the following input choosing it from a probability distribution. We study an automatic text generation problem, where we need to predict the following character in order to compose words and sentences, and a path prediction of walking mobile users in the central area of a city, as a sequence of crossroads. Then, we analyse the prediction of video frames, discovering a wide range of applications related to the prediction of movements. We study the collision problem of bouncing balls, taking into account only the sequence of video frames without any knowledge about the physical characteristics of the problem, and the distribution over days of mobile user in a city and in a whole region. Finally, we address the state-of-the-art problem of missing data imputation, analysing the incomplete spectrogram of audio signals. We restore audio signals with missing time-frequency data, demonstrating via numerical experiments that a performance improvement can be achieved involving recurrent neural networks.

Several lines of evidence from different laboratories suggest that hypothalamic beta-endorphinergic activity decreases around the time of initiation of the LH surge and may increase on estrus to extinguish the expression of the daily neuronal signal for the surge. In several hormone systems, factors that stimulate or suppress hormone release also stimulate or repress transcription of the hormone gene and translation of the messenger RNA encoding the hormone. Therefore, information about neurohormone activity may be inferred from data on changes in the levels of RNA species encoding these neurohormones. We used a solution hybridization/RNase protection assay to test the hypotheses that 1) the abundance of primary transcript of the hypothalamic POMC gene decreases at the time of initiation of the proestrous LH surge and 2) levels of POMC primary transcript (and by inference, levels of beta-endorphin neuronal activity and secretion) increase on estrus. 96 rats exhibiting at least two consecutive 4-day estrous cycles were killed at either 0600 or 1300 h on proestrus and estrus. Dissections of the medial basal hypothalamus were pooled into 4 samples at each time-point (6 rats per sample) and RNA was extracted from nuclear and cytoplasmic fractions separately. We measured levels of POMC primary transcript, processing intermediate and fully spliced mRNA in the nuclear fractions and POMC mRNA in cytoplasmic fractions. Compared to 0600 h, levels of POMC primary transcript decreased significantly during the afternoons of both proestrus and estrus (P < 0.05). Levels of nuclear processing intermediate RNA and cytoplasmic mRNA followed the same trend but the afternoon declines did not reach statistical significance. We conclude from these data that the afternoon decline in POMC gene expression is not unique to the day of proestrus and we speculate that an afternoon decline in beta-endorphinergic neuronal activity may instead be a component of the daily signal for the LH surge.