Characteristics of oligonucleotide frequencies across genomes: Conservation versus variation, strand symmetry, and evolutionary implications

One of the objectives of evolutionary genomics is to reveal the genetic information contained in the primordial genome (called the primary genetic information in this paper, with the primordial genome defined here as the most primitive nucleic acid genome for earth’s life) by searching for primitive traits or relics remained in modern genomes. As the shorter a sequence is, the less probable it would be modified during genome evolution. For that reason, some characteristics of very short nucleotide sequences would have considerable chances to persist during billions of years of evolution. Consequently, conservation of certain genomic features of mononucleotides, dinucleotides, and higher-order oligonucleotides across various genomes may exist; some, if not all, of these features would be relics of the primary genetic information. Based on this assumption, we analyzed the pattern of frequencies of mononucleotides, dinucleotides, and higher-order oligonucleotides of the whole-genome sequences from 458 species (including archaea, bacteria, and eukaryotes). Also, we studied the phenomenon of strand symmetry in these genomes. The results show that the conservation of frequencies of some dinucleotides and higher-order oligonucleotides across genomes does exist, and that strand symmetry is a ubiquitous and explicit phenomenon that may contribute to frequency conservation. We propose a new hypothesis for the origin of strand symmetry and frequency conservation as well as for the constitution of early genomes. We conclude that the phenomena of strand symmetry and the pattern of frequency conservation would be original features of the primary genetic information

A novel common triplet profile for GC-rich prokaryotic genomes

AbstractIt has been reported that there is a majority triplet profile among genomes, which was considered as a reflection of general mechanisms of genome evolution (Albrecht-Buehler, 2007). However, there are actually, according to our further analysis and at least among prokaryotic genomes, two common triplet profiles: one is from low-GC content genomes; the other is from high-GC content genomes. Both common profiles would be direct reflections of GC content variations and strand symmetry of genomic sequences

Magnetothermoelectric DC conductivities from holography models with hyperscaling factor in Lifshitz spacetime

We investigate an Einstein-Maxwell-Dilaton-Axion holographic model and obtain two branches of a charged black hole solution with a dynamic exponent and a hyperscaling violation factor when a magnetic field presents. The magnetothermoelectric DC conductivities are then calculated in terms of horizon data by means of holographic principle. We find that linear temperature dependence resistivity and quadratic temperature dependence inverse Hall angle can be achieved in our model. The well-known anomalous temperature scaling of the Nernst signal and the Seebeck coefficient of cuprate strange metals are also discussed.Comment: 1+23 pages, 4 figures, references adde

Coupled ocean-atmosphere dynamics of the 2017 extreme coastal El Niño.

In March 2017, sea surface temperatures off Peru rose above 28 °C, causing torrential rains that affected the lives of millions of people. This coastal warming is highly unusual in that it took place with a weak La Niña state. Observations and ocean model experiments show that the downwelling Kelvin waves caused by strong westerly wind events over the equatorial Pacific, together with anomalous northerly coastal winds, are important. Atmospheric model experiments further show the anomalous coastal winds are forced by the coastal warming. Taken together, these results indicate a positive feedback off Peru between the coastal warming, atmospheric deep convection, and the coastal winds. These coupled processes provide predictability. Indeed, initialized on as early as 1 February 2017, seasonal prediction models captured the extreme rainfall event. Climate model projections indicate that the frequency of extreme coastal El Niño will increase under global warming

Reform Exploration for Safety Course System of Oil and Gas Storage and Transportation Facilities

In recent years, the safety of oil and gas storage and transportation facilities has been paid more attention by the state and enterprises due to frequent accidents. The oil and gas storage and transportation facilities safety courses in China University of Petroleum (Beijing) includes “Engineering mechanics”, “Strength design of pipelines and tanks” and “Safety and integrity management of oil and gas storage and transportation facilities”. The three courses lack relevance and the teaching mode is too rigid, resulting in students losing their initiative in learning. If students can’t use the knowledge flexibly, it will affect the achievement of the objectives of the training program. Therefore, oil and gas storage and transportation facilities safety courses are reformed, training plans are adjusted and teaching methods are improved. The practice shows that the reform enriches the teaching content, improves the teaching quality, stimulates classroom activity and gets a good evaluation of students. The reform of safety courses has a certain significance for cultivating compound talents who have the ability to solve practical problems in engineering

Students of Chinese Language Major and Their Attitude Towards the Current Learning Study in Vietnam

Chinese language has recently grown so rapidly that people compared it to a storm overflowing into Vietnam. Thus, education managers and teachers can only respond promptly by immediate emergency measures, but have not found measures for stable development. The learning situation therefore also becomes chaotic and the quality does not meet social requirements.This article aims to analyze the current situation of Vietnamese students studying Chinese language by applying methods of current situation survey by questionnaires, observations in actuality and document research. Through this, the author figure out the true situation of learning attitude and student’s assessment of their schools’ quality of teaching. Results of the research will help teachers to better adjust their teaching methods, and help educational managers have more effective education policies

Assessment of Long-Term Watershed Management on Reservoir Phosphorus Concentrations and Export Fluxes.

Source water nutrient management to prevent eutrophication requires critical strategies to reduce watershed phosphorus (P) loadings. Shanxi Drinking-Water Source Area (SDWSA) in eastern China experienced severe water quality deterioration before 2010, but showed considerable improvement following application of several watershed management actions to reduce P. This paper assessed the changes in total phosphorus (TP) concentrations and fluxes at the SDWSA outlet relative to watershed anthropogenic P sources during 2005⁻2016. Overall anthropogenic P inputs decreased by 21.5% over the study period. Domestic sewage, livestock, and fertilizer accounted for (mean ± SD) 18.4 ± 0.6%, 30.1 ± 1.9%, and 51.5 ± 1.5% of total anthropogenic P inputs during 2005⁻2010, compared to 24.3 ± 2.7%, 8.8 ± 10.7%, and 66.9 ± 8.0% for the 2011⁻2016 period, respectively. Annual average TP concentrations in SDWSA decreased from 0.041 ± 0.019 mg/L in 2009 to 0.025 ± 0.013 mg/L in 2016, a total decrease of 38.2%. Annual P flux exported from SDWSA decreased from 0.46 ± 0.04 kg P/(ha·a) in 2010 to 0.25 ± 0.02 kg P/(ha·a) in 2016, a decrease of 44.9%. The success in reducing TP concentrations was mainly due to the development of domestic sewage/refuse collection/treatment and improved livestock management. These P management practices have prevented harmful algal blooms, providing for safe drinking water

Involvement of TRPC Channels in Lung Cancer Cell Differentiation and the Correlation Analysis in Human Non-Small Cell Lung Cancer

The canonical transient receptor potential (TRPC) channels are Ca2+-permeable cationic channels controlling the Ca2+ influx evoked by G protein-coupled receptor activation and/or by Ca2+ store depletion. Here we investigate the involvement of TRPCs in the cell differentiation of lung cancer. The expression of TRPCs and the correlation to cancer differentiation grade in non-small cell lung cancer (NSCLC) were analyzed by real-time PCR and immunostaining using tissue microarrays from 28 patient lung cancer samples. The association of TRPCs with cell differentiation was also investigated in the lung cancer cell line A549 by PCR and Western blotting. The channel activity was monitored by Ca2+ imaging and patch recording after treatment with all-trans-retinoic acid (ATRA). The expression of TRPC1, 3, 4 and 6 was correlated to the differentiation grade of NSCLC in patients, but there was no correlation to age, sex, smoking history and lung cancer cell type. ATRA upregulated TRPC3, TRPC4 and TRPC6 expression and enhanced Ca2+ influx in A549 cells, however, ATRA showed no direct effect on TRPC channels. Inhibition of TRPC channels by pore-blocking antibodies decreased the cell mitosis, which was counteracted by chronic treatment with ATRA. Blockade of TRPC channels inhibited A549 cell proliferation, while overexpression of TRPCs increased the proliferation. We conclude that TRPC expression correlates to lung cancer differentiation. TRPCs mediate the pharmacological effect of ATRA and play important roles in regulating lung cancer cell differentiation and proliferation, which gives a new understanding of lung cancer biology and potential anti-cancer therapy. © 2013 Jiang et al