The Jackprot Simulation Couples Mutation Rate with Natural Selection to Illustrate How Protein Evolution Is Not Random

Protein evolution is not a random process. Views which attribute randomness to molecular change, deleterious nature to single-gene mutations, insufficient geological time, or population size for molecular improvements to occur, or invoke “design creationism” to account for complexity in molecular structures and biological processes, are unfounded. Scientific evidence suggests that natural selection tinkers with molecular improvements by retaining adaptive peptide sequence. We used slot-machine probabilities and ion channels to show biological directionality on molecular change. Because ion channels reside in the lipid bilayer of cell membranes, their residue location must be in balance with the membrane’s hydrophobic/philic nature; a selective “pore” for ion passage is located within the hydrophobic region. We contrasted the random generation of DNA sequence for KcsA, a bacterial two-transmembrane-domain (2TM) potassium channel, from Streptomyces lividans, with an under-selection scenario, the “jackprot,” which predicted much faster evolution than by chance. We wrote a computer program in JAVA APPLET version 1.0 and designed an online interface, The Jackprot Simulation http://faculty.rwu.edu/cbai/JackprotSimulation.htm, to model a numerical interaction between mutation rate and natural selection during a scenario of polypeptide evolution. Winning the “jackprot,” or highest-fitness complete-peptide sequence, required cumulative smaller “wins” (rewarded by selection) at the first, second, and third positions in each of the 161 KcsA codons (“jackdons” that led to “jackacids” that led to the “jackprot”). The “jackprot” is a didactic tool to demonstrate how mutation rate coupled with natural selection suffices to explain the evolution of specialized proteins, such as the complex six-transmembrane (6TM) domain potassium, sodium, or calcium channels. Ancestral DNA sequences coding for 2TM-like proteins underwent nucleotide “edition” and gene duplications to generate the 6TMs. Ion channels are essential to the physiology of neurons, ganglia, and brains, and were crucial to the evolutionary advent of consciousness. The Jackprot Simulation illustrates in a computer model that evolution is not and cannot be a random process as conceived by design creationists

An undulation theory for condensation in open end slit pores: Critical hysteresis temperature & critical hysteresis pore size

A new theory of condensation in an open end slit pore, based on the concept of temperature dependent undulation, at the interface separating the adsorbed phase and the gas-like region, is presented. The theory, describes, for the first time, the microscopic origin of the critical hysteresis temperature and the critical hysteresis pore size, properties which are not accessible to any classical theories

A Maritime Advanced Geospatial Intelligence Craft for Oil Spill Response: White Paper

In line with current research thrusts on unmanned systems, the University of New Orleans has formed a collaborative team from industry, academia, and government (e.g., Department of Homeland Security). UNO’s intent is to work with organizations such as the Bureau of Safety and Environmental Enforcement (BSEE) to experiment and demonstrate the potential offered by Unmanned Surface Vessels within the Gulf of Mexico

A Maritime Advanced Geospatial Intelligence Craft for Oil Spill Response: White Paper

In line with current research thrusts on unmanned systems, the University of New Orleans has formed a collaborative team from industry, academia, and government (e.g., Department of Homeland Security). UNO’s intent is to work with organizations such as the Bureau of Safety and Environmental Enforcement (BSEE) to experiment and demonstrate the potential offered by Unmanned Surface Vessels within the Gulf of Mexico

Preferential Growth of Semiconducting Single-Walled Carbon Nanotubes on Substrate by Europium Oxide

In this paper, we have demonstrated that europium oxide (Eu2O3) is a new type of active catalyst for single-walled carbon nanotubes (SWNTs) growth under suitable conditions. Both random SWNT networks and horizontally aligned SWNT arrays are efficiently grown on silicon wafers. The density of the SWNT arrays can be altered by the CVD conditions. This result further provides the experimental evidence that the efficient catalyst for SWNT growth is more size dependent than the catalysts themselves. Furthermore, the SWNTs from europium sesquioxides have compatibly higher quality than that from Fe/Mo catalyst. More importantly, over 80% of the nanotubes from Eu2O3 are semiconducting SWNTs (s-SWNTs), indicating the preferential growth of s-SWNTs from Eu2O3. This new finding could open a way for selective growth of s-SWNTs, which can be used as high-current nanoFETs and sensors. Moreover, the successful growth of SWNTs by Eu2O3 catalyst provides new experimental information for understanding the preferential growth of s-SWNTs from Eu2O3, which may be helpful for their controllable synthesis

Groundwater Nitrogen Pollution and Assessment of Its Health Risks: A Case Study of a Typical Village in Rural-Urban Continuum, China

Protecting groundwater from nitrogen contamination is an important public-health concern and a major national environmental issue in China. In this study, we monitored water quality in 29 wells from 2009 to 2010 in a village in Shanghai city, whick belong to typical rural-urban continuum in China. The total N and NO3-N exhibited seasonal changes, and there were large fluctuations in NH4-N in residential areas, but without significant seasonal patterns. NO2-N in the water was not stable, but was present at high levels. Total N and NO3-N were significantly lower in residential areas than in agricultural areas. The groundwater quality in most wells belonged to Class III and IV in the Chinese water standard, which defines water that is unsuitable for human consumption. Our health risk assessments showed that NO3-N posed the greatest carcinogenic risk, with risk values ranging from 19×10−6 to 80×10−6, which accounted for more than 90% of the total risk in the study area

Characterization of global microRNA expression reveals oncogenic potential of miR-145 in metastatic colorectal cancer

Background: MicroRNAs (MiRNAs) are short non-coding RNAs that control protein expression through various mechanisms. Their altered expression has been shown to be associated with various cancers. The aim of this study was to profile miRNA expression in colorectal cancer (CRC) and to analyze the function of specific miRNAs in CRC cells. MirVana miRNA Bioarrays were used to determine the miRNA expression profile in eight CRC cell line models, 45 human CRC samples of different stages, and four matched normal colon tissue samples. SW620 CRC cells were stably transduced with miR-143 or miR-145 expression vectors and analyzed in vitro for cell proliferation, cell differentiation and anchorage-independent growth. Signalling pathways associated with differentially expressed miRNAs were identified using a gene set enrichment analysis. Results: The expression analysis of clinical CRC samples identified 37 miRNAs that were differentially expressed between CRC and normal tissue. Furthermore, several of these miRNAs were associated with CRC tumor progression including loss of miR-133a and gain of miR-224. We identified 11 common miRNAs that were differentially expressed between normal colon and CRC in both the cell line models and clinical samples. In vitro functional studies indicated that miR-143 and miR-145 appear to function in opposing manners to either inhibit or augment cell proliferation in a metastatic CRC model. The pathways targeted by miR-143 and miR-145 showed no significant overlap. Furthermore, gene expression analysis of metastatic versus non-metastatic isogenic cell lines indicated that miR-145 targets involved in cell cycle and neuregulin pathways were significantly down-regulated in the metastatic context. Conclusion: MiRNAs showing altered expression at different stages of CRC could be targets for CRC therapies and be further developed as potential diagnostic and prognostic analytes. The identified biological processes and signalling pathways collectively targeted by co-expressed miRNAs in CRC provide a basis for understanding the functional role of miRNAs in cancer. © 2009 Arndt et al; licensee BioMed Central Ltd