Long-wavelength sensitive visual pigments of the guppy (Poecilia reticulata): six opsins expressed in a single individual

BACKGROUND: The diversity of visual systems in fish has long been of interest for evolutionary biologists and neurophysiologists, and has recently begun to attract the attention of molecular evolutionary geneticists. Several recent studies on the copy number and genomic organization of visual pigment proteins, the opsins, have revealed an increased opsin diversity in fish relative to most vertebrates, brought about through recent instances of opsin duplication and divergence. However, for the subfamily of opsin genes that mediate vision at the long-wavelength end of the spectrum, the LWS opsins, it appears that most fishes possess only one or two loci, a value comparable to most other vertebrates. Here, we characterize the LWS opsins from cDNA of an individual guppy, Poecilia reticulata, a fish that is known exhibit variation in its long-wavelength sensitive visual system, mate preferences and colour patterns. RESULTS: We identified six LWS opsins expressed within a single individual. Phylogenetic analysis revealed that these opsins descend from duplication events both pre-dating and following the divergence of the guppy lineage from that of the bluefin killifish, Lucania goodei, the closest species for which comparable data exists. Numerous amino acid substitutions exist among these different LWS opsins, many at sites known to be important for visual pigment function, including spectral sensitivity and G-protein activation. Likelihood analyses using codon-based models of evolution reveal significant changes in selective constraint along two of the guppy LWS opsin lineages. CONCLUSION: The guppy displays an unusually high number of LWS opsins compared to other fish, and to vertebrates in general. Observing both substitutions at functionally important sites and the persistence of lineages across species boundaries suggests that these opsins might have functionally different roles, especially with regard to G-protein activation. The reasons why are currently unknown, but may relate to aspects of the guppy's behavioural ecology, in which both male colour patterns and the female mate preferences for these colour patterns experience strong, highly variable selection pressures

Structure-mechanics relationships of collagen fibrils in the Osteogenesis Imperfecta Mouse model

The collagen molecule, which is the building block of collagen fibrils, is a triple helix of two α1(I) chains and one α2(I) chain. However, in the severe mouse model of osteogenesis imperfecta (OIM), deletion of the COL1A2 gene results in the substitution of the α2(I) chain by one α1(I) chain. As this substitution severely impairs the structure and mechanics of collagen-rich tissues at the tissue and organ level, the main aim of this study was to investigate how the structure and mechanics are altered in OIM collagen fibrils. Comparing results from atomic force microscopy imaging and cantilever-based nanoindentation on collagen fibrils from OIM and wild-type (WT) animals, we found a 33% lower indentation modulus in OIM when air-dried (bound water present) and an almost fivefold higher indentation modulus in OIM collagen fibrils when fully hydrated (bound and unbound water present) in phosphate-buffered saline solution (PBS) compared with WT collagen fibrils. These mechanical changes were accompanied by an impaired swelling upon hydration within PBS. Our experimental and atomistic simulation results show how the structure and mechanics are altered at the individual collagen fibril level as a result of collagen gene mutation in OIM. We envisage that the combination of experimental and modelling approaches could allow mechanical phenotyping at the collagen fibril level of virtually any alteration of collagen structure or chemistry.United States. Dept. of Defense. Presidential Early Career Award for Scientists and EngineersNational Science Foundation (U.S.) (CAREER Award

Short-wavelength sensitive opsin (SWS1) as a new marker for vertebrate phylogenetics

BACKGROUND: Vertebrate SWS1 visual pigments mediate visual transduction in response to light at short wavelengths. Due to their importance in vision, SWS1 genes have been isolated from a surprisingly wide range of vertebrates, including lampreys, teleosts, amphibians, reptiles, birds, and mammals. The SWS1 genes exhibit many of the characteristics of genes typically targeted for phylogenetic analyses. This study investigates both the utility of SWS1 as a marker for inferring vertebrate phylogenetic relationships, and the characteristics of the gene that contribute to its phylogenetic utility. RESULTS: Phylogenetic analyses of vertebrate SWS1 genes produced topologies that were remarkably congruent with generally accepted hypotheses of vertebrate evolution at both higher and lower taxonomic levels. The few exceptions were generally associated with areas of poor taxonomic sampling, or relationships that have been difficult to resolve using other molecular markers. The SWS1 data set was characterized by a substantial amount of among-site rate variation, and a relatively unskewed substitution rate matrix, even when the data were partitioned into different codon sites and individual taxonomic groups. Although there were nucleotide biases in some groups at third positions, these biases were not convergent across different taxonomic groups. CONCLUSION: Our results suggest that SWS1 may be a good marker for vertebrate phylogenetics due to the variable yet consistent patterns of sequence evolution exhibited across fairly wide taxonomic groups. This may result from constraints imposed by the functional role of SWS1 pigments in visual transduction

Duplicate dmbx1 genes regulate progenitor cell cycle and differentiation during zebrafish midbrain and retinal development

Abstract Background The Dmbx1 gene is important for the development of the midbrain and hindbrain, and mouse gene targeting experiments reveal that this gene is required for mediating postnatal and adult feeding behaviours. A single Dmbx1 gene exists in terrestrial vertebrate genomes, while teleost genomes have at least two paralogs. We compared the loss of function of the zebrafish dmbx1a and dmbx1b genes in order to gain insight into the molecular mechanism by which dmbx1 regulates neurogenesis, and to begin to understand why these duplicate genes have been retained in the zebrafish genome. Results Using gene knockdown experiments we examined the function of the dmbx1 gene paralogs in zebrafish, dmbx1a and dmbx1b in regulating neurogenesis in the developing retina and midbrain. Dose-dependent loss of dmbx1a and dmbx1b function causes a significant reduction in growth of the midbrain and retina that is evident between 48-72 hpf. We show that this phenotype is not due to patterning defects or persistent cell death, but rather a deficit in progenitor cell cycle exit and differentiation. Analyses of the morphant retina or anterior hindbrain indicate that paralogous function is partially diverged since loss of dmbx1a is more severe than loss of dmbx1b. Molecular evolutionary analyses of the Dmbx1 genes suggest that while this gene family is conservative in its evolution, there was a dramatic change in selective constraint after the duplication event that gave rise to the dmbx1a and dmbx1b gene families in teleost fish, suggestive of positive selection. Interestingly, in contrast to zebrafish dmbx1a, over expression of the mouse Dmbx1 gene does not functionally compensate for the zebrafish dmbx1a knockdown phenotype, while over expression of the dmbx1b gene only partially compensates for the dmbx1a knockdown phenotype. Conclusion Our data suggest that both zebrafish dmbx1a and dmbx1b genes are retained in the fish genome due to their requirement during midbrain and retinal neurogenesis, although their function is partially diverged. At the cellular level, Dmbx1 regulates cell cycle exit and differentiation of progenitor cells. The unexpected observation of putative post-duplication positive selection of teleost Dmbx1 genes, especially dmbx1a, and the differences in functionality between the mouse and zebrafish genes suggests that the teleost Dmbx1 genes may have evolved a diverged function in the regulation of neurogenesis

Microalgae biomass from swine wastewater and its conversion to bioenergy

© 2018 Elsevier Ltd Ever-increasing swine wastewater (SW) has become a serious environmental concern. High levels of nutrients and toxic contaminants in SW significantly impact on the ecosystem and public health. On the other hand, swine wastewater is considered as valuable water and nutrient source for microalgae cultivation. The potential for converting the nutrients from SW into valuable biomass and then generating bioenergy from it has drawn increasing attention. For this reason, this review comprehensively discussed the biomass production, SW treatment efficiencies, and bioenergy generation potentials through cultivating microalgae in SW. Microalgae species grow well in SW with large amounts of biomass being produced, despite the impact of various parameters (e.g., nutrients and toxicants levels, cultivation conditions, and bacteria in SW). Pollutants in SW can effectively be removed by harvesting microalgae from SW, and the harvested microalgae biomass elicits high potential for conversion to valuable bioenergy

Neuroprotective effects of minocycline on double-stranded RNA-induced neurotoxicity in cultured cortical neurons

1. Minocycline, memantine,and glycoconjugate were assessed for their ability to protect cultured primary cortical neurons against double-stranded RNA-induced neurotoxicity. 2. Minocycline but not memantine or glycoconjugate protected cultured cells and warrants further investigation.published_or_final_versio

Influences of operational parameters on phosphorus removal in batch and continuous electrocoagulation process performance

© 2017, Springer-Verlag GmbH Germany. Performance of an electrocoagulation (EC) process in batch and continuous operating modes was thoroughly investigated and evaluated for enhancing wastewater phosphorus removal under various operating conditions, individually or combined with initial phosphorus concentration, wastewater conductivity, current density, and electrolysis times. The results revealed excellent phosphorus removal (72.7–100%) for both processes within 3–6 min of electrolysis, with relatively low energy requirements, i.e., less than 0.5 kWh/m3 for treated wastewater. However, the removal efficiency of phosphorus in the continuous EC operation mode was better than that in batch mode within the scope of the study. Additionally, the rate and efficiency of phosphorus removal strongly depended on operational parameters, including wastewater conductivity, initial phosphorus concentration, current density, and electrolysis time. Based on experimental data, statistical model verification of the response surface methodology (RSM) (multiple factor optimization) was also established to provide further insights and accurately describe the interactive relationship between the process variables, thus optimizing the EC process performance. The EC process using iron electrodes is promising for improving wastewater phosphorus removal efficiency, and RSM can be a sustainable tool for predicting the performance of the EC process and explaining the influence of the process variables

Studies of chain substitution caused sub-fibril level differences in stiffness and ultrastructure of wildtype and oim/oim collagen fibers using multifrequency-AFM and molecular modeling.

Molecular alteration in type I collagen, i.e., substituting the α2 chain with α1 chain in tropocollagen molecule, can cause osteogenesis imperfecta (OI), a brittle bone disease, which can be represented by a mouse model (oim/oim). In this work, we use dual-frequency Atomic Force Microscopy (AFM) and incorporated with molecular modeling to quantify the ultrastructure and stiffness of the individual native collagen fibers from wildtype (+/+) and oim/oim diseased mice humeri. Our work presents direct experimental evidences that the +/+ fibers have highly organized and compact ultrastructure and corresponding ordered stiffness distribution. In contrast, oim/oim fibers have ordered but loosely packed ultrastructure with uncorrelated stiffness distribution, as well as local defects. The molecular model also demonstrates the structural and molecular packing differences between +/+ and oim/oim collagens. The molecular mutation significantly altered sub-fibril structure and mechanical property of collagen fibers. This study can give the new insight for the mechanisms and treatment of the brittle bone disease

Feasibility study on a double chamber microbial fuel cell for nutrient recovery from municipal wastewater

© 2018 Elsevier B.V. Microbial fuel cell (MFC) is currently considered a promising technology for wastewater treatment. This study aims to evaluate the feasibility of a double-chamber MFC in terms of: (i) operating mode (batch mode, self-circulation mode, single-continuous mode) of anolyte on the nutrient accumulation in the catholyte, (ii) aeration conditions (anode effluent with aeration supplied in catholyte; anode effluent without aeration supplied in catholyte; cathode effluent with aeration supplied in catholyte and cathode effluent without aeration supplied in catholyte) on the nutrient recovery and (iii) types of separators (cation exchange membrane (CEM), forward osmosis (FO), and nonwoven (NW)) to remove nutrients toward their recovery from municipal wastewater. Results showed that there was no negligible increase in the phosphate concentration of the catholyte at the three different modes but accumulation of ammonium. At different aeration conditions, nutrients can be recovered by chemical precipitation at high pH generated by the MFC itself. Basically, phosphate was removed by microbial absorption and recovered by chemical precipitation while ammonium was accumulated by current generation and recovered as precipitates. It was found that double-chamber MFC with the CEM as the separator reported the best nutrients removal with >97.58% of NH4+-N and >94.9% of PO43−-P removed/recovered, followed by the MFC with the nonwoven and FO membrane, respectively. Thus, the double-chamber MFC is feasible for recovering nutrients in a comprehensive bioelectrochemical system