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Extreme environments, such as Antarctic habitats, present major challenges for many biological processes. Antarctic icefishes (Crynotothenioidea) represent a compelling system to investigate the molecular basis of adaptation to cold temperatures. Here, we explore how the sub-zero habitats of Antarctic icefishes have impacted rhodopsin (RH1) function, the temperature-sensitive dim-light visual pigment found in rod photoreceptors. Using likelihood models and ancestral reconstruction, we find that accelerated evolutionary rates in icefish RH1 underlie unique amino acid mutations absent from other deep-dwelling fishes, introduced before (S160A) and during (V259M) the onset of modern polar conditions. Functional assays reveal that these mutations red-shift rhodopsin spectral absorbance, consistent with spectral irradiance under sea ice. These mutations also lower the activation energy associated with retinal release of the light-activated RH1, and accelerate its return to the dark state, likely compensating for a cold-induced decrease in kinetic rates. These are adaptations in key properties of rhodopsin that mediate rod sensitivity and visual performance in the cold dark seas of the Antarctic.

Inflammatory bowel disease (IBD) is a complex chronic inflammatory disorder of the gastrointestinal tract. Extracellular adenosine triphosphate (eATP) produced by the commensal microbiota and host cells activates purinergic signaling, promoting intestinal inflammation and pathology. Based on the role of eATP in intestinal inflammation, we developed yeast-based engineered probiotics that express a human P2Y2 purinergic receptor with up to a 1,000-fold increase in eATP sensitivity. We linked the activation of this engineered P2Y2 receptor to the secretion of the ATP-degrading enzyme apyrase, thus creating engineered yeast probiotics capable of sensing a pro-inflammatory molecule and generating a proportional self-regulated response aimed at its neutralization. These self-tunable yeast probiotics suppressed intestinal inflammation in mouse models of IBD, reducing intestinal fibrosis and dysbiosis with an efficacy similar to or higher than that of standard-of-care therapies usually associated with notable adverse events. By combining directed evolution and synthetic gene circuits, we developed a unique self-modulatory platform for the treatment of IBD and potentially other inflammation-driven pathologies.

In this work, a g-C3N4/porphyrin nanocomposite was fabricated through the self-assembling of monomeric Tetrakis (4-carboxyphenyl) porphyrin (TCPP) molecules with g-C3N4 nanomaterials. The characterizing results showed a good distribution of TCPP nanofibers with a diameter of < 100 nm and several micrometers in length on the g-C3N4 nanoflakes’ surfaces. The prepared g-C3N4/porphyrin nanocomposite had two bandgap energies of 2.38 and 2.7 eV, which could harvest a wide range of photon energy in the light spectrum, particularly in visible light. The obtained C3N4/TCPP nanocomposite revealed a remarkable photodegradation efficiency toward rhodamine B dyes, with a RhB removing rate of 3.3 × 10−2 min−1. The plausible mechanism for the photocatalytic performance of the g-C3N4/porphyrin photocatalyst for the RhB dye’s degradation was also studied and discussed.

Snakes are known to express a rod visual opsin and two cone opsins, only (SWS1, LWS), a reduced palette resulting from their supposedly fossorial origins. Dipsadid snakes in the genusHelicopsare highly visual predators that successfully invaded freshwater habitats from ancestral terrestrial-only habitats. Here we report the first case of multiple SWS1 visual pigments in a vertebrate, simultaneously expressed in different photoreceptors and conferring both UV and violet sensitivity toHelicopssnakes. Molecular analysis andin vitroexpression confirmed the presence of two functional SWS1 opsins, likely the result of recent gene duplication. Evolutionary analyses indicate that eachsws1variant has undergone different evolutionary paths, with strong purifying selection acting on the UV-sensitive copy and dN/dS∼1 on the violet-sensitive copy. Site-directed mutagenesis points to the functional role of a single amino acid substitution, Phe86Val, in the large spectral shift between UV and violet opsins. In addition, higher densities of photoreceptors and SWS1 cones in the ventral retina suggest improved acuity in the upper visual field possibly correlated with visually-guided behaviors. The expanded visual opsin repertoire and specialized retinal architecture are likely to improve photon uptake in underwater and terrestrial environments, and provide the neural substrate for a gain in chromatic discrimination, potentially conferring unique color vision in the UV-violet range. Our findings highlight the innovative solutions undertaken by a highly specialized lineage to tackle the challenges imposed by the invasion of novel photic environments and the extraordinary diversity of evolutionary trajectories taken by visual opsin-based perception in vertebrates.

A collection of the editors of Journal of Molecular Evolution have gotten together to pose a set of key challenges and future directions for the field of molecular evolution. Topics include challenges and new directions in prebiotic chemistry and the RNA world, reconstruction of early cellular genomes and proteins, macromolecular and functional evolution, evolutionary cell biology, genome evolution, molecular evolutionary ecology, viral phylodynamics, theoretical population genomics, somatic cell molecular evolution, and directed evolution. While our effort is not meant to be exhaustive, it reflects research questions and problems in the field of molecular evolution that are exciting to our editors.

Most vertebrates use a combination of rod and cone photoreceptors to enable vision in conditions ranging from starlight to direct sunlight. Nocturnal geckos, however, have simplex retinas that contain only rods in terms of morphology and physiology, but these rods are thought to be derived from cones through an evolutionary process known as photoreceptor transmutation. To investigate this, we generated eye transcriptomes and analyzed patterns of phototransduction gene evolution in geckos in comparison to other reptiles. We confirm that geckos have lost several major components of the rod phototransduction pathway, including rod opsin (RH1), which we identified as a pseudogene in multiple genomes. We also identified a partial rod transducin transcript, but found no evidence of the protein in retinal sections. However, we find that geckos express several complete rod phototransduction transcripts in the eye, which may contribute to the rod-like physiology of nocturnal gecko photoreceptors. Finally, we found surprising evidence that even though photoreceptor transmutation evolved independently in geckos and snakes, they have experienced parallel shifts in selective constraint on phototransduction genes. These results implicate adaptive change in the underlying molecular machinery of visual transduction, in addition to the convergent changes in cellular morphology, during photoreceptor transmutation.

Agrowaste sources can be utilized to produce biogas by anaerobic digestion reaction. Fossil fuels have damaged the environment, while the biogas rectifies the issues related to the environment and climate change problems. Techno-economic analysis of biogas production is followed by nutrient recycling, reducing the greenhouse gas level, biorefinery purpose, and global warming effect. In addition, biogas production is mediated by different metabolic reactions, the usage of different microorganisms, purification process, upgrading process and removal of CO₂ from the gas mixture techniques. This review focuses on pre-treatment, usage of waste, production methods and application besides summarizing recent advancements in biogas production. Economical, technical, environmental properties and factors affecting biogas production as well as the future perspective of bioenergy are highlighted in the review. Among all agro-industrial wastes, sugarcane straw produced 94% of the biogas. In the future, to overcome all the problems related to biogas production and modify the production process.

The bioremediation of emerging recalcitrant pollutants in wastewater via enzyme biotechnology has been evolving as cost-effective with an input of low-energy technological approach. However, the enzyme based bioremediation technology is still not fully developed at a commercial level. The oxidoreductases being the domineering biocatalysts are promising candidates for wastewater treatments. Henceforth, comprehending their global market and biotransformation efficacy is mandatory for establishing these techno-economic bio-enzymes in commercial scale. The biocatalytic strategy can be established as a combinatorial approach with existing treatment technology to achieve towering bioremediation and effective removal of emerging pollutants from wastewater. This review provides a novel insight on the toxicological xenobiotics released from industries such as paper and pulps, soap and detergents, pharmaceuticals, textiles, pesticides, explosives and aptitude of peroxidases, nitroreductase and cellobiose dehydrogenase in their bio-based treatment. Moreover, the review comprehensively covers environmental relevance of wastewater pollution and the critical challenges based on remediation achieved through biocatalysts for future prospectives.

Natural variation in the number, expression and function of sensory genes in an organism's genome is often tightly linked to different ecological and evolutionary forces. Opsin genes, which code for the first step in visual transduction, are ideal models for testing how ecological factors such as light environment may influence visual system adaptation. Neotropical cichlid fishes are a highly ecologically diverse group that evolved in a variety of aquatic habitats, including black (stained), white (opaque) and clear waters. We used cross-species exon capture to sequence Neotropical cichlid short wavelength-sensitive (SWS) opsins, which mediate ultraviolet (UV) to blue visual sensitivity. Neotropical cichlid SWS1 opsin (UV-sensitive) underwent a relaxation of selective constraint during the early phases of cichlid diversification in South America, leading to pseudogenization and loss. Conversely, SWS2a (blue-sensitive) experienced a burst of episodic positive selection at the base of the South American cichlid radiation. This burst coincides with SWS1 relaxation and loss, and is consistent with findings in ecomorphological studies characterizing a period of extensive ecological divergence in Neotropical cichlids. We use ancestral sequence reconstruction and protein modelling to investigate mutations along this ancestral branch that probably modified SWS2a function. Together, our results suggest that variable light environments played a prominent early role in shaping SWS opsin diversity during the Neotropical cichlid radiation. Our results also illustrate that long-term evolution under light-limited conditions in South America may have reduced visual system plasticity; specifically, early losses of UV sensitivity may have constrained the evolutionary trajectory of Neotropical cichlid vision.

Rhodopsin, the light-sensitive visual pigment expressed in rod photoreceptors, is specialized for vision in dim-light environments. Aquatic environments are particularly challenging for vision due to the spectrally dependent attenuation of light, which can differ greatly in marine and freshwater systems. Among fish lineages that have successfully colonized freshwater habitats from ancestrally marine environments, croakers are known as highly visual benthic predators. In this study, we isolate rhodopsins from a diversity of freshwater and marine croakers and find that strong positive selection in rhodopsin is associated with a marine to freshwater transition in South American croakers. In order to determine if this is accompanied by significant shifts in visual abilities, we resurrected ancestral rhodopsin sequences and tested the experimental properties of ancestral pigments bracketing this transition using in vitro spectroscopic assays. We found the ancestral freshwater croaker rhodopsin is redshifted relative to its marine ancestor, with mutations that recapitulate ancestral amino acid changes along this transitional branch resulting in faster kinetics that are likely to be associated with more rapid dark adaptation. This could be advantageous in freshwater due to the redshifted spectrum and relatively narrow interface and frequent transitions between bright and dim-light environments. This study is the first to experimentally demonstrate that positively selected substitutions in ancestral visual pigments alter protein function to freshwater visual environments following a transition from an ancestrally marine state and provides insight into the molecular mechanisms underlying some of the physiological changes associated with this major habitat transition.

LDH: Funda??o de Amparo ? Pesquisa do Estado de S?o Paulo (FAPESP) post-doctoral fellowship 2019/14606-4 and Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior (CAPES) doctoral scholarship; EH: FAPESP post-doctoral fellowships 2014/25743-9 and 2018/09321-8; BSWC: Natural Sciences and Engineering Research Council (NSERC) Discovery grant; OFG: Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico (CNPq) Research Productivity Fellowship; PRKG: CNPq grant 484228/2011-0; DFV: FAPESP grant 2014/26818-2, CAPES ProAmazonia 3263/2013-19 and CNPq 309409/2015-2. Universidade de S?o Paulo. Instituto de Psicologia. Departamento de Psicologia Experimental. S?o Paulo, SP, Brazil. Universidade de S?o Paulo. Instituto de Psicologia. Departamento de Psicologia Experimental. S?o Paulo, SP, Brazil / Hospital Israelita Albert Einstein. Instituto de Ensino e Pesquisa. S?o Paulo, SP, Brazil. Universidade de S?o Paulo. Instituto de Psicologia. Departamento de Psicologia Experimental. S?o Paulo, SP, Brazil. University of Toronto. Department of Cell and System Biology. Toronto, Canada. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Centro Nacional de Primatas. Ananindeua, PA, Brasil. Universidade Federal do Par?. N?cleo de Medicina Tropical. Bel?m, PA, Brazil / Universidade Federal do Par?. Instituto de Ci?ncias Biol?gicas. Bel?m, PA, Brazil. Universidade Federal do Par?. N?cleo de Medicina Tropical. Bel?m, PA, Brazil / Universidade Federal do Par?. Instituto de Ci?ncias Biol?gicas. Bel?m, PA, Brazil. Universidade Federal do Par?. N?cleo de Teoria e Pesquisa do Comportamento. Bel?m, PA, Brazil Universidade Federal do Par?. N?cleo de Teoria e Pesquisa do Comportamento. Bel?m, PA, Brazil Universidade de S?o Paulo. Instituto de Psicologia. Departamento de Psicologia Experimental. S?o Paulo, SP, Brazil / Hospital Israelita Albert Einstein. Instituto de Ensino e Pesquisa. S?o Paulo, SP, Brazil. Primate colour vision depends on a matrix of photoreceptors, a neuronal post receptoral structure and a combination of genes that culminate in different sensitivity through the visual spectrum. Along with a common cone opsin gene for short wavelengths (sws1), Neotropical primates (Platyrrhini) have only one cone opsin gene for medium-long wavelengths (mws/lws) per X chromosome while Paleotropical primates (Catarrhini), including humans, have two active genes. Therefore, while female platyrrhines may be trichromats, males are always dichromats. The genus Alouatta is inferred to be an exception to this rule, as electrophysiological, behavioural and molecular analyses indicated a potential for male trichromacy in this genus. However, it is very important to ascertain by a combination of genetic and behavioural analyses whether this potential translates in terms of colour discrimination capability. We evaluated two howler monkeys (Alouatta spp.), one male A. caraya and one female A. seniculus, using a combination of genetic analysis of the opsin gene sequences and a behavioral colour discrimination test not previously used in this genus. Both individuals completed the behavioural test with performances typical of trichromatic colour vision and the genetic analysis of the swsl, mws, and Iws opsin genes revealed three different opsin sequences in both subjects. These results are consistent with uniform trichromacy in both male and female, with presumed spectral sensitivity peaks similar to Catarrhini, at similar to 430 nm, 532 nm, and 563 nm for S-, M- and L-cones, respectively.

Inflammatory bowel disease (IBD) is a complex chronic inflammatory disorder of the gastrointestinal tract. Extracellular adenosine triphosphate (eATP) produced by the commensal microbiota and host cells activates purinergic signaling, promoting intestinal inflammation and pathology. Based on the role of eATP in intestinal inflammation, we developed yeast-based engineered probiotics that express a human P2Y2 purinergic receptor with up to a 1,000-fold increase in eATP sensitivity. We linked the activation of this engineered P2Y2 receptor to the secretion of the ATP-degrading enzyme apyrase, thus creating engineered yeast probiotics capable of sensing a pro-inflammatory molecule and generating a proportional self-regulated response aimed at its neutralization. These self-tunable yeast probiotics suppressed intestinal inflammation in mouse models of IBD, reducing intestinal fibrosis and dysbiosis with an efficacy similar to or higher than that of standard-of-care therapies usually associated with notable adverse events. By combining directed evolution and synthetic gene circuits, we developed a unique self-modulatory platform for the treatment of IBD and potentially other inflammation-driven pathologies.

Colubridae represents the most phenotypically diverse and speciose family of snakes, yet no well-assembled and annotated genome exists for this lineage. Here, we report and analyze the genome of the garter snake, Thamnophis sirtalis, a colubrid snake that is an important model species for research in evolutionary biology, physiology, genomics, behavior, and the evolution of toxin resistance. Using the garter snake genome, we show how snakes have evolved numerous adaptations for sensing and securing prey, and identify features of snake genome structure that provide insight into the evolution of amniote genomes. Analyses of the garter snake and other squamate reptile genomes highlight shifts in repeat element abundance and expansion within snakes, uncover evidence of genes under positive selection, and provide revised neutral substitution rate estimates for squamates. Our identification of Z and W sex chromosome-specific scaffolds provides evidence for multiple origins of sex chromosome systems in snakes and demonstrates the value of this genome for studying sex chromosome evolution. Analysis of gene duplication and loss in visual and olfactory gene families supports a dim-light ancestral condition in snakes and indicates that olfactory receptor repertoires underwent an expansion early in snake evolution. Additionally, we provide some of the first links between secreted venom proteins, the genes that encode them, and their evolutionary origins in a rear-fanged colubrid snake, together with new genomic insight into the coevolutionary arms race between garter snakes and highly toxic newt prey that led to toxin resistance in garter snakes.

Convergent evolution in response to similar selective pressures is a well-known phenomenon in evolutionary biology. Less well understood is how selection drives convergence in protein function, and the underlying mechanisms by which this can be achieved. Here we investigate functional convergence in the visual system of two distantly related lineages of high-altitude adapted Andean and Himalayan catfishes. Statistical analyses revealed in the two high-altitude lineages, a parallel acceleration of evolutionary rates in rhodopsin, the dim-light visual pigment. However, the elevated rates were found to be accompanied by substitutions at different sites in the protein. Experiments substituting Andean- or Himalayan-specific residues significantly accelerated the kinetic rates of rhodopsin, destabilizing the ligand-bound forms. As found in cold-adapted enzymes, this phenotype likely compensates for a cold-induced decrease in kinetic rates, properties of rhodopsin mediating rod sensitivity and visual performance. Our study suggests that molecular convergence in protein function can be driven by parallel shifts in evolutionary rates but via non-parallel molecular mechanisms. Signatures of natural selection may therefore be a powerful guide for identifying complex instances of functional convergence across a wider range of protein systems. This article is protected by copyright. All rights reserved

G protein-coupled receptors (GPCRs) must discriminate between hundreds of related signal molecules. In order to better understand how GPCR specificity can arise from a common promiscuous ancestor, we used laboratory evolution to invert the specificity of the Saccharomyces cerevisiae mating receptor Ste2. This GPCR normally responds weakly to the pheromone of the related species Kluyveromyces lactis, though we previously showed that mutation N216S is sufficient to make this receptor promiscuous. Here, we found that three additional substitutions, A265T, Y266F and P290Q, can act together to confer a novel specificity for K. lactis pheromone. Unlike wild-type Ste2, this new variant does not rely on differences in binding affinity to discriminate against its non-preferred ligand. Instead, the mutation P290Q is critical for suppressing the efficacy of the native pheromone. These two alternative methods of ligand discrimination were mapped to specific amino acid positions on the peptide pheromones. Our work demonstrates that changes in ligand efficacy can drive changes in GPCR specificity, thus obviating the need for extensive binding pocket re-modeling.

Background:Gout is the most common inflammatory arthritis worldwide with a diverse spectrum of clinical manifestations. Many studies indicated that gout is associated with hypertension, metabolic syndrome, chronic kidney disease and ischaemic heart diseases.Objectives:This study investigated the association between the compliance of urate-lowering agents (ULA) compliance and progression end-stage renal disease (ESRD) and all-cause mortality.Methods:We identified 53,917 patients with incident gout from 2002 to 2012. We followed up these patients till 31DEC2015. The primary data source was the National Health Insurance database of Taiwan. Proportion of days covered (PDC) was used to measure medication adherence. Patients with PDC≧80% more than two years defined adherence to ULA. Cox proportional hazards model was used to estimate difference and hazard ratios (HRs) for ESRD and all-cause mortality.Results:A total of 53,917 patients were included (figure 1). Patient with urate-lowering agent PDC≧80% more than 2 years were 2,371. After propensity score matched 1:4 with age, sex and comorbidities, PDC Table 1.Baseline characteristic of adherence and non-adherence of urate-lowering agent among patients with gout in matched and unmatched cohortUnmatched CohortPropensity-score Matched CohortVariablePDC≧80%N=2371^PDCN=51546^PPDC≧80%N=2371^PDCN=9484^PAge (years) (mean ± standard deviation)59.96±13.4451.52±15.6159.96±13.4460.23±13.410.3755follow-up duration (years) (mean ± standard deviation)12.30±2.459.52±3.46Gender0.30980.2855Male1929(81.36%)42358(82.18%)1929(81.36%)7624(80.39%)Female442(18.64%)9188(17.82%)442(18.64%)1860(19.61%)ComorbiditiesHypertension406(17.12%)3695(7.17%)1.71E-71406(17.12%)1571(16.56%)0.5138Diabetes Mellitus276(11.64%)2367(4.59%)1.78E-54276(11.64%)1080(11.39%)0.7291Ischemic heart disease109(4.60%)988(1.92%)1.58E-19109(4.60%)444(4.68%)0.8617Cerebrovascular disease113(4.77%)891(1.73%)1.05E-26113(4.77%)481(5.07%)0.5416Peripheral arterial disease20(0.84%)170(0.33%)3.67E-0520(0.84%)74(0.78%)0.7561Congestive heart failure81(3.42%)606(1.18%)1.88E-2181(3.42%)286(3.02%)0.3137Anemia182(7.68%)1559(3.02%)5.22E-36182(7.68%)769(8.11%)0.4882CKD266(11.22%)1978(3.84%)2.61E-69266(11.22%)963(10.15%)0.1281Table 2.hazard ratio of ESRD and all-cause mortality in patients with goutOutcomeHazard ratio (95% Confidence interval)ESRDULA adherence level PDCReference PDC≧80%0.91 (0.80-1.03)All-cause mortalityULA adherence level PDCReference PDC≧80%0.96 (0.88-1.03)PDC= Proportion of days coveredFigure 1.Flow chart for study designConclusion:Gout patients with/without two years adherence of urate-lowering agents does not have an impact on ESRD and all-cause mortality.References:NilDisclosure of Interests: :None declared

Snakes are known to express up to three visual pigments, a rhodopsin and two cone opsins, SWS1 and LWS. Colubrid snakes in the genus Helicops have invaded freshwater habitats from an ancestral terrestrial-only condition. Here we report, for the first time in a tetrapod, the presence of two distinct SWS1 opsins simultaneously expressed in different photoreceptors, conferring both UV and violet sensitivity in a Helicops species. Molecular analysis and in vitro expression confirm the presence of two functional SWS1 copies, likely the result of a recent gene duplication. Evolutionary analyses indicate that each sws1 has undergone different evolutionary paths, with strong purifying selection acting on the UV-sensitive copy and neutrality on the violet-sensitive copy. Site-directed mutagenesis shows, for the first time in snakes, the functional role of a single amino acid substitution, Phe86Val, in the large spectral shift between UV and violet opsins. In addition, higher densities of photoreceptors and SWS cones in the ventral retina suggest improved acuity in the upper visual field possibly correlated with visually-guided behaviors. The expanded visual opsin repertoire and the specialized retinal architecture are likely to improve photon uptake in underwater and terrestrial environments, and provide the neural substrate for a gain in chromatic discrimination, potentially conferring unique color vision in the UV-violet range. Our findings highlight the innovative mechanisms undertaken by a highly specialized tetrapod lineage to tackle the challenges imposed by the invasion of novel photic environments and the extraordinary diversity of evolutionary trajectories taken by visual opsin- based perception in vertebrates.

The ability to generate and detect electric fields has evolved in several groups of fishes as a means of communication, navigation and, occasionally, predation. The energetic burden required can account for up to 20% of electric fishes' daily energy expenditure. Despite this, molecular adaptations that enable electric fishes to meet the metabolic demands of bioelectrogenesis remain unknown. Here, we investigate the molecular evolution of the mitochondrial oxidative phosphorylation (OXPHOS) complexes in the two most diverse clades of weakly electric fishes—South American Gymnotiformes and African Mormyroidea, using codon-based likelihood approaches. Our analyses reveal that although mitochondrial OXPHOS genes are generally subject to strong purifying selection, this constraint is significantly reduced in electric compared to non-electric fishes, particularly for complexes IV and V. Moreover, analyses of concatenated mitochondrial genes show strong evidence for positive selection in complex I genes on the two branches associated with the independent evolutionary origins of electrogenesis. These results suggest that adaptive evolution of proton translocation in the OXPHOS cellular machinery may be associated with the evolution of bioelectrogenesis. Overall, we find striking evidence for remarkably similar effects of electrogenesis on the molecular evolution of mitochondrial OXPHOS genes in two independently derived clades of electrogenic fishes.This article is part of the theme issue ‘Linking the mitochondrial genotype to phenotype: a complex endeavour’.

We report on Al(Ga,In)N HEMTs, MISHEMTs and MOSFETs integrated on 200 mm Si wafers using Au-free processing in standard Si CMOS tools, and discuss the performance tradeoffs, limitations and solutions. The main highlights of process optimization include low RF transmission loss (0.15 dB/mm at 20 GHz), state-of-the-art contact resistance (R C ) of 0.14 Ω mm for a non-Au, low thermal budget ( BD ) of >300 V (pre and post device processing). We show that MISHEMTs, which feature the highest field effect mobility (μ FE ), >2000 cm2/V.s, and the best 1/f noise performance, have the potential to outperform the other device types in terms of device scalability for high frequency operation.

Retinitis pigmentosa (RP) is a degenerative retinal disease, often caused by mutations in the G-protein-coupled receptor rhodopsin. The majority of pathogenic rhodopsin mutations cause rhodopsin to misfold, including P23H, disrupting its crucial ability to respond to light. Previous screens to discover pharmacological chaperones of rhodopsin have primarily been based on rescuing rhodopsin trafficking and localization to the plasma membrane. Here, we present methods utilizing a yeast-based assay to screen for compounds that rescue the ability of rhodopsin to activate an associated downstream G-protein signaling cascade. We engineered a yeast strain in which human rhodopsin variants were genomically integrated, and were able to demonstrate functional coupling to the yeast mating pathway, leading to fluorescent protein expression. We confirmed that a known pharmacological chaperone, 9

Since 2014, the National Comprehensive Cancer Network (NCCN) has recommended that colorectal carcinoma (CRC) be universally tested for high microsatellite instability (MSI-H) which is present in 15% of such cancers. Fidelity of resultant microsatellites during DNA replication is contingent upon an intact mismatch repair (MMR) system and lack of fidelity can result in tumourigenesis. Prior to commencing routine screening for MSI-H, we assessed two commonly used methods, immunohistochemical (IHC) determination of loss of MMR gene products viz MLH1, MSH2, MSH6 and PMS2 against PCR amplification and subsequent fragment analysis of microsatellite markers, BAT25, BAT26, D2S123, D5S346 and D17S250 (Bethesda markers) in 73 unselected primary CRC. 15.1% (11/73) were categorized as MSI-H while deficient MMR (dMMR) was detected in 16.4% (12/73). Of the dMMR, 66.7% (8/12) were classified MSI-H, while 33.3% (4/12) were microsatellite stable/low microsatellite instability (MSS/MSI-L). Of the proficient MMR (pMMR), 95.1% (58/61) were MSS/MSI-L and 4.9% (3/61) were MSI-H. The κ value of 0.639 (standard error =0.125; p = 0.000) indicated substantial agreement between detection of loss of DNA mismatch repair using immunohistochemistry and the detection of downstream microsatellite instability using PCR. After consideration of advantages and shortcomings of both methods, it is our opinion that the choice of preferred technique for MSI analysis would depend on the type of laboratory carrying out the testing.

Functional variation in rhodopsin, the dim-light-specialized visual pigment, frequently occurs in species inhabiting light-limited environments. Variation in visual function can arise through two processes: relaxation of selection or adaptive evolution improving photon detection in a given environment. Here, we investigate the molecular evolution of rhodopsin in Gymnotiformes, an order of mostly nocturnal South American fishes that evolved sophisticated electrosensory capabilities. Our initial sequencing revealed a mutation associated with visual disease in humans. As these fishes are thought to have poor vision, this would be consistent with a possible sensory trade-off between the visual system and a novel electrosensory system. To investigate this, we surveyed rhodopsin from 147 gymnotiform species, spanning the order, and analysed patterns of molecular evolution. In contrast with our expectation, we detected strong selective constraint in gymnotiform rhodopsin, with rates of non-synonymous to synonymous substitutions lower in gymnotiforms than in other vertebrate lineages. In addition, we found evidence for positive selection on the branch leading to gymnotiforms and on a branch leading to a clade of deep-channel specialized gymnotiform species. We also found evidence that deleterious effects of a human disease-associated substitution are likely to be masked by epistatic substitutions at nearby sites. Our results suggest that rhodopsin remains an important component of the gymnotiform sensory system alongside electrolocation, and that photosensitivity of rhodopsin is well adapted for vision in dim-light environments.

Rhodopsin is the visual pigment responsible for initiating the phototransduction cascade in vertebrate rod photoreceptors. Although well-characterized in a few model systems, comparative studies of rhodopsin function, particularly for nonmammalian vertebrates are comparatively lacking. Bowerbirds are rare among passerines in possessing a key substitution, D83N, at a site that is otherwise highly conserved among G protein-coupled receptors. While this substitution is present in some dim-light adapted vertebrates, often accompanying another unusual substitution, A292S, its functional relevance in birds is uncertain. To investigate functional effects associated with these two substitutions, we use the rhodopsin gene from the great bowerbird (Ptilonorhynchus nuchalis) as a background for site-directed mutagenesis, in vitro expression and functional characterization. We also mutated these sites in two additional rhodopsins that do not naturally possess N83, chicken and bovine, for comparison. Both sites were found to contribute to spectral blue-shifts, but had opposing effects on kinetic rates. Substitutions at site 83 were found to primarily affect the kinetics of light-activated rhodopsin, while substitutions at site 292 had a larger impact on spectral tuning. The contribution of substitutions at site 83 to spectral tuning in particular depended on genetic background, but overall, the effects of substitutions were otherwise surprisingly additive, and the magnitudes of functional shifts were roughly similar across all three genetic backgrounds. By employing a comparative approach with multiple species, our study provides new insight into the joint impact of sites 83 and 292 on rhodopsin structure-function as well as their evolutionary significance for dim-light vision across vertebrates.

We report the first demonstration of InAs FinFETs with fin width $\textrm {W}_{{\mathrm{fin}}}$ in the range 25–35 nm, formed by inductively coupled plasma etching. The channel comprises defect-free, lattice-matched InAs with fin height $\textrm {H}_{{\mathrm{fin}}}=20$ nm controlled by the use of an etch stop layer incorporated into the device heterostructure. For a gate length $\textrm {L}_{{{\textrm {g}}}}=1~\mu \text{m}$ , peak transconductance $\textrm {g}_{{{\textrm {m},{\mathrm{ peak}}}}}=1430~\mu \text{S}/\mu \text{m}$ is measured at $\textrm {V}_{{\textrm {d}}}=0.5$ V demonstrating that electron transport in InAs fins can match planar devices.

Snakes are descended from highly visual lizards [1] but have limited (probably dichromatic) color vision attributed to a dim-light lifestyle of early snakes [2, 3, 4]. The living species of front-fanged elapids, however, are ecologically very diverse, with ∼300 terrestrial species (cobras, taipans, etc.) and ∼60 fully marine sea snakes, plus eight independently marine, amphibious sea kraits [1]. Here, we investigate the evolution of spectral sensitivity in elapids by analyzing their opsin genes (which are responsible for sensitivity to UV and visible light), retinal photoreceptors, and ocular lenses. We found that sea snakes underwent rapid adaptive diversification of their visual pigments when compared with their terrestrial and amphibious relatives. The three opsins present in snakes (SWS1, LWS, and RH1) have evolved under positive selection in elapids, and in sea snakes they have undergone multiple shifts in spectral sensitivity toward the longer wavelengths that dominate below the sea surface. Several relatively distantly related Hydrophis sea snakes are polymorphic for shortwave sensitive visual pigment encoded by alleles of SWS1. This spectral site polymorphism is expected to confer expanded “UV-blue” spectral sensitivity and is estimated to have persisted twice as long as the predicted survival time for selectively neutral nuclear alleles. We suggest that this polymorphism is adaptively maintained across Hydrophis species via balancing selection, similarly to the LWS polymorphism that confers allelic trichromacy in some primates. Diving sea snakes thus appear to share parallel mechanisms of color vision diversification with fruit-eating primates.

Typhula incarnata, the causal agent of gray snow mold, is an important winter pathogen of turfgrasses in the northern United States. The relative susceptibility of cultivars of three bent-grass species (creeping, colonial, and velvet bentgrass) to Typhula incarnata and the aggressiveness of 15 T. incarnata isolates obtained from infected turfgrasses on golf courses in Michigan, Minnesota, and Wisconsin were evaluated under controlled conditions. A hypersensitive type of resistance response to T. incarnata was not observed in any cultivar. Disease severity increased with higher inoculum concentration of T. incarnata. Colonization by gray snow mold gradually decreased with increasing plant age from 11 weeks after seeding in most cultivars tested, suggesting that age-related resistance was expressed over time. There were significant differences in disease severity among the three bentgrass species, particularly between tetraploid (creeping and colonial) and diploid (velvet) species, and among cultivars within each species, indicating varying levels of susceptibility to T. incarnata. All 15 isolates were pathogenic on bentgrass and were significantly different in aggressiveness, but aggressiveness was not related to geographic origin. Therefore, turfgrass breeders should be able to use one or a few virulent representative isolates of the pathogen to screen for resistance.

Speckled snow mold, caused by Typhula ishikariensis, is one of the most important Typhula snow molds in subarctic zones of the Northern Hemisphere. Nine isolates of three T. ishikariensis varieties (var. ishikariensis, var. canadensis, and var. idahoensis) isolated from infected turfgrasses on golf course fairways throughout Wisconsin were evaluated for their aggressiveness toward nine cultivars of three bentgrass species (three creeping, three colonial, and three velvet cultivars) under controlled environmental conditions. Speckled snow mold severity increased as inoculum concentration of T. ishikariensis was increased. In general, bentgrass susceptibility increased between 9 and 11 weeks after seeding but gradually decreased thereafter, suggesting expression of age-related resistance as plants matured. Significant differences in aggressiveness were detected within and among T. ishikariensis varieties. Significant interactions between T. ishikariensis varieties or isolates and bentgrass species were detected, but there was no interaction between pathogen isolates and bentgrass cultivars. Disease severity evaluations showed significant differences among bentgrass cultivars and species in their response to T. ishikariensis. Since bentgrass species exhibit differential responses to T. ishikariensis varieties, representative isolates of each variety should be employed for screening of bentgrass germplasm for resistance to speckled snow mold.

Bats are excellent models for studying the molecular basis of sensory adaptation. In Chiroptera, a sensory trade-off has been proposed between the visual and auditory systems, though the extent of this association has yet to be fully examined. To investigate whether variation in visual performance is associated with echolocation, we experimentally assayed the dim-light visual pigment rhodopsin from bat species with differing echolocation abilities. While spectral tuning properties were similar among bats, we found that the rate of decay of their light-activated state was significantly slower in a nonecholocating bat relative to species that use distinct echolocation strategies, consistent with a sensory trade-off hypothesis. We also found that these rates of decay were remarkably slower compared with those of other mammals, likely indicating an adaptation to dim light. To examine whether functional changes in rhodopsin are associated with shifts in selection intensity upon bat Rh1 sequences, we implemented selection analyses using codon-based likelihood clade models. While no shifts in selection were identified in response to diverse echolocation abilities of bats, we detected a significant increase in the intensity of evolutionary constraint accompanying the diversification of Chiroptera. Taken together, this suggests that substitutions that modulate the stability of the light-activated rhodopsin state were likely maintained through intensified constraint after bats diversified, being finely tuned in response to novel sensory specializations. Our study demonstrates the power of combining experimental and computational approaches for investigating functional mechanisms underlying the evolution of complex sensory adaptations.