Genetically modified bacteriophages in applied microbiology

Bacteriophages represent a simple viral model of basic research with many possibilities for practical application. Due to their ability to infect and kill bacteria, their potential in the treatment of bacterial infection has been examined since their discovery. With advances in molecular biology and gene engineering, the phage application spectrum has been expanded to various medical and biotechnological fields. The construction of bacteriophages with an extended host range or longer viability in the mammalian bloodstream enhances their potential as an alternative to conventional antibiotic treatment. Insertion of active depolymerase genes to their genomes can enforce the biofilm disposal. They can also be engineered to transfer various compounds to the eukaryotic organisms and the bacterial culture, applicable for the vaccine, drug or gene delivery. Phage recombinant lytic enzymes can be applied as enzybiotics in medicine as well as in biotechnology for pathogen detection or programmed cell death in bacterial expression strains. Besides, modified bacteriophages with high specificity can be applied as bioprobes in detection tools to estimate the presence of pathogens in food industry, or utilized in the control of food‐borne pathogens as part of the constructed phage‐based biosorbents.     

Dietary adaptations in the teeth of murine rodents (Muridae): a test of biomechanical predictions

Functional dental theory predicts that tooth shape responds evolutionarily to the mechanical properties of food. Most studies of mammalian teeth have focused on qualitative measures of dental anatomy and have not formally tested how the functional components of teeth adapt in response to diet. Here we generated a series of predictions for tooth morphology based on biomechanical models of food processing. We used murine rodents (Old World rats and mice) to test these predictions for the relationship between diet and morphology and to identify a suite of functional dental characteristics that best predict diets. One hundred and five dental characteristics were extracted from images of the upper and lower tooth rows and incisors for 98 species. After accounting for phylogenetic relationships, we showed that species evolving plant‐dominated diets evolved deeper incisors, longer third molars, longer molar crests, blunter posteriorly angled cusps, and more expanded laterally oriented occlusal cusps than species adapting to animal‐dominated diets. Measures of incisor depth, crest length, cusp angle and sharpness, occlusal cusp orientation, and the lengths of third molars proved the best predictors of dietary adaptation. Accounting for evolutionary history in a phylogenetic discriminant function analysis notably improved the classification accuracy. Molar morphology is strongly correlated with diet and we suggest that these dental traits can be used to infer diet with good accuracy for both extinct and extant murine species.     

Repeated invasions into the twilight zone: evolutionary origins of a novel assemblage of fishes from deep Caribbean reefs

Mesophotic and deeper reefs of the tropics are poorly known and underexplored ecosystems worldwide. Collectively referred to as the ‘twilight zone’, depths below ~30–50 m are home to many species of reef fishes that are absent from shallower depths, including many undescribed and endemic species. We currently lack even a basic understanding of the diversity and evolutionary origins of fishes on tropical mesophotic reefs. Recent submersible collections in the Caribbean have provided new specimens that are enabling phylogenetic reconstructions that incorporate deep‐reef representatives of tropical fish genera. Here, we investigate evolutionary depth transitions in the family Gobiidae (gobies), the most diverse group of tropical marine fishes. Using divergence‐time estimation coupled with stochastic character mapping to infer the timing of shallow‐to‐deep habitat transitions in gobies, we demonstrate at least four transitions from shallow to mesophotic depths. Habitat transitions occurred in two broad time periods (Miocene, Pliocene–Pleistocene), and may have been linked to the availability of underutilized niches, as well as the evolution of morphological/behavioural adaptations for life on deep reefs. Further, our analysis shows that at least three evolutionary lineages that invaded deep habitats subsequently underwent speciation, reflecting another unique mode of radiation within the Gobiidae. Lastly, we synthesize depth distributions for 95 species of Caribbean gobies, which reveal major bathymetric faunal breaks at the boundary between euphotic and mesophotic reefs. Ultimately, our study is the first rigorous investigation into the origin of Caribbean deep‐reef fishes and provides a framework for future studies that utilize rare, deep‐reef specimens.     

Removal of ammonium from aqueous solutions using alkali-modified biochars

Biochars converted from agricultural residuals can effectively remove ammonium from water. This work further improved the sorption ability of biochars to aqueous ammonium through alkali modification. Three modified biochars were prepared from agricultural residuals pre-treated with NaOH solution through low-temperature (300 °C) slow pyrolysis. The modified biochars effectively removed ammonium ions from water under various conditions with relatively fast adsorption kinetics (reached equilibrium within 10 h) and extremely high adsorption capacity (>200 mg/g). The Langmuir maximum capacity of the three modified biochars were between 313.9 and 518.9 mg/g, higher than many other ammonium adsorbents. Although the sorption of ammonium onto the modified biochar was affected by pH and temperature, it was high under all of the tested conditions. Findings from this work indicated that alkali-modified biochars can be used as an alternative adsorbent for the removal of ammonium from wastewater.     

Synthesis,Characterization, Molecular Modeling,and DNA Interaction Studies of Copper Complex Containing Food Additive Carmoisine Dye

A copper complex of carmoisine dye; [Cu(carmoisine)₂(H₂O)₂]; was synthesized and characterized by using physico-chemical and spectroscopic methods. The binding of this complex with calf thymus (ct) DNA was investigated by circular dichroism, absorption studies, emission spectroscopy, and viscosity measurements. UV-vis results confirmed that the Cu complex interacted with DNA to form a ground-state complex and the observed binding constant (2× 10⁴ M^?1) is more in keeping with the groove bindings with DNA. Furthermore, the viscosity measurement result showed that the addition of complex causes no significant change on DNA viscosity and it indicated that the intercalation mode is ruled out. The thermodynamic parameters are calculated by van't Hoff equation, which demonstrated that hydrogen bonds and van der Waals interactions played major roles in the reaction. The results of circular dichroism (CD) suggested that the complex can change the conformation of DNA from B-like form toward A-like conformation. The cytotoxicity studies of the carmoisine dye and its copper complex indicated that both of them had anticancer effects on HT-29 (colon cancer) cell line and they may be new candidates for treatment of the colon cancer.     

Evolution of risk assessment strategies for food and feed uses of stacked GM events

Data requirements are not harmonized globally for the regulation of food and feed derived from stacked genetically modified (GM) events, produced by combining individual GM events through conventional breeding. The data required by some regulatory agencies have increased despite the absence of substantiated adverse effects to animals or humans from the consumption of GM crops. Data from studies conducted over a 15‐year period for several stacked GM event maize (Zea mays L.) products (Bt11 ×  GA21, Bt11 ×  MIR604, MIR604 ×  GA21, Bt11 ×  MIR604 ×  GA21, Bt11 ×  MIR162 ×  GA21 and Bt11 ×  MIR604 ×  MIR162 ×  GA21), together with their component single events, are presented. These data provide evidence that no substantial changes in composition, protein expression or insert stability have occurred after combining the single events through conventional breeding. An alternative food and feed risk assessment strategy for stacked GM events is suggested based on a problem formulation approach that utilizes (i) the outcome of the single event risk assessments, and (ii) the potential for interactions in the stack, based on an understanding of the mode of action of the transgenes and their products.     

Are all GMOs the same? Consumer acceptance of cisgenic rice in India

India has more than 215 million food‐insecure people, many of whom are farmers. Genetically modified (GM) crops have the potential to alleviate this problem by increasing food supplies and strengthening farmer livelihoods. For this to occur, two factors are critical: (i) a change in the regulatory status of GM crops, and (ii) consumer acceptance of GM foods. There are generally two classifications of GM crops based on how they are bred: cisgenically bred, containing only DNA sequences from sexually compatible organisms; and transgenically bred, including DNA sequences from sexually incompatible organisms. Consumers may view cisgenic foods as more natural than those produced via transgenesis, thus influencing consumer acceptance. This premise was the catalyst for our study—would Indian consumers accept cisgenically bred rice and if so, how would they value cisgenics compared to conventionally bred rice, GM‐labelled rice and ‘no fungicide’ rice? In this willingness‐to‐pay study, respondents did not view cisgenic and GM rice differently. However, participants were willing‐to‐pay a premium for any aforementioned rice with a ‘no fungicide’ attribute, which cisgenics and GM could provide. Although not significantly different (P = 0.16), 76% and 73% of respondents stated a willingness‐to‐consume GM and cisgenic foods, respectively.     

Going against the flow: a case for upstream dispersal and detection of uncommon dispersal events

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Stream diatom assemblages as predictors of climate

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An appraisal of seed enumeration and videographic techniques for determining seed removal rates by birds

We examined the efficacy of seed enumeration and videographic techniques for determining seed removal by birds from indigenous (Chrysanthemoides monilifera and Olea europaea subsp africana) and alien (Lantana camara and Solanum mauritianum) shrubs at different study sites in the Cape Floristic Region. The seed enumeration technique involved counting the numbers of fruits and associated seeds removed monthly by birds, excluding those naturally abscised, from the shrub canopy. The videographic technique involved visual counts from images of the numbers of fruits and associated seeds consumed by birds over specific time intervals captured by a digital camcorder. Daily seed removal rates by all birds, irrespective of species, measured by both techniques were similar with no significant interactions evident between measuring techniques, site and shrub species. Both techniques displayed higher seed removal from tiny‐seeded S. mauritianum than other shrub species; this was also evident among individual bird species. However, the seed enumeration technique was unable to discriminate between foraging organisms, contamination of traps by wind‐blown fruits abscised from neighbouring branches and fruit theft from the canopy and the traps. In contrast, the videographic technique provided permanent visual and time‐lapse records for individual foraging bird species allowing greater measurement precision and interpretation of fruit removal behaviour by birds. We recommend use of the videographic technique over the seed enumeration technique for studying vertebrates’ seed removal in a detailed manner.