Beyond barcoding: A mitochondrial genomics approach to molecular phylogenetics and diagnostics of blowflies (Diptera: Calliphoridae)

Members of the Calliphoridae (blowflies) are significant for medical and veterinary management, due to the ability of some species to consume living flesh as larvae, and for forensic investigations due to the ability of others to develop in corpses. Due to the difficulty of accurately identifying larval blowflies to species there is a need for DNA-based diagnostics for this family, however the widely used DNA-barcoding marker, cox1, has been shown to fail for several groups within this family. Additionally, many phylogenetic relationships within the Calliphoridae are still unresolved, particularly deeper level relationships. Sequencing whole mt genomes has been demonstrated both as an effective method for identifying the most informative diagnostic markers and for resolving phylogenetic relationships. Twenty-seven complete, or nearly so, mt genomes were sequenced representing 13 species, seven genera and four calliphorid subfamilies and a member of the related family Tachinidae. PCR and sequencing primers developed for sequencing one calliphorid species could be reused to sequence related species within the same superfamily with success rates ranging from 61% to 100%, demonstrating the speed and efficiency with which an mt genome dataset can be assembled. Comparison of molecular divergences for each of the 13 protein-coding genes and 2 ribosomal RNA genes, at a range of taxonomic scales identified novel targets for developing as diagnostic markers which were 117–200% more variable than the markers which have been used previously in calliphorids. Phylogenetic analysis of whole mt genome sequences resulted in much stronger support for family and subfamily-level relationships. The Calliphoridae are polyphyletic, with the Polleninae more closely related to the Tachinidae, and the Sarcophagidae are the sister group of the remaining calliphorids. Within the Calliphoridae, there was strong support for the monophyly of the Chrysomyinae and Luciliinae and for the sister-grouping of Luciliinae with Calliphorinae. Relationships within Chrysomya were not well resolved. Whole mt genome data, supported the previously demonstrated paraphyly of Lucilia cuprina with respect to L. sericata and allowed us to conclude that it is due to hybrid introgression prior to the last common ancestor of modern sericata populations, rather than due to recent hybridisation, nuclear pseudogenes or incomplete lineage sorting.     

Is caprine arthritis encephalitis virus (CAEV) transmitted vertically to early embryo development stages (morulae or blastocyst) via in vitro infected frozen semen?

The aim of this study was to determine, in vivo, whether in vitro infected cryopreserved caprine sperm is capable of transmitting caprine arthritis-encephalitis virus (CAEV) vertically to early embryo development stages via artificial insemination with in vitro infected semen. Sperm was collected from CAEV-free bucks by electroejaculation. Half of each ejaculate was inoculated with CAEV-pBSCA at a viral concentration of 10⁴ TCID₅₀/mL. The second half of each ejaculate was used as a negative control. The semen was then frozen. On Day 13 of superovulation treatment, 14 CAEV-free does were inseminated directly into the uterus under endoscopic control with thawed infected semen. Six CAEV-free does, used as a negative control, were inseminated intrauterine with thawed CAEV-free sperm, and eight CAEV-free does were mated with naturally infected bucks. Polymerase chain reaction (PCR) was used to detect CAEV proviral-DNA in the embryos at the D7 stage, in the embryo washing media, and in the uterine secretions of recipient does. At Day 7, all the harvested embryos were PCR-negative for CAEV proviral-DNA; however, CAEV proviral-DNA was detected in 8/14 uterine smears, and 9/14 flushing media taken from does inseminated with infected sperm, and in 1/8 uterine swabs taken from the does mated with infected bucks. The results of this study confirm that (i) artificial insemination with infected semen or mating with infected bucks may result in the transmission of CAEV to the does genital tack seven days after insemination, and (ii) irrespective of the medical status of the semen or the recipient doe, it is possible to obtain CAEV-free early embryos usable for embryo transfer.     

Glucosylation of the flavonoid, astragalin by Leuconostoc mesenteroides B-512FMCM dextransucrase acceptor reactions and characterization of the products

Astragalin (kaempferol-3-O-β-d-glucopyranoside, Ast) glucosides were synthesized by the acceptor reaction of a dextransucrase produced by Leuconostoc mesenteroides B-512FMCM with astragalin and sucrose. Each glucoside was purified and their structures were assigned as kaempferol-3-O-β-d-glucopyranosyl-(1 → 3)-O-α-d-glucopyranoside (or kaempferol-3-O-β-d-nigeroside, Ast-G1′) and kaempferol-3-O-β-d-glucopyranosyl-(1 → 6)-O-α-d-glucopyranoside (or kaempferol-3-O-β-d-isomaltoside, Ast-G1) for one glucose transferred, and kaempferol-3-O-β-d-isomaltooligosacharide (Ast-IMO or Ast-Gn; n = 2-8). The astragalin glucosides exhibited 8.3-60.6% higher inhibitory effects on matrix metalloproteinase-1 expression, 18.8-20.3% increased antioxidant effects, and 3.8-18.8% increased inhibition activity of melanin synthesis compared to control (without the addition of compound), depending on the number of glucosyl residues linked to astragalin. These novel compounds could be used to further expand the industrial applications of astragalin glucosides, in particular in the cosmetics industry.     

Chitosan-based heterogeneous catalysts for enantioselective Michael reaction

Novel chitosan-supported cinchona alkaloids have been developed as heterogeneous catalysts for enantioselective Michael reaction. As-synthesized products as organocatalysts for asymmetric Michael reaction have a high efficiency, providing highly functionalized products (containing adjacent quaternary and tertiary stereocenters) with good stereoselectivity (up to 93% enantiomeric excess) in high yields and recyclability (up to five runs).     

The mechanism of background extinction

Following publication of On the Origin of Species, biologists concentrated on and resolved the mechanisms of adaptation and speciation, but largely ignored extinction. Thus, extinction remained essentially a discipline of palaeontology. Adequate language is not available to describe extinction phenomena because they must be discussed in the passive voice, wherein populations simply ‘go extinct’ without reference to process, specifics, effects, or causality. Extinction is also described typically in terms of its dynamics (including rate or risk), and although correlative variables enhance our ability to predict extinction, they do not necessarily enable an understanding of process. Yet background extinction, like evolution, is a process requiring a functional explanation, without which it is impossible to formulate mechanisms. We define the mechanism of background extinction as a typically long‐term, multi‐generational loss of reproductive fitness. This simple concept has received little credence because of a perception that excess generation of progeny ensures population sustainability, and perhaps the misconception that the loss of reproductive fitness somehow constitutes selection against reproduction itself. During environmental shifts, reproductive fitness is compromised when biotic or abiotic extremes consistently exceed existing norms of reaction. Subsequent selection will now favour individual survival over reproductive fitness, initiating long‐term negative selection pressure and population decline. Background extinction consists typically of two intergrading phases: habitat attenuation and habitat dissolution. These processes generate the relict populations that characterize many species undergoing background extinction. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 255–268.     

Effects of brown and turbid water on piscivore–prey fish interactions along a visibility gradient

1. Environmental changes such as eutrophication and increasing inputs of humic matter (brownification) may have strong effects on predator–prey interactions in lakes through a reduction in the visual conditions affecting foraging behaviour of visually oriented predators. 2. In this experiment, we studied the effects of visual range (25–200 cm) in combination with optically deteriorating treatments (algae, clay or brown humic water) on predator–prey interactions between pike (Esox lucius) and roach (Rutilus rutilus). We measured effects on reaction distance and strike distance for pike and escape distance for roach, when pike individuals were exposed to free‐swimming roach as well as to roach held in a glass cylinder. 3. We found that reaction distance decreased with decreasing visual range caused by increasing levels of algae, clay or humic matter. The effect of reaction distance was stronger in turbid water (clay, algae) than in the brown water treatment. 4. Strike distance was neither affected by visual range nor by optical treatment, but we found shorter strike distances when pike attacked roach using visual cues only (roach held in a cylinder) compared to when pike could use multiple senses (free‐swimming roach). Escape distance for roach was longer in turbid than in brown water treatments. 5. Changes in environmental drivers, such as eutrophication and brownification, affecting the optical climate should thus have consequences for the strength of predator–prey interactions through changes in piscivore foraging efficiency and prey escape behaviour. This in turn may affect lake ecosystems through higher‐order interactions.     

Kidney proteome responses in the teleost fish Paralichthys olivaceus indicate a putative immune response against Streptococcus parauberis

The proteomic response to bacterial infection in a teleost fish (Paralichthys olivaceus) infected with Streptococcus parauberis was analyzed using label-free protein quantitation coupled with LC-MS(E) tandem mass spectrometry. A total of 82 proteins from whole kidney, a major lymphoid organ in this fish, were found to be differentially expressed between healthy and diseased fish analyzed 6, 24, 72 and 120 h post-infection. Among the differentially expressed proteins, those involved in mediating immune responses (e.g., heat shock proteins, cathepsins, goose-type lysozyme and complement components) were most significantly up-regulated by infection. In addition, cell division cycle 48 (CDC48) and calreticulin, which are associated with cellular recovery and glycoprotein synthesis, were up-regulated in the universal protein group, whereas the other proteins in that group were down-regulated. There was continuous activation of expression of immune-associated proteins during infection, but there was also loss of expression of proteins not involved in immune function. We expect that our findings regarding immune response at the protein level would offer new insight into the systemic response to bacterial infection of a major immune organ in teleost fish.     

Thermal luminescence spectra of polyamides and their Maillard reaction with reducing sugars

Thermal luminescence (TL) spectra of polyamides were measured with a Fourier‐transform chemiluminescence spectrometer to elucidate the emission mechanism. A TL band of ε‐polylysine with a peak at 542 nm observed at 403 K was assigned to the emission due to the interaction of the –CO–NH– group with oxygen molecules by comparison with nylon‐6, polyglycine, and polyalanine. When the sample was kept at 453 K, the intensity of the TL band decreased and the wavelength of the peak shifted to 602 nm, which was assigned to the emission due to the interaction of the NH₂ group on the side chain with oxygen molecules by comparison with monomeric lysine. A weak emission with a peak at 668 nm was assigned to the advanced glycosylation end products (AGEs) yielded by the Maillard reaction with a catalytic amount of water. To understand this reaction and to examine the TL emission of AGEs, we measured TL spectra of mixtures of polylysine and reducing sugars such as glucose, maltose, lactose, and dextrin. The minimum temperature for TL emission, wavelength of the peak and the relative intensities of the TL emission were found to depend on the size of the sugars. Copyright © 2011 John Wiley & Sons, Ltd.