Orphan genes: Function,evolution, and composition

The origin and function of orphan genes (OGs) is a mysterious problem in modern molecular biology. The recently developed PHOG database helped to shed light on some aspects in the evolution of these genes. Presumably, a rapid evolution is the main factor that influences the origin of OGs. The evolutionary rate of particular genes reflects the degree of their conservation, although exceptions from this rule contribute to the dynamic process of genome evolution during speciation. It is demonstrated that a great number of OGs detected is an artifact of insufficient sequencing. If DNAs of all organisms living on Earth were sequenced, then the OG number would be greatly reduced, giving the way to genes specific of particular taxonomic groups.     

Dipeptidase-C inDrosophila melanogaster: Genetic,ontogenetic, and tissue-specific variation

Dip-A, Dip-B, and Dip-C constitute structural genes for three peptidic enzymes in Drosophila melanogaster distinct from the leucine aminopeptidases. Their ontogenetic and tissue distributions of activities suggest the involvement of these enzymes in a general metabolic role, such as the regulation of amino acid and oligopeptide pools to make amino acids available for protein synthesis. Screening of chromosome substitution isogenic lines for DIP-C activity indicated that, like DIP-A and DIP-B, unlinked activity modifiers exist for Dip-C. The developmental profiles of dipeptidase activities are very similar, except in the pupal stage, during which DIP-C activity is markedly low compared to the other two enzymes. Intercorrelations of dipeptidase activities vary ontogenetically, which is consistent with the need for coordinate expression of these enzymes during certain developmental stages. Tissue-specific expression of dipeptidases in larvae and adults are also similar, although the relative levels of DIP-A activity differ from those of DIP-B and DIP-C in certain organs and body parts. Some of the differences among chromosome substitution lines for dipeptidase activities appear to be systemic, while others are developmental stage-specific and tissue-specific. Second- and third-chromosome variants for DIP-C activity differed in their tissue distribution. This is consistent with the presence of temporal and spatial variants in natural populations for other Drosophila enzymes.     

Macroborings in Otodus megalodon and Otodus chubutensis shark teeth from the submerged shelf of Onslow Bay,North Carolina,USA: implications for processes of lag deposit formation

Abstract

The shallow continental shelf in the Cape Fear Region of southwestern Onslow Bay, North Carolina, contains lag deposits with an abundance of megatoothed shark teeth belonging to Otodus megalodon (Agassiz 1835) and Otodus chubutensis (Ameghino 1906) that derive from the Pliocene Yorktown and Miocene Pungo River formations, respectively. These teeth exhibit different frequencies and orientations of macroborings identified as Gastrochaenolites torpedo Kelly and Bromley (1984 Kelly, S., and R. Bromley. 1984. “Ichnological Nomenclature of Clavate Borings.” Palaeontology 27: 793–807.[Web of Science ®] , [Google Scholar]), Gastrochaenolites lapidicus Kelly and Bromley (1984 Kelly, S., and R. Bromley. 1984. “Ichnological Nomenclature of Clavate Borings.” Palaeontology 27: 793–807.[Web of Science ®] , [Google Scholar]), Maeandropolydora sulcans Voigt (1965 Voigt, E. 1965. “Über parasitische Polychaeten in Kreide-Austern sowie einige andere in Muschelschalen bohrende Würmer.” Paläontologische Zeitschrift 39 (3–4): 193–211.[Crossref] , [Google Scholar]) and ?Entobia isp. attributed to endolithic bivalves, serpulid worms and clionaid sponges. Different frequencies and orientations of macroborings seen in lag deposits containing O. megalodon and O. chubutensis teeth are the result of repeated exhumation and reworking in response to bathymetrically controlled wave-based erosion during storm events and glacioeustatically driven sea-level cyclicity across Onslow Bay. Chronological ranges of O. megalodon and O. chubutensis teeth that contain macroborings indicate that these lag deposits may have been forming since the late early Miocene.     

Fabrication and Operation of Acoustofluidic Devices Supporting Bulk Acoustic Standing Waves for Sheathless Focusing of Particles

Acoustophoresis refers to the displacement of suspended objects in response to directional forces from sound energy. Given that the suspended objects must be smaller than the incident wavelength of sound and the width of the fluidic channels are typically tens to hundreds of micrometers across, acoustofluidic devices typically use ultrasonic waves generated from a piezoelectric transducer pulsating at high frequencies (in the megahertz range). At characteristic frequencies that depend on the geometry of the device, it is possible to induce the formation of standing waves that can focus particles along desired fluidic streamlines within a bulk flow. Here, we describe a method for the fabrication of acoustophoretic devices from common materials and clean room equipment. We show representative results for the focusing of particles with positive or negative acoustic contrast factors, which move towards the pressure nodes or antinodes of the standing waves, respectively. These devices offer enormous practical utility for precisely positioning large numbers of microscopic entities (e.g., cells) in stationary or flowing fluids for applications ranging from cytometry to assembly.     

Novel diversity within Roseofilum (Desertifilaceae,Cyanobacteria) from marine benthic mats with description of four new species

Benthic cyanobacterial mats (BCMs) are natural phenomena in marine environments. Reports of BCMs occurring across coastal marine environments have increased, partly driven by nutrient loading and climate change; thus, there is a need to understand the diversity involved in the proliferations and potential toxicity of the BCMs. Furthermore, marine cyanobacterial mats are observed growing on and affecting the health of corals with one specific cyanobacterial genus, Roseofilum, dominating the microbial mats associated with black band disease (BBD), a destructive polymicrobial disease that affects corals. To explore the diversity of Roseofilum, cyanobacterial mats from various marine habitats were sampled, and individual isolates were identified based on morphology, 16S rRNA gene phylogenies, 16S–23S ITS rRNA region sequence dissimilarities, and phylogenomics. Four novel species of Roseofilum were isolated from benthic marine mats, three from the coasts of Florida, United States (R. capinflatum sp. nov., R. casamattae sp. nov., and R. acuticapitatum sp. nov.) and one from the coast of France (R. halophilum sp. nov.). Our analyses revealed that Roseofilum associated with coral BBD and those not associated with corals but rather from coastal benthic mats are systematically distinct based on both phylogenetic and phylogenomic analyses. Enzyme-linked immunosorbent assay (ELISA) and LC–MS data indicated that microcystin production was found in one of the four species.