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The haloarchaeon Haloferax volcanii was shown to contain 145 intergenic and 45 antisense sRNAs. In a comprehensive approach to unravel various biological roles of haloarchaeal sRNAs in vivo, 27 sRNA genes were selected and deletion mutants were generated. The phenotypes of these mutants were compared to that of the parent strain under ten different conditions, i.e. growth on four different carbon sources, growth at three different salt concentrations, and application of four different stress conditions. In addition, cell morphologies in exponential and stationary phase were observed. Furthermore, swarming of 17 mutants was analyzed. 24 of the 27 mutants exhibited a difference from the parent strain under at least one condition, revealing that haloarchaeal sRNAs are involved in metabolic regulation, growth under extreme conditions, regulation of morphology and behavior, and stress adaptation. Notably, 7 deletion mutants showed a gain of function phenotype, which has not yet been described for any other prokaryotic sRNA gene deletion mutant. Comparison of the transcriptomes of one sRNA gene deletion mutant and the parent strain led to the identification of differentially expressed genes. Genes for flagellins and chemotaxis were up-regulated in the mutant, in accordance with its gain of function swarming phenotype. While the deletion mutant analysis underscored that haloarchaeal sRNAs are involved in many biological functions, the degree of conservation is extremely low. Only 3 of the 27 genes are conserved in more than 10 haloarchaeal species. 22 of the 27 genes are confined to H. volcanii, indicating a fast evolution of haloarchaeal sRNA genes.
Genome-wide association studies are widely used to correlate phenotypic traits with genetic variants. These studies usually compare the genetic variation between two groups to single out certain Single Nucleotide Polymorphisms (SNPs) that are linked to a phenotypic variation in one of the groups. However, it is necessary to have a large enough sample size to find statistically significant correlations. Direct-To-Consumer (DTC) genetic testing can supply additional data: DTC-companies offer the analysis of a large amount of SNPs for an individual at low cost without the need to consult a physician or geneticist. Over 100,000 people have already been genotyped through Direct-To-Consumer genetic testing companies. However, this data is not public for a variety of reasons and thus cannot be used in research. It seems reasonable to create a central open data repository for such data. Here we present the web platform openSNP, an open database which allows participants of Direct-To-Consumer genetic testing to publish their genetic data at no cost along with phenotypic information. Through this crowdsourced effort of collecting genetic and phenotypic information, openSNP has become a resource for a wide area of studies, including Genome-Wide Association Studies. openSNP is hosted at http://www.opensnp.org, and the code is released under MIT-license at http://github.com/gedankenstuecke/snpr.
Three neonicotinoids, imidacloprid, clothianidin and thiacloprid, agonists of the nicotinic acetylcholine receptor in the central brain of insects, were applied at non-lethal doses in order to test their effects on honeybee navigation. A catch-and-release experimental design was applied in which feeder trained bees were caught when arriving at the feeder, treated with one of the neonicotinoids, and released 1.5 hours later at a remote site. The flight paths of individual bees were tracked with harmonic radar. The initial flight phase controlled by the recently acquired navigation memory (vector memory) was less compromised than the second phase that leads the animal back to the hive (homing flight). The rate of successful return was significantly lower in treated bees, the probability of a correct turn at a salient landscape structure was reduced, and less directed flights during homing flights were performed. Since the homing phase in catch-and-release experiments documents the ability of a foraging honeybee to activate a remote memory acquired during its exploratory orientation flights, we conclude that non-lethal doses of the three neonicotinoids tested either block the retrieval of exploratory navigation memory or alter this form of navigation memory. These findings are discussed in the context of the application of neonicotinoids in plant protection.
A novel xanthomonadin-dialkylresorcinol hybrid named arcuflavin was identified in Azoarcus sp. BH72 by a combination of feeding experiments, HPLC-MS and MALDI-MS and gene clusters encoding the biosynthesis of this non-isoprenoid aryl-polyene containing pigment are reported. A chorismate-utilizing enzyme from the XanB2-type producing 3- and 4-hydroxybenzoic acid and an AMP-ligase encoded by these gene clusters were characterized, that might perform the first two steps of the polyene biosynthesis. Furthermore, a detailed analysis of the already known or novel biosynthesis gene clusters involved in the biosynthesis of polyene containing pigments like arcuflavin, flexirubin and xanthomonadin revealed the presence of similar gene clusters in a wide range of bacterial taxa, suggesting that polyene and polyene-dialkylresorcinol pigments are more widespread than previously realized.
A revision of the genus Asterostegus Mortensen, 1933 (Echinodermata: Ophiuroidea: Euryalidae) is based on seven specimens, including the holotype of Asterostegus maini McKnight, 2003. A new species, Asterostegus sabineae sp. nov., is described from off Reunion Island and two other species, A. tuberculatus Mortensen, 1933 and A. maini, are redescribed. A tabular key to the three species of the genus Asterostegus is provided. Some terminology of the taxonomy of euryalid ophiuroids is revised.
The types of nominal species of Diapriinae in the collection of the Natural History Museum, London, are catalogued. Lectotypes are designated for the following taxa: Diapria peraffinis Ashmead, 1896; D. smithii Ashmead, 1896; Galesus bipunctatus Ashmead,1894; G. (G.) foersteri var. nigricornis Kieffer, 1911; G. sexpunctatus Ashmead, 1893; G. walkeri Kieffer, 1907; Idiotypa nigriceps Kieffer, 1909; I. nigriceps Kieffer, 1911; I. pallida Ashmead, 1893; I. pallida Ashmead in Riley, Ashmead & Howard, 1894; Paramesius angustipennis Kieffer, 1911; P. cameroni Kieffer, 1911; Phaenopria cameroni Kieffer, 1911; P. halterata Kieffer, 1911; P. magniclavata Ashmead, 1896; Tropidopsis clavata Ashmead, 1893; T. clavata Ashmead in Riley, Ashmead & Howard, 1894. New combinations are proposed: Aneuropria bifurcata comb. nov. for Mantara bifurcata Dodd, 1920; Basalys quadridens comb. nov. for Microgalesus quadridens Kieffer, 1912; Coptera cratocerus comb. nov. for Galesus cratocerus Cameron, 1912; Coptera sexpunctata comb. nov. for Galesus sexpunctatus Ashmead, 1893; Doliopria magniclavata comb. nov. for Phaenopria magniclavata Ashmead, 1896; Spilomicrus aterrimus comb. nov. for Hoplopria aterrima Dodd,
1920; Spilomicrus campbellanus comb. nov. for Antarctopria campbellana Yoshimoto, 1964; Spilomicrus coelopae comb. nov. for Antarctopria coelopae Early, 1978; Spilomicrus diomedeae comb. nov. for Antarctopria diomedeae Early, 1978; Spilomicrus helosciomyzae comb. nov. for Malvina helosciomyzae Early & Horning, 1978; Spilomicrus insulae comb. nov. for Malvina insulae Early, 1980; Spilomicrus latigaster comb. nov. for Antarctopria latigaster Brues in Tillyard, 1920; Spilomicrus punctatus comb. nov. for Malvina punctata Cameron, 1889; Spilomicrus rekohua comb. nov. for Antarctopria rekohua Early, 1978; Trichopria bouceki comb. nov. for Oxypria bouceki Masner, 1959; Trichopria nigriceps comb. nov. for Tropidopria nigriceps Ashmead in Riley, Ashmead & Howard, 1894; Trichopria nigriceps comb. nov. for Xyalopria nigriceps Kieffer, 1907; Trichopria spinosiceps comb. nov. for Acidopria spinosiceps Dodd, 1920; Trichopria walkeri comb. nov. for Diapria walkeri Dalla Torre, 1890. New replacement names are proposed: Coptera mosselensis nom. nov. for C. nigricornis Nixon, 1930 preocc.; Coptera pijiguaorum nom. nov. for C. sexpunctata Montilla & García, 2008 preocc.; Spilomicrus kozlovi nom. nov. for S. punctatus Kozlov, 1978 preocc.; Trichopria fluminis nom. nov. for T. nigriceps (Kieffer, 1907) preocc.; T. thermarum nom. nov. for T. nigriceps (Kieffer, 1913) preocc. New specific synonyms are proposed: Basalys cursitans (Kieffer, 1911) = B. pedisequa (Kieffer, 1911) syn. nov. (the former removed from synonymy with B. parvus Thomson, 1858); B. iphicla Nixon, 1980 = B. macroptera (Kieffer, 1911) syn. nov.; Coptera bipunctata (Ashmead in Riley, Ashmead & Howard, 1894) = C. sexpunctata (Ashmead, 1893) syn. nov.; Idiotypa nigriceps Kieffer, 1911 = I. nigriceps Kieffer, 1909 syn. nov.; I. pallida Ashmead in Riley, Ashmead & Howard, 1894 = I. pallida Ashmead, 1893 syn. nov.; Psilus nigricornis (Kieffer, 1911) = P. fuscipennis (Curtis, 1831) syn. nov.; P. walkeri (Kieffer, 1907) = P. fuscipennis (Curtis, 1831) syn. nov.; T. bouceki (Masner, 1959) = T. conotoma (Kieffer, 1911) syn. nov.; Trichopria halterata (Kieffer, 1911) = T. halterata (Kieffer, 1909) syn. nov. New generic synonyms are proposed: Antarctopria Brues in Tillyard, 1920 = Spilomicrus Westwood, 1832 syn. nov.; Malvina Cameron, 1889 = Spilomicrus Westwood, 1832 syn. nov.; Mantara Dodd, 1920 = Aneuropria Kieffer, 1905 syn. nov.; Microgalesus Kieffer, 1912 = Basalys Westwood, 1833 syn. nov.; Xyalopria Kieffer, 1907 = Trichopria Ashmead, 1893 syn. nov. (Xyalopria is removed from synonymy with Megaplastopria Ashmead, 1903). A brief account of some aspects of the history of these types is given.
Three fossil leafhopper inclusions from Eocene Baltic amber, representing three new extinct genera and species, are described and illustrated. Eomegophthalmus lithuaniensis gen. et sp. nov. is tentatively placed in Megophthalminae, although it may represent the stem group from which Megophthalminae, Ulopinae, and Membracidae arose. Xestocephalites balticus gen. et sp. nov. and Brevaphrodella nigra gen. et sp. nov. are placed in Aphrodinae: Xestocephalini based on the structure of the head, leg chaetotaxy, and male genital capsule. These new genera and species represent the oldest known representatives of their respective subfamilies and the latter is the oldest known brachypterous adult leafhopper.
The study of the Portuguese marine ichthyofauna has a long historical tradition, rooted back in the 18th Century. Here we present an annotated checklist of the marine fishes from Portuguese waters, including the area encompassed by the proposed extension of the Portuguese continental shelf and the Economic Exclusive Zone (EEZ). The list is based on historical literature records and taxon occurrence data obtained from natural history collections, together with new revisions and occurrences. It comprises a total of 1191 species, distributed among 3 superclasses, 4 classes, 42 orders, 212 families and 617 genera. If considering only the EEZ and present territorial waters, this list represents an increase of 230 species (27.8%) and of 238 species (29.0%), when compared to the information available in FishBase (2012) and in the last checklist of marine and estuarine fishes of Portugal (1993), respectively. The order Perciformes shows the highest diversity, with 54 families, 162 genera and 299 species. Stomiidae (80 species), Myctophidae (71 species) and Macrouridae (37 species) are the richest families. From the listed species, 734 are present off mainland Portugal, 857 off the Azores and 766 off Madeira. Within the limits of the examined area, three species are reported for the first time in mainland Portugal and twenty-nine records are identified as doubtful. A total of 133 species have been recorded from the extended Portuguese continental shelf (2 off mainland Portugal, 117 off the Azores and 14 off Madeira), two of which are common to the Azores and Madeira extensions. Biogeographically, the Atlantic group is the most important (548 species – 46.01%), followed by the Lusitanian group (256 species – 21.49%), the African group (71 species – 5.96%), the Boreal group (34 species – 2.85%), the Mediterranean group (31 species – 2.60%), the Macaronesian group (21 species – 1.76%), the Atlantic/African group (19 species – 1.60%) and the Mediterranean/African and the Arctic groups, each with only 1 species (0.08%). Regarding the preferences for vertical habitat, the demersal fishes are the most important group (305 species – 25.61%), followed by the mesopelagic group (228 species – 19.14%), the bathypelagic group (164 species – 13.77%), the benthopelagic group (147 species – 12.34%), the bathydemersal group (115 species – 9.66%), the reef-associated group (88 species – 7.39%), the pelagic group (74 species – 6.21%), the epipelagic group (58 species – 4.87%) and 1 species (0.08%) of the benthic group. The oceanic habitat is the best represented group comprising 446 species (37.45%), followed by the shelf group (199 species – 16.71%), the slope group (164 species – 13.77%), the inner shelf group (89 species – 7.47%), the coastal group (70 species – 5.88%), the outer shelf group (29 species – 2.43%) and the oceanic/shelf group (7 species – 0.59%).