Data mining for simple sequence repeats in expressed sequence tags from barley,maize, rice,sorghum and wheat

Plant genomics projects involving model species and many agriculturally important crops are resulting in a rapidly increasing database of genomic and expressed DNA sequences. The publicly available collection of expressed sequence tags (ESTs) from several grass species can be used in the analysis of both structural and functional relationships in these genomes. We analyzed over 260000 EST sequences from five different cereals for their potential use in developing simple sequence repeat (SSR) markers. The frequency of SSR-containing ESTs (SSR-ESTs) in this collection varied from 1.5% for maize to 4.7% for rice. In addition, we identified several ESTs that are related to the SSR-ESTs by BLAST analysis. The SSR-ESTs and the related sequences were clustered within each species in order to reduce the redundancy and to produce a longer consensus sequence. The consensus and singleton sequences from each species were pooled and clustered to identify cross-species matches. Overall a reduction in the redundancy by 85% was observed when the resulting consensus and singleton sequences (3569) were compared to the total number of SSR-EST and related sequences analyzed (24606). This information can be useful for the development of SSR markers that can amplify across the grass genera for comparative mapping and genetics. Functional analysis may reveal their role in plant metabolism and gene evolution.     

N-acetylcysteine inhibits in vivo nitric oxide production by inducible nitric oxide synthase.

This in vivo study evaluates the effect of N-acetylcysteine (NAC) administration on nitric oxide (NO) production by the inducible form of nitric oxide synthase (iNOS). NO production was induced in the rat by the ip administration of 2 mg/100 g lipopolysaccharide (LPS). This treatment caused: (1) a decrease in body temperature within 90 min, followed by a slow return to normal levels; (2) an increase in plasma levels of urea, nitrite/nitrate, and citrulline; (3) the appearance in blood of nitrosyl-hemoglobin (NO-Hb) and in liver of dinitrosyl-iron-dithiolate complexes (DNIC); and (4) increased expression of iNOS mRNA in peripheral blood mononuclear cells (PBMC). Rat treatment with 15 mg/100 g NAC ip, 30 min before LPS, resulted in a significant decrease in blood NO-Hb levels, plasma nitrite/nitrate and citrulline concentrations, and liver DNIC complexes. PBMC also showed a decreased expression of iNOS mRNA. NAC pretreatment did not modify the increased levels of plasma urea or the hypothermic effect induced by the endotoxin. The administration of NAC following LPS intoxication (15 min prior to sacrifice) did not affect NO-Hb levels. These results demonstrate that NAC administration can modulate the massive NO production induced by LPS. This can be attributed mostly to the inhibitory effect of NAC on one of the events leading to iNOS protein expression. This hypothesis is also supported by the lack of effect of late NAC administration.     

Notable plesiomorphies and notable specializations: Head structure of the primitive “tongue moth” Acanthopteroctetes unifascia (lepidoptera: Acanthopteroctetidae)

The Acanthopteroctetidae are one of the first‐originated family‐group lineages within “tongue moths” (Lepidoptera‐Glossata). The purpose of this study is to provide a comprehensive account (based on whole mount preparations, serial sections, and Scanning electron microscopy) of the cephalic structure of an adult exemplar of the family, to supplement the sparse available information. Notable plesiomorphies include the retention of frontal retractors of the narrow labrum, a high supraocular index linked to strong development of cranio‐mandibular ad‐ and abductors, and perhaps the unusually short but still coilable (just ca. 1.5 turns) galeal “tongue.” Notable specializations (probably mostly family autapomorphies) include a complement of large sensilla placodea on the male antennae, an apical attachment of the long dorsal tentorial arm to the cranium, an extreme reduction of the single‐segmented labial palps, a particularly strong subgenal bridge and a surface structure of near‐parallel ridges on the ommatidial corneae. The presence of sizable saccular mandibular (type 1) glands opening into the adductor apodeme is unexpected, no counterparts being known from neighboring taxa. The same is true for ventral salivarium dilator muscles originating on the prelabium; and tentatively suggested to be homologues of the extrinsic palp flexors (the insertion shift being related to loss of original function due to palp reduction), rather than to the ventral salivarium muscles of more basal insects. A complete “deutocerebral loop”' may or may not be developed, as is true for a mutual appression of the optic lobe and circumoesophageal connective/suboesophageal ganglion, enclosing the anterior tentorial arm between them; a suboesophageal innervation of the retrocerebral complex was not observed. No characters bearing on the monophyly of the Coelolepida were identified. The scapo‐pedicellar articulation with a scapal process and a smooth intercalary sclerite is reminiscent of conditions in Neopseustidae, but remains debatable as a synapomorphy of the two families. J. Morphol. 275:153–172, 2014. © 2013 Wiley Periodicals, Inc.     

Netguns: a technique for capturing Black‐backed Woodpeckers

ABSTRACT Effective capture techniques are essential for studying bird populations, but commonly used techniques have proven ineffective for capturing Black‐backed Woodpeckers (Picoides arcticus) during the nonbreeding period. As a result, little is known about the winter ecology of Black‐backed Woodpeckers. We used two netguns, one powered with a 0.308 cartridge and another with CO₂ propellant, to capture 101 Black‐backed Woodpeckers (N= 75 initial captures and 26 recaptures) in the Black Hills of South Dakota from 2008 to 2011. Captures with the 0.308 netgun resulted in an impact mortality probability of 0.061 ± 0.034 (SE), whereas no impact mortalities were associated with the CO₂ netgun. We also tracked birds for 72 h post‐release, and determined a capture‐related mortality rate of 0.102 ± 0.04 with the 0.308 netgun and 0.038 ± 0.027 with the CO₂ netgun. With the CO₂ netgun, we captured woodpeckers in 31 of 43 net deployments (72%), with an average of 7.2 ± 0.4 h of capture effort for each bird. Many unsuccessful attempts were caused by tree branches that prevented net deployment. Netguns powered by CO₂ provide an effective capture technique that we recommend for studies of Black‐backed Woodpeckers and possibly other species of birds that forage low on trees.     

The effect of growth regulators on shoot propagation and rooting of common lavender (Lavandula vera DC)

Nodal segments from micropropagated plants were used to evaluate the effect of growth regulators on the in vitro shoot proliferation and rooting of Lavandula vera DC. The highest multiplication rate was obtained using MS medium supplemented with 1.0 mg l^-1 of TDZ (2.25 μM) or BA (2 μM). Hyperhydricity occurred at high concentrations of these growth regulators. Rooting of the plantlets was obtained in all the media evaluated. However, rooting rates and root growth increased with increased concentrations of NAA and the reduction of the salt strength of the media. The plantlets were successfully transferred to soil and grown to maturity, exhibiting a normal development, with high uniformity and no evidences of somaclonal variation. This revised version was published online in June 2006 with corrections to the Cover Date.     

Exploration of data partitioning in an eight‐gene data set: phylogeny of metalmark moths (Lepidoptera,Choreutidae)

Rota, J. & Wahlberg, N. (2012). Exploration of data partitioning in an eight‐gene data set: phylogeny of metalmark moths (Lepidoptera, Choreutidae). —Zoologica Scripta, 41, 536–546. Molecular data sets for phylogenetic inference continue to increase in size, especially with respect to the number of genes sampled. As more and more genes are included in analyses, the importance of partitioning the data to avoid problems that can arise from underparameterization becomes more apparent. With an eight‐gene data set from 38 metalmark moth species (12 genera represented) and three outgroups, we explored different data partitioning strategies and their influence on convergence and mixing of Markov Chains Monte Carlo in a Bayesian setting. We found that in larger data sets, with an increase in the number of partitions that are made a priori (e.g. by gene and codon position), convergence and mixing become poor. This problem can be overcome by using a recently published algorithm in which homologous sites are grouped into blocks with similar evolutionary rates that can then be modelled as separate data subsets. Using this novel approach to data partitioning, our analyses resolve with strong support relationships among the genera of metalmark moths. Support for the monophyly of the family, the two subfamilies and all genera except Hemerophila is strong. Hemerophila is broken into two separate clades, Hemerophila sensu stricto and another well‐supported clade. To render Hemerophila monophyletic, we describe a new genus, Ornarantia Rota, gen. nov., and transfer 18 species from Hemerophila to it. The type species of Ornarantia is Hemerophila laciniosella Busck, 1914.     

Revised systematics and higher classification of pierid butterflies (Lepidoptera: Pieridae) based on molecular data

The butterfly family Pieridae comprises approximately 1000 described species placed in 85 genera, but the higher classification has not yet been settled. We used molecular data from eight gene regions (one mitochondrial and seven nuclear protein‐coding genes) comprising a total of ~6700 bp from 96 taxa to infer a well‐supported phylogenetic hypothesis for the family. Based on this hypothesis, we revise the higher classification for all pierid genera. We resurrect the tribe Teracolini stat. rev. in the subfamily Pierinae to include the genera Teracolus, Pinacopteryx, Gideona, Ixias, Eronia, Colotis and most likely Calopieris. We transfer Hebomoia to the tribe Anthocharidini and assign the previously unplaced genera Belenois and Dixeia to the subtribe Aporiina. Three lineages near the base of Pierinae (Leptosia, Elodina and Nepheronia + Pareronia) remain unplaced. For each of these, we describe and delineate new tribes: Elodinini Braby tribus nova, Leptosiaini Braby tribus nova and Nepheroniini Braby tribus nova. The proposed higher classification is based on well‐supported monophyletic groups and is likely to remain stable even with the addition of more data.