Integrated modeling of protein-coding genes in the Manduca sexta genome using RNA-Seq data from the biochemical model insect

The genome sequence of Manduca sexta was recently determined using 454 technology. Cufflinks and MAKER2 were used to establish gene models in the genome assembly based on the RNA-Seq data and other species' sequences. Aided by the extensive RNA-Seq data from 50 tissue samples at various life stages, annotators over the world (including the present authors) have manually confirmed and improved a small percentage of the models after spending months of effort. While such collaborative efforts are highly commendable, many of the predicted genes still have problems which may hamper future research on this insect species. As a biochemical model representing lepidopteran pests, M. sexta has been used extensively to study insect physiological processes for over five decades. In this work, we assembled Manduca datasets Cufflinks 3.0, Trinity 4.0, and Oases 4.0 to assist the manual annotation efforts and development of Official Gene Set (OGS) 2.0. To further improve annotation quality, we developed methods to evaluate gene models in the MAKER2, Cufflinks, Oases and Trinity assemblies and selected the best ones to constitute MCOT 1.0 after thorough crosschecking. MCOT 1.0 has 18,089 genes encoding 31,666 proteins: 32.8% match OGS 2.0 models perfectly or near perfectly, 11,747 differ considerably, and 29.5% are absent in OGS 2.0. Future automation of this process is anticipated to greatly reduce human efforts in generating comprehensive, reliable models of structural genes in other genome projects where extensive RNA-Seq data are available.     

HEMIFLAGELLOCHLORIS KAZAKHSTANICA GEN. ET SP. NOV.: A NEW COCCOID GREEN ALGA WITH FLAGELLA OF CONSIDERABLY UNEQUAL LENGTHS FROM A SALINE IRRIGATION LAND IN KAZAKHSTAN (CHLOROPHYCEAE,CHLOROPHYTA)1

A coccoid green alga, Hemiflagellochloris kazakhstanica S. Watanabe, S. Tsujimura, T. Misono, S. Nakamura et H. Inoue, gen. et sp. nov., was described from soil samples of a saline irrigation land in Ili River basin, Kazakhstan. This alga had a parietal chloroplast with a pyrenoid, which was covered with starch segments and penetrated with thylakoid membranes. Reproduction occurred by the formation of aplanospores and zoospores. The aplanospores frequently formed tetrad aggregations in a mother cell. The zoospores were covered by a single‐layered cell wall and lacked stigmata. The zoospores had two flagella of considerably unequal lengths; the longer flagellum was 17–19 lm in length and the shorter one was 9–10 lm. The flagellar apparatus architecture was of the clockwise orientation group type in the Chlorophyceae. Molecular phylogenetic analysis using 18S and 28S rDNA sequence data resolved this organism in a separate clade from the green algae that had flagella of slightly unequal lengths. It was suggested that features such as inequality in flagellar lengths, parallel exsertion of basal bodies, and subapical position of the flagellar apparatus were sporadically evolved.     

Real-time ultrasonic evaluation of the baboon pregnancy: biometric measurements

Ultrasonic and direct biometric measurements of nine fetal baboons were made during 23 evaluations. Both the femur length and the biparietal diameter were correlated to gestational age. These initial results have facilitated intrauterine surgery. The data presented will help in determining adequate fetal growth and in dating the baboon pregnancy.     

Effect of aqueous leaf extract of common lambsquarters (Chenopodium album L.) and NaCl on germination and seedling growth of rice

Aqucous leaf extract of common lambsquarters (Chenopodium album L.) was evaluated alone or in combination with NaCl for its effect on germination and rice seedling growth. The treatments have no effect on germination. However, growth of both shoot and root significantly decreased under NaCl alone and in combination with leaf extract. Root growth was affected more than the shoot and the effect of NaCl was accentuated in the presence of leaf extract.     

Digit length may reveal unusual breeding behaviour in a seabird

The hormonal environment experienced during prenatal development may affect adult phenotype and behaviour. Digit lengths may provide an estimate of steroid levels encountered during embryonic development in humans and other vertebrates. Finger patterns in humans have been shown to reveal sexual orientation or cooperative behaviour. We explored individual breeding behaviour in a monogamous seabird, the Balearic shearwater Puffinus mauretanicus and unexpectedly detected some cooperative breeders. Furthermore, we show evidence of correlation between digit lengths and cooperative breeding in this species. Additionally, we suggest that the first digit could be a possible indicator of prenatal steroid levels. These results are the starting point for further tests of the hypothesis that first digit length is an indicator of prenatal hormone levels in other vertebrate species. Moreover, these results may offer practical use in wild populations to study the implications of the changes in prenatal environment for adult social behaviour.     

Very long chain alkylresorcinols accumulate in the intracuticular wax of rye (Secale cereale L.) leaves near the tissue surface

Alkylresorcinols (ARs) are bioactive compounds occurring in many members of the Poaceae, likely at or near the surface of various organs. Here, we investigated AR localization within the cuticular wax layers of rye (Secale cereale) leaves. The total wax mixture from both sides of the leaves was found to contain primary alcohols (71%), alkyl esters (11%), aldehydes (5%), and small amounts (<3%) of alkanes, steroids, secondary alcohols, fatty acids and unknowns. A homologous series of ARs (3%) was identified by GC-MS and comparison with a synthetic standard of nonadecylresorcinol. The alkyl side chains of the wax ARs contained odd numbers of carbons ranging from C19 to C27, with a prevalence of C21, C23 and C25. Waxes from both sides of the leaf, analyzed separately in a second experiment, comprised the same compound classes in similar relative amounts and with similar homolog patterns. Finally, the epicuticular and intracuticular wax layers were sampled separately from the abaxial side of the leaf. While ARs accounted for 2% of the intracuticular wax, they were not detectable in the epicuticular wax. The intracuticular wax was also slightly enriched in steroids, whereas the epicuticular layer contained more primary alcohols. All other wax constituents were distributed evenly between both wax layers.     

Neuroprotective effects of purslane herb aquenous extracts against D-galactose induced neurotoxicity

In order to evaluate mechanisms of natural plant purslane herb aquenous extracts (PHAS) for neuroprotective, we assessed neuroprotective effects of PHAS at doses of 2.5, 5 and 10 mg/(kg day) on SD mice injected daily with D-gal (50 mg/(kg day)) by behavioral tests. PHAS-fed mice showed higher activity upon induction by new environmental stimuli, lower anxiety and higher novelty-seeking behavior in the open field tasks, and significantly improved learning and memory ability in step-through compared with D-gal-treated mice. We further examined the mechanisms involved in neuroprotective effects of PHAS on mouse brain. PHAS significantly increased superoxide dismutase (SOD) activity and decreased the malondialdehyde (MDA) level. Meanwhile, PHAS also could up-regulate telomere lengths and telomerase activity in PHAS-fed groups. Furthermore, we examined the expression of p21(waf1) and p53 mRNA and protein in mouse brain by western blot analysis and real-time RT-PCR. We found that p21(waf1)was down-regulated by PHAS without changing the expression of p53. The results of this study suggested that the PHAS might be a primary target of p21(waf1)and the neuroprotective effect of PHAS might be carried out through a p21(waf1)-dependent and p53-independent pathway.