Complete mitochondrial genome of the Walking goby Scartelaos histophorus (Perceformes, Gobiidae)

The Walking goby Scartelaos histophorus (Perciformes, Gobiidae) is an amphibious gobioid fish. In this paper, the complete mitochondrial genome of S. histophorus was first determined. The genome is 16,496 bp in length and consists of 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes, and 1 control region. The overall base composition of S. histophorus is 27.5% for T, 28.0% for C, 28.3% for A, and 16.1% for G, with a slight A+T bias of 55.8%. It has the typical vertebrate mitochondrial gene arrangement.     

Complete mitochondrial genome of the mudskipper Boleophthalmus pectinirostris (Perciformes, Gobiidae): repetitive sequences in the control region

The mudskipper, Boleophthalmus pectinirostris (Perciformes, Gobiidae), is an amphibious gobioid fish. In this paper, the complete mitochondrial genome of B. pectinirostris was firstly determined. The mitogenome (17,111 bp) comprises 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 putative control region. 130-bp tandem repeat was identified in the control region, which was almost identical among the 10 individuals examined, and three different frequencies of the repeat unit (five, six or seven) were found among these individuals.     

Atypical reproductive cycles in a population of Sceloporus grammicus (Squamata: Phrynosomatidae) from the Mexican Plateau

The spiny lizard Sceloporus grammicus (Squamata: Phrynosomatidae) is a small reptile from central México and the southern United States, occurring in a wide geographic area characterized by extensive variation in topographic and climatic regimes. Genetic variation among lineages from central México is substantial, though the extent to which this variation corresponds with life-history traits remains obscure. To address part of this puzzle, we studied a population of S. grammicus from Tepeapulco, Hidalgo, México. Male-biased sexual dimorphism was extensive in this population; males were larger than females overall, and expressed proportionately larger heads and longer limbs. Minimum size at sexual maturity was similar in the sexes (males: 43 mm; females: 42 mm). In contrast to other populations from the Central Plateau, reproductive activity of males and females was synchronous. Testicular recrudescence of adult males was initiated in October-November, and maximum testis size maintained from December to July. Female reproductive activity showed no clear seasonal pattern: females had vitellogenic follicles from October to July, and pregnant females were found throughout the year. Female body size was not related to litter size. Neither male nor female gonadal mass was correlated with any abiotic environmental variable examined. Differences in reproductive characteristics among populations of S. grammicus might be indicative of plasticity in response to local environmental conditions, local adaptation, or complex gene × environment interactions. We consider these results in the context of previously studied populations of S. grammicus from the Central Plateau and elsewhere, and propose directions for future research.     

Mechanisms of activation and repression by the alternative splicing factors RBFOX1/2

RBFOX1 and RBFOX2 are alternative splicing factors that are predominantly expressed in the brain and skeletal muscle. They specifically bind the RNA element UGCAUG, and regulate alternative splicing positively or negatively in a position-dependent manner. The molecular basis for the position dependence of these and other splicing factors on alternative splicing of their targets is not known. We explored the mechanisms of RBFOX splicing activation and repression using an MS2-tethering assay. We found that the Ala/Tyr/Gly-rich C-terminal domain is sufficient for exon activation when tethered to the downstream intron, whereas both the C-terminal domain and the central RRM are required for exon repression when tethered to the upstream intron. Using immunoprecipitation and mass spectrometry, we identified hnRNP H1, RALY, and TFG as proteins that specifically interact with the C-terminal domain of RBFOX1 and RBFOX2. RNA interference experiments showed that hnRNP H1 and TFG modulate the splicing activity of RBFOX1/2, whereas RALY had no effect. However, TFG is localized in the cytoplasm, and likely modulates alternative splicing indirectly.     

YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops

The archaeal protein L7Ae and eukaryotic homologs such as L30e and 15.5kD comprise the best characterized family of K-turn-binding proteins. K-turns are an RNA motif comprised of a bulge flanked by canonical and noncanonical helices. They are widespread in cellular RNAs, including bacterial gene-regulatory RNAs such as the c-di-GMP-II, lysine, and SAM-I riboswitches, and the T-box. The existence in bacteria of K-turn-binding proteins of the L7Ae family has not been proven, although two hypothetical proteins, YbxF and YlxQ, have been proposed to be L7Ae homologs based on sequence conservation. Using purified, recombinant proteins, we show that Bacillus subtilis YbxF and YlxQ bind K-turns (K(d) ~270 nM and ~2300 nM, respectively). Crystallographic structure determination demonstrates that both YbxF and YlxQ adopt the same overall fold as L7Ae. Unlike the latter, neither bacterial protein recognizes K-loops, a structural motif that lacks the canonical helix of the K-turn. This property is shared between the bacterial and eukaryal family members. Comparison of our structure of YbxF in complex with the K-turn of the SAM-I riboswitch and previously determined structures of archaeal and eukaryal homologs bound to RNA indicates that L7Ae approaches the K-turn at a unique angle, which results in a considerably larger RNA-protein interface dominated by interactions with the noncanonical helix of the K-turn. Thus, the inability of the bacterial and eukaryal L7Ae homologs to bind K-loops probably results from their reliance on interactions with the canonical helix. The biological functions of YbxF and YlxQ remain to be determined.     

The importance of host plant-habitat substrate in the maintenance of a unique isolate of the Sandhill Rustic: disturbance, shingle matrix and bare ground indicators

The Sandhill Rustic moth Luperina nickerlii leechi is an isolate restricted to the beach of Loe Bar in Cornwall UK; it is a UK Priority taxon because of its unique status and small, declining population. The larval foodplant is Sand Couch-grass Elytrigia juncea; the larvae feed at first inside the stems and then on the rhizomes underground. The distribution of the moth and E. juncea were investigated in this study in relation to substrate conditions and other plants. E. juncea has an above-ground clumped distribution; near the sea the plants are linked by rhizomes, but away from the sea the apparent clumping is a probable historic record of previous connectivity where the rhizomes have disappeared. The adult moths were found to be associated with more vigorous E. juncea plants growing in sparsely vegetated, more disturbed ground near the sea, especially those plants with large rhizome systems along which later instar larvae can travel between plants. Emerging moths were associated with areas of extensive E. juncea surrounded by bare ground, where there was a substantial variation of shingle particles between 125?μm and 8?mm. The absence of vegetation and associated roots apart from E. juncea, and a coarse particle mix, may allow larvae to move through the shingle and the moths to push their way upwards from their subterranean pupae. We conclude that management should aim to create areas of bare ground with extensive patches of E. juncea growing in coarser shingle, with extensive underground connectivity and few other plants.     

Enzymatic transformation of the major ginsenoside Rb2 to minor compound Y and compound K by a ginsenoside-hydrolyzing β-glycosidase from Microbacterium esteraromaticum

The ginsenoside-hydrolyzing β-glycosidase (Bgp3) derived from Microbacterium esteraromaticum transformed the major ginsenoside Rb2 to more pharmacologically active minor ginsenosides including compounds Y and K. The bgp3 gene consists of 2,271?bp encoding 756 amino acids which have homology to the glycosyl hydrolase family 3 protein domain. Bgp3 is capable of hydrolyzing beta-glucose links and arabinose links. HPLC analysis of the time course of ginsenoside Rb2 hydrolysis by Bgp3 (0.1?mg?enzyme?ml(-1) in 20?mM sodium phosphate buffer at 40?°C and pH 7.0) showed that the glycosidase first hydrolyzed the inner glucose moiety attached to the C-3 position and then the arabinopyranose moiety attached to the C-20 position. Thus, Bgp3 hydrolyzed the ginsenoside Rb2 via the following pathway: Rb2?→?compound Y?→?compound K.     

The influence of light on microtubule dynamics and alignment in the Arabidopsis hypocotyl

Light and dark have antagonistic effects on shoot elongation, but little is known about how these effects are translated into changes of shape. Here we provide genetic evidence that the light/gibberellin-signaling pathway affects the properties of microtubules required to reorient growth. To follow microtubule dynamics for hours without triggering photomorphogenic inhibition of growth, we used Arabidopsis thaliana light mutants in the gibberellic acid/DELLA pathway. Particle velocimetry was used to map the mass movement of microtubule plus ends, providing new insight into the way that microtubules switch between orthogonal axes upon the onset of growth. Longitudinal microtubules are known to signal growth cessation, but we observed that cells also self-organize a strikingly bipolarized longitudinal array before bursts of growth. This gives way to a radial microtubule star that, far from being a random array, seems to be a key transitional step to the transverse array, forecasting the faster elongation that follows. Computational modeling provides mechanistic insight into these transitions. In the faster-growing mutants, the microtubules were found to have faster polymerization rates and to undergo faster reorientations. This suggests a mechanism in which the light-signaling pathway modifies the dynamics of microtubules and their ability to switch between orthogonal axes.