Two new dinosaur tracksites from the Lower Cretaceous Jiaguan Formation of Sichuan Basin,China: specific preservation and ichnotaxonomy

Two new dinosaur tracksites are reported from the Lower Cretaceous Jiaguan Formation in the Sichuan Basin, Qijiang District of Chongqing. These are the Gaoqing-Yongsheng and the Huibu tracksites, which represent the 13th and 14th reports from this formation. The Gaoqing-Yongsheng tracksite reveals the trackway of a large biped (ornithopod) in association with isolated sauropod tracks and large indeterminate undertracks with radial cracks. These features are preserved as natural casts with pebble infillings in a coarse, cross bedded and very thick bedded sandstone sequence. The Huibu tracksite reveals isolated theropod tracks and ornithopod tracks, the latter having a quadripartite, Caririchnium-like morphology, preserved in a thin bedded sandstone sequence with intercalated mudstone.     

Metabolic engineering of Escherichia coli for 1-butanol production

Compared to ethanol, butanol offers many advantages as a substitute for gasoline because of higher energy content and higher hydrophobicity. Typically, 1-butanol is produced by Clostridium in a mixed-product fermentation. To facilitate strain improvement for specificity and productivity, we engineered a synthetic pathway in Escherichia coli and demonstrated the production of 1-butanol from this non-native user-friendly host. Alternative genes and competing pathway deletions were evaluated for 1-butanol production. Results show promise for using E. coli for 1-butanol production.     

Inhibition of DNA-dependent protein kinase induces accelerated senescence in irradiated human cancer cells

DNA-dependent protein kinase (DNA-PK) plays a pivotal role in the repair of DNA double-strand breaks (DSB) and is centrally involved in regulating cellular radiosensitivity. Here, we identify DNA-PK as a key therapeutic target for augmenting accelerated senescence in irradiated human cancer cells. We find that BEZ235, a novel inhibitor of DNA-PK and phosphoinositide 3-kinase (PI3K)/mTOR, abrogates radiation-induced DSB repair resulting in cellular radiosensitization and growth delay of irradiated tumor xenografts. Importantly, radiation enhancement by BEZ235 coincides with a prominent p53-dependent accelerated senescence phenotype characterized by positive β-galactosidase staining, G(2)-M cell-cycle arrest, enlarged and flattened cellular morphology, and increased p21 expression and senescence-associated cytokine secretion. Because this senescence response to BEZ235 is accompanied by unrepaired DNA DSBs, we examined whether selective targeting of DNA-PK also induces accelerated senescence in irradiated cells. Significantly, we show that specific pharmacologic inhibition of DNA-PK, but not PI3K or mTORC1, delays DSB repair leading to accelerated senescence after radiation. We additionally show that PRKDC knockdown using siRNA promotes a striking accelerated senescence phenotype in irradiated cells comparable with that of BEZ235. Thus, in the context of radiation treatment, our data indicate that inhibition of DNA-PK is sufficient for the induction of accelerated senescence. These results validate DNA-PK as an important therapeutic target in irradiated cancer cells and establish accelerated senescence as a novel mechanism of radiosensitization induced by DNA-PK blockade.     

Integrin activation state determines selectivity for novel recognition sites in fibrillar collagens

Only three recognition motifs, GFOGER, GLOGER, and GASGER, all present in type I collagen, have been identified to date for collagen-binding integrins, such as alpha(2)beta(1). Sequence alignment was used to investigate the occurrence of related motifs in other human fibrillar collagens, and located a conserved array of novel GER motifs within their triple helical domains. We compared the integrin binding properties of synthetic triple helical peptides containing examples of such sequences (GLSGER, GMOGER, GAOGER, and GQRGER) or the previously identified motifs. Recombinant inserted (I) domains of integrin subunits alpha(1), alpha(2) and alpha(11) all bound poorly to all motifs other than GFOGER and GLOGER. Similarly, alpha(2)beta(1) -containing resting platelets adhered well only to GFOGER and GLOGER, while ADP-activated platelets, HT1080 cells and two active alpha(2)I domain mutants (E318W, locked open) bound all motifs well, indicating that affinity modulation determines the sequence selectivity of integrins. GxO/SGER peptides inhibited platelet adhesion to collagen monomers with order of potency F >/= L >/= M > A. These results establish GFOGER as a high affinity sequence, which can interact with the alpha(2)I domain in the absence of activation and suggest that integrin reactivity of collagens may be predicted from their GER content.     

Isobaric Labeling and Data Normalization without Requiring Protein Quantitation

Isobaric multiplexed quantitative proteomics can complement high-resolution sample isolation techniques. Here, we report a simple workflow exponentially modified protein abundance index (emPAI)-MW deconvolution (EMMOL) for normalizing isobaric reporter ratios within and between experiments, where small or unknown amounts of protein are used. EMMOL deconvolutes the isobaric tags for relative and absolute quantification (iTRAQ) data to yield the quantity of each protein of each sample in the pool, a new approach that enables the comparison of many samples without including a channel of reference standard. Moreover, EMMOL allows using a sufficient quantity of control sample to facilitate the peptide fractionation (isoelectric-focusing was used in this report), and mass spectrometry MS/MS sequencing yet relies on the broad dynamic range of iTRAQ quantitation to compare relative protein abundance. We demonstrated EMMOL by comparing four pooled samples with 20-fold range differences in protein abundance and performed data normalization without using prior knowledge of the amounts of proteins in each sample, simulating an iTRAQ experiment without protein quantitation prior to labeling. We used emPAI,¹ the target protein MW, and the iTRAQ reporter ratios to calculate the amount of each protein in each of the four channels. Importantly, the EMMOL-delineated proteomes from separate iTRAQ experiments can be assorted for comparison without using a reference sample. We observed no compression of expression in iTRAQ ratios over a 20-fold range for all protein abundances. To complement this ability to analyze minute samples, we report an optimized iTRAQ labeling protocol for using 5 μg protein as the starting material.     

Analysis of trimethyl carboxyphosphate by gas chromatography-mass spectrometry

Analysis of trimethyl carboxyphosphate samples by gas chromatography-mass spectrometry, using typical conditions resulted in significant decomposition of the analyte. Optimization of injection conditions, including conditioning of the injection port liner, produced a dramatic increase in observed peak areas and afforded an effective method for detection of trimethyl carboxyphosphate at the <1μg mL⁻¹ level.     

Subcellular Localization of "Peripheral-Type" Binding Sites for Benzodiazepines in Rat Brain

The binding of [3H]Ro 5-4864, a specific ligand for "peripheral-type" benzodiazepine binding sites and [3H]Ro 15-1788, a specific ligand for the central benzodiazepine receptors, was determined in subcellular fractions of rat brain. As previously reported, the highest levels of "peripheral-type" benzodiazepine binding sites and benzodiazepine receptors were found in the crude P1 and P2 fractions, respectively. Purification of these crude fractions revealed that high levels of both [3H]Ro 5-4864 and [3H]Ro 15-1788 binding were present in the mitochondrial and synaptosomal fractions. In contrast, the purified nuclei and myelin contained low levels of both [3H]Ro 5-4864 and [3H]Ro 15-1788 binding.     

Lateral variability of shallow-water facies and high-frequency cycles in foreland basin carbonate platforms (Pennsylvanian,NW Spain)

The kilometer-sized and 100-meter-thick carbonate platforms of the Escalada Fm. I and II (Middle Pennsylvanian) accumulated in the foredeep of a marine foreland basin during the transgressive phases of 3rd-order sequences and were buried by prograding siliciclastic deltaic systems in the course of the subsequent highstand. The carbonate successions show a general upward trend from grain- to mud-supported carbonates, interfingering landwards with siliciclastic deposits of a mixed siliciclastic-carbonate shelf (Fito Fm.) adjacent to deltaic systems. The spatial variability of the carbonate facies and the high-frequency (4th–5th order) cycles, from the platform margin-outer platform to the deltaic systems, has been interpreted from basin reconstruction. Carbonate facies include skeletal grainstone to packstone, ooidal grainstone, burrowed skeletal wackestone, microbial and algal boundstone to wackestone forming mounds, various algal bafflestone and coral biostromes in areas with siliciclastic input. These high-frequency transgressive–regressive cycles are interpreted to record allocyclic forcing of high-amplitude glacioeustasy because they show characteristic features of icehouse cycles: thickness >5 m, absence of peritidal facies, and in some cases, subaerial exposure surfaces capping the cycles. In the mixed cycles, siliciclastics are interpreted as late highstand to lowstand regressive deposits, whereas carbonates as transgressive-early highstand deposition. The lateral and vertical variability of the facies in the glacioeustatic cycles was a response to deposition in a rapidly subsiding, active foreland basin subjected to siliciclastic input, conditions that might be detrimental to the growth of high-relief carbonate systems.     

Ontogenetic scaling of scansorial surface area and setal dimensions of Chondrodactylus bibronii (Gekkota: Gekkonidae): testing predictions derived from cross‐species comparisons of gekkotans

Little is known of how the adhesive apparatus of gekkotans scales with growth. Cross‐species comparisons of certain characteristics, using size as a comparator to investigate scaling relationships, suggest certain relationships between subdigital pad area and body size. The manner in which the adhesive apparatus grows and scales within any one species, however, remains unknown, and it is unclear whether interspecific and intraspecific patterns are similar. To address this, we examined a post‐hatching ontogenetic series of the southern African gecko Chondrodactylus bibronii and demonstrate that setal density, setal basal diameter and setal spacing remain relatively constant in relation to size, indicating conserved subdigital pad assembly rules that are independent of size. Conversely, however, average and maximal setal lengths increase slightly and isometrically with size, an outcome that is probably explained by setal row recruitment, and the surface area of the subdigital pads scales close to, but below, isometry with respect to body mass and snout–vent length, it therefore does not increase sufficiently with size to compensate for the increase in mass. As a result, relative adhesive capacity decreases with growth with a regression slope of –0.45.