Regulatory sequences of Arabidopsis drive reporter gene expression in nematode feeding structures.

In the quest for plant regulatory sequences capable of driving nematode-triggered effector gene expression in feeding structures, we show that promoter tagging is a valuable tool. A large collection of transgenic Arabidopsis plants was generated. They were transformed with a beta-glucuronidase gene functioning as a promoter tag. Three T-DNA constructs, pGV1047, p delta gusBin19, and pMOG553, were used. Early responses to nematode invasion were of primary interest. Six lines exhibiting beta-glucuronidase activity in syncytia induced by the beet cyst nematode were studied. Reporter gene activation was also identified in galls induced by root knot and ectoparasitic nematodes. Time-course studies revealed that all six tags were differentially activated during the development of the feeding structure. T-DNA-flanking regions responsible for the observed responses after nematode infection were isolated and characterized for promoter activity.     

Correlations between ultrastructural features and contraction rates in Rotiferan muscle

Summary The Rotifer Trichocerca rattus has striated longitudinal retractor muscles. These muscles can be divided into two categories: 1. The central and ventral retractor muscles which, after fixation, are found in a supercontracted state: they probably contract very quickly. 2. The lateral retractor muscles which are in a relaxed state after fixation. However, if the animal is mechanically stimulated before fixation, these are also fixed in a contracted state: so, normally, these muscles probably contract more slowly than the first category.In the relaxed state, thin myofilaments of the lateral retractor muscles are folded at the I band level; this is a consequence of their compression provoked by the contraction of central and ventral retractor muscles.In muscles of the first type, the thick myofilaments are shorter (<2 ) than in the second type (2.5 ).     

Efficient expression of vip184DeltaP gene under the control of promoters plus Shine-Dalgarno (SD) sequences of cry genes from Bacillus thuringiensis

AIMS: To compare vip184DeltaP gene expression time course and Vip184 protein yield under the control of promoters and Shine-Dalgarno (SD) sequences of vip184, cry3A and cry1A gene from Bacillus thuringiensis respectively. METHODS AND RESULTS: Derived from the shuttle vector pHT3101, recombinant plasmids pHPT3, pHTP3A(Delta)P and pHTP1A(Delta)P were constructed with the native vip184 gene and the vip184(Delta)P gene, either under the control of promoters and SD sequences of cry3A or cry1A genes. When the above plasmids were transformed into an acrystalliferous B. thuringiensis strain Cry(-)B, their expression time course were consistent with those of vip184, cry3A and cry1A gene respectively. The maximum yields of Vip184 protein were increased when under the control of promoters plus SD sequences of cry3A and cry1A gene. CONCLUSIONS: The results showed that both cry3A and cry1A promoter/SD sequence combinations were able to enhance synthesis of Vip184 and change its expression time course. SIGNIFICANCE AND IMPACT OF THE STUDY: Both cry3A and cry1A promoter/SD systems offer a method for improving the expression efficacy of the vip184 gene in B. thuringiensis and it is possible to co-express the vip184 gene and cry genes and accumulate Vip184 in the form of inclusion bodies by these systems in order to construct novel useful B. thuringiensis engineered strains.     

Clock gene expression levels and relationship with clinical and pathological features in colorectal cancer patients

The clock gene machinery controls cellular metabolism, proliferation, and key functions, such as DNA damage recognition and repair. Dysfunction of the circadian clock is involved in tumorigenesis, and altered expression of some clock genes has been found in cancer patients. The aim of this study was to evaluate the expression levels of core clock genes in colorectal cancer (CRC). Quantitative real-time polymerase chain reaction (qPCR) was used to examine ARNTL1, CLOCK, PER1, PER2, PER3, CRY1, CRY2, Timeless (TIM), TIPIN, and CSNK1? expression levels in the tumor tissue and matched apparently healthy mucosa of CRC patients. In the tumor tissue of CRC patients, compared to their matched healthy mucosa, expression levels of ARNTL1 (p=.002), PER1 (p=.002), PER2 (p=.011), PER3 (p=.003), and CRY2 (p=.012) were lower, whereas the expression level of TIM (p=.044) was higher. No significant difference was observed in the expression levels of CLOCK (p=.778), CRY1 (p=.600), CSNK1 (p=.903), and TIPIN (p=.136). As to the clinical and pathological features, a significant association was found between low CRY1 expression levels in tumor mucosa and age (p=.026), and female sex (p=.005), whereas high CRY1 expression levels in tumor mucosa were associated with cancer location in the distal colon (p?=?.015). Moreover, high TIM mRNA levels in the tumor mucosa were prevalent whenever proximal lymph nodes were involved (p= .013) and associated with TNM stages III-IV (p=.005) and microsatellite instability (p=.015). Significantly poorer survival rates were evidenced for CRC patients with lower expression in the tumor tissue of PER1 (p=.010), PER3 (p= .010), and CSNKIE (p=.024). In conclusion, abnormal expression levels of core clock genes in CRC tissue may be related to the process of tumorigenesis and exert an influence on host/tumor interactions.     

Clinical drug response can be predicted using baseline gene expression levels and in vitro drug sensitivity in cell lines

We demonstrate a method for the prediction of chemotherapeutic response in patients using only before-treatment baseline tumor gene expression data. First, we fitted models for whole-genome gene expression against drug sensitivity in a large panel of cell lines, using a method that allows every gene to influence the prediction. Following data homogenization and filtering, these models were applied to baseline expression levels from primary tumor biopsies, yielding an in vivo drug sensitivity prediction. We validated this approach in three independent clinical trial datasets, and obtained predictions equally good, or better than, gene signatures derived directly from clinical data.     

The SRS 3D module: integrating structures, sequences and features

In this paper we present SRS 3D, a new service that allows users to easily and rapidly find all related structures for a given target sequence; structures can then be viewed together with sequences, alignments and sequence features (currently from UniProt, InterPro and PDB). Extensive user feedback confirms that SRS 3D is intuitive and useful especially for those not expert in structures. AVAILABILITY: An SRS 3D server is provided at http://srs3d.ebi.ac.uk/.     

Correlations between coding and contiguous non-coding sequences in isochore families from vertebrate genomes

Many years ago compositional correlations were found to hold between coding and contiguous non-coding sequences. These correlations were essentially studied in whole genomes of mammals, which are characterized by strong compositional heterogeneities. Here we investigated whether these correlations also hold within the much more homogeneous isochore families. This point was checked not only in the case of mammals, but also in that of phylogenetically distant vertebrates, which are characterized by very different compositional patterns. Indeed, these are remarkably different in cold- and warm-blooded vertebrates. Fish genomes, for instance, are much more homogeneous than those of mammals and birds. The compositional correlations between coding sequences and the corresponding introns, or their 5′ and 3′ flanking regions, were studied in the isochore families of the fully sequenced genomes from four fishes (Brachydanio rerio, Oryzias latipes, Gasterosteus aculeatus and Tetraodon nigroviridis), human and chicken.     

Correlations between spatiotemporal changes in gene expression and apoptosis underlie wing polyphenism in the ant Pheidole morrisi

Wing polyphenism, which is the ability of a single genome to produce winged and wingless castes in a colony in response to environmental cues, evolved just once and is a universal feature of ants. The gene network underlying wing polyphenism, however, is conserved in the winged castes of different ant species, but is interrupted at different points in the network in the wingless castes of these species. We previously constructed a mathematical model, which predicts that a key gene brinker (brk) mediates the development and evolution of these different "interruption points" in wingless castes of different ant species. According to this model, brk is upregulated throughout the vestigial wing discs of wingless ant castes to reduce growth and induce apoptosis. Here, we tested these predictions by examining the expression of brk, as well as three other genes up- and downstream of brk-decapentaplegic (dpp), spalt (sal), and engrailed (en)-in the winged reproductive and wingless soldier castes in the ant Pheidole morrisi. We show that expression of these genes is conserved in the wing disc of winged castes. Surprisingly, however, we found that brk expression is absent throughout development of the vestigial soldier forewing disc. This absence is correlated with abnormal growth of the soldier forewing disc as revealed by En expression and morphometric analyses. We also discovered that dpp and sal expression change dynamically during the transition from larval-to-prepupal development, and is spatiotemporally correlated with the induction of apoptosis in soldier forewing disc. Our results suggest that, contrary to our predictions, brk may not be a key gene in the network for suppressing wings in soldiers, and its absence may function to disrupt the normal growth of the soldier forewing disc. Furthermore, the dynamic changes in network interruptions we discovered may be important for the induction of apoptosis, and may be a general feature of gene networks that underlie polyphenism.